1
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Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S, Chandramouliswaran I, Splendiani A, Burdett T, Giessmann RT, Henderson D, Batista D, Emam I, Gadiya Y, Giovanni L, Willighagen E, Evelo C, Gray AJG, Gribbon P, Juty N, Welter D, Quast K, Peeters P, Plasterer T, Wood C, van der Horst E, Reilly D, van Vlijmen H, Scollen S, Lister A, Thurston M, Granell R, Sansone SA. The FAIR Cookbook - the essential resource for and by FAIR doers. Sci Data 2023; 10:292. [PMID: 37208467 PMCID: PMC10198982 DOI: 10.1038/s41597-023-02166-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for "FAIR doers" in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes.
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Affiliation(s)
- Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK.
- AstraZeneca, Data Office, Data Science & AI unit R&D, 136 Hills Rd, Cambridge, UK.
| | - Wei Gu
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367, Belval, Luxembourg
- Luxembourg National Data Service, 6 Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Vassilios Ioannidis
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tooba Abbassi-Daloii
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | | | - Ishwar Chandramouliswaran
- Office of Data Science Strategy, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892, USA
| | | | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - Robert T Giessmann
- Bayer AG, Business Development & Licensing & OI, Pharmaceuticals, 13342, Berlin, Germany
- Institute for Globally Distributed Open Research and Education (IGDORE), Berlin, Germany
| | - David Henderson
- Bayer AG, Business Development & Licensing & OI, Pharmaceuticals, 13342, Berlin, Germany
| | - Dominique Batista
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Ibrahim Emam
- Data Science Institute, Imperial College London, William Penney Laboratory, South Kensington Campus, London, SW7 2AZ, UK
| | - Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Lucas Giovanni
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Egon Willighagen
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Chris Evelo
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Alasdair J G Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland, UK
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Nick Juty
- The University of Manchester, Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
| | - Danielle Welter
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367, Belval, Luxembourg
- Luxembourg National Data Service, 6 Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
| | - Paul Peeters
- Janssen, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Tom Plasterer
- AstraZeneca Pharmaceuticals, 36 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Colin Wood
- AstraZeneca, da Vinci Building, Melbourn Science Park, Cambridge Road, Royston, SG8 6HM, UK
| | - Eelke van der Horst
- The Hyve BV, Arthur van Schendelstraat 650, 3511 MJ, Utrecht, The Netherlands
| | - Dorothy Reilly
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Allyson Lister
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Milo Thurston
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Ramon Granell
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK.
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2
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Schwartz U, Llamazares Prada M, Pohl ST, Richter M, Tamas R, Schuler M, Keller C, Mijosek V, Muley T, Schneider MA, Quast K, Hey J, Heußel CP, Warth A, Winter H, Serçin Ö, Karmouty-Quintana H, Jyothula SS, Patel MK, Herth F, Koch I, Petrosino G, Titimeaua A, Mardin BR, Weichenhan D, Jurkowski TP, Imbusch CD, Brors B, Benes V, Jung B, Wyatt D, Stahl HF, Plass C, Jurkowska RZ. High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD. EMBO J 2023:e111272. [PMID: 37143403 DOI: 10.15252/embj.2022111272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 03/14/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering its environmental cause, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) across COPD stages. We show that the epigenetic landscape is changed early in COPD, with DNA methylation changes occurring predominantly in regulatory regions. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Data integration identified 110 candidate regulators of disease phenotypes that were linked to fibroblast repair processes using phenotypic screens. Our study provides high-resolution multi-omic maps of HLFs across COPD stages. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic lung diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.
