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Lee-Ferris RE, Okuda K, Galiger JR, Schworer SA, Rogers TD, Dang H, Gilmore R, Edwards C, Nakano S, Cawley AM, Pickles RJ, Gallant SC, Crisci E, Rivier L, Hagood JS, O'Neal WK, Baric RS, Grubb BR, Boucher RC, Randell SH. Prolonged airway explant culture enables study of health, disease, and viral pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.03.578756. [PMID: 38370820 PMCID: PMC10871200 DOI: 10.1101/2024.02.03.578756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In vitro models play a major role in studying airway physiology and disease. However, the native lung's complex tissue architecture and non-epithelial cell lineages are not preserved in these models. Ex vivo tissue models could overcome in vitro limitations, but methods for long-term maintenance of ex vivo tissue has not been established. We describe methods to culture human large airway explants, small airway explants, and precision-cut lung slices for at least 14 days. Human airway explants recapitulate genotype-specific electrophysiology, characteristic epithelial, endothelial, stromal and immune cell populations, and model viral infection after 14 days in culture. These methods also maintain mouse, rabbit, and pig tracheal explants. Notably, intact airway tissue can be cryopreserved, thawed, and used to generate explants with recovery of function 14 days post-thaw. These studies highlight the broad applications of airway tissue explants and their use as translational intermediates between in vitro and in vivo studies.
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Lam M, Lamanna E, Organ L, Donovan C, Bourke JE. Perspectives on precision cut lung slices-powerful tools for investigation of mechanisms and therapeutic targets in lung diseases. Front Pharmacol 2023; 14:1162889. [PMID: 37261291 PMCID: PMC10228656 DOI: 10.3389/fphar.2023.1162889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/19/2023] [Indexed: 06/02/2023] Open
Abstract
Precision cut lung slices (PCLS) have emerged as powerful experimental tools for respiratory research. Pioneering studies using mouse PCLS to visualize intrapulmonary airway contractility have been extended to pulmonary arteries and for assessment of novel bronchodilators and vasodilators as therapeutics. Additional disease-relevant outcomes, including inflammatory, fibrotic, and regenerative responses, are now routinely measured in PCLS from multiple species, including humans. This review provides an overview of established and innovative uses of PCLS as an intermediary between cellular and organ-based studies and focuses on opportunities to increase their application to investigate mechanisms and therapeutic targets to oppose excessive airway contraction and fibrosis in lung diseases.
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Affiliation(s)
- Maggie Lam
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Emma Lamanna
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institut Pasteur, Unit of Antibodies in Therapy and Pathology, INSERM UMR1222, Paris, France
| | - Louise Organ
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Chantal Donovan
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Jane E. Bourke
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
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3
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Nußbaum SM, Krabbe J, Böll S, Babendreyer A, Martin C. Functional changes in long-term incubated rat precision-cut lung slices. Respir Res 2022; 23:261. [PMID: 36127699 PMCID: PMC9490993 DOI: 10.1186/s12931-022-02169-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background Respiratory diseases represent a global health burden. Because research on therapeutic strategies of airway diseases is essential, the technique of precision-cut lung slices (PCLS) has been developed and widely studied. PCLS are an alternative ex vivo model and have the potential to replace and reduce in vivo animal models. So far, the majority of studies was conducted with short-term cultivated PCLS (≤ 72 h). As there is large interest in research of chronic diseases and chronic toxicity, feasibility of cultivating human PCLS long-term over 2 weeks and recently over 4 weeks was investigated by another research group with successful results. Our aim was to establish a model of long-term cultivated rat PCLS over a period of 29 days. Methods Rat PCLS were cultured for 29 days and analysed regarding viability, histopathology, reactivity and gene expression at different time points during cultivation. Results Cultivation of rat PCLS over a 29-day time period was successful with sustained viability. Furthermore, the ability of bronchoconstriction was maintained between 13 and 25 days, depending on the mediator. However, reduced relaxation, altered sensitivity and increased respiratory tone were observed. Regarding transcription, alteration in gene expression pattern of the investigated target genes was ascertained during long-term cultivation with mixed results. Furthermore, the preparation of PCLS seems to influence messenger ribonucleic acid (mRNA) expression of most target genes. Moreover, the addition of fetal bovine serum (FBS) to the culture medium did not improve viability of PCLS. In contrast to medium without FBS, FBS seems to affect measurements and resulted in marked cellular changes of metaplastic and/or regenerative origin. Conclusions Overall, a model of long-term cultivated rat PCLS which stays viable for 29 days and reactive for at least 13 days could be established. Before long-term cultivated PCLS can be used for in-depth study of chronic diseases and chronic toxicity, further investigations have to be made. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02169-5.
