51
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Zhang N, Wang H, Xie Q, Cao H, Wu F, Di Wu DB, Wan Y. Identification of potential diagnostic and therapeutic target genes for lung squamous cell carcinoma. Oncol Lett 2019; 18:169-180. [PMID: 31289486 PMCID: PMC6539486 DOI: 10.3892/ol.2019.10300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022] Open
Abstract
The purpose of this study was to identify potential molecular markers of lung squamous cell carcinoma (LUSC). Three datasets containing LUSC mRNA sequencing data were downloaded from the Gene Expression Omnibus, The Cancer Genome Atlas and the Gene Expression Profiling Interactive Analysis databases. These datasets were used to identify significantly differentially expressed genes (DEGs) in LUSC. A protein-protein interaction network of the DEGs was constructed followed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and overall survival analyses of the DEGs. A total of 37 DEGs between LUSC and normal tissues were identified, including 26 downregulated genes and 11 upregulated genes. Biological Process enrichment analysis revealed that the DEGs were mainly enriched in ‘cell adhesion’, ‘cell-matrix adhesion’, ‘anatomical structure morphogenesis’, ‘ECM-receptor interaction’ and ‘focal adhesion’. Overall survival analysis demonstrated that transcription factor 21, α-2-macroglobulin, acyl-CoA synthetase long chain family member 5, integrin subunit β8, meiotic nuclear divisions 1 and secretoglobin family 1A member 1 were significantly associated with the occurrence and development of lung cancer, and these genes were selected as hub genes. The results obtained in the present study may aid the elucidation of the molecular mechanisms involved in the development of LUSC and may provide potential targets for LUSC treatment.
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Affiliation(s)
- Nana Zhang
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Hong Wang
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Qiqi Xie
- Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Hua Cao
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Fanqi Wu
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Dan Bei Di Wu
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yixin Wan
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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52
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Wang H, Xie Q, Ou-Yang W, Zhang M. Integrative analyses of genes associated with idiopathic pulmonary fibrosis. J Cell Biochem 2019; 120:8648-8660. [PMID: 30506760 DOI: 10.1002/jcb.28153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/09/2018] [Indexed: 01/24/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF), characterized by irreversible scarring and progressive destruction of the lung tissue, is one of the most common types of idiopathic interstitial pneumonia worldwide. However, there are no reliable candidates for curative therapies. Hence, elucidation of the mechanisms of IPF genesis and exploration of potential biomarkers and prognostic indicators are essential for accurate diagnosis and treatment of IPF. Recently, efficient microarray and bioinformatics analyses have promoted an understanding of the molecular mechanisms of disease occurrence and development, which is necessary to explore genetic alternations and identify potential diagnostic biomarkers. However, high false-positive rates results have been observed based on single microarray datasets. In the current study, we performed a comprehensive analysis of the differential expression, biological functions, and interactions of IPF-related genes. Three publicly available microarray datasets including 54 IPF samples and 34 normal samples were integrated by performing gene set enrichment analysis and analyzing differentially expressed genes (DEGs). Our results identified 350 DEGs genetically associated with IPF. Gene ontology analyses revealed that the changes in the modules were mostly enriched in the positive regulation of smooth muscle cell proliferation, positive regulation of inflammatory responses, and the extracellular space. Kyoto encyclopedia of genes and genomes enrichment analysis of DEGs revealed that IPF involves the TNF signaling pathway, NOD-like receptor signaling pathway, and PPAR signaling pathway. To identify key genes related to IPF in the protein-protein interaction network, 20 hub genes were screened out with highest scores. Our results provided a framework for developing new pathological molecular networks related to specific diseases in silico.
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Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, State Key Laboratory of Medical Neurobiology, Institute of Brain Science, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Qiqi Xie
- Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Wen Ou-Yang
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Mingwei Zhang
- Department of Radiotherapy, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, PR China
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53
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Yao L, Conforti F, Hill C, Bell J, Drawater L, Li J, Liu D, Xiong H, Alzetani A, Chee SJ, Marshall BG, Fletcher SV, Hancock D, Coldwell M, Yuan X, Ottensmeier CH, Downward J, Collins JE, Ewing RM, Richeldi L, Skipp P, Jones MG, Davies DE, Wang Y. Paracrine signalling during ZEB1-mediated epithelial-mesenchymal transition augments local myofibroblast differentiation in lung fibrosis. Cell Death Differ 2019; 26:943-957. [PMID: 30050057 PMCID: PMC6252080 DOI: 10.1038/s41418-018-0175-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023] Open
Abstract
The contribution of epithelial-mesenchymal transition (EMT) to human lung fibrogenesis is controversial. Here we provide evidence that ZEB1-mediated EMT in human alveolar epithelial type II (ATII) cells contributes to the development of lung fibrosis by paracrine signalling to underlying fibroblasts. Activation of EGFR-RAS-ERK signalling in ATII cells induced EMT via ZEB1. ATII cells had extremely low extracellular matrix gene expression even after induction of EMT, however conditioned media from ATII cells undergoing RAS-induced EMT augmented TGFβ-induced profibrogenic responses in lung fibroblasts. This epithelial-mesenchymal crosstalk was controlled by ZEB1 via the expression of tissue plasminogen activator (tPA). In human fibrotic lung tissue, nuclear ZEB1 expression was detected in alveolar epithelium adjacent to sites of extracellular matrix (ECM) deposition, suggesting that ZEB1-mediated paracrine signalling has the potential to contribute to early fibrotic changes in the lung interstitium. Targeting this novel ZEB1 regulatory axis may be a viable strategy for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Liudi Yao
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Franco Conforti
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Charlotte Hill
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joseph Bell
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Leena Drawater
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Juanjuan Li
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dian Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Aiman Alzetani
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- Department of Thoracic Surgery, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Serena J Chee
- University Hospital Southampton, Southampton, SO16 6YD, UK
- Cancer Sciences & NIHR and CRUK Experimental Cancer Sciences Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Ben G Marshall
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Sophie V Fletcher
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- University Hospital Southampton, Southampton, SO16 6YD, UK
| | - David Hancock
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mark Coldwell
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Christian H Ottensmeier
- Cancer Sciences & NIHR and CRUK Experimental Cancer Sciences Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Julian Downward
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Jane E Collins
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Rob M Ewing
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Luca Richeldi
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- Unità Operativa Complessa di Pneumologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico A. Gemelli, Rome, Italy
| | - Paul Skipp
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Proteomic Research, Institute for Life Sciences University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark G Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Donna E Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yihua Wang
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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54
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Ammar R, Sivakumar P, Jarai G, Thompson JR. A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection. PLoS One 2019; 14:e0215565. [PMID: 30998768 PMCID: PMC6472794 DOI: 10.1371/journal.pone.0215565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease affecting ~5 million people globally. We have constructed an accurate model of IPF disease status using elastic net regularized regression on clinical gene expression data. Leveraging whole transcriptome microarray data from 230 IPF and 89 control samples from Yang et al. (2013), sourced from the Lung Tissue Research Consortium (LTRC) and National Jewish Health (NJH) cohorts, we identify an IPF gene expression signature. We performed optimal feature selection to reduce the number of transcripts required by our model to a parsimonious set of 15. This signature enables our model to accurately separate IPF patients from controls. Our model outperforms existing published models when tested with multiple independent clinical cohorts. Our study underscores the utility of elastic nets for gene signature/panel selection which can be used for the construction of a multianalyte biomarker of disease. We also filter the gene sets used for model input to construct a model reliant on secreted proteins. Using this approach, we identify the preclinical bleomycin rat model that is most congruent with human disease at day 21 post-bleomycin administration, contrasting with earlier timepoints suggested by other studies.
