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Putri KSS, Adhyatmika A, Boorsma CE, Habibie H, Ruigrok MJR, Heukels P, Timens W, de Jager MH, Hinrichs WLJ, Olinga P, Melgert BN. Osteoprotegerin is an Early Marker of the Fibrotic Process and of Antifibrotic Treatment Responses in Ex Vivo Lung Fibrosis. Lung 2024:10.1007/s00408-024-00691-5. [PMID: 38642135 DOI: 10.1007/s00408-024-00691-5] [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] [Received: 01/30/2024] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Lung fibrosis is a chronic lung disease with a high mortality rate with only two approved drugs (pirfenidone and nintedanib) to attenuate its progression. To date, there are no reliable biomarkers to assess fibrosis development and/or treatment effects for these two drugs. Osteoprotegerin (OPG) is used as a serum marker to diagnose liver fibrosis and we have previously shown it associates with lung fibrosis as well. METHODS Here we used murine and human precision-cut lung slices to investigate the regulation of OPG in lung tissue to elucidate whether it tracks with (early) fibrosis development and responds to antifibrotic treatment to assess its potential use as a biomarker. RESULTS OPG mRNA expression in murine lung slices was higher after treatment with profibrotic cytokines TGFβ1 or IL13, and closely correlated with Fn and PAI1 mRNA expression. More OPG protein was released from fibrotic human lung slices than from the control human slices and from TGFβ1 and IL13-stimulated murine lung slices compared to control murine slices. This OPG release was inhibited when murine slices were treated with pirfenidone or nintedanib. OPG release from human fibrotic lung slices was inhibited by pirfenidone treatment. CONCLUSION OPG can already be detected during the early stages of fibrosis development and responds, both in early- and late-stage fibrosis, to treatment with antifibrotic drugs currently on the market for lung fibrosis. Therefore, OPG should be further investigated as a potential biomarker for lung fibrosis and a potential surrogate marker for treatment effect.
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Affiliation(s)
- Kurnia S S Putri
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
- Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
- Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
| | - Adhyatmika Adhyatmika
- Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
- Drug Targeting and Personalized Medicine Research Group, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Carian E Boorsma
- Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Habibie Habibie
- Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
- Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Mitchel J R Ruigrok
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Peter Heukels
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Marina H de Jager
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wouter L J Hinrichs
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Barbro N Melgert
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands.
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands.
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2
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Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, van Langelaar J, Schreurs RR, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SA, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, van Kempen LC, Groen HJ, Aerts JGJV, van Heesch S, Lowenberg B, Plasterk R, Kloosterman WP. The neo-open reading frame peptides that comprise the tumor framome are a rich source of neoantigens for cancer immunotherapy. Cancer Immunol Res 2024:742916. [PMID: 38573707 DOI: 10.1158/2326-6066.cir-23-0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate cancer whole genome and long-read transcript sequencing to identify the collection of novel open reading frame peptides (NOPs) expressed in tumors, termed the framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe an uncharacterized class of hidden NOPs, which derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of non-coding regions of the genome downstream of a rearrangement breakpoint. NOPs represent a vast amount of possible neoantigens particularly in tumors with many (complex) structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T-cells specific for hidden NOPs in lung cancer patient peripheral blood.
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Affiliation(s)
| | | | - Katka Franke
- CureVac Netherlands B.V., Amsterdam, Netherlands
| | | | | | | | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | | | - Jan Koster
- Amsterdam UMC, University of Amsterdam, Amsterdam, NH, Netherlands
| | - Wim Timens
- University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | | | | | | | | | - Emma V King
- University Hospitals Dorset, Poole, United Kingdom
| | | | | | | | - Sem Ag Engels
- The Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Ellen Oostenbach
- The Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, Netherlands
| | - Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, Sanquin, Amsterdam, Netherlands
| | | | | | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Dennis Poel
- Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - T Jeroen N Hiltermann
- University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Léon C van Kempen
- University Medical Center Groningen, Groningen, I am not in the U.S. or Canada, Netherlands
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3
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Nizamoglu M, Alleblas F, Koster T, Borghuis T, Vonk JM, Thomas MJ, White ES, Watson CK, Timens W, El Kasmi KC, Melgert BN, Heijink IH, Burgess JK. Three dimensional fibrotic extracellular matrix directs microenvironment fiber remodeling by fibroblasts. Acta Biomater 2024; 177:118-131. [PMID: 38350556 DOI: 10.1016/j.actbio.2024.02.008] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/12/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF), for which effective treatments are limited, results in excessive and disorganized deposition of aberrant extracellular matrix (ECM). An altered ECM microenvironment is postulated to contribute to disease progression through inducing profibrotic behavior of lung fibroblasts, the main producers and regulators of ECM. Here, we examined this hypothesis in a 3D in vitro model system by growing primary human lung fibroblasts in ECM-derived hydrogels from non-fibrotic (control) or IPF lung tissue. Using this model, we compared how control and IPF lung-derived fibroblasts responded in control and fibrotic microenvironments in a combinatorial manner. Culture of fibroblasts in fibrotic hydrogels did not alter in the overall amount of collagen or glycosaminoglycans but did cause a drastic change in fiber organization compared to culture in control hydrogels. High-density collagen percentage was increased by control fibroblasts in IPF hydrogels at day 7, but decreased at day 14. In contrast, IPF fibroblasts only decreased the high-density collagen percentage at day 14, which was accompanied by enhanced fiber alignment in IPF hydrogels. Similarly, stiffness of fibrotic hydrogels was increased only by control fibroblasts by day 14 while those of control hydrogels were not altered by fibroblasts. These data highlight how the ECM-remodeling responses of fibroblasts are influenced by the origin of both the cells and the ECM. Moreover, by showing how the 3D microenvironment plays a crucial role in directing cells, our study paves the way in guiding future investigations examining fibrotic processes with respect to ECM remodeling responses of fibroblasts. STATEMENT OF SIGNIFICANCE: In this study, we investigated the influence of the altered extracellular matrix (ECM) in Idiopathic Pulmonary Fibrosis (IPF), using a 3D in vitro model system composed of ECM-derived hydrogels from both IPF and control lungs, seeded with human IPF and control lung fibroblasts. While our results indicated that fibrotic microenvironment did not change the overall collagen or glycosaminoglycan content, it resulted in a dramatically alteration of fiber organization and mechanical properties. Control fibroblasts responded differently from IPF fibroblasts, highlighting the unique instructive role of the fibrotic ECM and the interplay with fibroblast origin. These results underscore the importance of 3D microenvironments in guiding pro-fibrotic responses, offering potential insights for future IPF therapies as well as other fibrotic diseases and cancer.
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Affiliation(s)
- Mehmet Nizamoglu
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands.
| | - Frederique Alleblas
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Taco Koster
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Theo Borghuis
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Matthew J Thomas
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Eric S White
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Carolin K Watson
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Karim C El Kasmi
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Barbro N Melgert
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, Groningen, the Netherlands
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, the Netherlands
| | - Janette K Burgess
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, Groningen, the Netherlands.
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4
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de Jager VD, Timens W, Bayle A, Botling J, Brcic L, Büttner R, Fernandes MGO, Havel L, Hochmair MJ, Hofman P, Janssens A, Johansson M, van Kempen L, Kern I, Lopez-Rios F, Lüchtenborg M, Machado JC, Mohorcic K, Paz-Ares L, Popat S, Ryška A, Taniere P, Wolf J, Schuuring E, van der Wekken AJ. Developments in predictive biomarker testing and targeted therapy in advanced stage non-small cell lung cancer and their application across European countries. Lancet Reg Health Eur 2024; 38:100838. [PMID: 38476742 PMCID: PMC10928289 DOI: 10.1016/j.lanepe.2024.100838] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 01/08/2024] [Indexed: 03/14/2024]
Abstract
In the past two decades, the treatment of metastatic non-small cell lung cancer (NSCLC), has undergone significant changes due to the introduction of targeted therapies and immunotherapy. These advancements have led to the need for predictive molecular tests to identify patients eligible for targeted therapy. This review provides an overview of the development and current application of targeted therapies and predictive biomarker testing in European patients with advanced stage NSCLC. Using data from eleven European countries, we conclude that recommendations for predictive testing are incorporated in national guidelines across Europe, although there are differences in their comprehensiveness. Moreover, the availability of recently EMA-approved targeted therapies varies between European countries. Unfortunately, routine assessment of national/regional molecular testing rates is limited. As a result, it remains uncertain which proportion of patients with metastatic NSCLC in Europe receive adequate predictive biomarker testing. Lastly, Molecular Tumor Boards (MTBs) for discussion of molecular test results are widely implemented, but national guidelines for their composition and functioning are lacking. The establishment of MTB guidelines can provide a framework for interpreting rare or complex mutations, facilitating appropriate treatment decision-making, and ensuring quality control.
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Affiliation(s)
- Vincent D. de Jager
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Arnaud Bayle
- Oncostat U1018, Inserm, Paris-Saclay University, Gustave Roussy, Villejuif, France
| | - Johan Botling
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy of University of Gothenburg, Gothenburg, Sweden
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Reinhard Büttner
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Libor Havel
- Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Maximilian J. Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Paul Hofman
- IHU RespirERA, FHU OncoAge, Nice University Hospital, Côte d’Azur University, Nice, France
| | - Annelies Janssens
- Department of Oncology, University Hospital Antwerp, University of Antwerp, Edegem, Belgium
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Léon van Kempen
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Edegem, Belgium
| | - Izidor Kern
- Laboratory for Cytology and Pathology, University Clinic Golnik, Golnik, Slovenia
| | - Fernando Lopez-Rios
- Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, Research Institute Hospital 12 de Octubre (i+12), Ciberonc, Madrid, Spain
| | - Margreet Lüchtenborg
- National Disease Registration Service, NHS England, London, United Kingdom
- Centre for Cancer, Society & Public Health, King’s College London, London, United Kingdom
| | - José Carlos Machado
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Medicine of the University of Porto, Institute for Research and Innovation in Health (i3S), Porto, Portugal
| | - Katja Mohorcic
- University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 de Octubre (i+12)/Spanish National Cancer Research Center (CNIO), Ciberonc, Madrid, Spain
| | - Sanjay Popat
- Lung Unit, Royal Marsden NHS Trust, London, United Kingdom
| | - Aleš Ryška
- The Fingerland Department of Pathology, Charles University Medical Faculty and University Hospital, Czech Republic
| | - Phillipe Taniere
- Department of Histopathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Department I for Internal Medicine and Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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5
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de Jager VD, Timens W, Bayle A, Botling J, Brcic L, Büttner R, Fernandes MGO, Havel L, Hochmair M, Hofman P, Janssens A, van Kempen L, Kern I, Machado JC, Mohorčič K, Popat S, Ryška A, Wolf J, Schuuring E, van der Wekken AJ. Future perspective for the application of predictive biomarker testing in advanced stage non-small cell lung cancer. Lancet Reg Health Eur 2024; 38:100839. [PMID: 38476751 PMCID: PMC10928270 DOI: 10.1016/j.lanepe.2024.100839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 01/08/2024] [Indexed: 03/14/2024]
Abstract
For patients with advanced stage non-small cell lung cancer (NSCLC), treatment strategies have changed significantly due to the introduction of targeted therapies and immunotherapy. In the last few years, we have seen an explosive growth of newly introduced targeted therapies in oncology and this development is expected to continue in the future. Besides primary targetable aberrations, emerging diagnostic biomarkers also include relevant co-occurring mutations and resistance mechanisms involved in disease progression, that have impact on optimal treatment management. To accommodate testing of pending biomarkers, it is necessary to establish routine large-panel next-generation sequencing (NGS) for all patients with advanced stage NSCLC. For cost-effectiveness and accessibility, it is recommended to implement predictive molecular testing using large-panel NGS in a dedicated, centralized expert laboratory within a regional oncology network. The central molecular testing center should host a regional Molecular Tumor Board and function as a hub for interpretation of rare and complex testing results and clinical decision-making.
