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Rusbjerg-Weberskov CE, Gant MS, Chamot-Rooke J, Nielsen NS, Enghild JJ. Development of a top-down MS assay for specific identification of human periostin isoforms. Front Mol Biosci 2024; 11:1399225. [PMID: 38962283 PMCID: PMC11220192 DOI: 10.3389/fmolb.2024.1399225] [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: 03/11/2024] [Accepted: 05/31/2024] [Indexed: 07/05/2024] Open
Abstract
Periostin is a matricellular protein encoded by the POSTN gene that is alternatively spliced to produce ten different periostin isoforms with molecular weights ranging from 78 to 91 kDa. It is known to promote fibrillogenesis, organize the extracellular matrix, and bind integrin-receptors to induce cell signaling. As well as being a key component of the wound healing process, it is also known to participate in the pathogenesis of different diseases including atopic dermatitis, asthma, and cancer. In both health and disease, the functions of the different periostin isoforms are largely unknown. The ability to precisely determine the isoform profile of a given human sample is fundamental for characterizing their functional significance. Identification of periostin isoforms is most often carried out at the transcriptional level using RT-PCR based approaches, but due to high sequence homogeneity, identification on the protein level has always been challenging. Top-down proteomics, where whole proteins are measured by mass spectrometry, offers a fast and reliable method for isoform identification. Here we present a fully developed top-down mass spectrometry assay for the characterization of periostin splice isoforms at the protein level.
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Affiliation(s)
| | - Megan S. Gant
- Mass Spectrometry for Biology, Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Paris, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology, Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Paris, France
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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2
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Lin KZ, Qiu Y, Roeder K. eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings. BMC Bioinformatics 2024; 25:113. [PMID: 38486150 PMCID: PMC10941434 DOI: 10.1186/s12859-024-05724-7] [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: 12/06/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. RESULTS We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. CONCLUSIONS eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
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Affiliation(s)
- Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Yixuan Qiu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, People's Republic of China
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
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3
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Lin KZ, Qiu Y, Roeder K. eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568369. [PMID: 38045428 PMCID: PMC10690270 DOI: 10.1101/2023.11.22.568369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. Results We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. Conclusions eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
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Affiliation(s)
- Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Yixuan Qiu
- School of Statistics & Management, Shanghai University of Finance and Economics, Shanghai,People's Republic of China
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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Russo RC, Quesniaux VFJ, Ryffel B. Homeostatic chemokines as putative therapeutic targets in idiopathic pulmonary fibrosis. Trends Immunol 2023; 44:1014-1030. [PMID: 37951789 DOI: 10.1016/j.it.2023.10.003] [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: 09/22/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal chronic interstitial lung disease (ILD) that affects lung mechanical functions and gas exchange. IPF is caused by increased fibroblast activity and collagen deposition that compromise the alveolar-capillary barrier. Identifying an effective therapy for IPF remains a clinical challenge. Chemokines are key proteins in cell communication that have functions in immunity as well as in tissue homeostasis, damage, and repair. Chemokine receptor signaling induces the activation and proliferation of lung-resident cells, including alveolar macrophages (AMs) and fibroblasts. AMs are an important source of chemokines and cytokines during IPF. We highlight the complexity of this system and, based on insights from genetic and transcriptomic studies, propose a new role for homeostatic chemokine imbalance in IPF, with implications for putative therapeutic targets.
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Affiliation(s)
- Remo C Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
| | - Valerie F J Quesniaux
- Experimental and Molecular Immunology and Neurogenetics (INEM), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7355, University of Orleans, Orleans 45071, France.
| | - Bernhard Ryffel
- Experimental and Molecular Immunology and Neurogenetics (INEM), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7355, University of Orleans, Orleans 45071, France.
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Rusbjerg-Weberskov C, Johansen ML, Nowak JS, Otzen DE, Pedersen JS, Enghild JJ, Nielsen NS. Periostin C-Terminal Is Intrinsically Disordered and Interacts with 143 Proteins in an In Vitro Epidermal Model of Atopic Dermatitis. Biochemistry 2023; 62:2803-2815. [PMID: 37704583 PMCID: PMC10552548 DOI: 10.1021/acs.biochem.3c00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/18/2023] [Indexed: 09/15/2023]
Abstract
Human periostin is a 78-91 kDa matricellular protein implicated in extracellular matrix remodeling, tumor development, metastasis, and inflammatory diseases like atopic dermatitis, psoriasis, and asthma. The protein consists of six domains, including an N-terminal Cys-rich CROPT domain, four fasciclin-1 domains, and a C-terminal domain. The exons encoding the C-terminal domain may be alternatively spliced by shuffling four exons, generating ten variants of unknown function. Here, we investigate the structure and interactome of the full-length variant of the C-terminal domain with no exons spliced out. The structural analysis showed that the C-terminal domain lacked a tertiary structure and was intrinsically disordered. In addition, we show that the motif responsible for heparin-binding is in the conserved very C-terminal part of periostin. Pull-down confirmed three known interaction partners and identified an additional 140 proteins, among which nine previously have been implicated in atopic dermatitis. Based on our findings, we suggest that the C-terminal domain of periostin facilitates interactions between connective tissue components in concert with the four fasciclin domains.
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Affiliation(s)
| | - Mette Liere Johansen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Jan S. Nowak
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Daniel E. Otzen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan Skov Pedersen
- Department
of Chemistry, Aarhus University, Aarhus C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan J. Enghild
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Nadia Sukusu Nielsen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
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6
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Islam MA, Kibria MK, Hossen MB, Reza MS, Tasmia SA, Tuly KF, Mosharof MP, Kabir SR, Kabir MH, Mollah MNH. Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing. Sci Rep 2023; 13:4685. [PMID: 36949176 PMCID: PMC10031699 DOI: 10.1038/s41598-023-31276-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
Some recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein-protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk.
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Affiliation(s)
- Md Ariful Islam
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Kaderi Kibria
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Bayazid Hossen
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Selim Reza
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Samme Amena Tasmia
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Khanis Farhana Tuly
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Parvez Mosharof
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- School of Business, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Hadiul Kabir
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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7
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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8
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Huang Y, Guzy R, Ma SF, Bonham CA, Jou J, Schulte JJ, Kim JS, Barros AJ, Espindola MS, Husain AN, Hogaboam CM, Sperling AI, Noth I. Central lung gene expression associates with myofibroblast features in idiopathic pulmonary fibrosis. BMJ Open Respir Res 2023; 10:10/1/e001391. [PMID: 36725082 PMCID: PMC9896241 DOI: 10.1136/bmjresp-2022-001391] [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: 08/04/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023] Open
Abstract
RATIONALE Contribution of central lung tissues to pathogenesis of idiopathic pulmonary fibrosis (IPF) remains unknown. OBJECTIVE To ascertain the relationship between cell types of IPF-central and IPF-peripheral lung explants using RNA sequencing (RNA-seq) transcriptome. METHODS Biopsies of paired IPF-central and IPF-peripheral along with non-IPF lungs were selected by reviewing H&E data. Criteria for differentially expressed genes (DEG) were set at false discovery rate <5% and fold change >2. Computational cell composition deconvolution was performed. Signature scores were computed for each cell type. FINDINGS Comparison of central IPF versus non-IPF identified 1723 DEG (1522 upregulated and 201 downregulated). Sixty-two per cent (938/1522) of the mutually upregulated genes in central IPF genes were also upregulated in peripheral IPF versus non-IPF. Moreover, 85 IPF central-associated genes (CAG) were upregulated in central IPF versus both peripheral IPF and central non-IPF. IPF single-cell RNA-seq analysis revealed the highest CAG signature score in myofibroblasts and significantly correlated with a previously published activated fibroblasts signature (r=0.88, p=1.6×10-4). CAG signature scores were significantly higher in IPF than in non-IPF myofibroblasts (p=0.013). Network analysis of central-IPF genes identified a module significantly correlated with the deconvoluted proportion of myofibroblasts in central IPF and anti-correlated with inflammation foci trait in peripheral IPF. The module genes were over-represented in idiopathic pulmonary fibrosis signalling pathways. INTERPRETATION Gene expression in central IPF lung regions demonstrates active myofibroblast features that contributes to disease progression. Further elucidation of pathological transcriptomic state of cells in the central regions of the IPF lung that are relatively spared from morphological rearrangements may provide insights into molecular changes in the IPF progression.
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Affiliation(s)
- Yong Huang
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Rob Guzy
- Section of Pulmonary & Critical Care Medicine, University of Chicago, Chicago, Illinois, USA
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Catherine A Bonham
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Jonathan Jou
- Department of Surgery, University of Illinois, Peoria, Illinois, USA
| | - Jefree J Schulte
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - John S Kim
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Andrew J Barros
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Milena S Espindola
- Division of Pulmonary & Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Aliya N Husain
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Cory M Hogaboam
- Division of Pulmonary & Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anne I Sperling
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
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9
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Buratin A, Bortoluzzi S, Gaffo E. Systematic benchmarking of statistical methods to assess differential expression of circular RNAs. Brief Bioinform 2023; 24:6966517. [PMID: 36592056 PMCID: PMC9851295 DOI: 10.1093/bib/bbac612] [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: 09/26/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 01/03/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.
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Affiliation(s)
- Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Enrico Gaffo
- Corresponding author: Enrico Gaffo, Department of Molecular Medicine, University of Padova - Via G. Colombo, 3—35131 Padova, Italy. Phone +39 049 827 6502; Fax +39 049 827 6209; E-mail:
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10
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Karhadkar TR, Chen W, Pilling D, Gomer RH. Inhibitors of the Sialidase NEU3 as Potential Therapeutics for Fibrosis. Int J Mol Sci 2022; 24:239. [PMID: 36613682 PMCID: PMC9820515 DOI: 10.3390/ijms24010239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Fibrosing diseases are a major medical problem, and are associated with more deaths per year than cancer in the US. Sialidases are enzymes that remove the sugar sialic acid from glycoconjugates. In this review, we describe efforts to inhibit fibrosis by inhibiting sialidases, and describe the following rationale for considering sialidases to be a potential target to inhibit fibrosis. First, sialidases are upregulated in fibrotic lesions in humans and in a mouse model of pulmonary fibrosis. Second, the extracellular sialidase NEU3 appears to be both necessary and sufficient for pulmonary fibrosis in mice. Third, there exist at least three mechanistic ways in which NEU3 potentiates fibrosis, with two of them being positive feedback loops where a profibrotic cytokine upregulates NEU3, and the upregulated NEU3 then upregulates the profibrotic cytokine. Fourth, a variety of NEU3 inhibitors block pulmonary fibrosis in a mouse model. Finally, the high sialidase levels in a fibrotic lesion cause an easily observed desialylation of serum proteins, and in a mouse model, sialidase inhibitors that stop fibrosis reverse the serum protein desialylation. This then indicates that serum protein sialylation is a potential surrogate biomarker for the effect of sialidase inhibitors, which would facilitate clinical trials to test the exciting possibility that sialidase inhibitors could be used as therapeutics for fibrosis.
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Affiliation(s)
| | | | | | - Richard H. Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
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11
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The Multiple Roles of Periostin in Non-Neoplastic Disease. Cells 2022; 12:cells12010050. [PMID: 36611844 PMCID: PMC9818388 DOI: 10.3390/cells12010050] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Periostin, identified as a matricellular protein and an ECM protein, plays a central role in non-neoplastic diseases. Periostin and its variants have been considered to be normally involved in the progression of most non-neoplastic diseases, including brain injury, ocular diseases, chronic rhinosinusitis, allergic rhinitis, dental diseases, atopic dermatitis, scleroderma, eosinophilic esophagitis, asthma, cardiovascular diseases, lung diseases, liver diseases, chronic kidney diseases, inflammatory bowel disease, and osteoarthrosis. Periostin interacts with protein receptors and transduces signals primarily through the PI3K/Akt and FAK two channels as well as other pathways to elicit tissue remodeling, fibrosis, inflammation, wound healing, repair, angiogenesis, tissue regeneration, bone formation, barrier, and vascular calcification. This review comprehensively integrates the multiple roles of periostin and its variants in non-neoplastic diseases, proposes the utility of periostin as a biological biomarker, and provides potential drug-developing strategies for targeting periostin.