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Affiliation(s)
- Ron Ammar
- Translational Bioinformatics, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, United States of America
- * E-mail:
| | - Pitchumani Sivakumar
- Fibrosis, Translational Research & Development, Bristol-Myers Squibb, Princeton, NJ, United States of America
| | - Gabor Jarai
- Fibrosis, Translational Research & Development, Bristol-Myers Squibb, Princeton, NJ, United States of America
| | - John Ryan Thompson
- Translational Bioinformatics, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, United States of America
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55
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Sheu CC, Chang WA, Tsai MJ, Liao SH, Chong IW, Kuo PL. Bioinformatic analysis of next‑generation sequencing data to identify dysregulated genes in fibroblasts of idiopathic pulmonary fibrosis. Int J Mol Med 2019; 43:1643-1656. [PMID: 30720061 PMCID: PMC6414167 DOI: 10.3892/ijmm.2019.4086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/29/2019] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease with an increasing global burden. It is hypothesized that fibroblasts have a number of functions that may affect the development and progression of IPF. However, the present understanding of cellular and molecular mechanisms associated with fibroblasts in IPF remains limited. The present study aimed to identify the dysregulated genes in IPF fibroblasts, elucidate their functions and explore potential microRNA (miRNA)-mRNA interactions. mRNA and miRNA expression profiles were obtained from IPF fibroblasts and normal lung fibroblasts using a next-generation sequencing platform, and bioinformatic analyses were performed in a step-wise manner. A total of 42 dysregulated genes (>2 fold-change of expression) were identified, of which 5 were verified in the Gene Expression Omnibus (GEO) database analysis, including the upregulation of neurotrimin (NTM), paired box 8 (PAX8) and mesoderm development LRP chaperone, and the downregulation of ITPR interacting domain containing 2 and Inka box actin regulator 2 (INKA2). Previous data indicated that PAX8 and INKA2 serve roles in cell growth, proliferation and survival. Gene Ontology analysis indicated that the most significant function of these 42 dysregulated genes was associated with the composition and function of the extracellular matrix (ECM). A total of 60 dysregulated miRNAs were also identified, and 1,908 targets were predicted by the miRmap database. The integrated analysis of mRNA and miRNA expression data, combined with GEO verification, finally identified Homo sapiens (hsa)-miR-1254-INKA2 and hsa-miR-766-3p-INKA2 as the potential miRNA-mRNA interactions in IPF fibroblasts. In summary, the results of the present study suggest that dysregulation of PAX8, hsa-miR-1254-INKA2 and hsa-miR-766-3p-INKA2 may promote the proliferation and survival of IPF fibroblasts. In the functional analysis of the dysregulated genes, a marked association between fibroblasts and the ECM was identified. These data improve the current understanding of fibroblasts as key cells in the pathogenesis of IPF. As a screening study using bioinformatics approaches, the results of the present study require additional validation.
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Affiliation(s)
- Chau-Chyun Sheu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Ming-Ju Tsai
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Ssu-Hui Liao
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Inn-Wen Chong
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
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56
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Lodyga M, Cambridge E, Karvonen HM, Pakshir P, Wu B, Boo S, Kiebalo M, Kaarteenaho R, Glogauer M, Kapoor M, Ask K, Hinz B. Cadherin-11-mediated adhesion of macrophages to myofibroblasts establishes a profibrotic niche of active TGF-β. Sci Signal 2019; 12:12/564/eaao3469. [PMID: 30647145 DOI: 10.1126/scisignal.aao3469] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Macrophages contribute to the activation of fibroblastic cells into myofibroblasts, which secrete collagen and contract the collagen matrix to acutely repair injured tissue. Persistent myofibroblast activation leads to the accumulation of fibrotic scar tissue that impairs organ function. We investigated the key processes that turn acute beneficial repair into destructive progressive fibrosis. We showed that homotypic cadherin-11 interactions promoted the specific binding of macrophages to and persistent activation of profibrotic myofibroblasts. Cadherin-11 was highly abundant at contacts between macrophages and myofibroblasts in mouse and human fibrotic lung tissues. In attachment assays, cadherin-11 junctions mediated specific recognition and strong adhesion between macrophages and myofibroblasts. One functional outcome of cadherin-11-mediated adhesion was locally restricted activation of latent transforming growth factor-β (TGF-β) between macrophage-myofibroblast pairs that was not observed in cocultures of macrophages and myofibroblasts that were not in contact with one another. Our data suggest that cadherin-11 junctions maintain latent TGF-β-producing macrophages and TGF-β-activating myofibroblasts in close proximity to one another. Inhibition of homotypic cadherin-11 interactions could be used to cause macrophage-myofibroblast separation, thereby destabilizing the profibrotic niche.
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Affiliation(s)
- Monika Lodyga
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Elizabeth Cambridge
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Henna M Karvonen
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.,Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland
| | - Pardis Pakshir
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Brian Wu
- Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5T 2S8, Canada.,Arthritis Program, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Stellar Boo
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Melanie Kiebalo
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Riitta Kaarteenaho
- Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Mohit Kapoor
- Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5T 2S8, Canada.,Arthritis Program, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kjetil Ask
- Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, Hamilton, Ontario L8N 4A6, Canada
| | - Boris Hinz
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada. .,Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland.,Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
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57
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Wang L, Huang W, Zhang L, Chen Q, Zhao H. Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network. Mol Med Rep 2018; 18:4365-4373. [PMID: 30221703 PMCID: PMC6172385 DOI: 10.3892/mmr.2018.9456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/06/2018] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is considered to be an ailment of the lungs that cannot be cured, wherein the lung tissues are characterized by increased thickness and stiffness, and/or scars. Despite the fact that extensive success has been achieved regarding the molecular diagnostics and pathobiology, the basic pathogenesis associated with IPF has not yet been fully elucidated and requires further clarification. In the current research, the changes in microRNA (miRNA) and mRNA expression in IPF were investigated through an integrative network technique. The authentic miRNA and mRNA expression profiling datasets were downloaded from Gene Expression Omnibus, followed by identification of differentially expressed miRNAs and mRNAs with use of the Significance Analysis of Microarrays algorithm. Expansion of the molecular targets associated with miRNAs was performed with the use of CyTargetLinker in Cytoscape, which was succeeded by validation with the use of mRNA array expression profiling. The incorporated miRNA‑mRNA network covered 27 genes, in addition to 22 miRNAs that were associated with IPF development. As revealed by the functional enrichment analysis, the cytokine‑cytokine receptor interaction and glycine, serine and threonine metabolism signalling pathways were extensively associated with IPF development. Overall, the present incorporated network illustrated the key link between miRNA and genes in IPF; in particular, it was elucidated that miR‑409‑5p and has‑miR‑376c, together with their target genes (C‑C motif chemokine ligand 20 and oncostatin M), are likely candidates involved in the promotion of IPF initiation and progression.
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Affiliation(s)
- Lijing Wang
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wei Huang
- Division of Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - Lemeng Zhang
- Department of Thoracic Oncology, Hunan Cancer Hospital, Changsha, Hunan 410008, P.R. China
| | - Qiong Chen
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hongjun Zhao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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58
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Díaz-Piña G, Ordoñez-Razo RM, Montes E, Páramo I, Becerril C, Salgado A, Santibañez-Salgado JA, Maldonado M, Ruiz V. The Role of ADAR1 and ADAR2 in the Regulation of miRNA-21 in Idiopathic Pulmonary Fibrosis. Lung 2018; 196:393-400. [PMID: 29637273 DOI: 10.1007/s00408-018-0115-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
INTRODUCTION microRNAs (miRNAs) are small non-coding 1RNAs that post-transcriptionally regulate gene expression. Recent evidence shows that adenosine deaminases that act on RNA (ADAR) can edit miRNAs. miRNAs are involved in the development of different diseases, such as idiopathic pulmonary fibrosis (IPF). In IPF, about 40% of the miRNAs are differentially expressed with respect to controls. Among these miRNAs, miRNA-21 has been found over-expressed in IPF and its targets are anti-fibrosing molecules such as PELI1 and SPRY2. The objective of this study is to determine the role of ADAR1 and 2 on the expression of miRNA-21 in human lung fibroblasts trough quantification of gene expression, protein levels, and overexpression of ADAR1 and 2. METHODS Six control and six fibrotic primary fibroblast cell cultures were used for RNA extraction, ADAR1, ADAR2, PELI1, SPRY2, miRNA-21, and pri-miRNA-21 expression was measured. Subsequently, two fibrotic fibroblast cultures were used for overexpression of ADAR1 and ADAR2, and they were stimulated with TGFβ1. Real-time PCR and Western blot were performed. RESULTS ADAR1 is significantly downregulated in IPF fibroblasts; the overexpression of ADAR1 and ADAR2 reestablishes the expression levels of miRNA-21, PELI1, and SPRY2 in fibroblasts of patients with IPF. CONCLUSION These changes in the processing of miRNAs have great value in pathology diagnosis, including lung diseases, and play an important role in the understanding of molecular mechanisms involved in the development of different pathologies, as well as representing new therapeutic targets.