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Affiliation(s)
- Vincent D. de Jager
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Arnaud Bayle
- Oncostat U1018, Inserm, Paris-Saclay University, Gustave Roussy, Villejuif, France
| | - Johan Botling
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy of University of Gothenburg, Gothenburg, Sweden
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Reinhard Büttner
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Libor Havel
- Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Maximilian Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Paul Hofman
- IHU RespirERA, FHU OncoAge, Nice University Hospital, Côte d’Azur University, Nice, France
| | - Annelies Janssens
- Department of Oncology, University Hospital Antwerp, University of Antwerp, Edegem, Belgium
| | - Léon van Kempen
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Edegem, Belgium
| | - Izidor Kern
- Laboratory for Cytology and Pathology, University Clinic Golnik, Golnik, Slovenia
| | - José Carlos Machado
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Medicine of the University of Porto, Portugal
- Institute for Research and Innovation in Health (i3S), Porto, Portugal
| | - Katja Mohorčič
- University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Sanjay Popat
- Lung Unit, Royal Marsden NHS Trust, London, England, UK
| | - Aleš Ryška
- The Fingerland Department of Pathology, Charles University Medical Faculty and University Hospital, Czech Republic
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Department I for Internal Medicine and Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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6
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Steinkühler T, Yang S, Hu MA, Jainandunsing JS, Jager NM, Erasmus ME, Struys MMRF, Bosch DJ, van Meurs M, Jabaudon M, Richard D, Timens W, Leuvenink HGD, Nieuwenhuijs-Moeke GJ. Ex Vivo Optimization of Donor Lungs with Inhaled Sevoflurane during Normothermic Ex Vivo Lung Perfusion (VITALISE): A Pilot and Feasibility Study in Sheep. Int J Mol Sci 2024; 25:2413. [PMID: 38397090 PMCID: PMC10888671 DOI: 10.3390/ijms25042413] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Volatile anesthetics have been shown in different studies to reduce ischemia reperfusion injury (IRI). Ex vivo lung perfusion (EVLP) facilitates graft evaluation, extends preservation time and potentially enables injury repair and improvement of lung quality. We hypothesized that ventilating lungs with sevoflurane during EVLP would reduce lung injury and improve lung function. We performed a pilot study to test this hypothesis in a slaughterhouse sheep DCD model. Lungs were harvested, flushed and stored on ice for 3 h, after which EVLP was performed for 4 h. Lungs were ventilated with either an FiO2 of 0.4 (EVLP, n = 5) or FiO2 of 0.4 plus sevoflurane at a 2% end-tidal concentration (Cet) (S-EVLP, n = 5). Perfusate, tissue samples and functional measurements were collected and analyzed. A steady state of the target Cet sevoflurane was reached with measurable concentrations in perfusate. Lungs in the S-EVLP group showed significantly better dynamic lung compliance than those in the EVLP group (p = 0.003). Oxygenation capacity was not different in treated lungs for delta partial oxygen pressure (PO2; +3.8 (-4.9/11.1) vs. -11.7 (-12.0/-3.2) kPa, p = 0.151), but there was a trend of a better PO2/FiO2 ratio (p = 0.054). Perfusate ASAT levels in S-EVLP were significantly reduced compared to the control group (198.1 ± 93.66 vs. 223.9 ± 105.7 IU/L, p = 0.02). We conclude that ventilating lungs with sevoflurane during EVLP is feasible and could be useful to improve graft function.
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Affiliation(s)
- Timo Steinkühler
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Shuqi Yang
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Michiel A. Hu
- Department of Thoracic Surgery, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Jayant S. Jainandunsing
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Neeltina M. Jager
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Michiel E. Erasmus
- Department of Thoracic Surgery, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Michel M. R. F. Struys
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Department of Basic and Applied Medical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dirk J. Bosch
- Department of Anesthesiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Matijs van Meurs
- Department of Critical Care, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Matthieu Jabaudon
- Department of Perioperative Medicine, University Hospital Clermont-Ferrand, 63001 Clermont-Ferrand, France
- Institute of Genetics, Reproduction & Development, University Clermont Auvergne, 63001 Clermont-Ferrand, France
- National Institute of Health and Medical Research (INSERM), National Center for Scientific Research (CNRS), 75794 Paris, France
| | - Damien Richard
- Department of Pharmacology and Toxicology, University Hospital Clermont-Ferrand, University Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Henri G. D. Leuvenink
- Department of Surgery, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
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7
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Khalenkow D, Brandsma CA, Timens W, Choy DF, Grimbaldeston MA, Rosenberger CM, Slebos DJ, Kerstjens HAM, Faiz A, Koppelman GH, Nawijn MC, van den Berge M, Guryev V. Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe COPD. Am J Respir Cell Mol Biol 2024. [PMID: 38315810 DOI: 10.1165/rcmb.2023-0296oc] [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] [Received: 08/10/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
The role of alternative splicing in Chronic Obstructive Pulmonary Disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared to non-COPD controls and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-seq analysis of bronchial brushings from 23 mild-to-moderate, 121 severe COPD patients, and 23 non-COPD controls. We found a significant difference in the frequency of alternative splicing events in mild-to-moderate and severe COPD compared to non-COPD controls. There were from 2x to 8x (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The samples from severe COPD patients showed less intron retention and more exon skipping. Interestingly, the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of COPD and control individuals, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The presented results provide a better understanding of COPD-related alternative splicing changes.
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Affiliation(s)
- Dmitry Khalenkow
- University Medical Centre Groningen, 10173, Department of Pulmonology and Pediatric Allergy, Groningen, Netherlands
- ERIBA, 548577, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Corry-Anke Brandsma
- University Medical Centre Groningen, 10173, Department of Pathology and Medical Biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Wim Timens
- University Medical Centre Groningen, 10173, Department of Pathology and Medical Biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - David F Choy
- Genentech Inc, 7412, South San Francisco, California, United States
| | | | | | - Dirk-Jan Slebos
- University Medical Centre Groningen, 10173, Department of Pulmonary diseases, Groningen, Netherlands
| | - Huib A M Kerstjens
- University Medical Centre Groningen, 10173, Department of Pulmonology and Tuberculosis, Groningen, Netherlands
| | - Alen Faiz
- University of Technology Sydney, 1994, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, New South Wales, Australia
| | - Gerard H Koppelman
- University Medical Centre Groningen, 10173, Department of Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Martijn C Nawijn
- University Medical Centre Groningen, 10173, Lab allergology and pulmonary diseases, department of pathology and medical biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Maarten van den Berge
- University Medical Centre Groningen, 10173, Department of Pulmonary Diseases, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Victor Guryev
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
- ERIBA, 548577, Groningen, Netherlands;
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8
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Faiz A, Wiersma VR, Salzbrunn JB, Brandsma CA, Timens W, Burgess JK, van den Berge M, Slebos DJ, Guryev V, Pouwels SD. COPD Patients Display Increased Peripheral Blood Somatic Mutations Which Associate With the Prevalence of Co-morbidities. Arch Bronconeumol 2024; 60:119-121. [PMID: 38212182 DOI: 10.1016/j.arbres.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/13/2024]
Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology Group, University of Technology Sydney, Australia; GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, The Netherlands
| | - Valerie R Wiersma
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jonas B Salzbrunn
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Janette K Burgess
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, The Netherlands
| | - Dirk-Jan Slebos
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, Groningen, The Netherlands
| | - Simon D Pouwels
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands.
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9
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Migulina N, de Hilster RHJ, Bartel S, Vedder RHJ, van den Berge M, Nagelkerke A, Timens W, Harmsen MC, Hylkema MN, Brandsma CA, Burgess JK. 3-D culture of human lung fibroblasts decreases proliferative and increases extracellular matrix remodeling genes. Am J Physiol Cell Physiol 2024; 326:C177-C193. [PMID: 37955339 DOI: 10.1152/ajpcell.00374.2023] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]
Abstract
Fibroblasts are the main producers of extracellular matrix (ECM) responsible for ECM maintenance and repair, a process often disrupted in chronic lung diseases. The accompanying mechanical changes adversely affect resident cells and overall lung function. Numerous models have been used to elucidate fibroblast behavior that are now evolving toward complex three-dimensional (3-D) models incorporating ECM, aiming to replicate the cells' native environment. Little is known about the cellular changes that occur when moving from two-dimensional (2-D) to 3-D cell culture. This study compared the gene expression profiles of primary human lung fibroblasts from seven subjects with normal lung function, that were cultured for 24 h on 2-D collagen I-coated tissue culture plastic and in 3-D collagen I hydrogels, which are commonly used to mimic ECM in various models, from contraction assays to intricate organ-on-a-chip models. Comparing 3-D with 2-D cell culture, 6,771 differentially expressed genes (2,896 up, 3,875 down) were found; enriched gene sets within the downregulated genes, identified through Gene Set Enrichment Analysis and Ingenuity Pathway Analysis, were involved in the initiation of DNA replication which implied downregulation of fibroblast proliferation in 3-D. Observation of cells for 72 h in 2-D and 3-D environments confirmed the reduced progression through the cell cycle in 3-D. A focused analysis, examining the Hippo pathway and ECM-associated genes, showed differential patterns of gene expression in the 3-D versus 2-D culture. Altogether, the transcriptional response of fibroblasts cultured in 3-D indicated inhibition of proliferation, and alterations in Hippo and ECM pathways indicating a complete switch from proliferation to ECM remodeling.NEW & NOTEWORTHY With the introduction of complex three-dimensional (3-D) lung models, comes a need for understanding cellular behavior in these models. We compared gene expression profiles of human lung fibroblasts grown on two-dimensional (2-D) collagen I-coated surfaces with those in 3-D collagen I hydrogels. RNA sequencing and subsequent pathway analyses showed decreased proliferation, increased extracellular matrix (ECM) remodeling, and altered Hippo signaling and ECM deposition-related gene signatures. These findings highlight unique responses of fibroblasts in 3-D models.
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Affiliation(s)
- Nataliya Migulina
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roderick H J de Hilster
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sabine Bartel
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H J Vedder
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anika Nagelkerke
- Pharmaceutical Analysis, Groningen Research Institute of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martin C Harmsen
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Machteld N Hylkema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Janette K Burgess
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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10
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Wu DD, Lau ATY, Xu YM, Reinders-Luinge M, Koncz M, Kiss A, Timens W, Rots MG, Hylkema MN. Targeted epigenetic silencing of UCHL1 expression suppresses collagen-1 production in human lung epithelial cells. Epigenetics 2023; 18:2175522. [PMID: 38016026 PMCID: PMC9980648 DOI: 10.1080/15592294.2023.2175522] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/17/2022] [Accepted: 01/11/2023] [Indexed: 02/24/2023] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is highly expressed in smokers, but little is known about the molecular mechanism of UCHL1 in airway epithelium and its possible role in affecting extracellular matrix (ECM) remodelling in the underlying submucosa. Since cigarette smoking is a major cause of lung diseases, we studied its effect on UCHL1 expression and DNA methylation patterns in human bronchial epithelial cells, obtained after laser capture micro-dissection (LCM) or isolated from residual tracheal/main stem bronchial tissue. Targeted regulation of UCHL1 expression via CRISPR/dCas9 based-epigenetic editing was used to explore the function of UCHL1 in lung epithelium. Our results show that cigarette smoke extract (CSE) stimulated the expression of UCHL1 in vitro. The methylation status of the UCHL1 gene was negatively associated with UCHL1 transcription in LCM-obtained airway epithelium at specific sites. Treatment with a UCHL1 inhibitor showed that the TGF-β1-induced upregulation of the ECM gene COL1A1 can be prevented by the inhibition of UCHL1 activity in cell lines. Furthermore, upon downregulation of UCHL1 by epigenetic editing using CRISPR/dCas-EZH2, mRNA expression of COL1A1 and fibronectin was reduced. In conclusion, we confirmed higher UCHL1 expression in current smokers compared to non- and ex-smokers, and induced downregulation of UCHL1 by epigenetic editing. The subsequent repression of genes encoding ECM proteins suggest a role for UCHL1 as a therapeutic target in fibrosis-related disease.