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Affiliation(s)
- Sarah Marie Nußbaum
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Julia Krabbe
- Institute of Occupational, Social and Environmental Medicine, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Svenja Böll
- Department of Pediatrics, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Christian Martin
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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4
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Varankar SS, Cardoso EC, Lee JH. Ex situ-armus: experimental models for combating respiratory dysfunction. Curr Opin Genet Dev 2022; 75:101946. [PMID: 35810725 DOI: 10.1016/j.gde.2022.101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 11/28/2022]
Abstract
Ex situ experimental models have become a main stay in pulmonary research. Organoids and explant systems have uncovered novel stem cell subsets, served as disease models, delineated cell fate transitions, and aided high throughput pre-clinical drug screening. Integration of gene-editing and bioengineering approaches have further generated novel avenues for regenerative medicine and transplantation strategies. In this article, we highlight recent studies, aided by ex situ systems, which have contributed to significant advances in our understanding of the human lower respiratory tract. We present key observations from these studies to gain improved insights into human disease. We conclude this article with a summary of existing challenges and potential technological advances to successfully mirror human tissue physiology.
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Affiliation(s)
- Sagar S Varankar
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Erik C Cardoso
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Joo-Hyeon Lee
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK.
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5
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Jeong MH, Han H, Lagares D, Im H. Recent Advances in Molecular Diagnosis of Pulmonary Fibrosis for Precision Medicine. ACS Pharmacol Transl Sci 2022; 5:520-538. [DOI: 10.1021/acsptsci.2c00028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Mi Ho Jeong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hongwei Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - David Lagares
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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6
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Ruggiero V, Aquino RP, Del Gaudio P, Campiglia P, Russo P. Post-COVID Syndrome: The Research Progress in the Treatment of Pulmonary sequelae after COVID-19 Infection. Pharmaceutics 2022; 14:pharmaceutics14061135. [PMID: 35745708 PMCID: PMC9229559 DOI: 10.3390/pharmaceutics14061135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022] Open
Abstract
Post-COVID syndrome or long COVID is defined as the persistence of symptoms after confirmed SARS-CoV-2 infection, the pathogen responsible for coronavirus disease. The content herein presented reviews the reported long-term consequences and aftereffects of COVID-19 infection and the potential strategies to adopt for their management. Recent studies have shown that severe forms of COVID-19 can progress into acute respiratory distress syndrome (ARDS), a predisposing factor of pulmonary fibrosis that can irreversibly compromise respiratory function. Considering that the most serious complications are observed in the airways, the inhalation delivery of drugs directly to the lungs should be preferred, since it allows to lower the dose and systemic side effects. Although further studies are needed to optimize these techniques, recent studies have also shown the importance of in vitro models to recreate the SARS-CoV-2 infection and study its sequelae. The information reported suggests the necessity to develop new inhalation therapies in order to improve the quality of life of patients who suffer from this condition.
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Affiliation(s)
- Valentina Ruggiero
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (V.R.); (R.P.A.); (P.D.G.); (P.C.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Italy
| | - Rita P. Aquino
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (V.R.); (R.P.A.); (P.D.G.); (P.C.)
| | - Pasquale Del Gaudio
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (V.R.); (R.P.A.); (P.D.G.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (V.R.); (R.P.A.); (P.D.G.); (P.C.)
| | - Paola Russo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (V.R.); (R.P.A.); (P.D.G.); (P.C.)