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Affiliation(s)
- Gabriela Díaz-Piña
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Rosa Ma Ordoñez-Razo
- Hospital de Pediatría, Centro Médico Siglo XXI, Instituto Mexicano del Seguro Social, Unidad de Investigación Médica en Genética Humana, Av. Cuauhtémoc 330, Col. Doctores, 06720, Mexico City, Mexico
| | - Eduardo Montes
- Clínica de Asma, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Ignacio Páramo
- Clínica de Asma, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Carina Becerril
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Alfonso Salgado
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - J Alfredo Santibañez-Salgado
- Departamento de Cirugía Experimental, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Mariel Maldonado
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico
| | - Victor Ruiz
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico. .,Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calz. Tlalpan 4502, Col. Sección XVI, 14080, Mexico City, Mexico.
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59
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Kuo CHS, Liu CY, Pavlidis S, Lo YL, Wang YW, Chen CH, Ko HW, Chung FT, Lin TY, Wang TY, Lee KY, Guo YK, Wang TH, Yang CT. Unique Immune Gene Expression Patterns in Bronchoalveolar Lavage and Tumor Adjacent Non-Neoplastic Lung Tissue in Non-Small Cell Lung Cancer. Front Immunol 2018; 9:232. [PMID: 29483918 PMCID: PMC5816075 DOI: 10.3389/fimmu.2018.00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022] Open
Abstract
Background The immune cells in the local environments surrounding non-small cell lung cancer (NSCLC) implicate the balance of pro- and antitumor immunity; however, their transcriptomic profiles remain poorly understood. Methods A transcriptomic microarray study of bronchoalveolar lavage (BAL) cells harvested from tumor-bearing lung segments was performed in a discovery group. The findings were validated (1) in published microarray datasets, (2) in an independent group by RT-qPCR, and (3) in non-diseased and tumor adjacent non-neoplastic lung tissue by immunohistochemistry and in BAL cell lysates by immunoblotting. Result The differential expression of 129 genes was identified in the discovery group. These genes revealed functional enrichment in Fc gamma receptor-dependent phagocytosis and circulating immunoglobulin complex among others. Microarray datasets analysis (n = 607) showed that gene expression of BAL cells of tumor-bearing lung segment was also the unique transcriptomic profile of tumor adjacent non-neoplastic lung of early stage NSCLC and a significantly gradient increase of immunoglobulin genes’ expression for non-diseased lungs, tumor adjacent non-neoplastic lungs, and tumors was identified (ANOVA, p < 2 × 10−16). A 53-gene signature was determined with significant correlation with inhibitory checkpoint PDCD1 (r = 0.59, p = 0.0078) among others, where the nine top genes including IGJ and IGKC were RT-qPCR validated with high diagnostic performance (AUC: 0.920, 95% CI: 0.831–0.985, p = 2.98 × 10−7). Increased staining and expression of IGKC revealed by immunohistochemistry and immunoblotting in tumor adjacent non-neoplastic lung tissues (Wilcoxon signed-rank test, p < 0.001) and in BAL cell lysates (p < 0.01) of NSCLC, respectively, were noted. Conclusion The BAL cells of tumor-bearing lung segments and tumor adjacent non-neoplastic lung tissues present a unique gene expression characterized by IGKC in relation to inhibitory checkpoints. Further study of humoral immune responses to NSCLC is warranted.
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Affiliation(s)
- Chih-Hsi Scott Kuo
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan.,Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Chien-Ying Liu
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Stelios Pavlidis
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Yu-Lun Lo
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yen-Wen Wang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Chih-Hung Chen
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - How-Wen Ko
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Fu-Tsai Chung
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tin-Yu Lin
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tsai-Yu Wang
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Kang-Yun Lee
- Division of Thoracic Medicine, Taipei Medical University Shuang Ho Hospital, New Taipei City, Taiwan
| | - Yi-Ke Guo
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Tzu-Hao Wang
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Cheng-Ta Yang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
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60
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Wang Y, Yella J, Chen J, McCormack FX, Madala SK, Jegga AG. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulm Med 2017; 17:133. [PMID: 29058630 PMCID: PMC5649521 DOI: 10.1186/s12890-017-0472-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/01/2017] [Indexed: 12/30/2022] Open
Abstract
Background Idiopathic Pulmonary Fibrosis (IPF) is a fatal fibrotic lung disease occurring predominantly in middle-aged and older adults. The traditional diagnostic classification of IPF is based on clinical, radiological, and histopathological features. However, the considerable heterogeneity in IPF presentation suggests that differences in gene expression profiles can help to characterize and distinguish disease severity. Methods We used data-driven unsupervised clustering analysis, combined with a knowledge-based approach to identify and characterize IPF subgroups. Results Using transcriptional profiles on lung tissue from 131 patients with IPF/UIP and 12 non-diseased controls, we identified six subgroups of IPF that generally correlated with the disease severity and lung function decline. Network-informed clustering identified the most severe subgroup of IPF that was enriched with genes regulating inflammatory processes, blood pressure and branching morphogenesis of the lung. The differentially expressed genes in six subgroups of IPF compared to healthy control include transcripts of extracellular matrix, epithelial-mesenchymal cell cross-talk, calcium ion homeostasis, and oxygen transport. Further, we compiled differentially expressed gene signatures to identify unique gene clusters that can segregate IPF from normal, and severe from mild IPF. Additional validations of these signatures were carried out in three independent cohorts of IPF/UIP. Finally, using knowledge-based approaches, we identified several novel candidate genes which may also serve as potential biomarkers of IPF. Conclusions Discovery of unique and redundant gene signatures for subgroups in IPF can be greatly facilitated through unsupervised clustering. Findings derived from such gene signatures may provide insights into pathogenesis of IPF and facilitate the development of clinically useful biomarkers. Electronic supplementary material The online version of this article (10.1186/s12890-017-0472-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jaswanth Yella
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francis X McCormack
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Satish K Madala
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH, USA.
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61
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease characterized by progressive lung scarring and the histological picture of usual interstitial pneumonia (UIP). It is associated with increasing cough and dyspnoea and impaired quality of life. IPF affects ∼3 million people worldwide, with incidence increasing dramatically with age. The diagnostic approach includes the exclusion of other interstitial lung diseases or overlapping conditions and depends on the identification of the UIP pattern, usually with high-resolution CT; lung biopsy might be required in some patients. The UIP pattern is predominantly bilateral, peripheral and with a basal distribution of reticular changes associated with traction bronchiectasis and clusters of subpleural cystic airspaces. The biological processes underlying IPF are thought to reflect an aberrant reparative response to repetitive alveolar epithelial injury in a genetically susceptible ageing individual, although many questions remain on how to define susceptibility. Substantial progress has been made in the understanding of the clinical management of IPF, with the availability of two pharmacotherapeutic agents, pirfenidone and nintedanib, that decrease physiological progression and likely improve progression-free survival. Current efforts are directed at identifying IPF early, potentially relying on combinations of biomarkers that include circulating factors, demographics and imaging data.