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Affiliation(s)
- Dan-Dan Wu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Marjan Reinders-Luinge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihaly Koncz
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Machteld N. Hylkema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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11
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Al-Adwi Y, Atzeni IM, Doornbos-van der Meer B, van der Leij MJ, Varkevisser RDM, Kroesen BJ, Stel A, Timens W, Gan CT, van Goor H, Westra J, Mulder DJ. High serum C-X-C motif chemokine ligand 10 (CXCL10) levels may be associated with new onset interstitial lung disease in patients with systemic sclerosis: evidence from observational, clinical, transcriptomic and in vitro studies. EBioMedicine 2023; 98:104883. [PMID: 37995465 PMCID: PMC10708993 DOI: 10.1016/j.ebiom.2023.104883] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Systemic sclerosis-interstitial lung disease (SSc-ILD) is the leading cause of death in patients with SSc. There is an unmet need for predictive biomarkers to identify patients with SSc at risk of ILD. Previous studies have shown that interferon (IFN) pathways may play a role in SSc. We assessed the use of C-X-C motif chemokine ligand 10 (CXCL10) as a predictive biomarker for new onset of ILD in patients with SSc. METHODS One-hundred-sixty-five (Female, N = 130) patients with SSc (SSc-ILD, N = 41) and 13 (Female, N = 8) healthy controls were investigated retrospectively. CXCL10 protein levels were measured by ELISA. We performed log rank analysis with baseline CXCL10 serum levels. CXCL10 nanoString data from lung tissues obtained from transplanted patients with SSc-ILD were extracted. Fifteen (Female, N = 10) patients with SSc (SSc-ILD, N = 7) were recruited for bronchoalveolar lavage (BAL) procedure. Lung fibroblasts were treated with BAL-fluid or serum from patients with SSc with or without ILD. Inflammatory/fibrotic genes were assessed. FINDINGS Serum CXCL10 levels were higher in patients with SSc-ILD compared to SSc patients without ILD [Median (IQR):126 pg/ml (66-282.5) vs. 78.5 pg/ml (50-122), P = 0.029, 95% CI: 1.5 × 10-6 to 0.4284]. Survival analysis showed that baseline CXCL10 levels >78.5 pg/ml have a 2.74-fold increased risk of developing new onset of ILD (Log-rank: P = 0.119) on follow-up. CXCL10 levels in BAL supernatant were not different in patients with SSc-ILD compared to SSc without ILD [76.1 pg/ml (7.2-120.8) vs. 22.3 pg/ml (12.1-43.7), P = 0.24, 95% CI: -19.5 to 100]. NanoString showed that CXCL10 mRNA expression was higher in inflammatory compared to fibrotic lung tissues [4.7 (4.2-5.6) vs. 4.3 (3.6-4.7), P = 0.029]. Fibroblasts treated with SSc-ILD serum or BAL fluids overexpressed CXCL10. INTERPRETATIONS Clinical, transcriptomic, and in vitro data showed that CXCL10 is potentially involved in early SSc-ILD. More research is needed to confirm whether CXCL10 can be classified as a prospective biomarker to detect patients with SSc at higher risk of developing new onset ILD. FUNDING This collaborative project is co-financed by the Ministry of Economic Affairs and Climate Policy of the Netherlands utilizing the PPP-allowance made available by the Top Sector Life Sciences & Health to stimulate public-private partnerships (PPP-2019_007). Part of this study is financially supported by Sanofi Genzyme (NL8921).
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Affiliation(s)
- Yehya Al-Adwi
- University of Groningen, University Medical Centre Groningen, Department of Internal Medicine, Division of Vascular Medicine, Groningen, the Netherlands.
| | - Isabella Maria Atzeni
- University of Groningen, University Medical Centre Groningen, Department of Internal Medicine, Division of Vascular Medicine, Groningen, the Netherlands
| | - Berber Doornbos-van der Meer
- University of Groningen, University Medical Centre Groningen, Department of Rheumatology and Clinical Immunology, Groningen, the Netherlands
| | - Marcel John van der Leij
- University of Groningen, University Medical Centre Groningen, Department of Laboratory Medicine, Groningen, the Netherlands
| | | | - Bart-Jan Kroesen
- University of Groningen, University Medical Centre Groningen, Department of Laboratory Medicine, Groningen, the Netherlands
| | - Alja Stel
- University of Groningen, University Medical Centre Groningen, Department of Rheumatology and Clinical Immunology, Groningen, the Netherlands
| | - Wim Timens
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Christiaan Tji Gan
- University of Groningen, University Medical Centre Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, the Netherlands
| | - Harry van Goor
- Department of Endocrinology, University Medical Centre Groningen, Groningen, the Netherlands
| | - Johanna Westra
- University of Groningen, University Medical Centre Groningen, Department of Rheumatology and Clinical Immunology, Groningen, the Netherlands
| | - Douwe Johannes Mulder
- University of Groningen, University Medical Centre Groningen, Department of Internal Medicine, Division of Vascular Medicine, Groningen, the Netherlands
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12
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Faiz A, Mahbub RM, Boedijono FS, Tomassen MI, Kooistra W, Timens W, Nawijn M, Hansbro PM, Johansen MD, Pouwels SD, Heijink IH, Massip F, de Biase MS, Schwarz RF, Adcock IM, Chung KF, van der Does A, Hiemstra PS, Goulaouic H, Xing H, Abdulai R, de Rinaldis E, Cunoosamy D, Harel S, Lederer D, Nivens MC, Wark PA, Kerstjens HAM, Hylkema MN, Brandsma CA, van den Berge M. IL-33 Expression Is Lower in Current Smokers at both Transcriptomic and Protein Levels. Am J Respir Crit Care Med 2023; 208:1075-1087. [PMID: 37708400 PMCID: PMC10867944 DOI: 10.1164/rccm.202210-1881oc] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 09/14/2023] [Indexed: 09/16/2023] Open
Abstract
Rationale: IL-33 is a proinflammatory cytokine thought to play a role in the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD). A recent clinical trial using an anti-IL-33 antibody showed a reduction in exacerbation and improved lung function in ex-smokers but not current smokers with COPD. Objectives: This study aimed to understand the effects of smoking status on IL-33. Methods: We investigated the association of smoking status with the level of gene expression of IL-33 in the airways in eight independent transcriptomic studies of lung airways. Additionally, we performed Western blot analysis and immunohistochemistry for IL-33 in lung tissue to assess protein levels. Measurements and Main Results: Across the bulk RNA-sequencing datasets, IL-33 gene expression and its signaling pathway were significantly lower in current versus former or never-smokers and increased upon smoking cessation (P < 0.05). Single-cell sequencing showed that IL-33 is predominantly expressed in resting basal epithelial cells and decreases during the differentiation process triggered by smoke exposure. We also found a higher transitioning of this cellular subpopulation into a more differentiated cell type during chronic smoking, potentially driving the reduction of IL-33. Protein analysis demonstrated lower IL-33 levels in lung tissue from current versus former smokers with COPD and a lower proportion of IL-33-positive basal cells in current versus ex-smoking controls. Conclusions: We provide strong evidence that cigarette smoke leads to an overall reduction in IL-33 expression in transcriptomic and protein level, and this may be due to the decrease in resting basal cells. Together, these findings may explain the clinical observation that a recent antibody-based anti-IL-33 treatment is more effective in former than current smokers with COPD.
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Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Rashad M. Mahbub
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Fia Sabrina Boedijono
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Milan I. Tomassen
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wierd Kooistra
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon D. Pouwels
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Irene H. Heijink
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Massip
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
| | - Maria Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Ian M. Adcock
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Kian F. Chung
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Anne van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | | | - Sivan Harel
- Regeneron Pharmaceuticals, Tarrytown, New York
| | | | | | - Peter A. Wark
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
| | - Huib A. M. Kerstjens
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Machteld N. Hylkema
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - the Cambridge Lung Cancer Early Detection Programme
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
- Sanofi, Chilly-Mazarin, France
- Sanofi, Cambridge, Massachusetts
- Regeneron Pharmaceuticals, Tarrytown, New York
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
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13
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Nizamoglu M, Koloko Ngassie ML, Meuleman RA, Banchero M, Borghuis T, Timens W, Nawijn MC, Melgert BN, Heijink IH, Brandsma CA, Burgess JK. Collagen type XIV is proportionally lower in the lung tissue of patients with IPF. Sci Rep 2023; 13:19393. [PMID: 37938243 PMCID: PMC10632429 DOI: 10.1038/s41598-023-46733-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023] Open
Abstract
Abnormal deposition of extracellular matrix (ECM) in lung tissue is a characteristic of idiopathic pulmonary fibrosis (IPF). Increased collagen deposition is also accompanied by altered collagen organization. Collagen type XIV, a fibril-associated collagen, supports collagen fibril organization. Its status in IPF has not been described at the protein level yet. In this study, we utilized publicly available datasets for single-cell RNA-sequencing for characterizing collagen type XIV expression at the gene level. For protein level comparison, we applied immunohistochemical staining for collagen type XIV on lung tissue sections from IPF patients and compared it to lung tissue sections from never smoking and ex-smoking donors. Analyzing the relative amounts of collagen type XIV at the whole tissue level, as well as in parenchyma, airway wall and bronchial epithelium, we found consistently lower proportions of collagen type XIV in all lung tissue compartments across IPF samples. Our study suggests proportionally lower collagen type XIV in IPF lung tissues may have implications for the assembly of the ECM fibers potentially contributing to progression of fibrosis.
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Affiliation(s)
- Mehmet Nizamoglu
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maunick Lefin Koloko Ngassie
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rhode A Meuleman
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin Banchero
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Theo Borghuis
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Barbro N Melgert
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Irene H Heijink
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands.
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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14
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van Nijnatten J, Faiz A, Timens W, Guryev V, Slebos DJ, Klooster K, Hartman JE, Kole T, Choy DF, Chakrabarti A, Grimbaldeston M, Rosenberger CM, Kerstjens H, Brandsma CA, van den Berge M. A bronchial gene signature specific for severe COPD that is retained in the nose. ERJ Open Res 2023; 9:00354-2023. [PMID: 38020574 PMCID: PMC10680034 DOI: 10.1183/23120541.00354-2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction A subset of COPD patients develops advanced disease with severe airflow obstruction, hyperinflation and extensive emphysema. We propose that the pathogenesis in these patients differs from mild-moderate COPD and is reflected by bronchial gene expression. The aim of the present study was to identify a unique bronchial epithelial gene signature for severe COPD patients. Methods We obtained RNA sequencing data from bronchial brushes from 123 ex-smokers with severe COPD, 23 with mild-moderate COPD and 23 non-COPD controls. We identified genes specific to severe COPD by comparing severe COPD to non-COPD controls, followed by removing genes that were also differentially expressed between mild-moderate COPD and non-COPD controls. Next, we performed a pathway analysis on these genes and evaluated whether this signature is retained in matched nasal brushings. Results We identified 219 genes uniquely differentially expressed in severe COPD. Interaction network analysis identified VEGFA and FN1 as the key genes with the most interactions. Genes were involved in extracellular matrix regulation, collagen binding and the immune response. Of interest were 10 genes (VEGFA, DCN, SPARC, COL6A2, MGP, CYR61, ANXA6, LGALS1, C1QA and C1QB) directly connected to fibronectin 1 (FN1). Most of these genes were lower expressed in severe COPD and showed the same effect in nasal brushings. Conclusions We found a unique severe COPD bronchial gene signature with key roles for VEGFA and FN1, which was retained in the upper airways. This supports the hypothesis that severe COPD, at least partly, comprises a different pathology and supports the potential for biomarker development based on nasal brushes in COPD.