- Correspondence:
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7
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Baldassi D, Ambike S, Feuerherd M, Cheng CC, Peeler DJ, Feldmann DP, Porras-Gonzalez DL, Wei X, Keller LA, Kneidinger N, Stoleriu MG, Popp A, Burgstaller G, Pun SH, Michler T, Merkel OM. Inhibition of SARS-CoV-2 replication in the lung with siRNA/VIPER polyplexes. J Control Release 2022; 345:661-674. [PMID: 35364120 PMCID: PMC8963978 DOI: 10.1016/j.jconrel.2022.03.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 01/11/2023]
Abstract
SARS-CoV-2 has been the cause of a global pandemic since 2019 and remains a medical urgency. siRNA-based therapies are a promising strategy to fight viral infections. By targeting a specific region of the viral genome, siRNAs can efficiently downregulate viral replication and suppress viral infection. However, to achieve the desired therapeutic activity, siRNA requires a suitable delivery system. The VIPER (virus-inspired polymer for endosomal release) block copolymer has been reported as promising delivery system for both plasmid DNA and siRNA in the past years. It is composed of a hydrophilic block for condensation of nucleic acids as well as a hydrophobic, pH-sensitive block that, at acidic pH, exposes the membrane lytic peptide melittin, which enhances endosomal escape. In this study, we aimed at developing a formulation for pulmonary administration of siRNA to suppress SARS-CoV-2 replication in lung epithelial cells. After characterizing siRNA/VIPER polyplexes, the activity and safety profile were confirmed in a lung epithelial cell line. To further investigate the activity of the polyplexes in a more sophisticated cell culture system, an air-liquid interface (ALI) culture was established. siRNA/VIPER polyplexes reached the cell monolayer and penetrated through the mucus layer secreted by the cells. Additionally, the activity against wild-type SARS-CoV-2 in the ALI model was confirmed by qRT-PCR. To investigate translatability of our findings, the activity against SARS-CoV-2 was tested ex vivo in human lung explants. Here, siRNA/VIPER polyplexes efficiently inhibited SARS-CoV-2 replication. Finally, we verified the delivery of siRNA/VIPER polyplexes to lung epithelial cells in vivo, which represent the main cellular target of viral infection in the lung. In conclusion, siRNA/VIPER polyplexes efficiently delivered siRNA to lung epithelial cells and mediated robust downregulation of viral replication both in vitro and ex vivo without toxic or immunogenic side effects in vivo, demonstrating the potential of local siRNA delivery as a promising antiviral therapy in the lung.
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Affiliation(s)
- Domizia Baldassi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-University of Munich, Butenandtstraße 5, 81377 Munich, Germany
| | - Shubhankar Ambike
- Institute of Virology, School of Medicine, Technical University of Munich / Helmholtz Zentrum Munich, Trogerstr.30, 81675 Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, School of Medicine, Technical University of Munich / Helmholtz Zentrum Munich, Trogerstr.30, 81675 Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, School of Medicine, Technical University of Munich / Helmholtz Zentrum Munich, Trogerstr.30, 81675 Munich, Germany
| | - David J Peeler
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, United States
| | - Daniel P Feldmann
- Department of Oncology, Wayne State University School of Medicine, 4100 John R St, Detroit, MI 48201, United States
| | - Diana Leidy Porras-Gonzalez
- Institute of Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Xin Wei
- Institute of Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Lea-Adriana Keller
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-University of Munich, Butenandtstraße 5, 81377 Munich, Germany; Preclinical Safety, AbbVie Deutschland GmbH & Co. KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, University Hospital, LMU, Munich, Member of the German Center for Lung Research (DZL), Germany
| | - Mircea Gabriel Stoleriu
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Pulmonary Hospital; Marchioninistraße 15, 81377 Munich and Robert-Koch-Allee 2, 82131 Gauting, Germany
| | - Andreas Popp
- Preclinical Safety, AbbVie Deutschland GmbH & Co. KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Gerald Burgstaller
- Institute of Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, United States
| | - Thomas Michler
- Institute of Virology, School of Medicine, Technical University of Munich / Helmholtz Zentrum Munich, Trogerstr.30, 81675 Munich, Germany; Institute of Laboratory Medicine, University Hospital, LMU, Munich, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-University of Munich, Butenandtstraße 5, 81377 Munich, Germany; Institute of Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.
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8
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Gerckens M, Schorpp K, Pelizza F, Wögrath M, Reichau K, Ma H, Dworsky AM, Sengupta A, Stoleriu MG, Heinzelmann K, Merl-Pham J, Irmler M, Alsafadi HN, Trenkenschuh E, Sarnova L, Jirouskova M, Frieß W, Hauck SM, Beckers J, Kneidinger N, Behr J, Hilgendorff A, Hadian K, Lindner M, Königshoff M, Eickelberg O, Gregor M, Plettenburg O, Yildirim AÖ, Burgstaller G. Phenotypic drug screening in a human fibrosis model identified a novel class of antifibrotic therapeutics. SCIENCE ADVANCES 2021; 7:eabb3673. [PMID: 34936468 PMCID: PMC8694600 DOI: 10.1126/sciadv.abb3673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Fibrogenic processes instigate fatal chronic diseases leading to organ failure and death. Underlying biological processes involve induced massive deposition of extracellular matrix (ECM) by aberrant fibroblasts. We subjected diseased primary human lung fibroblasts to an advanced three-dimensional phenotypic high-content assay and screened a repurposing drug library of small molecules for inhibiting ECM deposition. Fibrotic Pattern Detection by Artificial Intelligence identified tranilast as an effective inhibitor. Structure-activity relationship studies confirmed N-(2-butoxyphenyl)-3-(phenyl)acrylamides (N23Ps) as a novel and highly potent compound class. N23Ps suppressed myofibroblast transdifferentiation, ECM deposition, cellular contractility, and altered cell shapes, thus advocating a unique mode of action. Mechanistically, transcriptomics identified SMURF2 as a potential therapeutic target network. Antifibrotic activity of N23Ps was verified by proteomics in a human ex vivo tissue fibrosis disease model, suppressing profibrotic markers SERPINE1 and CXCL8. Conclusively, N23Ps are a novel class of highly potent compounds inhibiting organ fibrosis in patients.