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62
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García-Heredia JM, Carnero A. The cargo protein MAP17 (PDZK1IP1) regulates the immune microenvironment. Oncotarget 2017; 8:98580-98597. [PMID: 29228712 PMCID: PMC5716752 DOI: 10.18632/oncotarget.21651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023] Open
Abstract
Inflammation is a complex defensive response activated after various harmful stimuli allowing the clearance of damaged cells and initiating healing and regenerative processes. Chronic, or pathological, inflammation is also one of the causes of neoplastic transformation and cancer development. MAP17 is a cargo protein that transports membrane proteins from the endoplasmic reticulum. Therefore, its overexpression may be linked to an excess of membrane proteins that may be recognized as an unwanted signal, triggering local inflammation. Therefore, we analyzed whether its overexpression is related to an inflammatory phenotype. In this work, we found a correlation between MAP17 expression and inflammatory phenotype in tumors and in other inflammatory diseases such as Crohn's disease, Barrett's esophagus, COPD or psoriasis. MAP17 expression correlated also with the markers of inflammation HLAs, BBS10, HERC2, ADNP and PYCARD. Furthermore, we found that MAP17 expression directly regulates NFAT2 and IL-6 activation, inducing the differentiation of monocytes to dendritic cells and suggesting a causal role of MAP17 in inflammation. Immunohistochemistry confirms local inflammation, mainly CD45+ cells, at the site of expression of MAP17, at least in tumors, Crohn's and psoriasis. Therefore, our data indicates that the overexpression of the protein MAP17 plays important role in diseases involving chronic inflammation.
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Affiliation(s)
- José M García-Heredia
- Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, Seville, Spain.,Department of Vegetal Biochemistry and Molecular Biology, University of Seville, Seville, Spain.,CIBER de Cáncer, Instituto de Salud Carlos III, Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, Seville, Spain.,CIBER de Cáncer, Instituto de Salud Carlos III, Madrid, Spain
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63
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Karatzas E, Bourdakou MM, Kolios G, Spyrou GM. Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score. Sci Rep 2017; 7:12569. [PMID: 28974751 PMCID: PMC5626774 DOI: 10.1038/s41598-017-12849-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/14/2017] [Indexed: 12/19/2022] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a rare disease of the respiratory system in which the lungs stiffen and get scarred, resulting in breathing weakness and eventually leading to death. Drug repurposing is a process that provides evidence for existing drugs that may also be effective in different diseases. In this study, we present a computational pipeline having as input a number of gene expression datasets from early and advanced stages of IPF and as output lists of repurposed drugs ranked with a novel composite score. We have devised and used a scoring formula in order to rank the repurposed drugs, consolidating the standard repurposing score with structural, functional and side effects' scores for each drug per stage of IPF. The whole pipeline involves the selection of proper gene expression datasets, data preprocessing and statistical analysis, selection of the most important genes related to the disease, analysis of biological pathways, investigation of related molecular mechanisms, identification of fibrosis-related microRNAs, drug repurposing, structural and literature-based analysis of the repurposed drugs.
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Affiliation(s)
- E Karatzas
- Department of Informatics and Telecommunications, University of Athens, 15784, Ilissia Athens, Greece
| | - M M Bourdakou
- Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27, Athens, Greece
- Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Nicosia, 2370, Cyprus
| | - G Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - G M Spyrou
- Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Nicosia, 2370, Cyprus.
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64
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Murray LA, Habiel DM, Hohmann M, Camelo A, Shang H, Zhou Y, Coelho AL, Peng X, Gulati M, Crestani B, Sleeman MA, Mustelin T, Moore MW, Ryu C, Osafo-Addo AD, Elias JA, Lee CG, Hu B, Herazo-Maya JD, Knight DA, Hogaboam CM, Herzog EL. Antifibrotic role of vascular endothelial growth factor in pulmonary fibrosis. JCI Insight 2017; 2:92192. [PMID: 28814671 PMCID: PMC5621899 DOI: 10.1172/jci.insight.92192] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 07/06/2017] [Indexed: 01/07/2023] Open
Abstract
The chronic progressive decline in lung function observed in idiopathic pulmonary fibrosis (IPF) appears to result from persistent nonresolving injury to the epithelium, impaired restitution of the epithelial barrier in the lung, and enhanced fibroblast activation. Thus, understanding these key mechanisms and pathways modulating both is essential to greater understanding of IPF pathogenesis. We examined the association of VEGF with the IPF disease state and preclinical models in vivo and in vitro. Tissue and circulating levels of VEGF were significantly reduced in patients with IPF, particularly in those with a rapidly progressive phenotype, compared with healthy controls. Lung-specific overexpression of VEGF significantly protected mice following intratracheal bleomycin challenge, with a decrease in fibrosis and bleomycin-induced cell death observed in the VEGF transgenic mice. In vitro, apoptotic endothelial cell–derived mediators enhanced epithelial cell injury and reduced epithelial wound closure. This process was rescued by VEGF pretreatment of the endothelial cells via a mechanism involving thrombospondin-1 (TSP1). Taken together, these data indicate beneficial roles for VEGF during lung fibrosis via modulating epithelial homeostasis through a previously unrecognized mechanism involving the endothelium. Elevated VEGF is associated with less severe disease in IPF patients, and VEGF overexpression ameliorates bleomycin-induced lung fibrosis in a murine model.
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Affiliation(s)
| | - David M Habiel
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Miriam Hohmann
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ana Camelo
- MedImmune Ltd., Cambridge, England, United Kingdom
| | - Huilan Shang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yang Zhou
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ana Lucia Coelho
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Xueyan Peng
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mridu Gulati
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bruno Crestani
- APHP, Hôpital Bichat, Service de Pneumologie A, Centre de Compétences des Maladies Pulmonaires Rares, Paris, France Université Paris Diderot, Sorbonne Paris Cité, INSERM Unité 1152, Paris
| | | | | | - Meagan W Moore
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Changwan Ryu
- Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jack A Elias
- Warren Alpert School of Medicine, Providence, Rhode Island, USA
| | - Chun G Lee
- Warren Alpert School of Medicine, Providence, Rhode Island, USA
| | - Buqu Hu
- Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Darryl A Knight
- Viva program, Hunter Medical Research Institute, Newcastle, NSW, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Cory M Hogaboam
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Erica L Herzog
- Yale University School of Medicine, New Haven, Connecticut, USA
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65
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Chen C, Deng J, Yu X, Wu F, Men K, Yang Q, Zhu Y, Liu X, Jiang Q. Identification of novel inhibitors of DDR1 against idiopathic pulmonary fibrosis by integrative transcriptome meta-analysis, computational and experimental screening. MOLECULAR BIOSYSTEMS 2017; 12:1540-51. [PMID: 26956955 DOI: 10.1039/c5mb00911a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a kind of a chronic and fatal lung disease leading to progressive lung function decline. Although several RNA microarray studies on IPF patients have been reported, their results were merely specific to each study with distinct platforms or sample types. In the current study, an integrative transcriptome meta-analysis of IPF was performed to explore regulated pathways, based on four independent expression profiling microarrays of IPF datasets, including 73 samples from IPF tissues or lung fibroblast cells. The results suggested the discoidin domain receptor 1 (DDR1) and downstream c-Jun N-terminal kinases (JNK) pathway may play important roles in the progression of IPF. To our knowledge, discoidin domain receptor 1 (DDR1) is a kind of receptor tyrosine kinase (RTK) with a unique ability to bind both fibrillar and non-fibrillar collagens. Based on the crystallographic structures of DDR1, the combination of molecular dynamics simulation and a hybrid protocol of a virtual screening method, comprised of PBVS (multicomplex-pharmacophore based virtual screening) and DBVS (docking based virtual screening) methods were used for retrieving novel DDR1 inhibitors from the SPECS database. Twelve hit compounds were selected from the hit compounds and shifted to experimental validations, and the most potent compound was evaluated for its anti-IPF capacity on murine IPF models. Thus, these results may provide valuable information for further discovery of potential lead compounds for IPF therapy.