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12
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Tanzir Mehedi S, Ahmed K, Bui FM, Rahaman M, Hossain I, Tonmoy TM, Limon RA, Ibrahim SM, Moni MA. MLBioIGE: Integration and Interplay of Machine Learning and Bioinformatics Approach to Identify the Genetic Effect of SARS-COV-2 on Idiopathic Pulmonary Fibrosis Patients. Biol Methods Protoc 2022; 7:bpac013. [PMID: 35734766 PMCID: PMC9210941 DOI: 10.1093/biomethods/bpac013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/18/2022] [Accepted: 05/25/2022] [Indexed: 11/15/2022] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19, is a current concern for people worldwide. The virus has recently spread worldwide and is out of control in several countries, putting the outbreak into a terrifying phase. Machine learning with transcriptome analysis has advanced in recent years. Its outstanding performance in several fields has emerged as a potential option to find out how SARS-CoV-2 is related to other diseases. Idiopathic pulmonary fibrosis (IPF) disease is caused by long-term lung injury, a risk factor for SARS-CoV-2. In this article, we used a variety of combinatorial statistical approaches, machine learning, and bioinformatics tools to investigate how the SARS-CoV-2 affects IPF patients’ complexity. For this study, we employed two RNA-seq datasets. The unique contributions include common genes identification to identify shared pathways and drug targets, PPI network to identify hub-genes and basic modules, and the interaction of transcription factors (TFs) genes and TFs–miRNAs with common differentially expressed genes also placed on the datasets. Furthermore, we used gene ontology and molecular pathway analysis to do functional analysis and discovered that IPF patients have certain standard connections with the SARS-CoV-2 virus. A detailed investigation was carried out to recommend therapeutic compounds for IPF patients affected by the SARS-CoV-2 virus.
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Affiliation(s)
| | - Kawsar Ahmed
- Correspondence address. (K.A.) Department of Information and Communication Technology, Group of Bio-Photomatix, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh. E-mail: and (M.A.M.) Faculty of Health and Behavioural Sciences, School of Health and Rehabilitation Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia. E-mail: ,
| | - Francis M Bui
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Musfikur Rahaman
- Department of Information Technology, University of Information Technology and Sciences, Baridhara, Dhaka-1212, Bangladesh
| | - Imran Hossain
- Department of Information Technology, University of Information Technology and Sciences, Baridhara, Dhaka-1212, Bangladesh
| | - Tareq Mahmud Tonmoy
- Department of Information Technology, University of Information Technology and Sciences, Baridhara, Dhaka-1212, Bangladesh
| | - Rakibul Alam Limon
- Department of Information Technology, University of Information Technology and Sciences, Baridhara, Dhaka-1212, Bangladesh
| | - Sobhy M Ibrahim
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Ali Moni
- Correspondence address. (K.A.) Department of Information and Communication Technology, Group of Bio-Photomatix, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh. E-mail: and (M.A.M.) Faculty of Health and Behavioural Sciences, School of Health and Rehabilitation Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia. E-mail: ,
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13
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Santos-Álvarez JC, Velázquez-Enríquez JM, García-Carrillo R, Rodríguez-Beas C, Ramírez-Hernández AA, Reyes-Jiménez E, González-García K, López-Martínez A, Pérez-Campos Mayoral L, Aguilar-Ruiz SR, Romero-Tlalolini MDLÁ, Torres-Aguilar H, Castro-Sánchez L, Arellanes-Robledo J, Vásquez-Garzón VR, Baltiérrez-Hoyos R. miRNAs Contained in Extracellular Vesicles Cargo Contribute to the Progression of Idiopathic Pulmonary Fibrosis: An In Vitro Aproach. Cells 2022; 11:cells11071112. [PMID: 35406675 PMCID: PMC8997737 DOI: 10.3390/cells11071112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease. Lesions in the lung epithelium cause alterations in the microenvironment that promote fibroblast accumulation. Extracellular vesicles (EVs) transport proteins, lipids, and nucleic acids, such as microRNAs (miRNAs). The aim of this study was to characterize the differentially expressed miRNAs in the cargo of EVs obtained from the LL97 and LL29 fibroblast cell lines isolated from IPF lungs versus those derived from the CCD19 fibroblast cell line isolated from a healthy donors. We characterized EVs by ultracentrifugation, Western blotting, and dynamic light scattering. We identified miRNAs by small RNA-seq, a total of 1144 miRNAs, of which 1027 were known miRNAs; interestingly, 117 miRNAs were novel. Differential expression analysis showed that 77 miRNAs were upregulated and 68 were downregulated. In addition, pathway enrichment analyses from the Gene Ontology and Kyoto Encyclopedia of Genomes identified several miRNA target genes in the categories, cell proliferation, regulation of apoptosis, pathways in cancer, and proteoglycans in cancer. Our data reveal that miRNAs contained in EVs cargo could be helpful as biomarkers for fibrogenesis, diagnosis, and therapeutic intervention of IPF.
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Affiliation(s)
- Jovito Cesar Santos-Álvarez
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Juan Manuel Velázquez-Enríquez
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Rosendo García-Carrillo
- Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima 28045, Mexico;
| | | | - Alma Aurora Ramírez-Hernández
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Edilburga Reyes-Jiménez
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Karina González-García
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Armando López-Martínez
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación, Facultad de Medicina, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico;
| | - Sergio Roberto Aguilar-Ruiz
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (E.R.-J.); (K.G.-G.); (A.L.-M.); (S.R.A.-R.)
| | | | - Honorio Torres-Aguilar
- Facultad de Ciencias Químicas, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico;
| | - Luis Castro-Sánchez
- Centro Universitario de Investigaciones Biomédicas, CONACYT-Universidad de Colima, Universidad de Colima, Colima 28045, Mexico;
| | | | - Verónica Rocío Vásquez-Garzón
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (M.d.l.Á.R.-T.); (V.R.V.-G.)
| | - Rafael Baltiérrez-Hoyos
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico; (M.d.l.Á.R.-T.); (V.R.V.-G.)
- Correspondence:
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14
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Higo H, Ohashi K, Tomida S, Okawa S, Yamamoto H, Sugimoto S, Senoo S, Makimoto G, Ninomiya K, Nakasuka T, Nishii K, Taniguchi A, Kubo T, Ichihara E, Hotta K, Miyahara N, Maeda Y, Toyooka S, Kiura K. Identification of targetable kinases in idiopathic pulmonary fibrosis. Respir Res 2022; 23:20. [PMID: 35130915 PMCID: PMC8822646 DOI: 10.1186/s12931-022-01940-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Tyrosine kinase activation plays an important role in the progression of pulmonary fibrosis. In this study, we analyzed the expression of 612 kinase-coding and cancer-related genes using next-generation sequencing to identify potential therapeutic targets for idiopathic pulmonary fibrosis (IPF). Methods Thirteen samples from five patients with IPF (Cases 1–5) and eight samples from four patients without IPF (control) were included in this study. Six of the thirteen samples were obtained from different lung segments of a single patient who underwent bilateral pneumonectomy. Gene expression analysis of IPF lung tissue samples (n = 13) and control samples (n = 8) was performed using SureSelect RNA Human Kinome Kit. The expression of the selected genes was further confirmed at the protein level by immunohistochemistry (IHC). Results Gene expression analysis revealed a correlation between the gene expression signatures and the degree of fibrosis, as assessed by Ashcroft score. In addition, the expression analysis indicated a stronger heterogeneity among the IPF lung samples than among the control lung samples. In the integrated analysis of the 21 samples, DCLK1 and STK33 were found to be upregulated in IPF lung samples compared to control lung samples. However, the top most upregulated genes were distinct in individual cases. DCLK1, PDK4, and ERBB4 were upregulated in IPF case 1, whereas STK33, PIM2, and SYK were upregulated in IPF case 2. IHC revealed that these proteins were expressed in the epithelial layer of the fibrotic lesions. Conclusions We performed a comprehensive kinase expression analysis to explore the potential therapeutic targets for IPF. We found that DCLK1 and STK33 may serve as potential candidate targets for molecular targeted therapy of IPF. In addition, PDK4, ERBB4, PIM2, and SYK might also serve as personalized therapeutic targets of IPF. Additional large-scale studies are warranted to develop personalized therapies for patients with IPF. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-01940-y.
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Affiliation(s)
- Hisao Higo
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Kadoaki Ohashi
- Department of Respiratory Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Sachi Okawa
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Hiromasa Yamamoto
- Department of Thoracic Surgery, Okayama University Hospital, Okayama, Japan
| | | | - Satoru Senoo
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Go Makimoto
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Kiichiro Ninomiya
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Takamasa Nakasuka
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Kazuya Nishii
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Akihiko Taniguchi
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Toshio Kubo
- Center for Clinical Oncology, Okayama University Hospital, Okayama, Japan
| | - Eiki Ichihara
- Department of Respiratory Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Katsuyuki Hotta
- Center for Innovative Clinical Medicine, Okayama University Hospital, Okayama, Japan
| | - Nobuaki Miyahara
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan.,Department of Medical Technology, Okayama University Graduate School of Health Sciences, Okayama, Japan
| | - Yoshinobu Maeda
- Department of Hematology, Oncology and Respiratory Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Katsuyuki Kiura
- Department of Respiratory Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
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15
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Zheng P, Sun S, Wang J, Cheng ZJ, Lei KC, Xue M, Zhang T, Huang H, Zhang XD, Sun B. Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis. Cell Mol Life Sci 2022; 79:66. [PMID: 35015148 PMCID: PMC11075137 DOI: 10.1007/s00018-021-04094-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.
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Affiliation(s)
- Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shixue Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Jingxian Wang
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guizhou, 550025, China
| | - Zhangkai Jason Cheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Mingshan Xue
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Teng Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Huimin Huang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | | | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
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16
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Li H, Zhu B, Xu Z, Adams T, Kaminski N, Zhao H. A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. BMC Bioinformatics 2021; 22:524. [PMID: 34702190 PMCID: PMC8549347 DOI: 10.1186/s12859-021-04412-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. In this article, we propose to borrow information through known biological networks to increase statistical power to identify differentially expressed genes (DEGs). RESULTS We develop MRFscRNAseq, which is based on a Markov random field (MRF) model to appropriately accommodate gene network information as well as dependencies among cell types to identify cell-type specific DEGs. We implement an Expectation-Maximization (EM) algorithm with mean field-like approximation to estimate model parameters and a Gibbs sampler to infer DE status. Simulation study shows that our method has better power to detect cell-type specific DEGs than conventional methods while appropriately controlling type I error rate. The usefulness of our method is demonstrated through its application to study the pathogenesis and biological processes of idiopathic pulmonary fibrosis (IPF) using a single-cell RNA-sequencing (scRNA-seq) data set, which contains 18,150 protein-coding genes across 38 cell types on lung tissues from 32 IPF patients and 28 normal controls. CONCLUSIONS The proposed MRF model is implemented in the R package MRFscRNAseq available on GitHub. By utilizing gene-gene and cell-cell networks, our method increases statistical power to detect differentially expressed genes from scRNA-seq data.