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Affiliation(s)
- Jos van Nijnatten
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology, Sydney, NSW, Australia
| | - Alen Faiz
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology, Sydney, NSW, Australia
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Victor Guryev
- University of Groningen University Medical Center Groningen, European Research Institute for the Biology of Ageing, Groningen, the Netherlands
| | - Dirk-Jan Slebos
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Karin Klooster
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Jorine E. Hartman
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Tessa Kole
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | | | | | | | | | - Huib Kerstjens
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- These authors contributed equally
| | - Maarten van den Berge
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
- These authors contributed equally
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15
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Wisman M, Nizamoglu M, Noordhoek JA, Timens W, Burgess JK, Heijink IH. Dysregulated cross-talk between alveolar epithelial cells and stromal cells in idiopathic pulmonary fibrosis reduces epithelial regenerative capacity. Front Med (Lausanne) 2023; 10:1182368. [PMID: 37621459 PMCID: PMC10446880 DOI: 10.3389/fmed.2023.1182368] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
In idiopathic pulmonary fibrosis (IPF) constant epithelial micro-injury and aberrant interactions within the stromal micro-environment lead to abnormal alveolar repair and fibrosis. We hypothesized that alveolar epithelial regenerative responses in IPF are impaired due to disturbed crosstalk between epithelial cells and their stromal niche. We established organoid cultures from unfractionated suspensions and isolated EpCAM+ cells from distal lung tissue of patients with and without IPF. We observed significantly more organoids being formed from unfractionated suspensions compared to isolated EpCAM+ cell cultures, indicating the presence of supportive cells in the unfractionated suspensions. Importantly, lower organoid numbers were observed in unfractionated cultures from IPF lungs compared to non-IPF lungs. This difference was not found when comparing organoid formation from isolated EpCAM+ cells alone between IPF and non-IPF groups, suggesting that crosstalk between the supportive population and epithelial cells is impaired in lungs from IPF patients. Additionally, organoids grown from IPF lung-derived cells were larger in size compared to those from non-IPF lungs in both unfractionated and EpCAM+ cultures, indicating an intrinsic abnormality in epithelial progenitors from IPF lungs. Together, our observations suggest that dysregulated crosstalk between alveolar progenitor cells and the stromal niche affects the regenerative capacity, potentially contributing to alveolar impairment in IPF.
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Affiliation(s)
- Marissa Wisman
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - Mehmet Nizamoglu
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - Jacobien A. Noordhoek
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - Janette K. Burgess
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, Groningen, Netherlands
| | - Irene H. Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, Netherlands
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16
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Atzeni IM, Al-Adwi Y, Doornbos-van der Meer B, Roozendaal C, Stel A, van Goor H, Gan CT, Dickinson M, Timens W, Smit AJ, Westra J, Mulder DJ. The soluble receptor for advanced glycation end products is potentially predictive of pulmonary arterial hypertension in systemic sclerosis. Front Immunol 2023; 14:1189257. [PMID: 37409127 PMCID: PMC10318928 DOI: 10.3389/fimmu.2023.1189257] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Pulmonary arterial hypertension (PAH) and interstitial lung disease (ILD) are the leading causes of death in systemic sclerosis (SSc). Until now, no prospective biomarker to predict new onset of SSc-ILD or SSc-PAH in patients with SSc has reached clinical application. In homeostasis, the receptor for advanced glycation end products (RAGE) is expressed in lung tissue and involved in cell-matrix adhesion, proliferation and migration of alveolar epithelial cells, and remodeling of the pulmonary vasculature. Several studies have shown that sRAGE levels in serum and pulmonary tissue vary according to the type of lung-related complication. Therefore, we investigated levels of soluble RAGE (sRAGE) and its ligand high mobility group box 1 (HMGB1) in SSc and their abilities to predict SSc-related pulmonary complications. Methods One hundred eighty-eight SSc patients were followed retrospectively for the development of ILD, PAH, and mortality for 8 years. Levels of sRAGE and HMGB1 were measured in serum by ELISA. Kaplan-Meier survival curves were performed to predict lung events and mortality and event rates were compared with a log-rank test. Multiple linear regression analysis was performed to examine the association between sRAGE and important clinical determinants. Results At baseline, levels of sRAGE were significantly higher in SSc-PAH-patients (median 4099.0 pg/ml [936.3-6365.3], p = 0.011) and lower in SSc-ILD-patients (735.0 pg/ml [IQR 525.5-1988.5], p = 0.001) compared to SSc patients without pulmonary involvement (1444.5 pg/ml [966.8-2276.0]). Levels of HMGB1 were not different between groups. After adjusting for age, gender, ILD, chronic obstructive pulmonary disease, anti-centromere antibodies, the presence of puffy fingers or sclerodactyly, use of immunosuppression, antifibrotic therapy, or glucocorticoids, and use of vasodilators, higher sRAGE levels remained independently associated with PAH. After a median follow-up of 50 months (25-81) of patients without pulmonary involvement, baseline sRAGE levels in the highest quartile were predictive of development of PAH (log-rank p = 0.01) and of PAH-related mortality (p = 0.001). Conclusions High systemic sRAGE at baseline might be used as a prospective biomarker for patients with SSc at high risk to develop new onset of PAH. Moreover, high sRAGE levels could predict lower survival rates due to PAH in patients with SSc.
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Affiliation(s)
- Isabella M. Atzeni
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Yehya Al-Adwi
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Berber Doornbos-van der Meer
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Caroline Roozendaal
- Department of Laboratory Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Alja Stel
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Harry van Goor
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - C. Tji Gan
- Department of Pulmonary Diseases and Tuberculosis, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Michael Dickinson
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Andries J. Smit
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Johanna Westra
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Douwe J. Mulder
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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17
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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18
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Pouwels SD, van den Berge M, Vasse GF, Timens W, Brandsma CA, Aliee H, Hiemstra PS, Guryev V, Faiz A. Smoking increases expression of the SARS-CoV-2 spike protein-binding long ACE2 isoform in bronchial epithelium. Respir Res 2023; 24:130. [PMID: 37170105 PMCID: PMC10174605 DOI: 10.1186/s12931-023-02430-5] [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] [Received: 03/23/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
After more than two years the COVID-19 pandemic, that is caused by infection with the respiratory SARS-CoV-2 virus, is still ongoing. The risk to develop severe COVID-19 upon SARS-CoV-2 infection is increased in individuals with a high age, high body mass index, and who are smoking. The SARS-CoV-2 virus infects cells of the upper respiratory tract by entering these cells upon binding to the Angiotensin-converting enzyme 2 (ACE2) receptor. ACE2 is expressed in various cell types in the lung but the expression is especially high in goblet and ciliated cells. Recently, it was shown that next to its full-length isoform, ACE2 also has a short isoform. The short isoform is unable to bind SARS-CoV-2 and does not facilitate viral entry. In the current study we investigated whether active cigarette smoking increases the expression of the long or the short ACE2 isoform. We showed that in active smokers the expression of the long, active isoform, but not the short isoform of ACE2 is higher compared to never smokers. Additionally, it was shown that the expression of especially the long, active isoform of ACE2 was associated with secretory, club and goblet epithelial cells. This study increases our understanding of why current smokers are more susceptible to SARS-CoV-2 infection, in addition to the already established increased risk to develop severe COVID-19.
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Affiliation(s)
- Simon D Pouwels
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gwenda F Vasse
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Victor Guryev
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, University of Technology Sydney, Building 4, Room 04.07.418, Thomas St, Ultimo, NSW, 2007, Australia.
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19
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Kortekaas RK, Geillinger-Kästle KE, Borghuis T, Belharch K, Webster M, Timens W, Burgess JK, Gosens R. Interleukin-11 disrupts alveolar epithelial progenitor function. ERJ Open Res 2023; 9:00679-2022. [PMID: 37228276 PMCID: PMC10204861 DOI: 10.1183/23120541.00679-2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 05/27/2023] Open
Abstract
Background Interleukin-11 (IL-11) is linked to the pathogenesis of idiopathic pulmonary fibrosis (IPF), since IL-11 induces myofibroblast differentiation and stimulates their excessive collagen deposition in the lung. In IPF there is disrupted alveolar structural architecture, yet the effect of IL-11 on the dysregulated alveolar repair remains to be elucidated. Methods We hypothesised that epithelial-fibroblast communication associated with lung repair is disrupted by IL-11. Thus, we studied whether IL-11 affects the repair responses of alveolar lung epithelium using mouse lung organoids and precision-cut lung slices (PCLS). Additionally, we assessed the anatomical distribution of IL-11 and IL-11 receptor (IL-11R) in human control and IPF lungs using immunohistochemistry. Results IL-11 protein was observed in airway epithelium, macrophages and in IPF lungs, also in areas of alveolar type 2 (AT2) cell hyperplasia. IL-11R staining was predominantly present in smooth muscle and macrophages. In mouse organoid co-cultures of epithelial cells with lung fibroblasts, IL-11 decreased organoid number and reduced the fraction of Prosurfactant Protein C-expressing organoids, indicating dysfunctional regeneration initiated by epithelial progenitors. In mouse PCLS exposed to IL-11, ciliated cell markers were increased. The response of primary human fibroblasts to IL-11 on gene expression level was minimal, though bulk RNA-sequencing revealed IL-11 modulated various processes which are associated with IPF, including unfolded protein response, glycolysis and Notch signalling. Conclusions IL-11 disrupts alveolar epithelial regeneration by inhibiting progenitor activation and suppressing the formation of mature alveolar epithelial cells. Evidence for a contribution of dysregulated fibroblast-epithelial communication to this process is limited.
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Affiliation(s)
- Rosa K. Kortekaas
- Department of Molecular Pharmacology, University of Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Kerstin E. Geillinger-Kästle
- Department of Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Theo Borghuis
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Kaoutar Belharch
- Department of Molecular Pharmacology, University of Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Megan Webster
- Department of Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Janette K. Burgess
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- These authors contributed equally
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
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20
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Koloko Ngassie ML, de Vries M, Borghuis T, Timens W, Sin DD, Nickle D, Joubert P, Horvatovich P, Marko-Varga G, Teske JJ, Vonk JM, Gosens R, Prakash YS, Burgess JK, Brandsma CA. Age-associated Differences in the Human Lung Extracellular Matrix. Am J Physiol Lung Cell Mol Physiol 2023; 324:L799-L814. [PMID: 37039368 DOI: 10.1152/ajplung.00334.2022] [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] [Indexed: 04/12/2023] Open
Abstract
Extracellular matrix (ECM) remodeling has been associated with chronic lung diseases. However, information about specific age‑associated differences in lung ECM is currently limited. In this study we aimed to identify and localize age‑associated ECM differences in human lung using comprehensive transcriptomic, proteomic and immunohistochemical analyses. Our previously identified age-associated gene expression signature of the lung was re‑analyzed limiting it to an aging signature based on 270 control patients (37-80 years) and focused on the Matrisome core geneset using geneset enrichment analysis. To validate the age‑associated transcriptomic differences on protein level, we compared the age-associated ECM genes (FDR <0.05) with a profile of age‑associated proteins identified from a lung tissue proteomics dataset from 9 control patients (49-76 years) (FDR<0.05). Extensive immunohistochemical analysis was used to localize and semi-quantify the age-associated ECM differences in lung tissues from 62 control patients (18-82 years). Comparative analysis of transcriptomic and proteomic data identified 7 ECM proteins with higher expression with age at both gene and protein level: COL1A1, COL6A1, COL6A2, COL14A1, FBLN2, LTBP4 and LUM. With immunohistochemistry we demonstrated higher protein level with age for COL6A2 in whole tissue, parenchyma, airway wall and blood vessel, for COL14A1 and LUM in bronchial epithelium, and COL1A1 in lung parenchyma. Our study revealed that higher age is associated with lung ECM remodeling, with specific differences occurring in defined regions within the lung. These differences may affect lung structure and physiology with aging and as such may increase susceptibility for developing chronic lung diseases.