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Affiliation(s)
- Can Chen
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China.
| | - Jingjing Deng
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China.
| | - Xiaoping Yu
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China. and Department of Public Health, Chengdu Medical College, Chengdu, 610050, P. R. China
| | - Fengbo Wu
- State Key laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Ke Men
- State Key laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Qian Yang
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China.
| | - Yanfeng Zhu
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China. and Department of Public Health, Chengdu Medical College, Chengdu, 610050, P. R. China
| | - Xiaogang Liu
- Department of Gastroenterology, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, 610065, P. R. China
| | - Qinglin Jiang
- School of Pharmacy and the First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610050, P. R. China. and State Key laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
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66
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Walsh SLF. Multidisciplinary evaluation of interstitial lung diseases: current insights: Number 1 in the Series "Radiology" Edited by Nicola Sverzellati and Sujal Desai. Eur Respir Rev 2017; 26:26/144/170002. [PMID: 28515041 DOI: 10.1183/16000617.0002-2017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/18/2017] [Indexed: 11/05/2022] Open
Abstract
Multidisciplinary team (MDT) diagnosis is regarded as the diagnostic reference standard for interstitial lung disease (ILD). Several studies have reported that MDT diagnosis is associated with higher levels of diagnostic confidence and better interobserver agreement when compared to the individual components of the MDT in isolation. Although this recommendation is widely accepted, no guideline statement specifies what constitutes an MDT meeting and how its participants should govern it. Furthermore, the precise role of an MDT meeting in the setting of ILD may vary from one group to another. For example, in some cases, the meeting will confine its discussion to characterising the disease and formulating diagnosis. In others, management decisions may also be part of the discussion. Surprisingly, there is no consensus on how MDT diagnosis is validated. As multidisciplinary evaluation contains all the available clinical information on an individual patient, there is no reference standard against which the veracity of MDT diagnosis can be tested. Finally, many of these uncertainties surrounding MDT meeting practice are unlikely to be answered by traditional evidence-based studies, which create difficulties when generating guideline recommendations. There is clearly a need for expert consensus on what constitutes acceptable MDT meeting practice. This consensus will need to be flexible to accommodate the variability in resources available to fledgling MDT groups and the variable nature of patients requiring discussion.
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67
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Gangwar I, Kumar Sharma N, Panzade G, Awasthi S, Agrawal A, Shankar R. Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis. Sci Rep 2017; 7:1554. [PMID: 28484236 PMCID: PMC5431532 DOI: 10.1038/s41598-017-01765-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/12/2017] [Indexed: 01/22/2023] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is an incurable progressive fibrotic disease of the lungs. We currently lack a systematic understanding of IPF biology and a systems approach may offer new therapeutic insights. Here, for the first time, a large volume of high throughput genomics data has been unified to derive the most common molecular signatures of IPF. A set of 39 differentially expressed genes (DEGs) was found critical to distinguish IPF. Using high confidence evidences and experimental data, system level networks for IPF were reconstructed, involving 737 DEGs found common across at least two independent studies. This all provided one of the most comprehensive molecular system views for IPF underlining the regulatory and molecular consequences associated. 56 pathways crosstalks were identified which included critical pathways with specified directionality. The associated steps gained and lost due to crosstalk during IPF were also identified. A serially connected system of five crucial genes was found, potentially controlled by nine miRNAs and eight transcription factors exclusively in IPF when compared to NSIP and Sarcoidosis. Findings from this study have been implemented into a comprehensive molecular and systems database on IPF to facilitate devising diagnostic and therapeutic solutions for this deadly disease.
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Affiliation(s)
- Indu Gangwar
- Studio of Computational Biology & Bioinformatics, CSIR-IHBT, Palampur, HP, India.,Academy of Scientific and Innovative Research (AcSIR), Chennai, TN, India
| | - Nitesh Kumar Sharma
- Studio of Computational Biology & Bioinformatics, CSIR-IHBT, Palampur, HP, India.,Academy of Scientific and Innovative Research (AcSIR), Chennai, TN, India
| | - Ganesh Panzade
- Studio of Computational Biology & Bioinformatics, CSIR-IHBT, Palampur, HP, India.,Academy of Scientific and Innovative Research (AcSIR), Chennai, TN, India
| | - Supriya Awasthi
- Studio of Computational Biology & Bioinformatics, CSIR-IHBT, Palampur, HP, India
| | - Anurag Agrawal
- Centre of Excellence for Translational Research in Asthma & Lung Diseases, CSIR-IGIB, Mall Road, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Chennai, TN, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, CSIR-IHBT, Palampur, HP, India. .,Academy of Scientific and Innovative Research (AcSIR), Chennai, TN, India.
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Martinez FJ, Chisholm A, Collard HR, Flaherty KR, Myers J, Raghu G, Walsh SLF, White ES, Richeldi L. The diagnosis of idiopathic pulmonary fibrosis: current and future approaches. THE LANCET RESPIRATORY MEDICINE 2016; 5:61-71. [PMID: 27932290 DOI: 10.1016/s2213-2600(16)30325-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/20/2016] [Accepted: 09/22/2016] [Indexed: 12/13/2022]
Abstract
With the recent development of two effective treatments for patients with idiopathic pulmonary fibrosis, an accurate diagnosis is crucial. The traditional approach to diagnosis emphasises the importance of thorough clinical and laboratory evaluations to exclude secondary causes of disease. High-resolution CT is a critical initial diagnostic test and acts as a tool to identify patients who should undergo surgical lung biopsy to secure a definitive histological diagnosis of usual interstitial pneumonia pattern. This diagnostic approach faces several challenges. Many patients with suspected idiopathic pulmonary fibrosis present with atypical high-resolution CT characteristics but are unfit for surgical lung biopsy, therefore preventing a confident diagnosis. The state of the art suggests an iterative, multidisciplinary process that incorporates available clinical, laboratory, imaging, and histological features. Recent research has explored genomic techniques to molecularly phenotype patients with interstitial lung disease. In the future, clinicians will probably use blood-specific or lung-specific molecular markers in combination with other clinical, physiological, and imaging features to enhance diagnostic efforts, refine prognostic recommendations, and influence the initial or subsequent treatment options. There is an urgent and increasing need for well designed, large, prospective studies measuring the effect of different diagnostic approaches. Ultimately, this will help to inform the development of guidelines and tailor clinical practice for the benefit of patients.
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Affiliation(s)
- Fernando J Martinez
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA.
| | | | - Harold R Collard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kevin R Flaherty
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey Myers
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ganesh Raghu
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Simon L F Walsh
- Department of Radiology, Royal Brompton Hospital, London, UK
| | - Eric S White
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Luca Richeldi
- Catholic University of the Sacred Heart, A. Gemelli University Hospital, Rome, Italy; Academic Unit of Clinical and Experimental Sciences, NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
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69
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Kurowska-Stolarska M, Hasoo MK, Welsh DJ, Stewart L, McIntyre D, Morton BE, Johnstone S, Miller AM, Asquith DL, Millar NL, Millar AB, Feghali-Bostwick CA, Hirani N, Crick PJ, Wang Y, Griffiths WJ, McInnes IB, McSharry C. The role of microRNA-155/liver X receptor pathway in experimental and idiopathic pulmonary fibrosis. J Allergy Clin Immunol 2016; 139:1946-1956. [PMID: 27746237 PMCID: PMC5457127 DOI: 10.1016/j.jaci.2016.09.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 08/10/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is progressive and rapidly fatal. Improved understanding of pathogenesis is required to prosper novel therapeutics. Epigenetic changes contribute to IPF; therefore, microRNAs may reveal novel pathogenic pathways. Objectives We sought to determine the regulatory role of microRNA (miR)-155 in the profibrotic function of murine lung macrophages and fibroblasts, IPF lung fibroblasts, and its contribution to experimental pulmonary fibrosis. Methods Bleomycin-induced lung fibrosis in wild-type and miR-155−/− mice was analyzed by histology, collagen, and profibrotic gene expression. Mechanisms were identified by in silico and molecular approaches and validated in mouse lung fibroblasts and macrophages, and in IPF lung fibroblasts, using loss-and-gain of function assays, and in vivo using specific inhibitors. Results miR-155−/− mice developed exacerbated lung fibrosis, increased collagen deposition, collagen 1 and 3 mRNA expression, TGF-β production, and activation of alternatively activated macrophages, contributed by deregulation of the miR-155 target gene the liver X receptor (LXR)α in lung fibroblasts and macrophages. Inhibition of LXRα in experimental lung fibrosis and in IPF lung fibroblasts reduced the exacerbated fibrotic response. Similarly, enforced expression of miR-155 reduced the profibrotic phenotype of IPF and miR-155−/− fibroblasts. Conclusions We describe herein a molecular pathway comprising miR-155 and its epigenetic LXRα target that when deregulated enables pathogenic pulmonary fibrosis. Manipulation of the miR-155/LXR pathway may have therapeutic potential for IPF.