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Affiliation(s)
- Hongyu Li
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06511 USA
| | - Biqing Zhu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 USA
| | - Zhichao Xu
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06511 USA
| | - Taylor Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520 USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520 USA
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06511 USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 USA
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17
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Nakanishi T, Cerani A, Forgetta V, Zhou S, Allen RJ, Leavy OC, Koido M, Assayag D, Jenkins RG, Wain LV, Yang IV, Lathrop GM, Wolters PJ, Schwartz DA, Richards JB. Genetically increased circulating FUT3 level leads to reduced risk of Idiopathic Pulmonary Fibrosis: a Mendelian Randomisation Study. Eur Respir J 2021; 59:13993003.03979-2020. [PMID: 34172473 PMCID: PMC8828995 DOI: 10.1183/13993003.03979-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/14/2021] [Indexed: 11/05/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal fibrotic interstitial lung disease. Few circulating biomarkers have been identified to have causal effects on IPF.To identify candidate IPF-influencing circulating proteins, we undertook an efficient screen of circulating proteins by applying a two-sample Mendelian randomisation (MR) approach with existing publicly available data. For instruments we used genetic determinants of circulating proteins which reside cis to the encoded gene (cis-SNPs), identified by two genome-wide association studies (GWASs) in European individuals (3301 and 3200 subjects). We then applied MR methods to test if the levels of these circulating proteins influenced IPF susceptibility in the largest IPF GWAS (2668 cases and 8591 controls). We validated the MR results using colocalization analyses to ensure that both the circulating proteins and IPF shared a common genetic signal.MR analyses of 834 proteins found that a one sd increase in circulating FUT3 and FUT5 was associated with a reduced risk of IPF (OR: 0.81, 95%CI: 0.74-0.88, p=6.3×10-7, and OR: 0.76, 95%CI: 0.68-0.86, p=1.1×10-5). Sensitivity analyses including multiple-cis SNPs provided similar estimates both for FUT3 (inverse variance weighted [IVW] OR: 0.84, 95%CI: 0.78-0.91, p=9.8×10-6, MR-Egger OR: 0.69, 95%CI: 0.50-0.97, p=0.03) and FUT5 (IVW OR: 0.84, 95%CI: 0.77-0.92, p=1.4×10-4, MR-Egger OR: 0.59, 95%CI: 0.38-0.90, p=0.01) FUT3 and FUT5 signals colocalized with IPF signals, with posterior probabilities of a shared genetic signal of 99.9% and 97.7%. Further transcriptomic investigations supported the protective effects of FUT3 for IPF.An efficient MR scan of 834 circulating proteins provided evidence that genetically increased circulating FUT3 level is associated with reduced risk of IPF.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Agustin Cerani
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Sirui Zhou
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Masaru Koido
- Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Deborah Assayag
- Department of Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Translational Research in Respiratory Diseases, Research Institute McGill University Health Centre, Montréal, Québec, Canada
| | - R Gisli Jenkins
- National Institute for Health Research, Nottingham Biomedical Research Centre Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.,Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom.,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Ivana V Yang
- Center for Genes, Environment and Health and Department of Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - G Mark Lathrop
- McGill Genome Centre and Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Paul J Wolters
- Department of Medicine, School of Medicine, University of California, San Francisco, California, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA.,Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - J Brent Richards
- Department of Human Genetics, McGill University, Montréal, Québec, Canada .,Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada.,Division of Endocrinology, Departments of Medicine, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Twin Research, King's College London, London, United Kingdom
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18
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Sun S, Huang C, Leng D, Chen C, Zhang T, Lei KC, Zhang XD. Gene fusion of IL7 involved in the regulation of idiopathic pulmonary fibrosis. Ther Adv Respir Dis 2021; 15:1753466621995045. [PMID: 33878985 PMCID: PMC8064517 DOI: 10.1177/1753466621995045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a rare form of immune-mediated interstitial lung disease characterized by progressive pulmonary fibrosis and scarring. The pathogenesis of IPF is still unclear. Gene fusion events exist universally during transcription and show alternated patterns in a variety of lung diseases. Therefore, the comprehension of the function of gene fusion in IPF might shed light on IPF pathogenesis research and facilitate treatment development. Methods: In this study, we included 91 transcriptome datasets from the National Center for Biotechnology Information (NCBI), including 52 IPF patients and 39 healthy controls. We detected fusion events in these datasets and probed gene fusion-associated differential gene expression and functional pathways. To obtain robust results, we corrected the batch bias across different projects. Results: We identified 1550 gene fusion events in all transcriptomes and studied the possible impacts of IL7 = AC083837.1 gene fusion. The two genes locate adjacently in chromosome 8 and share the same promoters. Their fusion is associated with differential expression of 282 genes enriched in six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 35 functional gene sets. Gene ontology (GO) enrichment analysis shows that IL7 = AC083837.1 gene fusion is associated with the enrichment of 187 gene sets. The co-expression network of interleukin-7 (IL7) indicates that decreased IL7 expression is associated with many pathways that regulate IPF progress. Conclusion: Based on the results, we conclude that IL7 = AC083837.1 gene fusion might exacerbate fibrosis in IPF via enhancing activities of natural killer cell-mediated cytotoxicity, skin cell apoptosis, and vessel angiogenesis, the interaction of which contributes to the development of fibrosis and the deterioration of respiratory function of IPF patients. Our work unveils the possible roles of gene fusion in regulating IPF and demonstrates that gene fusion investigation is a valid approach in probing immunologic mechanisms and searching potential therapeutic targets for treating IPF. The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Shixue Sun
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chen Huang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Dongliang Leng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chang Chen
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Teng Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Kuan Cheok Lei
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Xiaohua Douglas Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR, China
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19
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Mahmud SMH, Al-Mustanjid M, Akter F, Rahman MS, Ahmed K, Rahman MH, Chen W, Moni MA. Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients. Brief Bioinform 2021; 22:6224261. [PMID: 33847347 PMCID: PMC8083324 DOI: 10.1093/bib/bbab115] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/25/2021] [Accepted: 03/13/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), better known as COVID-19, has become a current threat to humanity. The second wave of the SARS-CoV-2 virus has hit many countries, and the confirmed COVID-19 cases are quickly spreading. Therefore, the epidemic is still passing the terrible stage. Having idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are the risk factors of the COVID-19, but the molecular mechanisms that underlie IPF, COPD, and CVOID-19 are not well understood. Therefore, we implemented transcriptomic analysis to detect common pathways and molecular biomarkers in IPF, COPD, and COVID-19 that help understand the linkage of SARS-CoV-2 to the IPF and COPD patients. Here, three RNA-seq datasets (GSE147507, GSE52463, and GSE57148) from Gene Expression Omnibus (GEO) is employed to detect mutual differentially expressed genes (DEGs) for IPF, and COPD patients with the COVID-19 infection for finding shared pathways and candidate drugs. A total of 65 common DEGs among these three datasets were identified. Various combinatorial statistical methods and bioinformatics tools were used to build the protein–protein interaction (PPI) and then identified Hub genes and essential modules from this PPI network. Moreover, we performed functional analysis under ontologies terms and pathway analysis and found that IPF and COPD have some shared links to the progression of COVID-19 infection. Transcription factors–genes interaction, protein–drug interactions, and DEGs-miRNAs coregulatory network with common DEGs also identified on the datasets. We think that the candidate drugs obtained by this study might be helpful for effective therapeutic in COVID-19.
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Affiliation(s)
- S M Hasan Mahmud
- Computer Science and Technology from the University of Electronic Science and Technology of China, China
| | | | - Farzana Akter
- Computer Science and Engineering from Daffodil International University, Bangladesh
| | | | - Kawsar Ahmed
- Information and Communication Technology (ICT) at Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Habibur Rahman
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Wenyu Chen
- University of Electronic Science and Technology of China, China
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20
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Nambiar S, Clynick B, How BS, King A, Walters EH, Goh NS, Corte TJ, Trengove R, Tan D, Moodley Y. There is detectable variation in the lipidomic profile between stable and progressive patients with idiopathic pulmonary fibrosis (IPF). Respir Res 2021; 22:105. [PMID: 33836757 PMCID: PMC8033725 DOI: 10.1186/s12931-021-01682-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/11/2021] [Indexed: 01/10/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial lung disease characterized by fibrosis and progressive loss of lung function. The pathophysiological pathways involved in IPF are not well understood. Abnormal lipid metabolism has been described in various other chronic lung diseases including asthma and chronic obstructive pulmonary disease (COPD). However, its potential role in IPF pathogenesis remains unclear. Methods In this study, we used ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) to characterize lipid changes in plasma derived from IPF patients with stable and progressive disease. We further applied a data-independent acquisition (DIA) technique called SONAR, to improve the specificity of lipid identification. Results Statistical modelling showed variable discrimination between the stable and progressive subjects, revealing differences in the detection of triglycerides (TG) and phosphatidylcholines (PC) between progressors and stable IPF groups, which was further confirmed by mass spectrometry imaging (MSI) in IPF tissue. Conclusion This is the first study to characterise lipid metabolism between stable and progressive IPF, with results suggesting disparities in the circulating lipidome with disease progression.
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Affiliation(s)
- Shabarinath Nambiar
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, WA, Australia
| | - Britt Clynick
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia. .,Institute for Respiratory Health, Nedlands, WA, Australia.
| | - Bong S How
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, WA, Australia.,Metabolomics Australia, Murdoch University, Murdoch, WA, Australia
| | - Adam King
- Scientific Operations, Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX, UK
| | - E Haydn Walters
- Alfred Hospital, Melbourne, VIC, Australia.,University of Tasmania, Hobart, TAS, Australia.,University of Melbourne, Parkville, VIC, Australia.,Royal Hobart Hospital, Hobart, TAS, Australia
| | - Nicole S Goh
- Austin Hospital, Heidelberg, VIC, Australia.,Institute of Breathing and Sleep, Heidelberg, VIC, Australia
| | - Tamera J Corte
- University of Sydney, Camperdown, NSW, Australia.,Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Robert Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, WA, Australia.,Metabolomics Australia, Murdoch University, Murdoch, WA, Australia
| | - Dino Tan
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia.,Institute for Respiratory Health, Nedlands, WA, Australia
| | - Yuben Moodley
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia.,Institute for Respiratory Health, Nedlands, WA, Australia.,Fiona Stanley Hospital, Murdoch, WA, Australia
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21
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Iyer GR, Samajder S, Zubeda S, S DSN, Mali V, Pv SK, Sharma A, Abbas NZ, Bora NS, Narravula A, Hasan Q. Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants. Front Genet 2020; 11:861. [PMID: 33101356 PMCID: PMC7500201 DOI: 10.3389/fgene.2020.00861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has spread around the globe. Susceptibility has been associated with age, biological sex, and other prior existing health conditions. However, host genes are involved in viral infectivity and pathogenicity, and polymorphisms in these could be responsible for the interethnic/interindividual variability observed in infection and progression of COVID-19. Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. Results: A total of 497 polymorphisms were identified in the five selected genes in the exomes analyzed. Thirty-eight polymorphisms identified in our cohort have been reported earlier in literature and have functional significance or association with health conditions. These variants were classified into three groups: protective, susceptible, and responsible for comorbidities. Discussion and Conclusion: The two polymorphisms described in literature as risk inducing are rs35705950 in MUC5B gene and TMPRSS2 haplotype (rs463727, rs34624090, rs55964536, rs734056, rs4290734, rs34783969, rs11702475, rs35899679, and rs35041537) were absent in our cohort explaining the slower infectivity of the disease in this part of India. The 38 functional variants identified can be used as a predisposition panel for the COVID-19 infectivity and progression and stratify individuals as "high or low risk," which would help in planning appropriate surveillance and management protocols. A larger study from different regions of India is warranted to validate these results.