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Affiliation(s)
- Michael Gerckens
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Francesco Pelizza
- Chemical and Process Engineering, Strathclyde University, Glasgow, Scotland, UK
| | - Melanie Wögrath
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
| | - Kora Reichau
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Leibniz Universität Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Hannover, Germany
| | - Huilong Ma
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Leibniz Universität Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Hannover, Germany
| | - Armando-Marco Dworsky
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
| | - Arunima Sengupta
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mircea Gabriel Stoleriu
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Asklepios Fachkliniken Munich-Gauting, Munich, Germany
| | - Katharina Heinzelmann
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Hani N. Alsafadi
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Wallenberg Center for Molecular Medicine (WCMM), Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Eduard Trenkenschuh
- Department of Pharmacy–Center for Drug Research, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximillians University of Munich, Munich, Germany
| | - Lenka Sarnova
- Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marketa Jirouskova
- Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Wolfgang Frieß
- Department of Pharmacy–Center for Drug Research, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximillians University of Munich, Munich, Germany
| | - Stefanie M. Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, 85354 Freising, Germany
| | - Nikolaus Kneidinger
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximillians University of Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Jürgen Behr
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Asklepios Fachkliniken Munich-Gauting, Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximillians University of Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Anne Hilgendorff
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Lindner
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Asklepios Fachkliniken Munich-Gauting, Munich, Germany
- Paracelsus Medical Private University, Salzburg, Austria
| | - Melanie Königshoff
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Martin Gregor
- Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Leibniz Universität Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Hannover, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Ali Önder Yildirim
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, Munich, Germany
- Corresponding author.
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9
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Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res 2021; 50:333-349. [PMID: 34928377 PMCID: PMC8754636 DOI: 10.1093/nar/gkab1248] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/10/2021] [Accepted: 12/05/2021] [Indexed: 01/08/2023] Open
Abstract
A promising approach to tackle the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. So far it is unclear, which viral replication steps can be efficiently inhibited with siRNAs. Here, we report that siRNAs can target genomic RNA (gRNA) of SARS-CoV-2 after cell entry, and thereby terminate replication before start of transcription and prevent virus-induced cell death. Coronaviruses replicate via negative sense RNA intermediates using a unique discontinuous transcription process. As a result, each viral RNA contains identical sequences at the 5′ and 3′ end. Surprisingly, siRNAs were not active against intermediate negative sense transcripts. Targeting common sequences shared by all viral transcripts allowed simultaneous suppression of gRNA and subgenomic (sg)RNAs by a single siRNA. The most effective suppression of viral replication and spread, however, was achieved by siRNAs that targeted open reading frame 1 (ORF1) which only exists in gRNA. In contrast, siRNAs that targeted the common regions of transcripts were outcompeted by the highly abundant sgRNAs leading to an impaired antiviral efficacy. Verifying the translational relevance of these findings, we show that a chemically modified siRNA that targets a highly conserved region of ORF1, inhibited SARS-CoV-2 replication ex vivo in explants of the human lung. Our work encourages the development of siRNA-based therapies for COVID-19 and suggests that early therapy start, or prophylactic application, together with specifically targeting gRNA, might be key for high antiviral efficacy.