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Affiliation(s)
- Maunick Lefin Koloko Ngassie
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Maaike de Vries
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, Netherlands
| | - Theo Borghuis
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Don D Sin
- Centre for Heart Lung Innovation at St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | | | - Philippe Joubert
- Pneumologie, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Canada
| | - Peter Horvatovich
- 7University of Groningen, Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, Netherlands
| | - György Marko-Varga
- Center of Excellence in Biological and Medical Mass Spectrometry, Biomedical Center, Lund University, Sweden
| | - Jacob J Teske
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, Netherlands
| | - Reinoud Gosens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Molecular Pharmacology, University of Groningen, Groningen, Netherlands
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
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21
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Faiz A, Pavlidis S, Kuo CH, Rowe A, Hiemstra PS, Timens W, Berg M, Wisman M, Guo YK, Djukanović R, Sterk P, Meyer KB, Nawijn MC, Adcock I, Chung KF, van den Berge M. Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD. Thorax 2023; 78:335-343. [PMID: 36598042 PMCID: PMC10086461 DOI: 10.1136/thorax-2021-217736] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
RATIONALE Severe asthma and chronic obstructive pulmonary disease (COPD) share common pathophysiological traits such as relative corticosteroid insensitivity. We recently published three transcriptome-associated clusters (TACs) using hierarchical analysis of the sputum transcriptome in asthmatics from the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort comprising one Th2-high inflammatory signature (TAC1) and two Th2-low signatures (TAC2 and TAC3). OBJECTIVE We examined whether gene expression signatures obtained in asthma can be used to identify the subgroup of patients with COPD with steroid sensitivity. METHODS Using gene set variation analysis, we examined the distribution and enrichment scores (ES) of the 3 TACs in the transcriptome of bronchial biopsies from 46 patients who participated in the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease COPD study that received 30 months of treatment with inhaled corticosteroids (ICS) with and without an added long-acting β-agonist (LABA). The identified signatures were then associated with longitudinal clinical variables after treatment. Differential gene expression and cellular convolution were used to define key regulated genes and cell types. MEASUREMENTS AND MAIN RESULTS Bronchial biopsies in patients with COPD at baseline showed a wide range of expression of the 3 TAC signatures. After ICS±LABA treatment, the ES of TAC1 was significantly reduced at 30 months, but those of TAC2 and TAC3 were unaffected. A corticosteroid-sensitive TAC1 signature was developed from the TAC1 ICS-responsive genes. This signature consisted of mast cell-specific genes identified by single-cell RNA-sequencing and positively correlated with bronchial biopsy mast cell numbers following ICS±LABA. Baseline levels of gene transcription correlated with the change in RV/TLC %predicted following 30-month ICS±LABA. CONCLUSION Sputum-derived transcriptomic signatures from an asthma cohort can be recapitulated in bronchial biopsies of patients with COPD and identified a signature of airway mast cells as a predictor of corticosteroid responsiveness.
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Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
- Pulmonary Diseases, UMCG, Groningen, The Netherlands
- GRAIC, University of Groningen, Groningen, The Netherlands
| | - Stelios Pavlidis
- Department of Computing and Data Science Institute, Imperial College London, London, UK
| | - Chih-Hsi Kuo
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Anthony Rowe
- Discovery IT, Janssen Research and Development LLC, High Wycombe, UK
| | - Pieter S Hiemstra
- Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim Timens
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marijn Berg
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marissa Wisman
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Yi-Ke Guo
- Department of Computing and Data Science Institute, Imperial College London, London, UK
| | - Ratko Djukanović
- Academic Unit of Clinical and Experimental Sciences, Southampton University Faculty of Medicine, Southampton, UK
| | - Peter Sterk
- Respiratory Medicine, Amsterdam UMC-Locatie AMC, Amsterdam, The Netherlands
| | - Kerstin B Meyer
- Gene expression genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Martijn C Nawijn
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Ian Adcock
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Kian Fan Chung
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Maarten van den Berge
- Pulmonary Diseases, UMCG, Groningen, The Netherlands
- GRAIC, University of Groningen, Groningen, The Netherlands
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22
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Meertens M, Muntinghe-Wagenaar MB, Sikkema BJ, Lopez-Yurda M, Retèl VP, Paats MS, Ter Heine R, Schuuring E, Timens W, Touw DJ, van Boven JFM, de Langen AJ, Hashemi SMS, Hendriks LEL, Croes S, van den Heuvel MM, Dingemans AMC, Mathijssen RHJ, Smit EF, Huitema ADR, Steeghs N, van der Wekken AJ. Therapeutic drug monitoring guided dosing versus standard dosing of alectinib in advanced ALK positive non-small cell lung cancer patients: Study protocol for an international, multicenter phase IV randomized controlled trial (ADAPT ALEC). Front Oncol 2023; 13:1136221. [PMID: 36969063 PMCID: PMC10035072 DOI: 10.3389/fonc.2023.1136221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundAlectinib is first-line therapy in patients with stage IV non-small cell lung carcinoma (NSCLC) and an anaplastic lymphoma kinase (ALK) fusion. A shorter median progression-free survival (mPFS) was observed when alectinib minimum plasma concentrations during steady state (Cmin,SS) were below 435 ng/mL. This may suggest that patients should have an alectinib Cmin,SS ≥ 435 ng/mL for a more favorable outcome. This potential target could be attained by using therapeutic drug monitoring (TDM), i.e. adjusting the dose based on measured plasma trough concentrations. Hypothetically, this will increase mPFS, but this has not yet been evaluated in a randomized controlled trial (RCT). Therefore, the ADAPT ALEC trial is designed, with the primary objective to prolong mPFS in NSCLC patients treated with alectinib by using TDM.MethodsADAPT ALEC is a multicenter, phase IV RCT, in which patients aged ≥ 18 years with advanced ALK positive (+) NSCLC eligible for alectinib in daily care are enrolled. Participants will be randomized (1:1 ratio) into intervention arm A (TDM) or B (control), stratified by brain metastases and prior ALK treatments. Starting dose in both arms is the approved flat fixed dose of alectinib 600 mg taken twice daily with food. In case of alectinib Cmin,SS < 435 ng/mL, arm A will receive increased doses of alectinib till Cmin,SS ≥ 435 ng/mL when considered tolerable. The primary outcome is mPFS, where progressive disease is defined according to RECIST v1.1 or all-cause death and assessed by CT-scans and MRI brain. Secondary endpoints are feasibility and tolerability of TDM, patient and physician adherence, overall response rate, median overall survival, intracranial PFS, quality of life, toxicity, alectinib-M4 concentrations and cost-effectiveness of TDM. Exploratory endpoints are circulating tumor DNA and body composition.DiscussionThe ADAPT ALEC will show whether treatment outcomes of patients with advanced ALK+ NSCLC improve when using TDM-guided dosing of alectinib instead of fixed dosing. The results will provide high quality evidence for deciding whether TDM should be implemented as standard of care and this will have important consequences for the prescribing of alectinib.Clinical trial registrationClinicalTrials.gov, identifier NCT05525338.
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Affiliation(s)
- Marinda Meertens
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - M. Benthe Muntinghe-Wagenaar
- Department of Pulmonology and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Barend J. Sikkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marta Lopez-Yurda
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Valesca P. Retèl
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marthe S. Paats
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rob Ter Heine
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Daan J. Touw
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Job F. M. van Boven
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Adrianus. J. de Langen
- Department of Thoracic Oncology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Sayed M. S. Hashemi
- Department of Pulmonary Medicine, Amsterdam University Medical Center, VU University Medical Center, Amsterdam, Netherlands
| | - Lizza E. L. Hendriks
- Department of Respiratory Medicine, Maastricht University Medical Center, GROW School for Oncology and Reproduction, Maastricht, Netherlands
| | - Sander Croes
- Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Center, CARIM School for Cardiovascular disease, Maastricht, Netherlands
| | | | - Anne-Marie C. Dingemans
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ron H. J. Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Egbert F. Smit
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Alwin D. R. Huitema
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Pharmacology, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Neeltje Steeghs
- Department of Clinical Pharmacology, Division of Medical Oncology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonology and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- *Correspondence: Anthonie J. van der Wekken,
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23
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Hiddinga BI, Slebos DJ, David Koster T, Hijmering-Kappelle LBM, Hiltermann TJN, Kievit H, van der Wekken AJ, de Jonge G, Vliegenthart R, Van De Wauwer C, Timens W, Bensch F. The additional diagnostic value of virtual bronchoscopy navigation in patients with pulmonary nodules - The NAVIGATOR study. Lung Cancer 2023; 177:37-43. [PMID: 36708592 DOI: 10.1016/j.lungcan.2023.01.012] [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] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND The number of solitary pulmonary nodules to be evaluated is expected to increase and therefore we need to improve diagnostic and therapeutic tools to approach these nodules. To prevent patients from futile invasive procedures and receiving treatment without histological confirmation of cancer, we evaluated the value of virtual bronchoscopy navigation to obtain a diagnosis of the solitary pulmonary nodule in a real-world clinical setting. METHODS In the NAVIGATOR single center, prospective, observational cohort study patients underwent a virtual bronchoscopy navigation procedure with or without guide sheet tunnelling to assess a solitary pulmonary nodule. Nodules were considered not accessible if a diagnosis could not be obtained by either by CT-guided transthoracic biopsy or conventional bronchoscopy. RESULTS Between February 2021 and January 2022 35 patients underwent the virtual bronchoscopy navigation procedure. The overall diagnostic yield was 77% and was dependent on size of the nodule and chosen path, with highest yield in lesions with an airway path. Adverse events were few and manageable. CONCLUSION Virtual bronchoscopy navigation with or without sheet tunnelling is a new technique with a good diagnostic yield, also in patients in whom previously performed procedures failed to establish a diagnosis and/or alternative procedures are considered not feasible based on expected yield and/or safety. Preventing futile or more invasive procedures like surgery or transthoracic punctures with a higher complication rate is beneficial for patients, and allowed treatment adaptation in two-third of the analyzed patient population.
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Affiliation(s)
- Birgitta I Hiddinga
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands.
| | - Dirk-Jan Slebos
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - T David Koster
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Lucie B M Hijmering-Kappelle
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Hanneke Kievit
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Anthonie J van der Wekken
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Gonda de Jonge
- Department of Radiology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Caroline Van De Wauwer
- Department of Cardiothoracic Surgery, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Frederike Bensch
- Department of Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, the Netherlands
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24
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Bekker NJ, van Pijkeren A, Wolters JC, Sánchez Brotons A, Guryev V, Woldhuis RR, Bischoff R, Alkema W, Horvatovich P, Van Nijnatten JLL, van den Berge M, Timens W, Brandsma CA. A proteomics approach to identify COPD-related changes in lung fibroblasts. Am J Physiol Lung Cell Mol Physiol 2023; 324:L521-L535. [PMID: 36808722 DOI: 10.1152/ajplung.00105.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/23/2023] Open
Abstract
BACKGROUND Lung fibroblasts are implicated in abnormal tissue repair in chronic obstructive pulmonary disease (COPD). The exact mechanisms are unknown and comprehensive analysis comparing COPD- and control fibroblasts is lacking. AIM To gain insight in the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. METHODS Protein and RNA was isolated from cultured parenchymal lung fibroblasts of 17 stage IV COPD patients and 16 non-COPD controls. Proteins were analyzed using LC-MS/MS and RNA through RNA sequencing. Differential protein and gene expression in COPD was assessed via linear regression, followed by pathway enrichment, correlation analysis and immunohistological staining in lung tissue. Proteomic and transcriptomic data was compared to investigate the overlap and correlation between both levels of data. RESULTS We identified 40 differentially expressed (DE) proteins and zero DE genes between COPD and control fibroblasts. The most significant DE proteins were HNRNPA2B1 and FHL1. Thirteen of the 40 proteins were previously associated with COPD, including FHL1 and GSTP1. Six of the 40 proteins were related to telomere maintenance pathways, and were positively correlated with the senescence marker LMNB1. No significant correlation between gene and protein expression was observed for the 40 proteins. CONCLUSIONS The 40 DE proteins in COPD fibroblasts include previously described COPD proteins (FHL1, GSTP1) and new COPD research targets like HNRNPA2B1. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis and indicates that different types of information are generated with both methods.