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Affiliation(s)
- Gayatri R Iyer
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Sayani Samajder
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Syeda Zubeda
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | | | - Vishakha Mali
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Sharath Krishnan Pv
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Anuradha Sharma
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | | | | | - Amulya Narravula
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
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22
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Strikoudis A, Cieślak A, Loffredo L, Chen YW, Patel N, Saqi A, Lederer DJ, Snoeck HW. Modeling of Fibrotic Lung Disease Using 3D Organoids Derived from Human Pluripotent Stem Cells. Cell Rep 2020; 27:3709-3723.e5. [PMID: 31216486 DOI: 10.1016/j.celrep.2019.05.077] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/27/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
The pathogenesis of idiopathic pulmonary fibrosis (IPF), an intractable interstitial lung disease, is unclear. Recessive mutations in some genes implicated in Hermansky-Pudlak syndrome (HPS) cause HPS-associated interstitial pneumonia (HPSIP), a clinical entity that is similar to IPF. We previously reported that HPS1-/- embryonic stem cell-derived 3D lung organoids showed fibrotic changes. Here, we show that the introduction of all HPS mutations associated with HPSIP promotes fibrotic changes in lung organoids, while the deletion of HPS8, which is not associated with HPSIP, does not. Genome-wide expression analysis revealed the upregulation of interleukin-11 (IL-11) in epithelial cells from HPS mutant fibrotic organoids. IL-11 was detected predominantly in type 2 alveolar epithelial cells in end-stage IPF, but was expressed more broadly in HPSIP. Finally, IL-11 induced fibrosis in WT organoids, while its deletion prevented fibrosis in HPS4-/- organoids, suggesting IL-11 as a therapeutic target. hPSC-derived 3D lung organoids are, therefore, a valuable resource to model fibrotic lung disease.
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Affiliation(s)
- Alexandros Strikoudis
- Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA; Division of Pulmonary Medicine, Allergy, and Critical Care, Columbia University Medical Center, New York, NY 10032, USA
| | - Anna Cieślak
- Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA; Division of Pulmonary Medicine, Allergy, and Critical Care, Columbia University Medical Center, New York, NY 10032, USA
| | - Lucas Loffredo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ya-Wen Chen
- Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA; Division of Pulmonary Medicine, Allergy, and Critical Care, Columbia University Medical Center, New York, NY 10032, USA
| | - Nina Patel
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Anjali Saqi
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - David J Lederer
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Hans-Willem Snoeck
- Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA; Division of Pulmonary Medicine, Allergy, and Critical Care, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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23
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Zhao H, Jiang Z, Lv R, Li X, Xing Y, Gao Y, Lv D, Si Y, Wang J, Li J, Zhao X, Cai L. Transcriptome profile analysis reveals a silica-induced immune response and fibrosis in a silicosis rat model. Toxicol Lett 2020; 333:42-48. [PMID: 32721576 DOI: 10.1016/j.toxlet.2020.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022]
Abstract
Silicosis is a type of pneumoconiosis caused by the inhalation of silica dust. It is characterized by inflammation and fibrosis of the lung. Although many studies have reported that crystalline silica-inhalation into the lung initiates the immune response, activating effector cells and triggering the inflammatory cascade with subsequent elaboration of the extracellular matrix and fibrosis, the mechanism of silicosis pathogenesis remains unclear. In the present study, we established a silica inhalation-induced silicosis rat model validated by histological and cytokine analyses. RNA-seq and bioinformatic analyses showed that 600 genes were upregulated and 537 genes were downregulated in the silica-treated group. GO enrichment analysis indicates that these differentially expressed genes are enriched in several biological processes including immune response and organism remodeling. KEGG enrichment analysis showed that 53 enriched pathways were mainly associated with human diseases, immune response, signal transduction, and fibrosis process. Since alternative splicing of pre-mRNAs is also essential for the regulation of gene expression, we identified several alternative pre-mRNA splicing events in the fibrotic process. This study will provide a foundation to understand the molecular mechanism of the pulmonary fibrosis caused by silica.
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Affiliation(s)
- Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Zhiyan Jiang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Runchao Lv
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xue Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yanrong Gao
- School of Public Health, Baotou Medical College, Baotou, 014010, China
| | - Da Lv
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yangming Si
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jingyan Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jun Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiujuan Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
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24
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Cui L, Chen SY, Lerbs T, Lee JW, Domizi P, Gordon S, Kim YH, Nolan G, Betancur P, Wernig G. Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity. Nat Commun 2020; 11:2795. [PMID: 32493933 PMCID: PMC7270081 DOI: 10.1038/s41467-020-16466-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 04/27/2020] [Indexed: 02/04/2023] Open
Abstract
The transcription factor JUN is highly expressed in pulmonary fibrosis. Its induction in mice drives lung fibrosis, which is abrogated by administration of anti-CD47. Here, we use high-dimensional mass cytometry to profile protein expression and secretome of cells from patients with pulmonary fibrosis. We show that JUN is activated in fibrotic fibroblasts that expressed increased CD47 and PD-L1. Using ATAC-seq and ChIP-seq, we found that activation of JUN rendered promoters and enhancers of CD47 and PD-L1 accessible. We further detect increased IL-6 that amplified JUN-mediated CD47 enhancer activity and protein expression. Using an in vivo mouse model of fibrosis, we found two distinct mechanisms by which blocking IL-6, CD47 and PD-L1 reversed fibrosis, by increasing phagocytosis of profibrotic fibroblasts and by eliminating suppressive effects on adaptive immunity. Our results identify specific immune mechanisms that promote fibrosis and suggest a therapeutic approach that could be used alongside conventional anti-fibrotics for pulmonary fibrosis. Fibroblast contributions to lung fibrosis and in particular their crosstalk with immune cells in the lung are incompletely understood. Here, the authors show an overall immune suppressive environment transcriptionally controlled and maintained by fibroblasts in lung fibrosis with possible therapeutic implications.
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Affiliation(s)
- Lu Cui
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Tristan Lerbs
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Pablo Domizi
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Sydney Gordon
- Orca Biosystems, 3475 Edison Way, Suite B, Menlo Park, 94025, CA, USA
| | - Yong-Hun Kim
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Garry Nolan
- Baxter Laboratories Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco, 94143, CA, USA
| | - Gerlinde Wernig
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA.
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25
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Ambrose RL, Brice AM, Caputo AT, Alexander MR, Tribolet L, Liu YC, Adams TE, Bean AG, Stewart CR. Molecular characterisation of ILRUN, a novel inhibitor of proinflammatory and antimicrobial cytokines. Heliyon 2020; 6:e04115. [PMID: 32518853 PMCID: PMC7270589 DOI: 10.1016/j.heliyon.2020.e04115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
Regulation of type-I interferon (IFN) production is essential to the balance between antimicrobial defence and autoimmune disorders. The human protein-coding gene ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains, previously C6orf106) was recently characterised as an inhibitor of antiviral and proinflammatory cytokine (interferon-alpha/beta and tumor necrosis factor alpha) transcription. Currently there is a paucity of information about the molecular characteristics of ILRUN, despite it being associated with several diseases including virus infection, coronary artery disease, obesity and cancer. Here, we characterise ILRUN as a highly phylogenetically conserved protein containing UBA-like and a NBR1-like domains that are both essential for inhibition of type-I interferon and tumor necrosis factor alpha) transcription in human cells. We also solved the crystal structure of the NBR1-like domain, providing insights into its potential role in ILRUN function. This study provides critical information for future investigations into the role of ILRUN in health and disease.
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Affiliation(s)
- Rebecca L. Ambrose
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Aaron M. Brice
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | | | - Marina R. Alexander
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Leon Tribolet
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Yu Chih Liu
- CSIRO Manufacturing, Parkville, Victoria, 3010, Australia
| | | | - Andrew G.D. Bean
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Cameron R. Stewart
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
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26
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Huang R, Liu X, Li H, Ning H, Zhou PK. PRKCSH Alternative Splicing Involves in Silica-Induced Expression of Epithelial-Mesenchymal Transition Markers and Cell Proliferation. Dose Response 2020; 18:1559325820923825. [PMID: 32425726 PMCID: PMC7218327 DOI: 10.1177/1559325820923825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/10/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Mounting evidence suggests that alternative splicing is one of the ways for cells to adapt to environmental stress insults. The aim of this study was firstly to examine the effect of silica on the alternative splicing of lung fibrosis–associated genes. Methods: Microarray analysis was used to construct the alternative splicing profile. Functional experiments were conducted using Cell Counting Kit-8, cell cycle, apoptosis, and epithelial–mesenchymal transition (EMT) analyses. Alternative splicing variants were verified by quantitative real-time polymerase chain reaction (qRT-PCR) polymerase chain reaction method. Results: A total of 1850 genes that have alternative splices in response to silica insult were identified. PCDHB11, MALAT1, MT2A, RP11-126D17.1, and RP11-415I12.2 are the top 5 upregulated genes with occurrence of alternative splice, whereas NDE1, RNPEPL1, TREML2, CSF2RB, and PRKCSH are the top 5 downregulated genes with occurrence of alternative splice. Bioinformatic analysis showed these genes with the occurrence of alternative splice mainly are associated with EMT pathway, N-Glycan biosynthesis, and leukocyte transendothelial migration. Further study indicated that PRKCSH-2 knockdown promotes A549 cell proliferation potential by partially promoting EMT signals. Conclusions: Significant changes in alternative splicing of silicosis-associated genes occur in patients with silicosis in silica conditions. Our study provides basic founding for further investigation into the detail molecular mechanisms underlying silica-induced silicosis.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Xiaodan Liu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - He Li
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Huacheng Ning
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China.,Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
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27
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Clynick B, Jo HE, Corte TJ, Glaspole IN, Grainge C, Hopkins PMA, Reynolds PN, Chapman S, Walters EH, Zappala C, Keir GJ, Cooper WA, Mahar AM, Ellis S, Goh NS, Baltic S, Ryan M, Tan DBA, Moodley YP. Circulating RNA differences between patients with stable and progressive idiopathic pulmonary fibrosis. Eur Respir J 2020; 56:13993003.02058-2019. [PMID: 32381494 DOI: 10.1183/13993003.02058-2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/08/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Britt Clynick
- Institute for Respiratory Health, Nedlands, Australia.,University of Western Australia, Crawley, Australia
| | - Helen E Jo
- University of Sydney, Camperdown, Australia.,Royal Prince Alfred Hospital, Camperdown, Australia
| | - Tamera J Corte
- University of Sydney, Camperdown, Australia.,Royal Prince Alfred Hospital, Camperdown, Australia
| | - Ian N Glaspole
- Monash University, Clayton, Australia.,Alfred Hospital, Melbourne, Australia
| | - Christopher Grainge
- University of Newcastle, Callaghan, Australia.,John Hunter Hospital, New Lambton Heights, Australia
| | - Peter M A Hopkins
- University of Queensland, St Lucia, Australia.,Prince Charles Hospital, Chermside, Australia
| | - Paul N Reynolds
- University of Adelaide, Adelaide, Australia.,Royal Adelaide Hospital, Adelaide, Australia
| | | | - E Haydn Walters
- Alfred Hospital, Melbourne, Australia.,University of Tasmania, Hobart, Australia.,University of Melbourne, Parkville, Australia.,Royal Hobart Hospital, Hobart, Australia
| | | | | | - Wendy A Cooper
- University of Sydney, Camperdown, Australia.,Royal Prince Alfred Hospital, Camperdown, Australia.,Western Sydney University, Sydney, Australia
| | - Annabelle M Mahar
- University of Sydney, Camperdown, Australia.,Royal Prince Alfred Hospital, Camperdown, Australia
| | | | - Nicole S Goh
- Austin Hospital, Heidelberg, Australia.,Institute of Breathing and Sleep, Heidelberg, Australia
| | - Svetlana Baltic
- Institute for Respiratory Health, Nedlands, Australia.,University of Western Australia, Crawley, Australia
| | - Marisa Ryan
- Institute for Respiratory Health, Nedlands, Australia.,University of Western Australia, Crawley, Australia
| | - Dino B A Tan
- Institute for Respiratory Health, Nedlands, Australia.,University of Western Australia, Crawley, Australia
| | - Yuben P Moodley
- Institute for Respiratory Health, Nedlands, Australia.,University of Western Australia, Crawley, Australia.,Fiona Stanley Hospital, Murdoch, Australia
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28
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Azuma A, Richeldi L. New Era of Management Concept on Pulmonary Fibrosis with Revisiting Framework of Interstitial Lung Diseases. Tuberc Respir Dis (Seoul) 2020; 83:195-200. [PMID: 32578412 PMCID: PMC7362754 DOI: 10.4046/trd.2020.0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/10/2020] [Indexed: 11/24/2022] Open
Abstract
The disease concept of interstitial lung disease with idiopathic pulmonary fibrosis at its core has been relied on for many years depending on morphological classification. The separation of non-specific interstitial pneumonia with a relatively good prognosis from usual interstitial pneumonia is also based on the perception that morphology enables predict the prognosis. Beginning with dust-exposed lungs, initially, interstitial pneumonia is classified by anatomical pathology. Diagnostic imaging has dramatically improved the diagnostic technology for surviving patients through the introduction of high-resolution computed tomography scan. And now, with the introduction of therapeutics, the direction of diagnosis is turning. It can be broadly classified into to make known the importance of early diagnosis, and to understand the importance of predicting the speed of progression/deterioration of pathological conditions. For this reason, the insight of “early lesions” has been discussed. There are reports that the presence or absence of interstitial lung abnormalities affects the prognosis. Searching for a biomarker is another prognostic indicator search. However, as is the case with many chronic diseases, pathological conditions that progress linearly are extremely rare. Rather, it progresses while changing in response to environmental factors. In interstitial lung disease, deterioration of respiratory functions most closely reflect prognosis. Treatment is determined by combining dynamic indicators as faithful indicators of restrictive impairments. Reconsidering the history being classified under the disease concept, the need to reorganize treatment targets based on common pathological phenotype is under discussed. What is the disease concept? That aspect changes with the discussion of improving prognosis.