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Affiliation(s)
- Shubhankar Ambike
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Stoyan Velkov
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Domizia Baldassi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Suliman Qadir Afridi
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Diana Porras-Gonzalez
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Xin Wei
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Philipp Hagen
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mircea Gabriel Stoleriu
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Pulmonary Hospital; Marchioninistraße 15, 81377 Munich and Robert-Koch-Allee 2, 82131 Gauting, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany.,Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,Infectious Diseases Therapeutic Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), 34114 Daejeon, Republic of Korea
| | - Thomas Michler
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
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10
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Burgstaller G, Gerckens M, Eickelberg O, Königshoff M. Decellularized Human Lung Scaffolds as Complex Three-Dimensional Tissue Culture Models to Study Functional Behavior of Fibroblasts. Methods Mol Biol 2021; 2299:447-456. [PMID: 34028760 DOI: 10.1007/978-1-0716-1382-5_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In vitro culturing of cells in two-dimensional (2D) environments is a widespread used methodology in biomedical research. Most commonly, cells are cultured on artificial plastic dish surfaces, which lead to abnormal functional behaviors, as plastic does not reflect the native microenvironment found in vivo or in situ. Therefore, a multitude of three-dimensional (3D) cell culture systems were developed in the past years, which aim to bridge the gap between 2D cell culture dishes and the in vivo situation. One of the more recent development in the field, the generation of viable precision-cut tissue slices from various organs emerged as an exciting approach to study complex interactions and biological processes ex vivo in 3D. Decellularization of such tissue slices leads to the removal of all functional cells, and leaves behind a scaffold of extracellular matrix (ECM), which closely recapitulates the molecular composition, mechanical properties, topology, and microarchitecture of native ECM. Subsequently, decellularized precision-cut lung slices (PCLS), also called 3D lung tissue culture (3D-LTCs), can be successfully reseeded with a variety of cell types, including fibroblasts, which attach to and engraft into the matrix. Here, we describe the generation of PCLS from resected human lung tissue and their decellularization and recellularization with primary human fibroblasts. This novel 3D tissue culture model allows for various functional studies of fibroblast behavior on native ECM composition and topology.
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Affiliation(s)
- Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany. .,CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, München, Germany.
| | - Michael Gerckens
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany.,CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, München, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melanie Königshoff
- CPC-M bioArchive, Helmholtz Zentrum München, Comprehensive Pneumology Center Munich DZL/CPC-M, München, Germany.,Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Comprehensive Pneumology Center (CPC), Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
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11
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Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R. An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices. Eur Respir J 2021; 58:13993003.00221-2020. [PMID: 33361096 PMCID: PMC8318569 DOI: 10.1183/13993003.00221-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
Fibrosis can affect any organ, resulting in the loss of tissue architecture and function with often life-threatening consequences. Pathologically, fibrosis is characterised by the expansion of connective tissue due to excessive deposition of extracellular matrix (ECM) proteins, including the fibrillar forms of collagen. A significant limitation for discovering cures for fibrosis is the availability of suitable human models and techniques to quantify mature fibrillar collagen deposition as close as possible to human physiological conditions. Here we have extensively characterised an ex vivo cultured human lung tissue-derived, precision-cut lung slices (hPCLS) model using label-free second harmonic generation (SHG) light microscopy to quantify fibrillar collagen deposition and mass spectrometry-based techniques to obtain a proteomic and metabolomic fingerprint of hPCLS in ex vivo culture. We demonstrate that hPCLS are viable and metabolically active, with mesenchymal, epithelial, endothelial and immune cell types surviving for at least 2 weeks in ex vivo culture. Analysis of hPCLS-conditioned supernatants showed a strong induction of pulmonary fibrosis-related ECM proteins upon transforming growth factor-β1 (TGF-β1) stimulation. This upregulation of ECM proteins was not translated into an increased deposition of fibrillar collagen. In support of this observation, we revealed the presence of a pro-ECM degradation activity in our ex vivo cultures of hPCLS, inhibition of which by a metalloproteinase inhibitor resulted in increased collagen deposition in response to TGF-β1 stimulation. Together the data show that an integrated approach of measuring soluble pro-fibrotic markers alongside quantitative SHG-based analysis of fibrillar collagen is a valuable tool for studying pro-fibrotic signalling and testing anti-fibrotic agents. Multiomic and label-free imaging-based characterisation of ex vivo cultured human precision-cut lung slices (hPCLS) reveals that MMP signalling is a rate-limiting factor necessary for deposition of fibrillar collagen in ECM of hPCLShttps://bit.ly/3rcUa0e
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Affiliation(s)
- Muzamil Majid Khan