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Affiliation(s)
- Uwe Schwartz
- BioMed X Institute, Heidelberg, Germany
- NGS Analysis Center Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Maria Llamazares Prada
- BioMed X Institute, Heidelberg, Germany
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stephanie T Pohl
- BioMed X Institute, Heidelberg, Germany
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | - Michael Schuler
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Corinna Keller
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Thomas Muley
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
| | - Karsten Quast
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Claus P Heußel
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
- Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Pathological Institute, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Department of Surgery, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Soma Sk Jyothula
- Center for Advanced Cardiopulmonary Therapies and Transplantation, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Manish K Patel
- Center for Advanced Cardiopulmonary Therapies and Transplantation, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Felix Herth
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine and Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, German Center for Lung Research (DZL), Munich, Germany
| | | | - Alexandru Titimeaua
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Vladimir Benes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Birgit Jung
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Wyatt
- Biotherapeutics Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Heiko F Stahl
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Renata Z Jurkowska
- BioMed X Institute, Heidelberg, Germany
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
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3
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Klee S, Picart-Armada S, Wenger K, Birk G, Quast K, Veyel D, Rist W, Violet C, Luippold A, Haslinger C, Thomas M, Fernandez-Albert F, Kästle M. Transcriptomic and proteomic profiling of young and old mice in the bleomycin model reveals high similarity. Am J Physiol Lung Cell Mol Physiol 2023; 324:L245-L258. [PMID: 36625483 DOI: 10.1152/ajplung.00253.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The most common preclinical, in vivo model to study lung fibrosis is the bleomycin-induced lung fibrosis model in 2- to 3-mo-old mice. Although this model resembles key aspects of idiopathic pulmonary fibrosis (IPF), there are limitations in its predictability for the human disease. One of the main differences is the juvenile age of animals that are commonly used in experiments, resembling humans of around 20 yr. Because IPF patients are usually older than 60 yr, aging appears to play an important role in the pathogenesis of lung fibrosis. Therefore, we compared young (3 months) and old mice (21 months) 21 days after intratracheal bleomycin instillation. Analyzing lung transcriptomics (mRNAs and miRNAs) and proteomics, we found most pathways to be similarly regulated in young and old mice. However, old mice show imbalanced protein homeostasis as well as an increased inflammatory state in the fibrotic phase compared to young mice. Comparisons with published human transcriptomic data sets (GSE47460, GSE32537, and GSE24206) revealed that the gene signature of old animals correlates significantly better with IPF patients, and it also turned human healthy individuals better into "IPF patients" using an approach based on predictive disease modeling. Both young and old animals show similar molecular hallmarks of IPF in the bleomycin-induced lung fibrosis model, although old mice more closely resemble several features associated with IPF in comparison to young animals.
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Affiliation(s)
- Stephan Klee
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sergio Picart-Armada
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kathrin Wenger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gerald Birk
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Daniel Veyel
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wolfgang Rist
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Coralie Violet
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andreas Luippold
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Haslinger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthew Thomas
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Marc Kästle
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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4
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Le HQ, Hill MA, Kollak I, Keck M, Schroeder V, Wirth J, Skronska‐Wasek W, Schruf E, Strobel B, Stahl H, Herrmann FE, Campos AR, Li J, Quast K, Knebel D, Viollet C, Thomas MJ, Lamb D, Garnett JP. An EZH2-dependent transcriptional complex promotes aberrant epithelial remodelling after injury. EMBO Rep 2021; 22:e52785. [PMID: 34224201 PMCID: PMC8339687 DOI: 10.15252/embr.202152785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Unveiling the molecular mechanisms of tissue remodelling following injury is imperative to elucidate its regenerative capacity and aberrant repair in disease. Using different omics approaches, we identified enhancer of zester homolog 2 (EZH2) as a key regulator of fibrosis in injured lung epithelium. Epithelial injury drives an enrichment of nuclear transforming growth factor-β-activated kinase 1 (TAK1) that mediates EZH2 phosphorylation to facilitate its liberation from polycomb repressive complex 2 (PRC2). This process results in the establishment of a transcriptional complex of EZH2, RNA-polymerase II (POL2) and nuclear actin, which orchestrates aberrant epithelial repair programmes. The liberation of EZH2 from PRC2 is accompanied by an EZH2-EZH1 switch to preserve H3K27me3 deposition at non-target genes. Loss of epithelial TAK1, EZH2 or blocking nuclear actin influx attenuates the fibrotic cascade and restores respiratory homeostasis. Accordingly, EZH2 inhibition significantly improves outcomes in a pulmonary fibrosis mouse model. Our results reveal an important non-canonical function of EZH2, paving the way for new therapeutic interventions in fibrotic lung diseases.