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Affiliation(s)
| | - Manhl K Hasoo
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - David J Welsh
- Scottish Pulmonary Vascular Unit, University of Glasgow, Glasgow, United Kingdom
| | - Lynn Stewart
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Donna McIntyre
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Brian E Morton
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Steven Johnstone
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ashley M Miller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Darren L Asquith
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Neal L Millar
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ann B Millar
- Academic Respiratory Unit, Learning and Research, University of Bristol, Bristol, United Kingdom
| | | | - Nikhil Hirani
- University of Edinburgh/MRC Centre for Inflammation Research, the Queen's Medical Research Institute, Edinburgh, United Kingdom
| | - Peter J Crick
- College of Medicine, Swansea University, Swansea, United Kingdom
| | - Yuqin Wang
- College of Medicine, Swansea University, Swansea, United Kingdom
| | | | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Charles McSharry
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom; Greater Glasgow and Clyde Clinical Research and Development, Yorkhill Hospital, Glasgow, United Kingdom.
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70
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Xie T, Liang J, Liu N, Huan C, Zhang Y, Liu W, Kumar M, Xiao R, D'Armiento J, Metzger D, Chambon P, Papaioannou VE, Stripp BR, Jiang D, Noble PW. Transcription factor TBX4 regulates myofibroblast accumulation and lung fibrosis. J Clin Invest 2016; 126:3063-79. [PMID: 27400124 DOI: 10.1172/jci85328] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/12/2016] [Indexed: 01/21/2023] Open
Abstract
Progressive tissue fibrosis is a major cause of the morbidity and mortality associated with repeated epithelial injuries and accumulation of myofibroblasts. Successful treatment options are limited by an incomplete understanding of the molecular mechanisms that regulate myofibroblast accumulation. Here, we employed in vivo lineage tracing and real-time gene expression transgenic reporting methods to analyze the early embryonic transcription factor T-box gene 4 (TBX4), and determined that TBX4-lineage mesenchymal progenitors are the predominant source of myofibroblasts in injured adult lung. In a murine model, ablation of TBX4-expressing cells or disruption of TBX4 signaling attenuated lung fibrosis after bleomycin-induced injury. Furthermore, TBX4 regulated hyaluronan synthase 2 production to enable fibroblast invasion of matrix both in murine models and in fibroblasts from patients with severe pulmonary fibrosis. These data identify TBX4 as a mesenchymal transcription factor that drives accumulation of myofibroblasts and the development of lung fibrosis. Targeting TBX4 and downstream factors that regulate fibroblast invasiveness could lead to therapeutic approaches in lung fibrosis.
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71
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Meshcheryakova A, Svoboda M, Tahir A, Köfeler HC, Triebl A, Mungenast F, Heinze G, Gerner C, Zimmermann P, Jaritz M, Mechtcheriakova D. Exploring the role of sphingolipid machinery during the epithelial to mesenchymal transition program using an integrative approach. Oncotarget 2016; 7:22295-323. [PMID: 26967245 PMCID: PMC5008362 DOI: 10.18632/oncotarget.7947] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/20/2016] [Indexed: 12/30/2022] Open
Abstract
The epithelial to mesenchymal transition (EMT) program is activated in epithelial cancer cells and facilitates their ability to metastasize based on enhanced migratory, proliferative, anti-apoptotic, and pluripotent capacities. Given the fundamental impact of sphingolipid machinery to each individual process, the sphingolipid-related mechanisms might be considered among the most prominent drivers/players of EMT; yet, there is still limited knowledge. Given the complexity of the interconnected sphingolipid system, which includes distinct sphingolipid mediators, their synthesizing enzymes, receptors and transporters, we herein apply an integrative approach for assessment of the sphingolipid-associated mechanisms underlying EMT program. We created the sphingolipid-/EMT-relevant 41-gene/23-gene signatures which were applied to denote transcriptional events in a lung cancer cell-based EMT model. Based on defined 35-gene sphingolipid/EMT-attributed signature of regulated genes, we show close associations between EMT markers, genes comprising the sphingolipid network at multiple levels and encoding sphingosine 1-phosphate (S1P)-/ceramide-metabolizing enzymes, S1P and lysophosphatidic acid (LPA) receptors and S1P transporters, pluripotency genes and inflammation-related molecules, and demonstrate the underlying biological pathways and regulators. Mass spectrometry-based sphingolipid analysis revealed an EMT-attributed shift towards increased S1P and LPA accompanied by reduced ceramide levels. Notably, using transcriptomics data across various cell-based perturbations and neoplastic tissues (24193 arrays), we identified the sphingolipid/EMT signature primarily in lung adenocarcinoma tissues; besides, bladder, colorectal and prostate cancers were among the top-ranked. The findings also highlight novel regulatory associations between influenza virus and the sphingolipid/EMT-associated mechanisms. In sum, data propose the multidimensional contribution of sphingolipid machinery to pathological EMT and may yield new biomarkers and therapeutic targets.
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Affiliation(s)
- Anastasia Meshcheryakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Martin Svoboda
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Ammar Tahir
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
- Mass Spectrometry Center, University of Vienna, Vienna, Austria
| | - Harald C. Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Felicitas Mungenast
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Georg Heinze
- Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University Vienna, Vienna, Austria
| | - Christopher Gerner
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
- Mass Spectrometry Center, University of Vienna, Vienna, Austria
| | | | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
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72
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Meltzer EB. The Bleomycin Model: In Pursuit of Relevant Biomakers. Am J Respir Cell Mol Biol 2015; 53:748. [DOI: 10.1165/rcmb.2015-0162le] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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73
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Bauer Y, Nayler O, Kaminski N. Reply: the bleomycin model: in pursuit of relevant biomakers. Am J Respir Cell Mol Biol 2015; 53:748-9. [PMID: 26517754 DOI: 10.1165/rcmb.2015-0196le] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Yasmina Bauer
- 1 Actelion Pharmaceuticals Ltd. Allschwil, Switzerland
| | - Oliver Nayler
- 1 Actelion Pharmaceuticals Ltd. Allschwil, Switzerland
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74
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Huan C, Yang T, Liang J, Xie T, Cheng L, Liu N, Kurkciyan A, Monterrosa Mena J, Wang C, Dai H, Noble PW, Jiang D. Methylation-mediated BMPER expression in fibroblast activation in vitro and lung fibrosis in mice in vivo. Sci Rep 2015; 5:14910. [PMID: 26442443 PMCID: PMC4595647 DOI: 10.1038/srep14910] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease. Although the pathogenesis is poorly understood, evidence suggests that genetic and epigenetic alterations, such as DNA methylation, may play a key role. Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-β (TGF-β) superfamily and are important regulators in IPF. Here we identified BMP endothelial cell precursor-derived regulator (BMPER) as a key regulator of fibroblast activation. BMPER is a secreted glycoprotein that binds directly to BMPs and may regulate TGF-β/BMP signaling, but its role in lung fibrosis is not clear. BMPER is highly expressed in human IPF lung fibroblasts compared to normal lung fibroblasts. Demethylation agent 5′-azacytidine decreased BMPER expression in fibroblasts, and attenuated the invasion and migration of IPF lung fibroblasts. Furthermore, siRNA-mediated reduction of BMPER in the human lung fibroblasts impaired cell migration and invasion. 5′-azacytidine treatment additionally regulated BMPER expression and reduced lung fibrosis in mice in vivo. These findings demonstrate that methylation of specific genes in fibroblasts may offer a new therapeutic strategy for IPF by modulating fibroblast activation.