- European Molecular Biology Laboratory, Heidelberg, Germany.,Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany.,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Daniel Poeckel
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- European Molecular Biology Laboratory, Heidelberg, Germany.,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | | | - Frank Stein
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Daniel C Sevin
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | | | - Nico Zinn
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | | | | | - Thomas Muley
- Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Biobank Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Biobank Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals, Newcastle upon Tyne, UK
| | | | - Giovanna Bergamini
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany.,G. Bergamini and R. Pepperkok contributed equally to this article as lead authors and supervised the work
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Heidelberg, Germany .,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,G. Bergamini and R. Pepperkok contributed equally to this article as lead authors and supervised the work
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12
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Wronski S, Beinke S, Obernolte H, Belyaev NN, Saunders KA, Lennon MG, Schaudien D, Braubach P, Jonigk D, Warnecke G, Zardo P, Fieguth HG, Wilkens L, Braun A, Hessel EM, Sewald K. Rhinovirus-induced Human Lung Tissue Responses Mimic COPD and Asthma Gene Signatures. Am J Respir Cell Mol Biol 2021; 65:544-554. [PMID: 34181859 PMCID: PMC8641849 DOI: 10.1165/rcmb.2020-0337oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Human rhinovirus (RV) is a major risk factor for chronic obstructive pulmonary disease (COPD) and asthma exacerbations. The exploration of RV pathogenesis has been hampered by a lack of disease-relevant model systems. We performed a detailed characterization of host responses to RV infection in human lung tissue ex vivo and investigated whether these responses are disease relevant for patients with COPD and asthma. In addition, impact of the viral replication inhibitor rupintrivir was evaluated. Human precision-cut lung slices (PCLS) were infected with RV1B with or without rupintrivir. At Days 1 and 3 after infection, RV tissue localization, tissue viability, and viral load were determined. To characterize host responses to infection, mediator and whole genome analyses were performed. RV successfully replicated in PCLS airway epithelial cells and induced both antiviral and proinflammatory cytokines such as IFNα2a, CXCL10, CXCL11, IFN-γ, TNFα, and CCL5. Genomic analyses revealed that RV not only induced antiviral immune responses but also triggered changes in epithelial cell–associated pathways. Strikingly, the RV response in PCLS was reflective of gene expression changes described in patients with COPD and asthma. Although RV-induced host immune responses were abrogated by rupintrivir, RV-triggered epithelial processes were largely refractory to antiviral treatment. Detailed analysis of RV-infected human PCLS and comparison with gene signatures of patients with COPD and asthma revealed that the human RV PCLS model represents disease-relevant biological mechanisms that can be partially inhibited by a well-known antiviral compound and provide an outstanding opportunity to evaluate novel therapeutics.
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Affiliation(s)
- Sabine Wronski
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of Fraunhofer international Consortium for Anti-Infective Research (iCAIR), Member of Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany;
| | - Soren Beinke
- Research and Development, GlaxoSmithKline, Stevenage, United Kingdom of Great Britain and Northern Ireland
| | - Helena Obernolte
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of Fraunhofer international Consortium for Anti-Infective Research (iCAIR), Member of Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Nikolai N Belyaev
- Research and Development, GlaxoSmithKline, Stevenage, United Kingdom of Great Britain and Northern Ireland
| | - Ken A Saunders
- Research and Development, GlaxoSmithKline, Stevenage, United Kingdom of Great Britain and Northern Ireland
| | - Mark G Lennon
- Research and Development, GlaxoSmithKline, Stevenage, United Kingdom of Great Britain and Northern Ireland
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of Fraunhofer international Consortium for Anti-Infective Research (iCAIR), Member of Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Dsease (BREATH), Hannover, Germany
| | - Peter Braubach
- Hannover Medical School, 9177, Department of Pathology, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Danny Jonigk
- Hannover Medical School, 9177, Department of Pathology, Hannover, Niedersachsen, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Gregor Warnecke
- Hannover Medical School, 9177, Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Patrick Zardo
- Hannover Medical School, 9177, Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover, Germany
| | | | | | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of Fraunhofer international Consortium for Anti-Infective Research (iCAIR), Member of Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Edith M Hessel
- Research and Development, GlaxoSmithKline, Stevenage, United Kingdom of Great Britain and Northern Ireland
| | - Katherina Sewald
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of Fraunhofer international Consortium for Anti-Infective Research (iCAIR), Member of Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany.,Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover, Germany
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13