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Affiliation(s)
- Huy Q Le
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew A Hill
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - Ines Kollak
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Martina Keck
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Victoria Schroeder
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Johannes Wirth
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Wioletta Skronska‐Wasek
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Eva Schruf
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Benjamin Strobel
- Drug Discovery SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Heiko Stahl
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Franziska E Herrmann
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | | | - Jun Li
- Immunology and Respiratory Disease Research DepartmentBoehringer Ingelheim Pharmaceuticals, IncRidgefieldCTUSA
| | - Karsten Quast
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Dagmar Knebel
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Coralie Viollet
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew J Thomas
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - David Lamb
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - James P Garnett
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- Translational and Clinical Research InstituteNewcastle UniversityNewcastleUK
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5
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Lamb D, De Sousa D, Quast K, Fundel-Clemens K, Erjefält JS, Sandén C, Hoffmann HJ, Kästle M, Schmid R, Menden K, Delic D. RORγt inhibitors block both IL-17 and IL-22 conferring a potential advantage over anti-IL-17 alone to treat severe asthma. Respir Res 2021; 22:158. [PMID: 34022896 PMCID: PMC8141258 DOI: 10.1186/s12931-021-01743-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND RORγt is a transcription factor that enables elaboration of Th17-associated cytokines (including IL-17 and IL-22) and is proposed as a pharmacological target for severe asthma. METHODS IL-17 immunohistochemistry was performed in severe asthma bronchial biopsies (specificity confirmed with in situ hybridization). Primary human small airway epithelial cells in air liquid interface and primary bronchial smooth muscle cells were stimulated with recombinant human IL-17 and/or IL-22 and pro-inflammatory cytokines measured. Balb/c mice were challenged intratracheally with IL-17 and/or IL-22 and airway hyperreactivity, pro-inflammatory cytokines and airway neutrophilia measured. Balb/c mice were sensitized intraperitoneally and challenged intratracheally with house dust mite extract and the effect of either a RORγt inhibitor (BIX119) or an anti-IL-11 antibody assessed on airway hyperreactivity, pro-inflammatory cytokines and airway neutrophilia measured. RESULTS We confirmed in severe asthma bronchial biopsies both the presence of IL-17-positive lymphocytes and that an IL-17 transcriptome profile in a severe asthma patient sub-population. Both IL-17 and IL-22 stimulated the release of pro-inflammatory cytokine and chemokine release from primary human lung cells and in mice. Furthermore, IL-22 in combination with IL-17, but neither alone, elicits airway hyperresponsiveness (AHR) in naïve mice. A RORγt inhibitor specifically blocked both IL-17 and IL-22, AHR and neutrophilia in a mouse house dust mite model unlike other registered or advanced pipeline modes of action. Full efficacy versus these parameters was associated with 90% inhibition of IL-17 and 50% inhibition of IL-22. In contrast, anti-IL-17 also blocked IL-17, but not IL-22, AHR or neutrophilia. Moreover, the deregulated genes in the lungs from these mice correlated well with deregulated genes from severe asthma biopsies suggesting that this model recapitulates significant severe asthma-relevant biology. Furthermore, these genes were reversed upon RORγt inhibition in the HDM model. Cell deconvolution suggested that the responsible cells were corticosteroid insensitive γδ-T-cells. CONCLUSION These data strongly suggest that both IL-17 and IL-22 are required for Th2-low endotype associated biology and that a RORγt inhibitor may provide improved clinical benefit in a severe asthma sub-population of patients by blocking both IL-17 and IL-22 biology compared with blocking IL-17 alone.
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MESH Headings
- Adolescent
- Adult
- Aged
- Animals
- Anti-Asthmatic Agents/pharmacology
- Asthma/drug therapy
- Asthma/immunology
- Asthma/metabolism
- Asthma/physiopathology
- Cells, Cultured
- Disease Models, Animal
- Epithelial Cells/drug effects
- Epithelial Cells/immunology
- Epithelial Cells/metabolism
- Female
- Humans
- Interleukin-17/metabolism
- Interleukins/antagonists & inhibitors
- Interleukins/metabolism
- Lung/drug effects
- Lung/immunology
- Lung/metabolism
- Lung/physiopathology
- Male
- Mice, Inbred BALB C
- Middle Aged
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/immunology
- Myocytes, Smooth Muscle/metabolism
- Nuclear Receptor Subfamily 1, Group F, Member 3/antagonists & inhibitors
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- Pyroglyphidae/immunology
- Signal Transduction
- Th17 Cells/drug effects
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Young Adult
- Interleukin-22
- Mice
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Affiliation(s)
- David Lamb
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany.
| | | | - Karsten Quast
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Katrin Fundel-Clemens
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | | | | | | | - Marc Kästle
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Ramona Schmid
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Kevin Menden
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Denis Delic
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
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6
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Nemeth J, Schundner A, Quast K, Winkelmann VE, Frick M. A Novel Fibroblast Reporter Cell Line for in vitro Studies of Pulmonary Fibrosis. Front Physiol 2020; 11:567675. [PMID: 33162897 PMCID: PMC7582034 DOI: 10.3389/fphys.2020.567675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease of the lower respiratory tract with restricted therapeutic options. Repetitive injury of the bronchoalveolar epithelium leads to activation of pulmonary fibroblasts, differentiation into myofibroblasts and excessive extracellular matrix (ECM) deposition resulting in aberrant wound repair. However, detailed molecular and cellular mechanisms underlying initiation and progression of fibrotic changes are still elusive. Here, we report the generation of a representative fibroblast reporter cell line (10-4A BFP ) to study pathophysiological mechanisms of IPF in high throughput or high resolution in vitro live cell assays. To this end, we immortalized primary fibroblasts isolated from the distal lung of Sprague-Dawley rats. Molecular and transcriptomic characterization identified clone 10-4A as a matrix fibroblast subpopulation. Mechanical or chemical stimulation induced a reversible fibrotic state comparable to effects observed in primary isolated fibroblasts. Finally, we generated a reporter cell line (10-4A BFP ) to express nuclear blue fluorescent protein (BFP) under the promotor of the myofibroblast marker alpha smooth muscle actin (Acta2) using CRISPR/Cas9 technology. We evaluated the suitability of 10-4A BFP as reporter tool in plate reader assays. In summary, the 10-4A BFP cell line provides a novel tool to study fibrotic processes in vitro to gain new insights into the cellular and molecular processes involved in fibrosis formation and propagation.