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Affiliation(s)
- Caijuan Huan
- Department of Respiratory and Critical Care Medicine, Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Chao-Yang Hospital-Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing 100020, China.,Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Ting Yang
- Department of Respiratory and Critical Care Medicine, Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Chao-Yang Hospital-Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing 100020, China
| | - Jiurong Liang
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Ting Xie
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Luis Cheng
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Ningshan Liu
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Adrianne Kurkciyan
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | | | - Chen Wang
- China-Japan Friendship Hospital, Beijing, China
| | - Huaping Dai
- Department of Respiratory and Critical Care Medicine, Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Chao-Yang Hospital-Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing 100020, China
| | - Paul W Noble
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
| | - Dianhua Jiang
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA 90048, USA
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75
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Clarke LA, Botelho HM, Sousa L, Falcao AO, Amaral MD. Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators. Genomics 2015. [PMID: 26225835 DOI: 10.1016/j.ygeno.2015.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease.
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Affiliation(s)
- Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Lisete Sousa
- University of Lisboa, Faculty of Sciences, DEIO and CEAUL, Portugal
| | - Andre O Falcao
- University of Lisboa, Faculty of Sciences, Department of Informatics, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
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76
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Luzina IG, Lockatell V, Todd NW, Kopach P, Pentikis HS, Atamas SP. Pharmacological In Vivo Inhibition of S-Nitrosoglutathione Reductase Attenuates Bleomycin-Induced Inflammation and Fibrosis. J Pharmacol Exp Ther 2015. [PMID: 26209236 DOI: 10.1124/jpet.115.224675] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Interstitial lung disease (ILD) characterized by pulmonary fibrosis and inflammation poses a substantial biomedical challenge due to often negative disease outcomes combined with the need to develop better, more effective therapies. We assessed the in vivo effect of administration of a pharmacological inhibitor of S-nitrosoglutathione reductase, SPL-334 (4-{[2-[(2-cyanobenzyl)thio]-4-oxothieno[3,2-d]pyrimidin-3(4H)-yl]methyl}benzoic acid), in a mouse model of ILD induced by intratracheal instillation of bleomycin (BLM). Daily i.p. administration of SPL-334 alone at 0.3, 1.0, or 3.0 mg/kg had no effect on animal body weight, appearance, behavior, total and differential bronchoalveolar lavage (BAL) cell counts, or collagen accumulation in the lungs, showing no toxicity of our investigational compound. Similar administration of SPL-334 for 7 days before and for an additional 14 days after BLM instillation resulted in a preventive protective effect on the BLM challenge-induced decline in total body weight and changes in total and differential BAL cellularity. In the therapeutic treatment regimen, SPL-334 was administered at days 7-21 after BLM challenge. Such treatment attenuated the BLM challenge-induced decline in total body weight, changes in total and differential BAL cellularity, and magnitudes of histologic changes and collagen accumulation in the lungs. These changes were accompanied by an attenuation of BLM-induced elevations in pulmonary levels of profibrotic cytokines interleukin-6, monocyte chemoattractant protein-1, and transforming growth factor-β (TGF-β). Experiments in cell cultures of primary normal human lung fibroblast have demonstrated attenuation of TGF-β-induced upregulation in collagen by SPL-334. It was concluded that SPL-334 is a potential therapeutic agent for ILD.
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Affiliation(s)
- Irina G Luzina
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
| | - Virginia Lockatell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
| | - Nevins W Todd
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
| | - Pavel Kopach
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
| | - Helen S Pentikis
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
| | - Sergei P Atamas
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland (I.G.L., V.L., N.W.T., P.K., S.P.A); and SAJE Pharma, Baltimore, Maryland (H.S.P.)
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77
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Foster MW, Morrison LD, Todd JL, Snyder LD, Thompson JW, Soderblom EJ, Plonk K, Weinhold KJ, Townsend R, Minnich A, Moseley MA. Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis. J Proteome Res 2015; 14:1238-49. [PMID: 25541672 DOI: 10.1021/pr501149m] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteomic analysis of bronchoalveolar lavage fluid (BALF) can give insight into pulmonary disease pathology and response to therapy. Here, we describe the first gel-free quantitative analysis of BALF in idiopathic pulmonary fibrosis (IPF), a chronic and fatal scarring lung disease. We utilized two-dimensional reversed-phase liquid chromatography and ion-mobility-assisted data-independent acquisition (HDMSE) for quantitation of >1000 proteins in immunodepleted BALF from the right middle and lower lobes of normal controls and patients with IPF. Among the analytes that were increased in IPF were well-described mediators of pulmonary fibrosis (osteopontin, MMP7, CXCL7, CCL18), eosinophil- and neutrophil-derived proteins, and proteins associated with fibroblast foci. For additional discovery and targeted validation, BALF was also screened by multiple reaction monitoring (MRM), using the JPT Cytokine SpikeMix library of >400 stable isotope-labeled peptides. A refined MRM assay confirmed the robust expression of osteopontin, and demonstrated, for the first time, upregulation of the pro-fibrotic cytokine, CCL24, in BALF in IPF. These results show the utility of BALF proteomics for the molecular profiling of fibrotic lung diseases and the targeted quantitation of soluble markers of IPF. More generally, this study addresses critical quality control measures that should be widely applicable to BALF profiling in pulmonary disease.
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Affiliation(s)
- Matthew W Foster
- Pulmonary, Allergy and Critical Care Medicine, ‡Duke Proteomics and Metabolomics Shared Resource, §Department of Surgery, Duke University Medical Center , Durham, North Carolina 27710, United States , and
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78
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Hamburg-Shields E, DiNuoscio GJ, Mullin NK, Lafyatis R, Atit RP. Sustained β-catenin activity in dermal fibroblasts promotes fibrosis by up-regulating expression of extracellular matrix protein-coding genes. J Pathol 2015; 235:686-97. [PMID: 25385294 DOI: 10.1002/path.4481] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/02/2014] [Accepted: 11/05/2014] [Indexed: 12/11/2022]
Abstract
Fibrosis is an end-stage response to tissue injury that is associated with loss of organ function as a result of excess extracellular matrix (ECM) production by fibroblasts. In skin, pathological fibrosis is evident during keloid scar formation, systemic sclerosis (SSc) and morphea. Dermal fibroblasts in these fibrotic diseases exhibit increased Wnt/β-catenin signalling, a pathway that is sufficient to cause fibrosis in mice. However, in the context of this complex pathology, the precise pro-fibrotic consequences of Wnt/β-catenin signalling are not known. We found that expression of stabilized β-catenin in mouse dermal fibroblasts resulted in spontaneous, progressive skin fibrosis with thickened collagen fibres and altered collagen fibril morphology. The fibrotic phenotype was predominated by resident dermal fibroblasts. Genome-wide profiling of the fibrotic mouse dermis revealed elevated expression of matrix-encoding genes, and the promoter regions of these genes were enriched for Tcf/Lef family transcription factor binding sites. Additionally, we identified 32 β-catenin-responsive genes in our mouse model that are also over-expressed in human fibrotic tissues and poised for regulation by Tcf/Lef family transcription factors. Therefore, we have uncovered a matrix-regulatory role for stabilized β-catenin in fibroblasts in vivo and have defined a set of β-catenin-responsive genes with relevance to fibrotic disease.
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79
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Meltzer EB, Barry WT, Yang IV, Brown KK, Schwarz MI, Patel H, Ashley A, Noble PW, Schwartz DA, Steele MP. Familial and sporadic idiopathic pulmonary fibrosis: making the diagnosis from peripheral blood. BMC Genomics 2014; 15:902. [PMID: 25318837 PMCID: PMC4288625 DOI: 10.1186/1471-2164-15-902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 07/10/2014] [Indexed: 12/26/2022] Open
Abstract
Background Peripheral blood biomarkers might improve diagnostic accuracy for idiopathic pulmonary fibrosis (IPF). Results Gene expression profiles were obtained from 89 patients with IPF and 26 normal controls. Samples were stratified according to severity of disease based on pulmonary function. The stratified dataset was split into subsets; two-thirds of the samples were selected to comprise the training set, while one-third was reserved for the validation set. Bayesian probit regression was used on the training set to develop a gene expression model for IPF versus normal. The gene expression model was tested by using it on the validation set to perform class prediction. Unsupervised clustering failed to discriminate between samples of different severity. Therefore, samples of all severities were included in the training and validation sets, in equal proportions. A gene signature model was developed from the training set. The model was built in an iterative fashion with the number of gene features selected to minimize the misclassification error in cross validation. The final model was based on the top 108 discriminating genes in the training set. The signature was successfully applied to the validation set, ROC area under the curve = 0.893, p < 0.0001. Using the optimal threshold (0.74) accurate class predictions were made for 77% of the test cases with sensitivity = 0.70, specificity = 1.00. Conclusions By using Bayesian probit regression to develop a model, we show that it is entirely possible to make a diagnosis of IPF from the peripheral blood with gene signatures. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-902) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mark P Steele
- Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, 1313 21st Avenue South, 1105 Oxford House, Nashville, TN, USA.