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Kiener M, Roldan N, Machahua C, Sengupta A, Geiser T, Guenat OT, Funke-Chambour M, Hobi N, Kruithof-de Julio M. Human-Based Advanced in vitro Approaches to Investigate Lung Fibrosis and Pulmonary Effects of COVID-19. Front Med (Lausanne) 2021; 8:644678. [PMID: 34026781 PMCID: PMC8139419 DOI: 10.3389/fmed.2021.644678] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused considerable socio-economic burden, which fueled the development of treatment strategies and vaccines at an unprecedented speed. However, our knowledge on disease recovery is sparse and concerns about long-term pulmonary impairments are increasing. Causing a broad spectrum of symptoms, COVID-19 can manifest as acute respiratory distress syndrome (ARDS) in the most severely affected patients. Notably, pulmonary infection with Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the causing agent of COVID-19, induces diffuse alveolar damage (DAD) followed by fibrotic remodeling and persistent reduced oxygenation in some patients. It is currently not known whether tissue scaring fully resolves or progresses to interstitial pulmonary fibrosis. The most aggressive form of pulmonary fibrosis is idiopathic pulmonary fibrosis (IPF). IPF is a fatal disease that progressively destroys alveolar architecture by uncontrolled fibroblast proliferation and the deposition of collagen and extracellular matrix (ECM) proteins. It is assumed that micro-injuries to the alveolar epithelium may be induced by inhalation of micro-particles, pathophysiological mechanical stress or viral infections, which can result in abnormal wound healing response. However, the exact underlying causes and molecular mechanisms of lung fibrosis are poorly understood due to the limited availability of clinically relevant models. Recently, the emergence of SARS-CoV-2 with the urgent need to investigate its pathogenesis and address drug options, has led to the broad application of in vivo and in vitro models to study lung diseases. In particular, advanced in vitro models including precision-cut lung slices (PCLS), lung organoids, 3D in vitro tissues and lung-on-chip (LOC) models have been successfully employed for drug screens. In order to gain a deeper understanding of SARS-CoV-2 infection and ultimately alveolar tissue regeneration, it will be crucial to optimize the available models for SARS-CoV-2 infection in multicellular systems that recapitulate tissue regeneration and fibrotic remodeling. Current evidence for SARS-CoV-2 mediated pulmonary fibrosis and a selection of classical and novel lung models will be discussed in this review.
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Affiliation(s)
- Mirjam Kiener
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research DBMR, Urology Research Laboratory, University of Bern, Bern, Switzerland
- Alveolix AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Nuria Roldan
- Alveolix AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Carlos Machahua
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research DBMR, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Arunima Sengupta
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
| | - Thomas Geiser
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research DBMR, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Olivier Thierry Guenat
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Manuela Funke-Chambour
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research DBMR, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Nina Hobi
- Alveolix AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research DBMR, Urology Research Laboratory, University of Bern, Bern, Switzerland
- Alveolix AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
- Organoid Core, Department for BioMedical Research, University of Bern, Bern, Switzerland
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14
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Stegmayr J, Alsafadi HN, Langwiński W, Niroomand A, Lindstedt S, Leigh ND, Wagner DE. Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts. Am J Physiol Lung Cell Mol Physiol 2020; 320:L232-L240. [PMID: 33112185 DOI: 10.1152/ajplung.00401.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Precision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology/disease and screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology/disease as compared with animal models. Several experimental readouts have been established for use with PCLS, but obtaining high-yield and -quality RNA for downstream analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for nonbiased and high-throughput analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high-quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis. We show that the RNA isolated using this method has sufficient quality for RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease.
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Affiliation(s)
- John Stegmayr
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hani N Alsafadi
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wojciech Langwiński
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Department of Pediatric Pulmonology, Allergy, and Clinical Immunology, Poznan University of Medical Science, Poznan, Poland
| | - Anna Niroomand
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Department of Thoracic Surgery, Lund University, Lund, Sweden
| | - Sandra Lindstedt
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Department of Thoracic Surgery, Lund University, Lund, Sweden
| | - Nicholas D Leigh
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.,Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Darcy E Wagner
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
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15
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Singh AK, Mishra G, Maurya A, Kulkarni GT, Awasthi R. Biofabrication: An interesting tool to create in vitro model for COVID-19 drug targets. Med Hypotheses 2020; 144:110059. [PMID: 32758895 PMCID: PMC7320859 DOI: 10.1016/j.mehy.2020.110059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/26/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Anurag Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Gaurav Mishra
- Institute of Medical Sciences, Faculty of Ayurveda, Department of Medicinal Chemistry, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Anand Maurya
- Institute of Medical Sciences, Faculty of Ayurveda, Department of Medicinal Chemistry, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Giriraj T Kulkarni
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida 201303, Uttar Pradesh, India
| | - Rajendra Awasthi
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida 201303, Uttar Pradesh, India.