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Affiliation(s)
- Julia Nemeth
- Institute of General Physiology, Ulm University, Ulm, Germany
| | | | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Manfred Frick
- Institute of General Physiology, Ulm University, Ulm, Germany
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7
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Zuo WL, Rostami MR, LeBlanc M, Kaner RJ, O’Beirne SL, Mezey JG, Leopold PL, Quast K, Visvanathan S, Fine JS, Thomas MJ, Crystal RG. Dysregulation of club cell biology in idiopathic pulmonary fibrosis. PLoS One 2020; 15:e0237529. [PMID: 32941426 PMCID: PMC7498242 DOI: 10.1371/journal.pone.0237529] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic fibrotic lung disease with an irreversible decline of lung function. "Bronchiolization", characterized by ectopic appearance of airway epithelial cells in the alveolar regions, is one of the characteristic features in the IPF lung. Based on the knowledge that club cells are the major epithelial secretory cells in human small airways, and their major secretory product uteroglobin (SCGB1A1) is significantly increased in both serum and epithelial lining fluid of IPF lung, we hypothesize that human airway club cells contribute to the pathogenesis of IPF. By assessing the transcriptomes of the single cells from human lung of control donors and IPF patients, we identified two SCGB1A1+ club cell subpopulations, highly expressing MUC5B, a significant genetic risk factor strongly associated with IPF, and SCGB3A2, a marker heterogeneously expressed in the club cells, respectively. Interestingly, the cellular proportion of SCGB1A1+MUC5B+ club cells was significantly increased in IPF patients, and this club cell subpopulation highly expressed genes related to mucous production and immune cell chemotaxis. In contrast, though the cellular proportion did not change, the molecular phenotype of the SCGB1A1+SCGB3A2high club cell subpopulation was significantly altered in IPF lung, with increased expression of mucins, cytokine and extracellular matrix genes. The single cell transcriptomic analysis reveals the cellular and molecular heterogeneity of club cells, and provide novel insights into the biological functions of club cells in the pathogenesis of IPF.
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Affiliation(s)
- Wu-Lin Zuo
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Mahboubeh R. Rostami
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Michelle LeBlanc
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Robert J. Kaner
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Sarah L. O’Beirne
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Philip L. Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sudha Visvanathan
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, United States of America
| | - Jay S. Fine
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, United States of America
| | - Matthew J. Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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8
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Schruf E, Schroeder V, Le HQ, Schönberger T, Raedel D, Stewart EL, Fundel-Clemens K, Bluhmki T, Weigle S, Schuler M, Thomas MJ, Heilker R, Webster MJ, Dass M, Frick M, Stierstorfer B, Quast K, Garnett JP. Recapitulating idiopathic pulmonary fibrosis related alveolar epithelial dysfunction in a human iPSC-derived air-liquid interface model. FASEB J 2020; 34:7825-7846. [PMID: 32297676 DOI: 10.1096/fj.201902926r] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/29/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown cause that is characterized by progressive fibrotic lung remodeling. An abnormal emergence of airway epithelial-like cells within the alveolar compartments of the lung, herein termed bronchiolization, is often observed in IPF. However, the origin of this dysfunctional distal lung epithelium remains unknown due to a lack of suitable human model systems. In this study, we established a human induced pluripotent stem cell (iPSC)-derived air-liquid interface (ALI) model of alveolar epithelial type II (ATII)-like cell differentiation that allows us to investigate alveolar epithelial progenitor cell differentiation in vitro. We treated this system with an IPF-relevant cocktail (IPF-RC) to mimic the pro-fibrotic cytokine milieu present in IPF lungs. Stimulation with IPF-RC during differentiation increases secretion of IPF biomarkers and RNA sequencing (RNA-seq) of these cultures reveals significant overlap with human IPF patient data. IPF-RC treatment further impairs ATII differentiation by driving a shift toward an airway epithelial-like expression signature, providing evidence that a pro-fibrotic cytokine environment can influence the proximo-distal differentiation pattern of human lung epithelial cells. In conclusion, we show for the first time, the establishment of a human model system that recapitulates aspects of IPF-associated bronchiolization of the lung epithelium in vitro.