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80
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Yang J, Wang Z, Leng D, Dai H, Wang J, Liang J, Jiang D, Wang C. G protein-coupled receptor 56 regulates matrix production and motility of lung fibroblasts. Exp Biol Med (Maywood) 2014; 239:686-96. [PMID: 24742924 DOI: 10.1177/1535370214529395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Idiopathic pulmonary fibrosis is a chronic, progressive, and fatal fibrotic lung disease with a poor prognosis, but no effective treatment is available. G protein-coupled receptor 56 (GPR56) plays a role in cell adhesion and tumor progression, but its function in fibrogenesis has not been explored. In this in vitro study, we found that GPR56 in IPF fibroblasts was lower than in normal fibroblasts. GPR56 regulated the production of fibronectin and type I collagen, and also changed the migratory and invasive capacity of lung fibroblasts. However, it was not sufficient to activate some classic markers of fibroblast and myofibroblast, such as α-smooth muscle actin and fibroblast specific protein 1. These findings demonstrate that reduced expression of GPR56 in lung fibroblasts may be an important link with pulmonary fibrosis, playing a role in regulating some important fibroblast functions.
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Affiliation(s)
- Jian Yang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
- Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Institute of Respiratory Medicine, Beijing 100020, China
| | - Zhanyong Wang
- Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
- Laboratory Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Dong Leng
- Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
- Laboratory Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Huaping Dai
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
- Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Institute of Respiratory Medicine, Beijing 100020, China
- Faculty of Respirology, Capital Medical University, Beijing 100069, China
| | - Jun Wang
- Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Institute of Respiratory Medicine, Beijing 100020, China
- Department of Physiology, Capital Medical University, Beijing 100069, China
| | - Jiurong Liang
- Cedars-Sinai Medical Center Department of Medicine, Los Angeles, CA 90048, USA
| | - Dianhua Jiang
- Cedars-Sinai Medical Center Department of Medicine, Los Angeles, CA 90048, USA
| | - Chen Wang
- Beijing Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Beijing Institute of Respiratory Medicine, Beijing 100020, China
- Faculty of Respirology, Capital Medical University, Beijing 100069, China
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81
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Yin T, Lallena MJ, Kreklau EL, Fales KR, Carballares S, Torrres R, Wishart GN, Ajamie RT, Cronier DM, Iversen PW, Meier TI, Foreman RT, Zeckner D, Sissons SE, Halstead BW, Lin AB, Donoho GP, Qian Y, Li S, Wu S, Aggarwal A, Ye XS, Starling JJ, Gaynor RB, de Dios A, Du J. A novel CDK9 inhibitor shows potent antitumor efficacy in preclinical hematologic tumor models. Mol Cancer Ther 2014; 13:1442-56. [PMID: 24688048 DOI: 10.1158/1535-7163.mct-13-0849] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA-dependent RNA polymerase II (RNAP II) largest subunit RPB1 C-terminal domain (CTD) kinases, including CDK9, are serine/threonine kinases known to regulate transcriptional initiation and elongation by phosphorylating Ser 2, 5, and 7 residues on CTD. Given the reported dysregulation of these kinases in some cancers, we asked whether inhibiting CDK9 may induce stress response and preferentially kill tumor cells. Herein, we describe a potent CDK9 inhibitor, LY2857785, that significantly reduces RNAP II CTD phosphorylation and dramatically decreases MCL1 protein levels to result in apoptosis in a variety of leukemia and solid tumor cell lines. This molecule inhibits the growth of a broad panel of cancer cell lines, and is particularly efficacious in leukemia cells, including orthotopic leukemia preclinical models as well as in ex vivo acute myeloid leukemia and chronic lymphocytic leukemia patient tumor samples. Thus, inhibition of CDK9 may represent an interesting approach as a cancer therapeutic target, especially in hematologic malignancies.
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Affiliation(s)
- Tinggui Yin
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Maria J Lallena
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Emiko L Kreklau
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Kevin R Fales
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Santiago Carballares
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Raquel Torrres
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Graham N Wishart
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Rose T Ajamie
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Damien M Cronier
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Phillip W Iversen
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Timothy I Meier
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Robert T Foreman
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Douglas Zeckner
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Sean E Sissons
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Bart W Halstead
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Aimee B Lin
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Gregory P Donoho
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Yuewei Qian
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Shuyu Li
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Song Wu
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Amit Aggarwal
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Xiang S Ye
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - James J Starling
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Richard B Gaynor
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Alfonso de Dios
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
| | - Jian Du
- Authors' Affiliations: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana; Eli Lilly and Company, Alcobendas, Madrid, Spain; and Eli Lilly and Company, Windlesham, United Kingdom
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Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB. Transcriptome analysis reveals differential splicing events in IPF lung tissue. PLoS One 2014; 9:e92111. [PMID: 24647608 PMCID: PMC3960165 DOI: 10.1371/journal.pone.0092111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/18/2014] [Indexed: 12/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%), and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%). We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10) and POSTN (RNA-Seq adjusted pval = 2.06e-09), which encode the extracellular matrix proteins collagen alpha-3(VI) and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.
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Affiliation(s)
- Tracy Nance
- Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail: (TN); (GR); (SBM)
| | - Kevin S. Smith
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Vanessa Anaya
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Rhea Richardson
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Lawrence Ho
- Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington, United States of America
| | - Mauro Pala
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Sara Mostafavi
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Alexis Battle
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Carol Feghali-Bostwick
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Glenn Rosen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Stanford University, Stanford, California, United States of America
- * E-mail: (TN); (GR); (SBM)
| | - Stephen B. Montgomery
- Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail: (TN); (GR); (SBM)
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83
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Meta-analysis of genetic programs between idiopathic pulmonary fibrosis and sarcoidosis. PLoS One 2013; 8:e71059. [PMID: 23967151 PMCID: PMC3743918 DOI: 10.1371/journal.pone.0071059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) and pulmonary sarcoidosis are typical interstitial lung diseases with unknown etiology that cause lethal lung damages. There are notable differences between these two pulmonary disorders, although they do share some similarities. Gene expression profiles have been reported independently, but differences on the transcriptional level between these two entities have not been investigated. Methods/Results All expression data of lung tissue samples for IPF and sarcoidosis were from published datasets in the Gene Expression Omnibus (GEO) repository. After cross platform normalization, the merged sample data were grouped together and were subjected to statistical analysis for finding discriminate genes. Gene enrichments with their corresponding functions were analyzed by the online analysis engine “Database for Annotation, Visualization and Integrated Discovery” (DAVID) 6.7, and genes interactions and functional networks were further analyzed by STRING 9.0 and Cytoscape 3.0.0 Beta1. One hundred and thirty signature genes could potentially differentiate one disease state from another. Compared with normal lung tissue, tissue affected by IPF and sarcoidosis displayed similar signatures that concentrated on proliferation and differentiation. Distinctly expressed genes that could distinguish IPF from sarcoidosis are more enriched in processes of cilium biogenesis or degradation and regulating T cell activations. Key discriminative network modules involve aspects of bone morphogenetic protein receptor two (BMPR2) related and v-myb myeloblastosis viral oncogene (MYB) related proliferation. Conclusions This study is the first attempt to examine the transcriptional regulation of IPF and sarcoidosis across different studies based on different working platforms. Groups of significant genes were found to clearly distinguish one condition from the other. While IPF and sarcoidosis share notable similarities in cell proliferation, differentiation and migration, remarkable differences between the diseases were found at the transcription level, suggesting that the two diseases are regulated by overlapping yet distinctive transcriptional networks.
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