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Affiliation(s)
- Arata Azuma
- Department of Pulmonary Medicine and Oncology, Nippon Medical School, Tokyo, Japan
| | - Luca Richeldi
- Respiratory Medicine, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
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29
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Huang C, Liang Y, Zeng X, Yang X, Xu D, Gou X, Sathiaseelan R, Senavirathna LK, Wang P, Liu L. Long Noncoding RNA FENDRR Exhibits Antifibrotic Activity in Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2020; 62:440-453. [PMID: 31697569 PMCID: PMC7110975 DOI: 10.1165/rcmb.2018-0293oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/07/2019] [Indexed: 01/01/2023] Open
Abstract
Abnormal activation of lung fibroblasts contributes to the initiation and progression of idiopathic pulmonary fibrosis (IPF). The objective of the present study was to investigate the role of fetal-lethal noncoding developmental regulatory RNA (FENDRR) in the activation of lung fibroblasts. Dysregulated long noncoding RNAs in IPF lungs were identified by next-generation sequencing analysis from the two online datasets. FENDRR expression in lung tissues from patients with IPF and mice with bleomycin-induced pulmonary fibrosis was determined by quantitative real-time PCR. IRP1 (iron-responsive element-binding protein 1), a protein partner of FENDRR, was identified by RNA pulldown-coupled mass spectrometric analysis and confirmed by RNA immunoprecipitation. The interaction region between FENDRR and IRP1 was determined by cross-linking immunoprecipitation. The in vivo role of FENDRR in pulmonary fibrosis was studied using adenovirus-mediated gene transfer in mice. The expression of FENDRR was downregulated in fibrotic human and mouse lungs as well as in primary lung fibroblasts isolated from bleomycin-treated mice. TGF-β1 (transforming growth factor-β1)-SMAD3 signaling inhibited FENDRR expression in lung fibroblasts. FENDRR was preferentially localized in the cytoplasm of adult lung fibroblasts and bound IRP1, suggesting its role in iron metabolism. FENDRR reduced pulmonary fibrosis by inhibiting fibroblast activation by reducing iron concentration and acting as a competing endogenous RNA of the profibrotic microRNA-214. Adenovirus-mediated FENDRR gene transfer in the mouse lung attenuated bleomycin-induced lung fibrosis and improved lung function. Our data suggest that FENDRR is an antifibrotic long noncoding RNA and a potential therapeutic target for pulmonary fibrosis.
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Affiliation(s)
- Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Xiangming Zeng
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Xiaoyun Yang
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Dao Xu
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Xuxu Gou
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Roshini Sathiaseelan
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Lakmini Kumari Senavirathna
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Pengcheng Wang
- Department of Immunology and Microbiology, Medical School of Jinan University, Guangdong, China
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, and
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
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30
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Chen W, Lamb TM, Gomer RH. TGF-β1 increases sialidase 3 expression in human lung epithelial cells by decreasing its degradation and upregulating its translation. Exp Lung Res 2020; 46:75-80. [PMID: 32102576 DOI: 10.1080/01902148.2020.1733135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Purpose: We previously found extensive desialylation of glycoconjugates and upregulation of the sialidase enzyme NEU3 in fibrotic lesions in human and mouse lungs. However, studies using microarray analysis of whole lung tissue mRNA and single cell RNA-seq found no significant difference in levels of NEU3 mRNA between IPF patients and controls. This study aimed to elucidate how NEU3 was upregulated in fibrotic lungs.Materials and methods: Transforming growth factor-β1 (TGF-β1), a key driver of fibrosis, was added to A549 human alveolar basal epithelial adenocarcinoma cells and human small airway epithelial cells (HSAEpC). NEU3 expression in A549 cells and HSAEpC was detected by immunofluorescence staining. NEU3 translation and degradation were assessed by polysome profiling (polysomes efficiently translate mRNAs; monosomes poorly translate mRNAs) and cycloheximide chase after treating cells with or without TGF-β1 for 48 h.Results: TGF-β1 increased NEU3 expression and secretion in A549 cells and HSAEpC but did not change total (nuclear + cytosolic) NEU3 mRNA levels. TGF-β1 decreased the degradation rate of NEU3 in A549 cells. TGF-β1 decreased NEU3 mRNA levels in monosomes and increased NEU3 mRNA level in polysomes.Conclusion: TGF-β1 upregulates levels of NEU3 in epithelial cells by both decreasing NEU3 degradation and by increasing the translation of NEU3 mRNA, explaining the apparent paradox of high levels of NEU3 protein in pulmonary fibrosis without a concomitant increase in the expression of NEU3 mRNA.
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Affiliation(s)
- Wensheng Chen
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, Texas, USA
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31
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Yoshihara T, Nanri Y, Nunomura S, Yamaguchi Y, Feghali-Bostwick C, Ajito K, Murakami S, Mawatari M, Izuhara K. Periostin plays a critical role in the cell cycle in lung fibroblasts. Respir Res 2020; 21:38. [PMID: 32000779 PMCID: PMC6993476 DOI: 10.1186/s12931-020-1299-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/19/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a devastating disease with a median survival of only three to 5 years. Fibroblast proliferation is a hallmark of IPF as is secretion of extracellular matrix proteins from fibroblasts. However, it is still uncertain how IPF fibroblasts acquire the ability to progressively proliferate. Periostin is a matricellular protein highly expressed in the lung tissues of IPF patients, playing a critical role in the pathogenesis of pulmonary fibrosis. However, it remains undetermined whether periostin affects lung fibroblast proliferation. METHODS In this study, we first aimed at identifying periostin-dependently expressed genes in lung fibroblasts using DNA microarrays. We then examined whether expression of cyclins and CDKs controlling cell cycle progression occur in a periostin-dependent manner. We next examined whether downregulation of cell proliferation-promoting genes by knockdown of periostin or integrin, a periostin receptor, using siRNA, is reflected in the cell proliferation of lung fibroblasts. We then looked at whether lung fibroblasts derived from IPF patients also require periostin for maximum proliferation. We finally investigated whether CP4715, a potent inhibitor against integrin αVβ3 (a periostin receptor), which we have recently found blocks TGF-β signaling, followed by reduced BLM-induced pulmonary fibrosis in mice, can block proliferation of lung fibroblasts derived from IPF patients. RESULTS Many cell-cycle-related genes are involved in the upregulated or downregulated genes by periostin knockdown. We confirmed that in lung fibroblasts, periostin silencing downregulates expression of several cell-cycle-related molecules, including the cyclin, CDK, and, E2F families, as well as transcription factors such as B-MYB and FOXM1. Periostin or integrin silencing slowed proliferation of lung fibroblasts and periostin silencing increased the distribution of the G0/G1 phase, whereas the distribution of the G2/M phase was decreased. Lung fibroblasts derived from IPF patients also required periostin for maximum proliferation. Moreover, CP4715 downregulated proliferation along with expression of cell-cycle-related genes in IPF lung fibroblasts as well as in normal lung fibroblasts. CONCLUSIONS Periostin plays a critical role in the proliferation of lung fibroblasts and the present results provide us a solid basis for considering inhibitors of the periostin/integrin αVβ3 interaction for the treatment of IPF patients.
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Affiliation(s)
- Tomohito Yoshihara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1 Nabeshima, Saga, 849-8501, Japan
| | - Yasuhiro Nanri
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1 Nabeshima, Saga, 849-8501, Japan
| | - Satoshi Nunomura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1 Nabeshima, Saga, 849-8501, Japan
| | - Yukie Yamaguchi
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Carol Feghali-Bostwick
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Keiichi Ajito
- Pharmaceutical Research Center, Meiji Seika Pharma Co. Ltd., Yokohama, 222-8567, Japan
| | - Shoichi Murakami
- Pharmaceutical Research Center, Meiji Seika Pharma Co. Ltd., Yokohama, 222-8567, Japan
| | - Masaaki Mawatari
- Department of Orthopaedic Surgery, Saga Medical School, Saga, 849-8501, Japan
| | - Kenji Izuhara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1 Nabeshima, Saga, 849-8501, Japan.
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32
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Idiopathic Pulmonary Fibrosis: Pathogenesis and the Emerging Role of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21020524. [PMID: 31947693 PMCID: PMC7013390 DOI: 10.3390/ijms21020524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive chronic disease characterized by excessing scarring of the lungs leading to irreversible decline in lung function. The aetiology and pathogenesis of the disease are still unclear, although lung fibroblast and epithelial cell activation, as well as the secretion of fibrotic and inflammatory mediators, have been strongly associated with the development and progression of IPF. Significantly, long non-coding RNAs (lncRNAs) are emerging as modulators of multiple biological processes, although their function and mechanism of action in IPF is poorly understood. LncRNAs have been shown to be important regulators of several diseases and their aberrant expression has been linked to the pathophysiology of fibrosis including IPF. This review will provide an overview of this emerging role of lncRNAs in the development of IPF.