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Affiliation(s)
- Eva Schruf
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Victoria Schroeder
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Huy Q Le
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tanja Schönberger
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dagmar Raedel
- Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Emily L Stewart
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Katrin Fundel-Clemens
- Global Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Teresa Bluhmki
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sabine Weigle
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michael Schuler
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthew J Thomas
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ralf Heilker
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Megan J Webster
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Dass
- Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Manfred Frick
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Birgit Stierstorfer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Global Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - James P Garnett
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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9
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Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2020; 199:622-630. [PMID: 30141961 DOI: 10.1164/rccm.201712-2551oc] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Idiopathic pulmonary fibrosis (IPF) is a fatal disease with a variable and unpredictable course. OBJECTIVES To determine whether BAL cell gene expression is predictive of survival in IPF. METHODS This retrospective study analyzed the BAL transcriptome of three independent IPF cohorts: Freiburg (Germany), Siena (Italy), and Leuven (Belgium) including 212 patients. BAL cells from 20 healthy volunteers, 26 patients with sarcoidosis stage III and IV, and 29 patients with chronic obstructive pulmonary disease were used as control subjects. Survival analysis was performed by Cox models and component-wise boosting. Presence of airway basal cells was tested by immunohistochemistry and flow cytometry. MEASUREMENTS AND MAIN RESULTS A total of 1,582 genes were predictive of mortality in the IPF derivation cohort in univariate analyses adjusted for age and sex at false discovery rate less than 0.05. A nine-gene signature, derived from the discovery cohort (Freiburg), performed well in both replication cohorts, Siena (P < 0.0032) and Leuven (P = 0.0033). nCounter expression analysis confirmed the array results (P < 0.0001). The genes associated with mortality in BAL cells were significantly enriched for genes expressed in airway basal cells. Further analyses by gene expression, flow cytometry, and immunohistochemistry showed an increase in airway basal cells in BAL and tissues of IPF compared with control subjects, but not in chronic obstructive pulmonary disease or sarcoidosis. CONCLUSIONS Our results identify and validate a BAL signature that predicts mortality in IPF and improves the accuracy of outcome prediction based on clinical parameters. The BAL signature associated with mortality unmasks a potential role for airway basal cells in IPF.
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Affiliation(s)
- Antje Prasse
- 1 Department of Pulmonology, Hannover Medical School, Hannover, Germany.,2 Department of Pneumology and.,3 Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.,4 German Center for Lung Research, BREATH, Hannover, Germany
| | - Harald Binder
- 5 Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | | | - Gian Kayser
- 6 Institute of Surgical Pathology, University Medical Center, Freiburg, Germany
| | - Elena Bargagli
- 7 Respiratory Diseases and Lung Transplantation Unit, AOUS and Siena University, Siena, Italy
| | - Benedikt Jaeger
- 3 Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.,4 German Center for Lung Research, BREATH, Hannover, Germany
| | - Moritz Hess
- 5 Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | | | - Louis Vuga
- 8 Division of Respiratory Medicine, Simmons Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Heather Lynn
- 9 Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | | | - Birgit Jung
- 11 Boehringer Ingelheim Pharma GmbH & Co. KG Research, Biberach, Germany
| | - Karsten Quast
- 11 Boehringer Ingelheim Pharma GmbH & Co. KG Research, Biberach, Germany
| | - Bart Vanaudenaerde
- 12 Department of Respiratory Medicine, University Hospitals Leuven, Leuven, Belgium; and
| | - Yan Xu
- 13 Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jens M Hohlfeld
- 3 Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.,4 German Center for Lung Research, BREATH, Hannover, Germany
| | - Norbert Krug
- 3 Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.,4 German Center for Lung Research, BREATH, Hannover, Germany
| | - Jose D Herazo-Maya
- 9 Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Paola Rottoli
- 7 Respiratory Diseases and Lung Transplantation Unit, AOUS and Siena University, Siena, Italy
| | - Wim A Wuyts
- 12 Department of Respiratory Medicine, University Hospitals Leuven, Leuven, Belgium; and
| | - Naftali Kaminski
- 9 Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
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10