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Affiliation(s)
- Nicolaas J Bekker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alejandro Sánchez Brotons
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Aging, University Medical Center Groningen, Groningen, Netherlands
| | - Roy R Woldhuis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Wynand Alkema
- Institute for Life Sciences and Technology, Hanze University of Applied Sciences, Groningen, Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Johannes L L Van Nijnatten
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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25
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Rathnayake SNH, Ditz B, van Nijnatten J, Sadaf T, Hansbro PM, Brandsma CA, Timens W, van Schadewijk A, Hiemstra PS, ten Hacken NHT, Oliver B, Kerstjens HAM, van den Berge M, Faiz A. Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier. Respirology 2023; 28:132-142. [PMID: 36414410 PMCID: PMC10947540 DOI: 10.1111/resp.14401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVE Smoking disturbs the bronchial-mucus-barrier. This study assesses the cellular composition and gene expression shifts of the bronchial-mucus-barrier with smoking to understand the mechanism of mucosal damage by cigarette smoke exposure. We explore whether single-cell-RNA-sequencing (scRNA-seq) based cellular deconvolution (CD) can predict cell-type composition in RNA-seq data. METHODS RNA-seq data of bronchial biopsies from three cohorts were analysed using CD. The cohorts included 56 participants with chronic obstructive pulmonary disease [COPD] (38 smokers; 18 ex-smokers), 77 participants without COPD (40 never-smokers; 37 smokers) and 16 participants who stopped smoking for 1 year (11 COPD and 5 non-COPD-smokers). Differential gene expression was used to investigate gene expression shifts. The CD-derived goblet cell ratios were validated by correlating with staining-derived goblet cell ratios from the COPD cohort. Statistics were done in the R software (false discovery rate p-value < 0.05). RESULTS Both CD methods indicate a shift in bronchial-mucus-barrier cell composition towards goblet cells in COPD and non-COPD-smokers compared to ex- and never-smokers. It shows that the effect was reversible within a year of smoking cessation. A reduction of ciliated and basal cells was observed with current smoking, which resolved following smoking cessation. The expression of mucin and sodium channel (ENaC) genes, but not chloride channel genes, were altered in COPD and current smokers compared to never smokers or ex-smokers. The goblet cell-derived staining scores correlate with CD-derived goblet cell ratios. CONCLUSION Smoking alters bronchial-mucus-barrier cell composition, transcriptome and increases mucus production. This effect is partly reversible within a year of smoking cessation. CD methodology can predict goblet-cell percentages from RNA-seq.
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Affiliation(s)
- Senani N. H. Rathnayake
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Benedikt Ditz
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Jos van Nijnatten
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | - Tayyaba Sadaf
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- Centre for InflammationCentenary Institute, and the University of Technology Sydney, Faculty of ScienceSydneyNew South WalesAustralia
| | - Philip M. Hansbro
- Centre for InflammationCentenary Institute, and the University of Technology Sydney, Faculty of ScienceSydneyNew South WalesAustralia
| | - Corry A. Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | | | - Peter S. Hiemstra
- Department of PulmonologyLeiden University Medical CenterLeidenthe Netherlands
| | - Nick H. T. ten Hacken
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Brian Oliver
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Huib A. M. Kerstjens
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Maarten van den Berge
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Alen Faiz
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
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26
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Rathnayake SNH, Ditz B, Willemse BWM, Timens W, Kooistra W, Heijink IH, Oliver BGG, van den Berge M, Faiz A. Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome. Chest 2023:S0012-3692(23)00158-7. [PMID: 36716955 DOI: 10.1016/j.chest.2022.12.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/30/2023] Open
Affiliation(s)
- Senani N H Rathnayake
- Respiratory Bioinformatics and Molecular Biology Group, Ultimo, NSW, Australia; School of Life Sciences, The University of Technology Sydney, Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology Group, Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - B Ditz
- Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Brigitte W M Willemse
- University of Technology Sydney; the Department of Paediatrics, Ultimo, NSW, Australia
| | - Wim Timens
- Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pathology & Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Wierd Kooistra
- Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pathology & Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Irene H Heijink
- Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pulmonary Diseases, Groningen, the Netherlands; Department of Pathology & Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Brian G G Oliver
- School of Life Sciences, The University of Technology Sydney, Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology Group, Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Maarten van den Berge
- Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology Group, Ultimo, NSW, Australia; School of Life Sciences, The University of Technology Sydney, Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology Group, Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia; Division of Paediatric Pulmonology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; Department of Pulmonary Diseases, Groningen, the Netherlands.
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27
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Kruk D, Yeung ACY, Faiz A, ten Hacken NHT, Timens W, van Kuppevelt TH, Daamen W, Hof D, Harmsen MC, Rojas M, Heijink IH. Gene expression profiles in mesenchymal stromal cells from bone marrow, adipose tissue and lung tissue of COPD patients and controls. Respir Res 2023; 24:22. [PMID: 36681830 PMCID: PMC9863276 DOI: 10.1186/s12931-023-02314-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/03/2023] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is characterized by irreversible lung tissue damage. Novel regenerative strategies are urgently awaited. Cultured mesenchymal stem/stromal cells (MSCs) have shown promising results in experimental models of COPD, but differences between sources may impact on their potential use in therapeutic strategies in patients. AIM To assess the transcriptome of lung-derived MSCs (LMSCs), bone marrow-derived MSCs (BM-MSC) and adipose-derived MSCs (AD-MSCs) from COPD patients and non-COPD controls. METHODS We studied differences in gene expression profiles between the MSC-subtypes, as well as between COPD and control using RNA sequencing (RNA-seq). RESULTS We show that besides heterogeneity between donors, MSCs from different sources have strongly divergent gene signatures. The growth factors FGF10 and HGF were predominantly expressed in LMSCs. MSCs from all sources displayed altered expression profiles in COPD, with most pronounced significantly up- and downregulated genes in MSCs from adipose tissue. Pathway analysis revealed that the most differentially expressed genes in COPD-derived AD-MSCs are involved in extracellular matrix (ECM) binding and expression. In LMSCs, the gene that differed most strongly between COPD and control was CSGALNACT1, an ECM modulating gene. CONCLUSION Autologous MSCs from COPD patients display abnormalities with respect to their transcriptome, which were surprisingly most profound in MSCs from extrapulmonary sources. LMSCs may be optimally equipped for lung tissue repair because of the expression of specific growth factor genes.
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Affiliation(s)
- Dennis Kruk
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anna C. Y. Yeung
- grid.117476.20000 0004 1936 7611Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW Australia ,grid.1013.30000 0004 1936 834XWoolcock Institute of Medical Research, The University of Sydney, Glebe, NSW Australia
| | - Alen Faiz
- grid.117476.20000 0004 1936 7611Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW Australia
| | - Nick H. T. ten Hacken
- grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Toin H. van Kuppevelt
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willeke Daamen
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danique Hof
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martin C. Harmsen
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands
| | - Mauricio Rojas
- grid.261331.40000 0001 2285 7943Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH USA
| | - Irene H. Heijink
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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28
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Qi C, Berg M, Chu X, Timens W, Kole T, van den Berge M, Xu CJ, Koppelman GH, Nawijn MC, Li Y. Cell-type eQTL deconvolution of bronchial epithelium through integration of single-cell and bulk RNA-seq. Allergy 2022; 77:3663-3666. [PMID: 35708915 DOI: 10.1111/all.15410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Marijn Berg
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Xiaojing Chu
- Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tessa Kole
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
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29
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Moonen L, Derks JL, Lap LMV, Marijnissen BJCA, Hillen LM, den Bakker MA, von der Thüsen JH, van Suylen RJ, Timens W, Bintanel M, Kuteeva E, Dingemans AMC, Speel EJM. Development and verification of new monoclonal orthopedia homeobox (OTP) specific antibodies for pulmonary carcinoid diagnostics. Transl Lung Cancer Res 2022; 11:2181-2191. [PMID: 36519022 PMCID: PMC9742615 DOI: 10.21037/tlcr-22-418] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022]
Abstract
Background Orthopedia homeobox (OTP) has shown to be a useful prognostic marker to predict outcome in pulmonary carcinoids, which is also supported by the World Health Organization. However, the discontinuation of the initially used polyclonal antibody and absence of a reliable routinely applicable monoclonal OTP antibody hampers implementation in routine diagnostics. Here, new monoclonal antibodies directed against OTP were developed and verified on formalin-fixed paraffin-embedded tissue of pulmonary neuroendocrine tumors (NETs) for clinical diagnostics. Methods OTP specific monoclonal antibodies were produced from mice immunised with a recombinant human OTP protein fragment. Enzyme-linked immunosorbent assay (ELISA) positive hybridomas were evaluated using immunohistochemistry (IHC). Following epitope-mapping and isotyping, purified monoclonal antibodies were validated for IHC in formalin-fixed paraffin-embedded tissues, the optimal dilution was determined, and results were cross validated with the OTP polyclonal antibody (HPA039365, Atlas Antibodies). Staining protocols were optimized on two automated staining platforms and performance was harmonized using a tissue microarray (TMA). Results Two clones (CL11222 and CL11225) were selected for purified monoclonal antibody (mAb) production. Intratumor heterogeneity assessment revealed similar performance for both clones. While clone CL11225 displayed a unique epitope compared to those present in the polyclonal antibody, this clone performed most similar to the polyclonal antibody. Cross-platform assessment revealed an excellent agreement for clone CL11225 while clone CL11222 showed somewhat discordant results on Dako. Conclusions New monoclonal OTP specific antibodies have been developed and verified on different automated immunohistochemical staining platforms. The OTP specific monoclonal antibodies showed excellent agreement with the often-used polyclonal antibody allowing application in routine diagnostics.
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Affiliation(s)
- Laura Moonen
- Department of Pathology GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jules L. Derks
- Department of Pulmonary Diseases, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Lisa M. V. Lap
- Department of Pathology GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Britney J. C. A. Marijnissen
- Department of Pathology GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Lisa M. Hillen
- Department of Pathology GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Jan H. von der Thüsen
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | - Anne-Marie C. Dingemans
- Department of Pulmonary Diseases, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands;,Department of Pulmonary Medicine, Erasmus MC Cancer institute, University Medical Center, Rotterdam, The Netherlands
| | - Ernst-Jan M. Speel
- Department of Pathology GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands
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30
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Zhang ZL, Moeslund N, Hu MA, Hoffmann R, Venema LH, Van De Wauwer C, Timens W, Okamoto T, Verschuuren EAM, Leuvenink HGD, Eiskjaer H, Erasmus ME. Establishing an economical and widely accessible donation after circulatory death animal abattoir model for lung research using ex vivo lung perfusion. Artif Organs 2022; 46:2179-2190. [PMID: 35730930 PMCID: PMC9796928 DOI: 10.1111/aor.14345] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/21/2022] [Accepted: 06/06/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Ex vivo lung perfusion (EVLP), is a platform that allows simultaneous testing and treatment of the lungs. However, use of EVLP is costly and requires access to lab animals and accompanying facilities. To increase the use of EVLP for research, we developed a method to perform EVLP using abattoir procured lungs. Furthermore, we were also able to significantly decrease costs. METHODS Six pair of lungs were procured from abattoir sheep. The lungs were then flushed and stored in ice for 3 h. A low-flow (20% of cardiac output) approach, a tidal volume of 6 ml/kg bodyweight and total perfusion time of 3 h were chosen. Perfusion fluids and circuits were self-made. Lung biopsies, perfusate collection, respiratory values, circulatory pressures were recorded and hourly blood gas analyses were performed. RESULTS Mean pO2 remained stable from 60 min (49.3 ± 7.1 kPa) to 180 min (51.5 kPa ± 8.0), p = 0.66. Pulmonary artery pressure remained ≤15 mm Hg and the left atrial pressure remained between 3 and 5 mm Hg and peak respiratory pressures ≤20 cmH2 O. Lactate dehydrogenase increased from start (96.3 ± 56.4 U/L) to the end of perfusion (315.8 ± 85.0 U/L), p < 0.05. No difference was observed in ATP between procurement and post-EVLP, 129.7 ± 37.4 μmol/g protein to 132.0 ± 23.4 μmol/g, p = 0.92. CONCLUSIONS Sheep lungs, acquired from an abattoir, can be ex vivo perfused under similar conditions as lab animal lungs with similar results regarding e.g., oxygenation and ATP restoration. Furthermore, costs can be significantly reduced by making use of this abattoir model. By increasing accessibility and lowering costs for experiments using lung perfusion, more results may be achieved in the field of lung diseases.