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33
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Ono J, Takai M, Kamei A, Nunomura S, Nanri Y, Yoshihara T, Ohta S, Yasuda K, Conway SJ, Yokosaki Y, Izuhara K. Periostin forms a functional complex with IgA in human serum. Allergol Int 2020; 69:111-120. [PMID: 31272904 DOI: 10.1016/j.alit.2019.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/12/2019] [Accepted: 05/28/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Periostin is a matricellular protein belonging to the fasciclin family, playing a role for the pathogenesis of allergic diseases by binding to integrins on cell surfaces. Serum periostin is elevated in various allergic diseases reflecting type 2 inflammation and tissue remodeling so that for allergic diseases, periostin is expected to be a novel biomarker for diagnosis, assessing severity or prognosis, and predicting responsiveness to treatments. We have previously shown that most serum periostin exists in the oligomeric form by intermolecular disulfide bonds. METHODS In this study, we examined how periostin forms a complex in serum, whether the periostin complex in serum is functional, and whether the complex formation interferes with reactivity to anti-periostin Abs. RESULTS We found that periostin formed a complex with IgA1 at a 1:1 ratio. The periostin in the serum complex contained at least five different isoforms. However, IgA was not essential for the oligomeric formation of periostin in mouse serum or in IgA-lacking serum. The periostin-IgA complex in human serum was functional, sustaining the ability to bind to αVβ3 integrin on cell surfaces. Moreover, periostin formed the complex with IgA broadly, which interferes the binding of the Abs recognizing all of the domains except the R4 domain to periostin. CONCLUSIONS Periostin is a novel member of the IgA-associated molecules. These results are of great potential use to understand the pathological roles of periostin in allergic diseases and, from a practical standpoint, to develop diagnostics or therapeutic agents against periostin.
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Affiliation(s)
- Junya Ono
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan; Shino-Test Corporation, Sagamihara, Japan
| | - Masayuki Takai
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan; Shino-Test Corporation, Sagamihara, Japan
| | | | - Satoshi Nunomura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan
| | - Yasuhiro Nanri
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan
| | - Tomohito Yoshihara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan
| | - Shoichiro Ohta
- Department of Laboratory Medicine, Saga Medical School, Saga, Japan
| | - Koubun Yasuda
- Department of Immunology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Simon J Conway
- HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yasuyuki Yokosaki
- Cell-Matrix Frontier Lab, Health Administration Office, Hiroshima University, Hiroshima, Japan
| | - Kenji Izuhara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan.
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34
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Vijayaraj P, Minasyan A, Durra A, Karumbayaram S, Mehrabi M, Aros CJ, Ahadome SD, Shia DW, Chung K, Sandlin JM, Darmawan KF, Bhatt KV, Manze CC, Paul MK, Wilkinson DC, Yan W, Clark AT, Rickabaugh TM, Wallace WD, Graeber TG, Damoiseaux R, Gomperts BN. Modeling Progressive Fibrosis with Pluripotent Stem Cells Identifies an Anti-fibrotic Small Molecule. Cell Rep 2019; 29:3488-3505.e9. [PMID: 31825831 PMCID: PMC6927560 DOI: 10.1016/j.celrep.2019.11.019] [Citation(s) in RCA: 15] [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: 01/09/2019] [Revised: 07/11/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
Progressive organ fibrosis accounts for one-third of all deaths worldwide, yet preclinical models that mimic the complex, progressive nature of the disease are lacking, and hence, there are no curative therapies. Progressive fibrosis across organs shares common cellular and molecular pathways involving chronic injury, inflammation, and aberrant repair resulting in deposition of extracellular matrix, organ remodeling, and ultimately organ failure. We describe the generation and characterization of an in vitro progressive fibrosis model that uses cell types derived from induced pluripotent stem cells. Our model produces endogenous activated transforming growth factor β (TGF-β) and contains activated fibroblastic aggregates that progressively increase in size and stiffness with activation of known fibrotic molecular and cellular changes. We used this model as a phenotypic drug discovery platform for modulators of fibrosis. We validated this platform by identifying a compound that promotes resolution of fibrosis in in vivo and ex vivo models of ocular and lung fibrosis.
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Affiliation(s)
- Preethi Vijayaraj
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Aspram Minasyan
- Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Abdo Durra
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Saravanan Karumbayaram
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Mehrsa Mehrabi
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Cody J Aros
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Sarah D Ahadome
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - David W Shia
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Katherine Chung
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jenna M Sandlin
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kelly F Darmawan
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kush V Bhatt
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Chase C Manze
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Manash K Paul
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Dan C Wilkinson
- Department of Materials Science and Engineering, UCLA, Los Angeles, CA 90095, USA
| | - Weihong Yan
- Department of Biology and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Amander T Clark
- Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA; Molecular Cell and Developmental Biology, UCLA, Los Angeles, CA 90095, USA
| | - Tammy M Rickabaugh
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - W Dean Wallace
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Robert Damoiseaux
- Department of Molecular & Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Brigitte N Gomperts
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA; UCLA Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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35
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Karhadkar TR, Chen W, Gomer RH. Attenuated pulmonary fibrosis in sialidase-3 knockout ( Neu3-/-) mice. Am J Physiol Lung Cell Mol Physiol 2019; 318:L165-L179. [PMID: 31617733 DOI: 10.1152/ajplung.00275.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pulmonary fibrosis involves the formation of inappropriate scar tissue in the lungs, but what drives fibrosis is unclear. Sialidases (also called neuraminidases) cleave terminal sialic acids from glycoconjugates. In humans and mice, pulmonary fibrosis is associated with desialylation of glycoconjugates and upregulation of sialidases. Of the four mammalian sialidases, we previously detected only NEU3 in the bronchoalveolar lavage fluid from mice with bleomycin-induced pulmonary fibrosis. In this report, we show that NEU3 upregulates extracellular accumulation of the profibrotic cytokines IL-6 and IL-1β, and IL-6 upregulates NEU3 in human peripheral blood mononuclear cells, suggesting that NEU3 may be part of a positive feedback loop potentiating fibrosis. To further elucidate the role of NEU3 in fibrosis, we used bleomycin to induce lung fibrosis in wild-type C57BL/6 and Neu3-/- mice. At 21 days after bleomycin, compared with male and female C57BL/6 mice, male and female Neu3-/- mice had significantly less inflammation, less upregulation of other sialidases and the profibrotic cytokine active transforming growth factor β1, and less fibrosis in the lungs. Our results suggest that NEU3 participates in fibrosis and that NEU3 could be a target to develop treatments for fibrosis.
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Affiliation(s)
| | - Wensheng Chen
- Department of Biology, Texas A&M University, College Station, Texas
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, Texas
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36
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Rubio K, Singh I, Dobersch S, Sarvari P, Günther S, Cordero J, Mehta A, Wujak L, Cabrera-Fuentes H, Chao CM, Braubach P, Bellusci S, Seeger W, Günther A, Preissner KT, Wygrecka M, Savai R, Papy-Garcia D, Dobreva G, Heikenwalder M, Savai-Pullamsetti S, Braun T, Barreto G. Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis. Nat Commun 2019; 10:2229. [PMID: 31110176 PMCID: PMC6527704 DOI: 10.1038/s41467-019-10066-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 04/12/2019] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and highly lethal lung disease with unknown etiology and poor prognosis. IPF patients die within 2 years after diagnosis mostly due to respiratory failure. Current treatments against IPF aim to ameliorate patient symptoms and to delay disease progression. Unfortunately, therapies targeting the causes of or reverting IPF have not yet been developed. Here we show that reduced levels of miRNA lethal 7d (MIRLET7D) in IPF compromise epigenetic gene silencing mediated by the ribonucleoprotein complex MiCEE. In addition, we find that hyperactive EP300 reduces nuclear HDAC activity and interferes with MiCEE function in IPF. Remarkably, EP300 inhibition reduces fibrotic hallmarks of in vitro (patient-derived primary fibroblast), in vivo (bleomycin mouse model), and ex vivo (precision-cut lung slices, PCLS) IPF models. Our work provides the molecular basis for therapies against IPF using EP300 inhibition. Idiopathic pulmonary fibrosis (IPF) is a lethal disease with insufficient treatment strategies. Here the authors show that reduction of the microRNA MIRLET7D and hyperactivation of EP300 contribute to impaired epigenetic silencing by the MiCEE complex in pulmonary fibroblasts of IPF patients, and demonstrate the benefit of inhibiting EP300 for the treatment of IPF.
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Affiliation(s)
- Karla Rubio
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Indrabahadur Singh
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany. .,Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
| | - Stephanie Dobersch
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Pouya Sarvari
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Stefan Günther
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Julio Cordero
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Anatomy and Developmental Biology, CBTM, Heidelberg University, Mannheim, 68167, Germany.,European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Aditi Mehta
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Pharmaceutical Technology and Biopharmaceutics, Department of Pharmacy, Ludwig-Maximilians-University of Munich, Munich, 81377, Germany
| | - Lukasz Wujak
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany
| | - Hector Cabrera-Fuentes
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,National Heart Research Institute, National Heart Centre Singapore, Singapore, 169609, Singapore.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Tecnologico de Monterrey, Centro de Biotecnologia-FEMSA, Monterrey, 64849, NL, Mexico.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, 169609, Singapore
| | - Cho-Ming Chao
- Chair for Lung Matrix Remodeling, Excellence Cluster Cardio Pulmonary System, Justus Liebig University, Giessen, 35392, Germany.,International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University and Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Department of General Pediatrics and Neonatology, University Children's Hospital Giessen, Justus Liebig University, Giessen, 35392, Germany
| | - Peter Braubach
- German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Institute for Pathology, Hanover Medical School, Hanover, 30625, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hanover (BREATH) Research Network, Hanover, 30625, Germany
| | - Saverio Bellusci
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Chair for Lung Matrix Remodeling, Excellence Cluster Cardio Pulmonary System, Justus Liebig University, Giessen, 35392, Germany.,International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University and Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,Department of General Pediatrics and Neonatology, University Children's Hospital Giessen, Justus Liebig University, Giessen, 35392, Germany.,Pulmonary and Critical Care Medicine, Department of Internal Medicine, Justus Liebig University, Giessen, 35392, Germany
| | - Andreas Günther
- Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Pulmonary and Critical Care Medicine, Department of Internal Medicine, Justus Liebig University, Giessen, 35392, Germany.,Agaplesion Lung Clinic Waldhof Elgershausen, Greifenstein, 35753, Germany
| | - Klaus T Preissner
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany
| | - Malgorzata Wygrecka
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Dulce Papy-Garcia
- Laboratoire Croissance, Réparation et Régénération Tissulaires (CRRET), CNRS ERL 9215, Université Paris Est Créteil, Université Paris Est, Créteil, F-94000, France
| | - Gergana Dobreva
- Anatomy and Developmental Biology, CBTM, Heidelberg University, Mannheim, 68167, Germany.,European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Mathias Heikenwalder
- Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Soni Savai-Pullamsetti
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Thomas Braun
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany. .,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation. .,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany. .,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany. .,Laboratoire Croissance, Réparation et Régénération Tissulaires (CRRET), CNRS ERL 9215, Université Paris Est Créteil, Université Paris Est, Créteil, F-94000, France.