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Wang G, Lou HH, Salit J, Leopold PL, Driscoll S, Schymeinsky J, Quast K, Visvanathan S, Fine JS, Thomas MJ, Crystal RG. Characterization of an immortalized human small airway basal stem/progenitor cell line with airway region-specific differentiation capacity. Respir Res 2019; 20:196. [PMID: 31443657 PMCID: PMC6708250 DOI: 10.1186/s12931-019-1140-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background The pathology of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF) and most lung cancers involves the small airway epithelium (SAE), the single continuous layer of cells lining the airways ≥ 6th generations. The basal cells (BC) are the stem/progenitor cells of the SAE, responsible for the differentiation into intermediate cells and ciliated, club and mucous cells. To facilitate the study of the biology of the human SAE in health and disease, we immortalized and characterized a normal human SAE basal cell line. Methods Small airway basal cells were purified from brushed SAE of a healthy nonsmoker donor with a characteristic normal SAE transcriptome. The BC were immortalized by retrovirus-mediated telomerase reverse transcriptase (TERT) transduction and single cell drug selection. The resulting cell line (hSABCi-NS1.1) was characterized by RNAseq, TaqMan PCR, protein immunofluorescence, differentiation capacity on an air-liquid interface (ALI) culture, transepithelial electrical resistance (TEER), airway region-associated features and response to genetic modification with SPDEF. Results The hSABCi-NS1.1 single-clone-derived cell line continued to proliferate for > 200 doubling levels and > 70 passages, continuing to maintain basal cell features (TP63+, KRT5+). When cultured on ALI, hSABCi-NS1.1 cells consistently formed tight junctions and differentiated into ciliated, club (SCGB1A1+), mucous (MUC5AC+, MUC5B+), neuroendocrine (CHGA+), ionocyte (FOXI1+) and surfactant protein positive cells (SFTPA+, SFTPB+, SFTPD+), observations confirmed by RNAseq and TaqMan PCR. Annotation enrichment analysis showed that “cilium” and “immunity” were enriched in functions of the top-1500 up-regulated genes. RNAseq reads alignment corroborated expression of CD4, CD74 and MHC-II. Compared to the large airway cell line BCi-NS1.1, differentiated of hSABCi-NS1.1 cells on ALI were enriched with small airway epithelial genes, including surfactant protein genes, LTF and small airway development relevant transcription factors NKX2–1, GATA6, SOX9, HOPX, ID2 and ETV5. Lentivirus-mediated expression of SPDEF in hSABCi-NS1.1 cells induced secretory cell metaplasia, accompanied with characteristic COPD-associated SAE secretory cell changes, including up-regulation of MSMB, CEACAM5 and down-regulation of LTF. Conclusions The immortalized hSABCi-NS1.1 cell line has diverse differentiation capacities and retains SAE features, which will be useful for understanding the biology of SAE, the pathogenesis of SAE-related diseases, and testing new pharmacologic agents. Electronic supplementary material The online version of this article (10.1186/s12931-019-1140-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guoqing Wang
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Howard H Lou
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Philip L Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Sharon Driscoll
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | | | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | - Jay S Fine
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Matthew J Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
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11
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Elefsinioti A, Bellaire T, Wang A, Quast K, Seidel H, Braxenthaler M, Goeller G, Christianson A, Henderson D, Reischl J. Key factors for successful data integration in biomarker research. Nat Rev Drug Discov 2016; 15:369-70. [DOI: 10.1038/nrd.2016.74] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Strobel B, Duechs MJ, Schmid R, Stierstorfer BE, Bucher H, Quast K, Stiller D, Hildebrandt T, Mennerich D, Gantner F, Erb KJ, Kreuz S. Modeling Pulmonary Disease Pathways Using Recombinant Adeno-Associated Virus 6.2. Am J Respir Cell Mol Biol 2015; 53:291-302. [PMID: 25845025 DOI: 10.1165/rcmb.2014-0338ma] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Viral vectors have been applied successfully to generate disease-related animal models and to functionally characterize target genes in vivo. However, broader application is still limited by complex vector production, biosafety requirements, and vector-mediated immunogenic responses, possibly interfering with disease-relevant pathways. Here, we describe adeno-associated virus (AAV) variant 6.2 as an ideal vector for lung delivery in mice, overcoming most of the aforementioned limitations. In a proof-of-concept study using AAV6.2 vectors expressing IL-13 and transforming growth factor-β1 (TGF-β1), we were able to induce hallmarks of severe asthma and pulmonary fibrosis, respectively. Phenotypic characterization and deep sequencing analysis of the AAV-IL-13 asthma model revealed a characteristic disease signature. Furthermore, suitability of the model for compound testing was also demonstrated by pharmacological intervention studies using an anti-IL-13 antibody and dexamethasone. Similarly, the AAV-TGF-β1 fibrosis model showed several disease-like pathophenotypes monitored by micro-computed tomography imaging and lung function measurement. Most importantly, analyses using stuffer control vectors demonstrated that in contrast to a common adenovirus-5 vector, AAV6.2 vectors did not induce any measurable inflammation and therefore carry a lower risk of altering relevant readouts. In conclusion, we propose AAV6.2 as an ideal vector system for the functional characterization of target genes in the context of pulmonary diseases in mice.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Florian Gantner