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Affiliation(s)
- Zhang Long Zhang
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Niels Moeslund
- Department of CardiologyAarhus University HospitalAarhusDenmark
| | - Michiel Andy Hu
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Roland Hoffmann
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Leonie Harmina Venema
- Department of Surgical ResearchUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Caroline Van De Wauwer
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Wim Timens
- Department of PathologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Toshihiro Okamoto
- Department of Thoracic Surgery and Lung TransplantationCleveland ClinicClevelandOhioUSA
| | - Erik Alfons Maria Verschuuren
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Henri Gerrit Derk Leuvenink
- Department of Surgical ResearchUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Hans Eiskjaer
- Department of CardiologyAarhus University HospitalAarhusDenmark
| | - Michiel Elardus Erasmus
- Department of Cardio‐Thoracic SurgeryUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
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31
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Gijtenbeek RG, van der Noort V, Aerts JG, Staal-van den Brekel JA, Smit EF, Krouwels FH, Wilschut FA, Hiltermann TJN, Timens W, Schuuring E, Janssen JD, Goosens M, van den Berg PM, de Langen AJ, Stigt JA, van den Borne BE, Groen HJ, van Geffen WH, van der Wekken AJ. Randomised controlled trial of first-line tyrosine-kinase inhibitor (TKI) versus intercalated TKI with chemotherapy for EGFR-mutated nonsmall cell lung cancer. ERJ Open Res 2022; 8:00239-2022. [PMID: 36267895 PMCID: PMC9574558 DOI: 10.1183/23120541.00239-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Previous studies have shown interference between epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and chemotherapy in the cell cycle, thus reducing efficacy. In this randomised controlled trial we investigated whether intercalated erlotinib with chemotherapy was superior compared to erlotinib alone in untreated advanced EGFR-mutated nonsmall cell lung cancer (NSCLC). Materials and methods Treatment-naïve patients with an activating EGFR mutation, ECOG performance score of 0-3 and adequate organ function were randomly assigned 1:1 to either four cycles of cisplatin-pemetrexed with intercalated erlotinib (day 2-16 out of 21 days per cycle) followed by pemetrexed and erlotinib maintenance (CPE) or erlotinib monotherapy. The primary end-point was progression-free survival (PFS). Secondary end-points were overall survival, objective response rate (ORR) and toxicity. Results Between April 2014 and September 2016, 22 patients were randomised equally into both arms; the study was stopped due to slow accrual. Median follow-up was 64 months. Median PFS was 13.7 months (95% CI 5.2-18.8) for CPE and 10.3 months (95% CI 7.1-15.5; hazard ratio (HR) 0.62, 95% CI 0.25-1.57) for erlotinib monotherapy; when compensating for number of days receiving erlotinib, PFS of the CPE arm was superior (HR 0.24, 95% CI 0.07-0.83; p=0.02). ORR was 64% for CPE versus 55% for erlotinib monotherapy. Median overall survival was 31.7 months (95% CI 21.8-61.9 months) for CPE compared to 17.2 months (95% CI 11.5-45.5 months) for erlotinib monotherapy (HR 0.58, 95% CI 0.22-1.41 months). Patients treated with CPE had higher rates of treatment-related fatigue, anorexia, weight loss and renal toxicity. Conclusion Intercalating erlotinib with cisplatin-pemetrexed provides a longer PFS compared to erlotinib alone in EGFR-mutated NSCLC at the expense of more toxicity.
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Affiliation(s)
- Rolof G.P. Gijtenbeek
- Dept of Respiratory Medicine, Medical Centre Leeuwarden, Leeuwarden, The Netherlands
| | - Vincent van der Noort
- Dept of Biometrics, Netherlands Cancer Institute – Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Joachim G.J.V. Aerts
- Dept of Pulmonary Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Egbert F. Smit
- Dept of Pulmonology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frans H. Krouwels
- Dept of Respiratory Medicine, Spaarne Hospital, Hoofddorp, The Netherlands
| | - Frank A. Wilschut
- Dept of Respiratory Medicine, Gelderse Vallei Hospital, Ede, The Netherlands
| | - T. Jeroen N. Hiltermann
- Dept of Pulmonary Diseases, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Wim Timens
- Dept of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Dept of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Joost D.J. Janssen
- Dept of Respiratory Medicine, Máxima Medical Centre, Eindhoven/Veldhoven, The Netherlands
| | - Martijn Goosens
- Dept of Pulmonary Medicine, Gelre Hospitals, Zutphen, The Netherlands
| | | | - A. Joop de Langen
- Dept of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos A. Stigt
- Dept of Respiratory Medicine, Isala Hospital, Zwolle, The Netherlands
| | | | - Harry J.M. Groen
- Dept of Pulmonary Diseases, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Wouter H. van Geffen
- Dept of Respiratory Medicine, Medical Centre Leeuwarden, Leeuwarden, The Netherlands
| | - Anthonie J. van der Wekken
- Dept of Pulmonary Diseases, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
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32
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Slob EMA, Faiz A, van Nijnatten J, Vijverberg SJH, Longo C, Kutlu M, Chew FT, Sio YY, Herrera-Luis E, Espuela-Ortiz A, Perez-Garcia J, Pino-Yanes M, Burchard EG, Potočnik U, Gorenjak M, Palmer C, Maroteau C, Turner S, Verhamme K, Karimi L, Mukhopadhyay S, Timens W, Hiemstra PS, Pijnenburg MW, Neighbors M, Grimbaldeston MA, Tew GW, Brandsma CA, Berce V, Aliee H, Theis F, Sin DD, Li X, van den Berge M, Maitland-van der Zee AH, Koppelman GH. Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response. Clin Transl Allergy 2022; 12:e12173. [PMID: 36036237 PMCID: PMC9421427 DOI: 10.1002/clt2.12173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Elise M A Slob
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Pharmacy, Haaglanden Medical Center, The Hague, The Netherlands
| | - Alen Faiz
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Jos van Nijnatten
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Susanne J H Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Cristina Longo
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Merve Kutlu
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Fook Tim Chew
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Colin Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, UK
| | - Cyrielle Maroteau
- Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Katia Verhamme
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leila Karimi
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Wim Timens
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariëlle W Pijnenburg
- Department of Pediatrics, Pediatric Pulmonology and Allergology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Margaret Neighbors
- OMNI Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | | | - Gaik W Tew
- Product Development Immunology, Infectious Disease & Ophtalmology, Genentech Inc, South San Francisco, California, USA
| | - Corry A Brandsma
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Center, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center, Munich, Germany.,Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
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Wildung M, Herr C, Riedel D, Wiedwald C, Moiseenko A, Ramírez F, Tasena H, Heimerl M, Alevra M, Movsisyan N, Schuldt M, Volceanov-Hahn L, Provoost S, Nöthe-Menchen T, Urrego D, Freytag B, Wallmeier J, Beisswenger C, Bals R, van den Berge M, Timens W, Hiemstra PS, Brandsma CA, Maes T, Andreas S, Heijink IH, Pardo LA, Lizé M. miR449 Protects Airway Regeneration by Controlling AURKA/HDAC6-Mediated Ciliary Disassembly. Int J Mol Sci 2022; 23:ijms23147749. [PMID: 35887096 PMCID: PMC9320302 DOI: 10.3390/ijms23147749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/23/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 01/25/2023] Open
Abstract
Airway mucociliary regeneration and function are key players for airway defense and are impaired in chronic obstructive pulmonary disease (COPD). Using transcriptome analysis in COPD-derived bronchial biopsies, we observed a positive correlation between cilia-related genes and microRNA-449 (miR449). In vitro, miR449 was strongly increased during airway epithelial mucociliary differentiation. In vivo, miR449 was upregulated during recovery from chemical or infective insults. miR0449−/− mice (both alleles are deleted) showed impaired ciliated epithelial regeneration after naphthalene and Haemophilus influenzae exposure, accompanied by more intense inflammation and emphysematous manifestations of COPD. The latter occurred spontaneously in aged miR449−/− mice. We identified Aurora kinase A and its effector target HDAC6 as key mediators in miR449-regulated ciliary homeostasis and epithelial regeneration. Aurora kinase A is downregulated upon miR449 overexpression in vitro and upregulated in miR449−/− mouse lungs. Accordingly, imaging studies showed profoundly altered cilia length and morphology accompanied by reduced mucociliary clearance. Pharmacological inhibition of HDAC6 rescued cilia length and coverage in miR449−/− cells, consistent with its tubulin-deacetylating function. Altogether, our study establishes a link between miR449, ciliary dysfunction, and COPD pathogenesis.
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Affiliation(s)
- Merit Wildung
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
| | - Christian Herr
- Department of Internal Medicine V, Saarland University, 66421 Homburg, Germany; (C.H.); (C.B.); (R.B.)
| | - Dietmar Riedel
- Laboratory for Electron Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany;
| | - Cornelia Wiedwald
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
| | - Alena Moiseenko
- Immunology & Respiratory Department, Boehringer Ingelheim Pharma GmbH, 88400 Biberach an der Riss, Germany;
| | - Fidel Ramírez
- Global Computational Biology and Digital Sciences Department, Boehringer Ingelheim Pharma GmbH, 88400 Biberach an der Riss, Germany;
| | - Hataitip Tasena
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (H.T.); (W.T.); (C.-A.B.); (I.H.H.)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands;
| | - Maren Heimerl
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
| | - Mihai Alevra
- Institute of Neuro- and Sensory Physiology, Goettingen University, 37073 Goettingen, Germany;
| | - Naira Movsisyan
- Oncophysiology Group, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany; (N.M.); (D.U.); (L.A.P.)
| | - Maike Schuldt
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
| | - Larisa Volceanov-Hahn
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
| | - Sharen Provoost
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (S.P.); (T.M.)
| | - Tabea Nöthe-Menchen
- Department of General Pediatrics, University Hospital Muenster, 48149 Muenster, Germany; (T.N.-M.); (J.W.)
| | - Diana Urrego
- Oncophysiology Group, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany; (N.M.); (D.U.); (L.A.P.)
| | - Bernard Freytag
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
| | - Julia Wallmeier
- Department of General Pediatrics, University Hospital Muenster, 48149 Muenster, Germany; (T.N.-M.); (J.W.)
| | - Christoph Beisswenger
- Department of Internal Medicine V, Saarland University, 66421 Homburg, Germany; (C.H.); (C.B.); (R.B.)
| | - Robert Bals
- Department of Internal Medicine V, Saarland University, 66421 Homburg, Germany; (C.H.); (C.B.); (R.B.)
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands;
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (H.T.); (W.T.); (C.-A.B.); (I.H.H.)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands;
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Centre, 2333 Leiden, The Netherlands;
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (H.T.); (W.T.); (C.-A.B.); (I.H.H.)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands;
| | - Tania Maes
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (S.P.); (T.M.)
| | - Stefan Andreas
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
| | - Irene H. Heijink
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (H.T.); (W.T.); (C.-A.B.); (I.H.H.)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands;
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands
| | - Luis A. Pardo
- Oncophysiology Group, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany; (N.M.); (D.U.); (L.A.P.)
| | - Muriel Lizé
- Molecular & Experimental Pneumology Group, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, 37075 Gottingen, Germany; (M.W.); (C.W.); (M.H.); (L.V.-H.); (S.A.)
- Molecular Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (M.S.); (B.F.)