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Precision medicine: integration of genetics and functional genomics in prediction of bronchiolitis obliterans after lung transplantation. Curr Opin Pulm Med 2019; 25:308-316. [PMID: 30883449 DOI: 10.1097/mcp.0000000000000579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Lung transplantation (LTx) can be a life saving treatment in end-stage pulmonary diseases, but survival after transplantation is still limited. Posttransplant development of chronic lung allograft dysfunction with bronchiolits obliterans syndrome (BOS) as the major subphenotype, is the main cause of morbidity and mortality. Early identification of high-risk patients for BOS is a large unmet clinical need. In this review, we discuss gene polymorphisms and gene expression related to the development of BOS. RECENT FINDINGS Candidate gene studies showed that donor and recipient gene polymorphisms affect transplant outcome and BOS-free survival after LTx. Both selective and nonselective gene expression studies revealed differentially expressed fibrosis and apoptosis-related genes in BOS compared with non-BOS patients. Significantly, recent microarray expression analysis of blood and broncho-alveolar lavage suggest a role for B-cell and T-cell responses prior to the development of BOS. Furthermore, 6 months prior to the development of BOS differentially expressed genes were identified in peripheral blood cells. SUMMARY Genetic polymorphisms and gene expression changes are associated with the development of BOS. Future genome wide studies are needed to identify easily accessible biomarkers for prediction of BOS toward precision medicine.
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38
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Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study. J Clin Med 2019; 8:jcm8030308. [PMID: 30841487 PMCID: PMC6462954 DOI: 10.3390/jcm8030308] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease. Therapeutic options for IPF remain limited. Nintedanib, a tyrosine kinase inhibitor approved for IPF treatment, is known to inhibit fibroblasts proliferation, migration and transformation to myofibroblasts. However, how nintedanib changes gene regulations in IPF has never been systematically investigated. We conducted a next-generation sequencing and bioinformatics study to evaluate the changes of mRNA and miRNA profiles in IPF fibroblasts treated with 2 µM and 4 µM nintedanib, compared to those without treatment. We identified 157 upregulated and 151 downregulated genes and used STRING and DAVID databases for analysis of protein⁻protein interactions, biological pathways, and molecular functions. We found strong protein⁻protein interactions within these dysregulated genes, mostly involved in the pathways of cell cycle and mitotic cell cycle. We also discovered 13 potential miRNA⁻mRNA interactions associated with nintedanib treatment. After validation using miRDB, TargetScan, and RT-qPCR, we identified 4 downregulated genes (DDX11, E2F1, NPTX1, and PLXNA4) which might be repressed by the upregulated hsa-miR-486-3p. According to the proposed functions of DDX11, E2F1, and PLXNA4 reported in previous studies, these gene expression changes together might contribute to decreased proliferation of fibroblasts and decreased angiogenesis in the microenvironment of IPF. Our findings need further studies to confirm.
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39
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The Structure of the Periostin Gene, Its Transcriptional Control and Alternative Splicing, and Protein Expression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1132:7-20. [PMID: 31037620 DOI: 10.1007/978-981-13-6657-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although many studies have described the role of periostin in various diseases, the functions of periostin derived from alternative splicing and proteinase cleavage at its C-terminus remain unknown. Further experiments investigating the periostin structures that are relevant to diseases are essential for an in-depth understanding of their functions, which would accelerate their clinical applications by establishing new approaches for curing intractable diseases. Furthermore, this understanding would enhance our knowledge of novel functions of periostin related to stemness and response to mechanical stress .
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40
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Ability of Periostin as a New Biomarker of Idiopathic Pulmonary Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1132:79-87. [PMID: 31037627 DOI: 10.1007/978-981-13-6657-4_9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The primarily pathogenesis of IPF, an incurable respiratory disease is believed to over-repair to lung injury. The development of new drugs for IPF has increased the necessity of identifying biomarkers for predicting clinical behavior and the selection of the appropriate treatment strategy for individual patient.We and another group found that periostin, a matricellular protein expressed specifically in areas of ongoing fibrotic lesions, such as fibroblastic foci in lung tissues from human IPF or murine bleomycin-induced lung injury models. Murine bleomycin-induced lung injury was improved by the constant suppression of periostin expression and treatment with neutralizing anti-periostin antibodies at the fibroproliferative phase. Moreover, total periostin can predict both short-term declines of pulmonary function and overall survival in IPF patients. Our group also established a new enzyme-linked immunosorbent assay (ELISA) kit that is more specific for IPF compared with the conventional kit. This new periostin ELISA kit specifically detects monomeric form, whereas the conventional kit detects both monomeric and oligomeric forms. The monomeric periostin levels can be used to predict pulmonary function decline and to distinguish IPF patients from healthy controls.In conclusion, periostin may play an important role in fibrogenesis and could be a potential biomarker for predicting disease progression and therapeutic effect in IPF patients.
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41
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Chambers DM, Moretti L, Zhang JJ, Cooper SW, Chambers DM, Santangelo PJ, Barker TH. LEM domain-containing protein 3 antagonizes TGFβ-SMAD2/3 signaling in a stiffness-dependent manner in both the nucleus and cytosol. J Biol Chem 2018; 293:15867-15886. [PMID: 30108174 DOI: 10.1074/jbc.ra118.003658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/31/2018] [Indexed: 12/28/2022] Open
Abstract
Transforming growth factor-β (TGFβ) signaling through SMAD2/3 is an important driver of pathological fibrosis in multiple organ systems. TGFβ signaling and extracellular matrix (ECM) stiffness form an unvirtuous pathological circuit in which matrix stiffness drives activation of latent TGFβ, and TGFβ signaling then drives cellular stress and ECM synthesis. Moreover, ECM stiffness also appears to sensitize cells to exogenously activated TGFβ through unknown mechanisms. Here, using human fibroblasts, we explored the effect of ECM stiffness on a putative inner nuclear membrane protein, LEM domain-containing protein 3 (LEMD3), which is physically connected to the cell's actin cytoskeleton and inhibits TGFβ signaling. We showed that LEMD3-SMAD2/3 interactions are inversely correlated with ECM stiffness and TGFβ-driven luciferase activity and that LEMD3 expression is correlated with the mechanical response of the TGFβ-driven luciferase reporter. We found that actin polymerization but not cellular stress or LEMD3-nuclear-cytoplasmic couplings were necessary for LEMD3-SMAD2/3 interactions. Intriguingly, LEMD3 and SMAD2/3 frequently interacted in the cytosol, and we discovered LEMD3 was proteolytically cleaved into protein fragments. We confirmed that a consensus C-terminal LEMD3 fragment binds SMAD2/3 in a stiffness-dependent manner throughout the cell and is sufficient for antagonizing SMAD2/3 signaling. Using human lung biopsies, we observed that these nuclear and cytosolic interactions are also present in tissue and found that fibrotic tissues exhibit locally diminished and cytoplasmically shifted LEMD3-SMAD2/3 interactions, as noted in vitro Our work reveals novel LEMD3 biology and stiffness-dependent regulation of TGFβ by LEMD3, providing a novel target to antagonize pathological TGFβ signaling.
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Affiliation(s)
- Dwight M Chambers
- From the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia 30332
| | - Leandro Moretti
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, and
| | - Jennifer J Zhang
- From the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia 30332
| | - Spencer W Cooper
- From the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia 30332
| | - Davis M Chambers
- the College of Arts and Sciences, Georgia State University, Atlanta, Georgia 30303
| | - Philip J Santangelo
- From the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia 30332
| | - Thomas H Barker
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, and
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42
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Barretto KT, Swanson CM, Nguyen CL, Annis DS, Esnault SJ, Mosher DF, Johansson MW. Control of cytokine-driven eosinophil migratory behavior by TGF-beta-induced protein (TGFBI) and periostin. PLoS One 2018; 13:e0201320. [PMID: 30048528 PMCID: PMC6062114 DOI: 10.1371/journal.pone.0201320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 01/05/2023] Open
Abstract
Periostin, which is induced by interleukin (IL)-13, is an extracellular matrix (ECM) protein that supports αMβ2 integrin-mediated adhesion and migration of IL-5-stimulated eosinophils. Transforming growth factor (TGF)-β-induced protein (TGFBI) is a widely expressed periostin paralog known to support monocyte adhesion. Our objective was to compare eosinophil adhesion and migration on TGFBI and periostin in the presence of IL-5-family cytokines. Eosinophil adhesion after 1 h and random motility over 20 h in the presence of various concentrations of IL-5, IL-3, or granulocyte macrophage-colony stimulating factor (GM-CSF) were quantified in wells coated with various concentrations of TGFBI or periostin. Results were compared to video microscopy of eosinophils. Cytokine-stimulated eosinophils adhered equivalently well to TGFBI or periostin in a coating concentration-dependent manner. Adhesion was blocked by anti-αMβ2 and stimulated at the lowest concentration by GM-CSF. In the motility assay, periostin was more potent than TGFBI, the coating-concentration effect was bimodal, and IL-3 was the most potent cytokine. Video microscopy revealed that under the optimal coating condition of 5 μg/ml periostin, most eosinophils migrated persistently and were polarized and acorn-shaped with a ruffling forward edge and granules gathered together, in front of the nucleus. On 10 μg/ml periostin or TGFBI, more eosinophils adopted a flattened pancake morphology with dispersed granules and nuclear lobes, and slower migration. Conversion between acorn and pancake morphologies were observed. We conclude that TGFBI or periostin supports two modes of migration by IL-5 family cytokine-activated eosinophils. The rapid mode is favored by intermediate protein coatings and the slower by higher coating concentrations. We speculate that eosinophils move by haptotaxis up a gradient of adhesive ECM protein and then slow down to surveil the tissue.
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Affiliation(s)
- Karina T. Barretto
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Calvin M. Swanson
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christopher L. Nguyen
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Douglas S. Annis
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Stephane J. Esnault
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Deane F. Mosher
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mats W. Johansson
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
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43
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Rodriguez LR, Emblom-Callahan M, Chhina M, Bui S, Aljeburry B, Tran LH, Novak R, Lemma M, Nathan SD, Grant GM. Global Gene Expression Analysis in an in vitro Fibroblast Model of Idiopathic Pulmonary Fibrosis Reveals Potential Role for CXCL14/CXCR4. Sci Rep 2018; 8:3983. [PMID: 29507348 PMCID: PMC5838110 DOI: 10.1038/s41598-018-21889-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a progressive disorder that is marked by an over accumulation of activated fibroblast populations. Despite the improved understanding of many mechanisms within this disease, global gene expression analysis has few focused studies on the fibroblast, the central effector cell of progressive fibrosis. We present a unique analysis of IPF pulmonary fibroblasts as they transition through cell culture and identify in vitro altered cellular processes. Fibroblasts were isolated from diseased (n = 8) and non-diseased (n = 4) lungs. Global gene expression analysis was carried out at the initial point of isolation and after 3 weeks of culture. We identify several genes that are altered by removal of the fibroblast from the IPF environment. Comparison of this subset of genes to four previously published whole lung analyses refined our list to a small subset of key fibroblast specific genes important in IPF. Application of STRING database analysis and confirmation via in-vitro and histological assay highlights the CXCL14/CXCR4 chemokine axis with a possible role in the progression and/or activation of fibroblasts within the IPF lung. Our findings, present a possible therapeutic target for IPF and a model for the study and discovery of novel protein and processes in this terrible disease.
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Affiliation(s)
- Luis R Rodriguez
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | | | - Mantej Chhina
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | - Sarah Bui
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | - Bilal Aljeburry
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | - Luc H Tran
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | - Rebecca Novak
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA
| | - Merte Lemma
- Inova Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Steven D Nathan
- Inova Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Geraldine M Grant
- Department of Biology, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA.