- 4 Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany
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13
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Baum P, Schmid R, Ittrich C, Rust W, Fundel-Clemens K, Siewert S, Baur M, Mara L, Gruenbaum L, Heckel A, Eils R, Kontermann RE, Roth GJ, Gantner F, Schnapp A, Park JE, Weith A, Quast K, Mennerich D. Phenocopy--a strategy to qualify chemical compounds during hit-to-lead and/or lead optimization. PLoS One 2010; 5:e14272. [PMID: 21170314 PMCID: PMC3000806 DOI: 10.1371/journal.pone.0014272] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/09/2010] [Indexed: 01/12/2023] Open
Abstract
A phenocopy is defined as an environmentally induced phenotype of one individual which is identical to the genotype-determined phenotype of another individual. The phenocopy phenomenon has been translated to the drug discovery process as phenotypes produced by the treatment of biological systems with new chemical entities (NCE) may resemble environmentally induced phenotypic modifications. Various new chemical entities exerting inhibition of the kinase activity of Transforming Growth Factor β Receptor I (TGF-βR1) were qualified by high-throughput RNA expression profiling. This chemical genomics approach resulted in a precise time-dependent insight to the TGF-β biology and allowed furthermore a comprehensive analysis of each NCE's off-target effects. The evaluation of off-target effects by the phenocopy approach allows a more accurate and integrated view on optimized compounds, supplementing classical biological evaluation parameters such as potency and selectivity. It has therefore the potential to become a novel method for ranking compounds during various drug discovery phases.
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Affiliation(s)
- Patrick Baum
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ramona Schmid
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Carina Ittrich
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Werner Rust
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | - Susanne Siewert
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Baur
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Lisa Mara
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, United States of America
| | - Lore Gruenbaum
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, United States of America
| | - Armin Heckel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Roland Eils
- Institute of Pharmacy and Molecular Biotechnology/BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Roland E. Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Gerald J. Roth
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Florian Gantner
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andreas Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - John E. Park
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andreas Weith
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Detlev Mennerich
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, United States of America
- * E-mail:
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14
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Schmid R, Baum P, Ittrich C, Fundel-Clemens K, Huber W, Brors B, Eils R, Weith A, Mennerich D, Quast K. Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics 2010; 11:349. [PMID: 20525181 PMCID: PMC3091625 DOI: 10.1186/1471-2164-11-349] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/02/2010] [Indexed: 11/26/2022] Open
Abstract
Background Normalization of microarrays is a standard practice to account for and minimize effects which are not due to the controlled factors in an experiment. There is an overwhelming number of different methods that can be applied, none of which is ideally suited for all experimental designs. Thus, it is important to identify a normalization method appropriate for the experimental setup under consideration that is neither too negligent nor too stringent. Major aim is to derive optimal results from the underlying experiment. Comparisons of different normalization methods have already been conducted, none of which, to our knowledge, comparing more than a handful of methods. Results In the present study, 25 different ways of pre-processing Illumina Sentrix BeadChip array data are compared. Among others, methods provided by the BeadStudio software are taken into account. Looking at different statistical measures, we point out the ideal versus the actual observations. Additionally, we compare qRT-PCR measurements of transcripts from different ranges of expression intensities to the respective normalized values of the microarray data. Taking together all different kinds of measures, the ideal method for our dataset is identified. Conclusions Pre-processing of microarray gene expression experiments has been shown to influence further downstream analysis to a great extent and thus has to be carefully chosen based on the design of the experiment. This study provides a recommendation for deciding which normalization method is best suited for a particular experimental setup.