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16
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Alsafadi HN, Uhl FE, Pineda RH, Bailey KE, Rojas M, Wagner DE, Königshoff M. Applications and Approaches for Three-Dimensional Precision-Cut Lung Slices. Disease Modeling and Drug Discovery. Am J Respir Cell Mol Biol 2020; 62:681-691. [PMID: 31991090 PMCID: PMC7401444 DOI: 10.1165/rcmb.2019-0276tr] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic lung diseases (CLDs), such as chronic obstructive pulmonary disease, interstitial lung disease, and lung cancer, are among the leading causes of morbidity globally and impose major health and financial burdens on patients and society. Effective treatments are scarce, and relevant human model systems to effectively study CLD pathomechanisms and thus discover and validate potential new targets and therapies are needed. Precision-cut lung slices (PCLS) from healthy and diseased human tissue represent one promising tool that can closely recapitulate the complexity of the lung's native environment, and recently, improved methodologies and accessibility to human tissue have led to an increased use of PCLS in CLD research. Here, we discuss approaches that use human PCLS to advance our understanding of CLD development, as well as drug discovery and validation for CLDs. PCLS enable investigators to study complex interactions among different cell types and the extracellular matrix in the native three-dimensional architecture of the lung. PCLS further allow for high-resolution (live) imaging of cellular functions in several dimensions. Importantly, PCLS can be derived from diseased lung tissue upon lung surgery or transplantation, thus allowing the study of CLDs in living human tissue. Moreover, CLDs can be modeled in PCLS derived from normal lung tissue to mimic the onset and progression of CLDs, complementing studies in end-stage diseased tissue. Altogether, PCLS are emerging as a remarkable tool to further bridge the gap between target identification and translation into clinical studies, and thus open novel avenues for future precision medicine approaches.
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Affiliation(s)
- Hani N. Alsafadi
- Lung Bioengineering and Regeneration, Department of Experimental Medical Science
- Wallenberg Center for Molecular Medicine
- Lund Stem Cell Center, Faculty of Medicine, and
- Helmholtz Zentrum Munich, Lung Repair and Regeneration, Comprehensive Pneumology Center, Member of the German Center for Lung Research, Munich, Germany
| | - Franziska E. Uhl
- Wallenberg Center for Molecular Medicine
- Vascular Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Ricardo H. Pineda
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Denver, Aurora, Colorado; and
| | - Kolene E. Bailey
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Denver, Aurora, Colorado; and
| | - Mauricio Rojas
- Division of Respiratory, Allergy and Critical Care Medicine, The Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Darcy E. Wagner
- Lung Bioengineering and Regeneration, Department of Experimental Medical Science
- Wallenberg Center for Molecular Medicine
- Lund Stem Cell Center, Faculty of Medicine, and
- Helmholtz Zentrum Munich, Lung Repair and Regeneration, Comprehensive Pneumology Center, Member of the German Center for Lung Research, Munich, Germany
| | - Melanie Königshoff
- Helmholtz Zentrum Munich, Lung Repair and Regeneration, Comprehensive Pneumology Center, Member of the German Center for Lung Research, Munich, Germany
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Denver, Aurora, Colorado; and
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17
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Oakley F, Gee LM, Sheerin NS, Borthwick LA. Implementation of pre-clinical methodologies to study fibrosis and test anti-fibrotic therapy. Curr Opin Pharmacol 2019; 49:95-101. [PMID: 31731225 PMCID: PMC6904905 DOI: 10.1016/j.coph.2019.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Diseases where fibrosis plays a major role accounts for enormous morbidity and mortality and yet we have very little in our therapeutic arsenal despite decades of research and clinical trials. Our understanding of fibrosis biology is primarily built on data generated in conventional mono-culture or co-culture systems and in vivo model systems. While these approaches have undoubtedly enhanced our understanding of basic mechanisms, they have repeatedly failed to translate to clinical benefit. Recently, there had been a push to generate more physiologically relevant platforms to study fibrosis and identify new therapeutic targets. Here we review the state-of-the-art regarding the development and application of 3D complex cultures, bio-printing and precision cut slices to study pulmonary, hepatic and renal fibrosis.
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Affiliation(s)
- Fiona Oakley
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Lucy M Gee
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Neil S Sheerin
- Renal Department, Freeman Hospital, Newcastle upon Tyne, UK; Applied Immunobiology and Transplantation Research Group, Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Lee A Borthwick
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
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