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44
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Chen J, Yao Y, Su X, Shi Y, Song X, Xie L, You J, Tian L, Yang L, Fang A, Xiong J. Comparative RNA-Seq transcriptome analysis on silica induced pulmonary inflammation and fibrosis in mice silicosis model. J Appl Toxicol 2018; 38:773-782. [PMID: 29341224 DOI: 10.1002/jat.3587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/08/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023]
Abstract
Silicosis is a long-established public health issue in developing countries due to increasingly serious air pollution and poorly implemented occupational safety regulation. Inhalation of silica triggers cytotoxicity, oxidative stress, pulmonary inflammation and eventually silicosis. Current understanding in the pathogenesis and mechanism of silicosis is limited, and no effective cure is clinically available once silicosis is developed. A number of studies were conducted to investigate silica-induced alternate gene expressions in pulmonary cells. However, transcriptome analysis in a silicosis animal model is needed. This study was performed to evaluate the transcriptional alternations in silicotic mice using comparative RNA-Seq. A silicosis mice model was established by intratracheal instillation of silica suspensions, and validated by histological examinations. High-throughput sequencing and differential gene expression analysis revealed 749 upregulated genes and 70 downregulated genes in the silicosis model. Genes related to immune cell interactions, immune cell responses and inflammation were significantly enriched. Cytokine-cytokine receptor interaction and downstream JAK-STAT signaling pathways were the most significantly enriched KEGG pathways. Reverse transcription-polymerase chain reaction analysis and immunohistochemistry were performed to validate further the differential expression patterns of representative genes. The reported results in this study provide the basis for elucidating the molecular mechanisms for silica-induced pulmonary inflammation and fibrosis, and support the prevention and treatment of silicosis.
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Affiliation(s)
- Jiayi Chen
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Yuqin Yao
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China.,Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaolan Su
- Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ying Shi
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Xuejiao Song
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Linshen Xie
- Research Center for Occupational Respiratory Diseases, No.4 West China Teaching Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Liantian Tian
- Research Center for Occupational Respiratory Diseases, No.4 West China Teaching Hospital, Sichuan University, Chengdu, 610041, China
| | - Luo Yang
- Research Center for Occupational Respiratory Diseases, No.4 West China Teaching Hospital, Sichuan University, Chengdu, 610041, China
| | - Aiping Fang
- Research Center for Occupational Respiratory Diseases, No.4 West China Teaching Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingyuan Xiong
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, 610041, China
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45
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Transcriptomic evidence of immune activation in macroscopically normal-appearing and scarred lung tissues in idiopathic pulmonary fibrosis. Cell Immunol 2018; 325:1-13. [PMID: 29329637 DOI: 10.1016/j.cellimm.2018.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/19/2017] [Accepted: 01/02/2018] [Indexed: 12/16/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease manifested by overtly scarred peripheral and basilar regions and more normal-appearing central lung areas. Lung tissues from macroscopically normal-appearing (IPFn) and scarred (IPFs) areas of explanted IPF lungs were analyzed by RNASeq and compared with healthy control (HC) lung tissues. There were profound transcriptomic changes in IPFn compared with HC tissues, which included elevated expression of numerous immune-, inflammation-, and extracellular matrix-related mRNAs, and these changes were similar to those observed with IPFs compared to HC. Comparing IPFn directly to IPFs, elevated expression of epithelial mucociliary mRNAs was observed in the IPFs tissues. Thus, despite the known geographic tissue heterogeneity in IPF, the entire lung is actively involved in the disease process, and demonstrates pronounced elevated expression of numerous immune-related genes. Differences between normal-appearing and scarred tissues may thus be driven by deranged epithelial homeostasis or possibly non-transcriptomic factors.
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46
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Kudo A. Introductory review: periostin-gene and protein structure. Cell Mol Life Sci 2017; 74:4259-4268. [PMID: 28884327 PMCID: PMC11107487 DOI: 10.1007/s00018-017-2643-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 01/08/2023]
Abstract
Although many studies have described the role of periostin in various diseases, the function of the periostin protein structures derived from alternative splicing and proteinase cleavage at the C-terminal remain unknown. Further experiments revealing the protein structures that are highly related to diseases are essential to understand the function of periostin in depth, which would accelerate its clinical application by establishing new approaches for curing intractable diseases. Furthermore, this understanding would enhance our knowledge of novel functions of periostin related to stemness and response to mechanical stress.
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Affiliation(s)
- Akira Kudo
- International Frontier, Tokyo Institute of Technology, S3-8, 2-12-1 Oookayama, Meguro-ku, Tokyo, 152-8550, Japan.
- Department of Pharmacology, School of Dentistry, Showa University, Tokyo, 142-8555, Japan.
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47
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Izuhara K, Nunomura S, Nanri Y, Ogawa M, Ono J, Mitamura Y, Yoshihara T. Periostin in inflammation and allergy. Cell Mol Life Sci 2017; 74:4293-4303. [PMID: 28887633 PMCID: PMC11107676 DOI: 10.1007/s00018-017-2648-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 12/26/2022]
Abstract
We found for the first time that IL-4 and IL-13, signature type 2 cytokines, are able to induce periostin expression. We and others have subsequently shown that periostin is highly expressed in chronic inflammatory diseases-asthma, atopic dermatitis, eosinophilc chronic sinusitis/chronic rhinosinusitis with nasal polyp, and allergic conjunctivitis-and that periostin plays important roles in the pathogenesis of these diseases. The epithelial/mesenchymal interaction via periostin is important for the onset of allergic inflammation, in which periostin derived from fibroblasts acts on epithelial cells or fibroblasts, activating their NF-κB. Moreover, the immune cell/non-immune cell interaction via periostin may be also involved. Now the significance of periostin has been expanded into other inflammatory or fibrotic diseases such as scleroderma and pulmonary fibrosis. The cross-talk of periostin with TGF-β or pro-inflammatory cytokines is important for the underlying mechanism of these diseases. Because of its pathogenic importance and broad expression, diagnostics or therapeutic drugs can be potentially developed to target periostin as a means of treating these diseases.
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Affiliation(s)
- Kenji Izuhara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan.
| | - Satoshi Nunomura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
| | - Yasuhiro Nanri
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
| | - Masahiro Ogawa
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
| | - Junya Ono
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
- Shino-Test Corporation, 2-29-14, Oonodai, Sagamihara, 229-0011, Japan
| | - Yasutaka Mitamura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
| | - Tomohito Yoshihara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, 5-1-1, Nabeshima, Saga, 849-8501, Japan
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48
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Karhadkar TR, Pilling D, Cox N, Gomer RH. Sialidase inhibitors attenuate pulmonary fibrosis in a mouse model. Sci Rep 2017; 7:15069. [PMID: 29118338 PMCID: PMC5678159 DOI: 10.1038/s41598-017-15198-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/23/2017] [Indexed: 01/14/2023] Open
Abstract
Fibrosis involves increasing amounts of scar tissue appearing in a tissue, but what drives this is unclear. In fibrotic lesions in human and mouse lungs, we found extensive desialylation of glycoconjugates, and upregulation of sialidases. The fibrosis-associated cytokine TGF-β1 upregulates sialidases in human airway epithelium cells, lung fibroblasts, and immune system cells. Conversely, addition of sialidases to human peripheral blood mononuclear cells induces accumulation of extracellular TGF-β1, forming what appears to be a sialidase - TGF-β1 - sialidase positive feedback loop. Monocyte-derived cells called fibrocytes also activate fibroblasts, and we found that sialidases potentiate fibrocyte differentiation. A sialylated glycoprotein called serum amyloid P (SAP) inhibits fibrocyte differentiation, and sialidases attenuate SAP function. Injections of the sialidase inhibitors DANA and oseltamivir (Tamiflu) starting either 1 day or 10 days after bleomycin strongly attenuate pulmonary fibrosis in the mouse bleomycin model, and by breaking the feedback loop, cause a downregulation of sialidase and TGF-β1 accumulation. Together, these results suggest that a positive feedback loop involving sialidases potentiates fibrosis, and suggest that sialidase inhibitors could be useful for the treatment of fibrosis.
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Affiliation(s)
- Tejas R Karhadkar
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Darrell Pilling
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Richard H Gomer
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA.
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49
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Herrmann FE, Wollin L, Wirth J, Gantner F, Lämmle B, Wex E. Olodaterol shows anti-fibrotic efficacy in in vitro and in vivo models of pulmonary fibrosis. Br J Pharmacol 2017; 174:3848-3864. [PMID: 28810065 DOI: 10.1111/bph.13982] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND AND PURPOSE Idiopathic pulmonary fibrosis (IPF) is a fatal respiratory disease characterized by excessive fibroblast activation ultimately leading to scarring of the lungs. Although, the activation of β2 -adrenoceptors (β2 -AR) has been shown to inhibit pro-fibrotic events primarily in cell lines, the role of β2 -adrenoceptor agonists has not yet been fully characterized. The aim of our study was to explore the anti-fibrotic activity of the long-acting β2 -adrenoceptor agonist olodaterol in primary human lung fibroblasts (HLF) and in murine models of pulmonary fibrosis. EXPERIMENTAL APPROACH We assessed the activity of olodaterol to inhibit various pro-fibrotic mechanisms, induced by different pro-fibrotic mediators, in primary HLF from control donors and patients with IPF (IPF-LF). The in vivo anti-fibrotic activity of olodaterol, given once daily by inhalation in either a preventive or therapeutic treatment regimen, was explored in murine models of lung fibrosis induced by either bleomycin or the overexpression of TGF-β1. KEY RESULTS In both HLF and IPF-LF, olodaterol attenuated TGF-β-induced expression of α-smooth muscle actin, fibronectin and endothelin-1 (ET-1), FGF- and PDGF-induced motility and proliferation and TGF-β/ET-1-induced contraction. In vivo olodaterol significantly attenuated the bleomycin-induced increase in lung weight, reduced bronchoalveolar lavage cell counts and inhibited release of pro-fibrotic mediators (TGF-ß, MMP-9 and tissue inhibitor of metalloproteinase-1). Forced vital capacity was increased only with the preventive treatment regimen. In the TGF-β-overexpressing model, olodaterol additionally reduced the Col3A1 mRNA expression. CONCLUSION AND IMPLICATIONS Olodaterol showed anti-fibrotic properties in primary HLF from control and IPF patients and in murine models of lung fibrosis.
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Affiliation(s)
- Franziska Elena Herrmann
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Lutz Wollin
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Johannes Wirth
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Florian Gantner
- Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Bärbel Lämmle
- Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Eva Wex
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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O'Dwyer DN, Moore BB. The role of periostin in lung fibrosis and airway remodeling. Cell Mol Life Sci 2017; 74:4305-4314. [PMID: 28918442 DOI: 10.1007/s00018-017-2649-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022]
Abstract
Periostin is a protein that plays a key role in development and repair within the biological matrix of the lung. As a matricellular protein that does not contribute to extracellular matrix structure, periostin interacts with other extracellular matrix proteins to regulate the composition of the matrix in the lung and other organs. In this review, we discuss the studies exploring the role of periostin to date in chronic respiratory diseases, namely asthma and idiopathic pulmonary fibrosis. Asthma is a major health problem globally affecting millions of people worldwide with significant associated morbidity and mortality. Periostin is highly expressed in the lungs of asthmatic patients, contributes to mucus secretion, airway fibrosis and remodeling and is recognized as a biomarker of Th2 high inflammation. Idiopathic pulmonary fibrosis is a fatal interstitial lung disease characterized by progressive aberrant fibrosis of the lung matrix and respiratory failure. It predominantly affects adults over 50 years of age and its incidence is increasing worldwide. Periostin is also highly expressed in the lungs of idiopathic pulmonary fibrosis patients. Serum levels of periostin may predict clinical progression in this disease and periostin promotes myofibroblast differentiation and type 1 collagen production to contribute to aberrant lung fibrosis. Studies to date suggest that periostin is a key player in several pathogenic mechanisms within the lung and may provide us with a useful biomarker of clinical progression in both asthma and idiopathic pulmonary fibrosis.
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Affiliation(s)
- David N O'Dwyer
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, 4053 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Bethany B Moore
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, 4053 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA. .,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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