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Affiliation(s)
- Ramona Schmid
- Boehringer Ingelheim Pharma GmbH & Co, KG, Birkendorfer Str, 65, 88397 Biberach/Riss, Germany
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Popova T, Mennerich D, Weith A, Quast K. Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. BMC Genomics 2008; 9:91. [PMID: 18298816 PMCID: PMC2268927 DOI: 10.1186/1471-2164-9-91] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 02/25/2008] [Indexed: 12/04/2022] Open
Abstract
Background Large-scale gene expression analysis of post-mortem brain tissue offers unique opportunities for investigating genetic mechanisms of psychiatric and neurodegenerative disorders. On the other hand microarray data analysis associated with these studies is a challenging task. In this publication we address the issue of low RNA quality data and corresponding data analysis strategies. Results A detailed analysis of effects of post chip RNA quality on the measured abundance of transcripts is presented. Overall Affymetrix GeneChip data (HG-U133_AB and HG-U133_Plus_2.0) derived from ten different brain regions was investigated. Post chip RNA quality being assessed by 5'/3' ratio of housekeeping genes was found to introduce a well pronounced systematic noise into the measured transcript expression levels. According to this study RNA quality effects have: 1) a "random" component which is introduced by the technology and 2) a systematic component which depends on the features of the transcripts and probes. Random components mainly account for numerous negative correlations of low-abundant transcripts. These negative correlations are not reproducible and are mainly introduced by an increased relative level of noise. Three major contributors to the systematic noise component were identified: the first is the probe set distribution, the second is the length of mRNA species, and the third is the stability of mRNA species. Positive correlations reflect the 5'-end to 3'-end direction of mRNA degradation whereas negative correlations result from the compensatory increase in stable and 3'-end probed transcripts. Systematic components affect the expressed transcripts by introducing irrelevant gene correlations and can strongly influence the results of the main experiment. A linear model correcting the effect of RNA quality on measured intensities was introduced. In addition the contribution of a number of pre-mortem and post-mortem attributes to the overall detected RNA quality effect was investigated. Brain pH, duration of agonal stage, post-mortem interval before sampling and donor's age of death within considered limits were found to have no significant contribution. Conclusion Basic conclusions for data analysis in expression profiling study are as follows: 1) testing for RNA quality dependency should be included in the preprocessing of the data; 2) investigating inter-gene correlation without regard to RNA quality effects could be misleading; 3) data normalization procedures relying on housekeeping genes either do not influence the correlation structure (if 3'-end intensities are used) or increase it for negatively correlated transcripts (if 5'-end or median intensities are included in normalization procedure); 4) sample sets should be matched with regard to RNA quality; 5) RMA preprocessing is more sensitive to RNA quality effect, than MAS 5.0.
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Affiliation(s)
- Tatiana Popova
- Boehringer Ingelheim Pharma GmbH Co & KG, Birkendorfer Str. 65, Biberach and der Riss, Germany.
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Abstract
DNA-microarrays find broad employment in biochemical research. This technology allows the monitoring of the expression levels of thousands of genes at the same time. Often, the goal of a microarray study is to find differentially expressed genes in two different types of tissue, for example normal and cancerous. Multiple hypothesis testing is a useful statistical tool for such studies. One approach using multiple hypothesis testing is nonparametric analysis for replicated microarray experiments. In this paper we present an improved version of this method. We also show how p-values are calculated for all significant genes detected with this testing procedure. All algorithms were implemented in an R-package, and instructions on it's use are included. The package can be downloaded at http://www.statistik.unidortmund.de/de/content/einrichtungen/lehrstuehle/personen/jung.html
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Affiliation(s)
- Klaus Jung
- Department of Statistics, University of Dortmund, D-44221 Dortmund, Germany.
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Quast K, Bathe B, Pühler A, Kalinowski J. The Corynebacterium glutamicum insertion sequence ISCg2 prefers conserved target sequences located adjacent to genes involved in aspartate and glutamate metabolism. Mol Gen Genet 1999; 262:568-78. [PMID: 10589846 DOI: 10.1007/s004380051119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An IS element, termed ISCg2, was identified in the chromosome of Corynebacterium glutamicum ATCC 13032. After screening a cosmid library of the C. glutamicum ATCC 13032 genome, six copies of ISCg2 including their flanking regions were sequenced and analyzed. ISCg2 is 1636 bp in length and has 26-bp imperfect inverted repeats flanked by 3-bp direct repeats. By comparisons with other IS elements, ISCg2 was classified as a member of the IS30 family of insertion sequences. The six copies of ISCg2 were identical at the nucleotide level and were located in intergenic, AT-rich regions of the chromosome. The regions in which the six copies of ISCg2 were inserted displayed significant similarities. This similarity extends over a region of 65 bp, which was assumed to be the target region for ISCg2. Interestingly, five of the six copies of ISCg2 were located adjacent to genes that may be involved in aspartate and glutamate metabolism or its regulation. Investigation of the distribution of ISCg2 showed that the IS element is restricted to certain C. glutamicum strains. Analysis of various integration regions indicates active transposition of ISCg2 in C. glutamicum.
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Affiliation(s)
- K Quast
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Germany
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