- Immunology & Respiratory Department, Boehringer Ingelheim Pharma GmbH, 88400 Biberach an der Riss, Germany;
- Correspondence:
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Du Y, Sidorenkov G, Groen HJ, Heuvelmans MA, Vliegenthart R, Dorrius MD, Timens W, de Bock GH. Airflow Limitation Increases Lung Cancer Risk in Smokers: The Lifelines Cohort Study. Cancer Epidemiol Biomarkers Prev 2022; 31:1442-1449. [PMID: 35534234 PMCID: PMC9377735 DOI: 10.1158/1055-9965.epi-21-1365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/29/2021] [Revised: 02/15/2022] [Accepted: 05/02/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The relationship between smoking, airflow limitation, and lung cancer occurrence is unclear. This study aims to evaluate the relationship between airflow limitation and lung cancer, and the effect modification by smoking status. METHODS We included participants with spirometry data from Lifelines, a population-based cohort study from the Northern Netherlands. Airflow limitation was defined as FEV1/FVC ratio < 0.7. The presence of pathology-confirmed primary lung cancer during a median follow-up of 9.5 years was collected. The Cox regression model was used and hazard ratios (HR) with 95% confidence interval (95% CI) were reported. Adjusted confounders included age, sex, educational level, smoking, passive smoking, asthma status and asbestos exposure. The effect modification by smoking status was investigated by estimating the relative excess risk due to interaction (RERI) and the ratio of HRs with 95% CI. RESULTS Out of 98,630 participants, 14,200 (14.4%) had airflow limitation. In participants with and without airflow limitation, lung cancer incidence was 0.8% and 0.2%, respectively. The adjusted HR between airflow limitation and lung cancer risk was 1.7 (1.4-2.3). The association between airflow limitation and lung cancer differed by smoking status [former smokers: 2.1 (1.4-3.2), current smokers: 2.2 (1.5-3.2)] and never smokers [0.9 (0.4-2.1)]. The RERI and ratio of HRs was 2.1 (0.7-3.4) and 2.5 (1.0-6.5) for former smokers, and 4.6 (95% CI, 1.8-7.4) and 2.5 (95% CI, 1.0-6.3) for current smokers, respectively. CONCLUSIONS Airflow limitation increases lung cancer risk and this association is modified by smoking status. IMPACT Ever smokers with airflow limitation are an important target group for the prevention of lung cancer.
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Affiliation(s)
- Yihui Du
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Grigory Sidorenkov
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Harry J.M. Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marjolein A. Heuvelmans
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Monique D. Dorrius
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Department of Radiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Geertruida H. de Bock
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Corresponding Author: Geertruida H. de Bock, University Medical Center Groningen, University of Groningen, PO Box 30.001, FA 40, Groningen 9700 RB, the Netherlands. Phone: 315-0361-0739; E-mail:
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Migulina N, Tjin G, Faiz A, Borghuis T, Zhao F, Kaper HJ, Metzlar M, van Dijk E, Sharma PK, Timens W, Gosens R, Brandsma CA, Burgess JK. Differential roles for lysyl oxidase (like), family members in chronic obstructive pulmonary disease; from gene and protein expression to function. FASEB J 2022; 36:e22374. [PMID: 35670745 DOI: 10.1096/fj.202101553r] [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] [Received: 10/12/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/11/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by long-term airflow obstruction with cigarette smoke as a key risk factor. Extracellular matrix (ECM) alterations in COPD may lead to small airway wall fibrosis. Altered collagen cross-linking, potentially mediated by the lysyl oxidase (LO) family of enzymes (LOX, LOXL1-4), orchestrates disturbed ECM homeostasis. In this study, we investigated the effects of smoking status and presence and severity of COPD on LOs gene and protein expression in the airways and the impact of LOs inhibition on airway contraction in an ex vivo mouse model. We used gene expression data from bronchial brushings, airway smooth muscle (ASM) cells in vitro and immunohistochemistry in lung tissue to assess smoke- and COPD-associated differences in LOs gene and protein expression in the small airways. We found higher LOX expression in current- compared to ex-smokers and higher LOXL1 expression in COPD compared to non-COPD patients. LOX and LOXL2 expression were upregulated in COPD ASM cells treated with cigarette smoke extract. LOXL1 and LOXL2 protein levels were higher in small airways from current- compared to non-smokers. In COPD patients, higher LOXL1 and lower LOX protein levels were observed, but no differences for LOXL2, LOXL3, and LOXL4 protein were detected in small airways. Inhibiting LOs activity increased airway contraction in murine lung slices. COPD-associated changes in LOs, in particular LOX and LOXL1, may be related to smoking and contribute to impaired airway function, providing potential novel targets for preventing or treating small airways changes in COPD.
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Affiliation(s)
- Nataliya Migulina
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gavin Tjin
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.,Discipline of Pharmacology, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Alen Faiz
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Faculty of Science, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Theo Borghuis
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Fenghua Zhao
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Biomedical Engineering-FB40, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hans J Kaper
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Biomedical Engineering-FB40, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marit Metzlar
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - Eline van Dijk
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - Prashant K Sharma
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Biomedical Engineering-FB40, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Janette K Burgess
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, KOLFF Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Al-Adwi Y, Gan TJ, Bosma J, Abdulahad W, Atzeni IM, Van der Leij M, Kroesen BJ, Stel AJ, Timens W, Burgess J, Van Goor H, Westra J, Mulder DJ. AB0659 Recruitment and prevalence of mixed phenotype macrophages is prominent in Bronchoalveolar Lavage (BAL) of Systemic Sclerosis (SSc) patients with Interstitial Lung Disease (ILD). Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundILD is a major problem in SSc for which no disease-modifying therapies are available. Many observations suggest monocyte/macrophage involvement in SSc and might be a key component in the development of ILD. Macrophages polarize into M1 and M2 phenotypes and thereby orchestrate inflammation and subsequent fibrosis by responding to and producing a vast array of cytokines and chemokines. Differences in the levels of the chemokines might explain variations in the recruitment and activation of macrophages in affected organs. In SSc, monocytes with a mixed phenotype (expressing both M1 and M2 markers) are prominent in peripheral blood. No previous study has investigated the mixed phenotype macrophages locally on the lung level.Objectivesa-to measure macrophage-related chemokines in BAL fluid obtained from SSc-ILD and SSc-no-ILD patients.b-to investigate levels of M1 and M2 macrophage markers in BAL cells obtained from SSc-ILD and SSc-no-ILD patients.MethodsA cross-sectional study in which BAL procedure was performed on 15 treatment-naïve SSc patients divided into two groups according to lung involvement determined by HRCT and lung function tests: SSc-no-ILD group and SSc-ILD group (Table 1). Levels of chemokines (CCL18, CXCL-10 and CCR2) were analysed using ELISA. mRNA expression levels of CD86 (M1; inflammatory macrophage marker) and CD206 (M2; fibrogenic macrophage marker) in cells isolated from BAL were assessed using RT-qPCR. In addition, immunofluorescence studies and flow cytometry analyses were performed to evaluate the expression of M1 (CD86) or M2 (CD206) markers in BAL macrophages.Table 1.Patient characteristicsno ILDILDNumber of patients87Age57 (51-68)60 (53-73)Female75%57%Raynauds phenomenon100%85%Age start of Raynauds36 (22-53)56 (41-66)Age start of non-Raynauds50 (33-60)49 (36-68)Skin thickening50%43%Digital ulcer at this moment0%29%Digital ulcer in the past38%29%Pitting scars38%43%Telangiectasia50%43%Calcinosis13%29%Cardiac25%14%Gastro-intestinal88%43%Kidney0%0%ResultsMacrophages were the predominant immune cell population in BAL of SSc patients (73%). The levels of CCL18, CCR2 and CXCL10 were slightly elevated in the SSc-ILD group compared to the SSc-no-ILD (Figure 1.1). RT-qPCR data showed that CD86 expression was elevated in the SSc-ILD group while no difference was observed in CD206 expression between the two groups (data not shown). The SSc-ILD group had higher proportions of double-positive (CD86+, CD206+) macrophages than SSc-no-ILD which, in contrast, had higher proportions of CD86+, CD206- macrophages (Figure 1.2). These results were supported by fluorescent microscopy images in which the SSc-ILD group had higher CD86 and CD206 expression than the SSc-no-ILD (Figure 1.3). Double staining clearly showed a more prevalent mixed activation of macrophages in the SSc-ILD group.ConclusionIn this pilot study, recruitment and activation of mixed phenotype macrophages was more prominent in SSc-ILD than in SSc-no-ILD. Although levels of chemokines were not profoundly different between both groups, studying extensively the macrophage activation patterns in BAL provided novel findings regarding differences between the two groups. Since SSc is characterised by inflammatory and fibrotic phases, the mixed polarization of macrophages we showed for the first time in SSc-ILD patients on an organ level is a key aspect in such disease and could potentially serve as a target for therapeutics.References[1]Perelas A, Silver RM, Arrossi AV, Highland KB. Systemic sclerosis-associated interstitial lung disease. Lancet Respir Med. 2020;8(3):304-320. doi:10.1016/S2213-2600(19)30480-1[2]Schmidt K, Martinez-Gamboa L, Meier S, et al. Bronchoalveoloar lavage fluid cytokines and chemokines as markers and predictors for the outcome of interstitial lung disease in systemic sclerosis patients. Arthritis Res Ther. 2009;11(4):R111. doi:10.1186/ar2766Disclosure of InterestsYehya Al-Adwi: None declared, Tji-Joong Gan: None declared, Janneke Bosma: None declared, Wayel Abdulahad: None declared, Isabella M. Atzeni: None declared, Marcel Van der Leij: None declared, Bart-Jan Kroesen: None declared, Alja J. Stel: None declared, Wim Timens: None declared, Janette Burgess: None declared, Harry van Goor: None declared, Johanna Westra: None declared, Douwe J Mulder Grant/research support from: Dr. DJ Mulder as an employee of the UMCG received research grants from Sanofi Genzyme which were paid to the UMCG
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van Nijnatten J, Brandsma CA, Steiling K, Hiemstra PS, Timens W, van den Berge M, Faiz A. High miR203a-3p and miR-375 expression in the airways of smokers with and without COPD. Sci Rep 2022; 12:5610. [PMID: 35379844 PMCID: PMC8980043 DOI: 10.1038/s41598-022-09093-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Smoking is a leading cause of chronic obstructive pulmonary disease (COPD). It is known to have a significant impact on gene expression and (inflammatory) cell populations in the airways involved in COPD pathogenesis. In this study, we investigated the impact of smoking on the expression of miRNAs in healthy and COPD individuals. We aimed to elucidate the overall smoking-induced miRNA changes and those specific to COPD. In addition, we investigated the downstream effects on regulatory gene expression and the correlation to cellular composition. We performed a genome-wide miRNA expression analysis on a dataset of 40 current- and 22 ex-smoking COPD patients and a dataset of 35 current- and 38 non-smoking respiratory healthy controls and validated the results in an independent dataset. miRNA expression was then correlated with mRNA expression in the same patients to assess potential regulatory effects of the miRNAs. Finally, cellular deconvolution analysis was used to relate miRNAs changes to specific cell populations. Current smoking was associated with increased expression of three miRNAs in the COPD patients and 18 miRNAs in the asymptomatic smokers compared to respiratory healthy controls. In comparison, four miRNAs were lower expressed with current smoking in asymptomatic controls. Two of the three smoking-related miRNAs in COPD, miR-203a-3p and miR-375, were also higher expressed with current smoking in COPD patients and the asymptomatic controls. The other smoking-related miRNA in COPD patients, i.e. miR-31-3p, was not present in the respiratory healthy control dataset. miRNA-mRNA correlations demonstrated that miR-203a-3p, miR-375 and also miR-31-3p expression were negatively associated with genes involved in pro-inflammatory pathways and positively associated with genes involved in the xenobiotic pathway. Cellular deconvolution showed that higher levels of miR-203a-3p were associated with higher proportions of proliferating-basal cells and secretory (club and goblet) cells and lower levels of fibroblasts, luminal macrophages, endothelial cells, B-cells, amongst other cell types. MiR-375 expression was associated with lower levels of secretory cells, ionocytes and submucosal cells, but higher levels of endothelial cells, smooth muscle cells, and mast cells, amongst other cell types. In conclusion, we identified two smoking-induced miRNAs (miR-375 and miR-203a-3p) that play a role in regulating inflammation and detoxification pathways, regardless of the presence or absence of COPD. Additionally, in patients with COPD, we identified miR-31-3p as a miRNA induced by smoking. Our identified miRNAs should be studied further to unravel which smoking-induced inflammatory mechanisms are reactive and which are involved in COPD pathogenesis.
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Koopman B, Kuijpers CCHJ, Groen HJM, Timens W, Schuuring E, Willems SM, van Kempen LC. Detection of NTRK Fusions and TRK Expression and Performance of pan-TRK Immunohistochemistry in Routine Diagnostics: Results from a Nationwide Community-Based Cohort. Diagnostics (Basel) 2022; 12:diagnostics12030668. [PMID: 35328221 PMCID: PMC8946871 DOI: 10.3390/diagnostics12030668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 02/16/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Gene fusions involving NTRK1, NTRK2, and NTRK3 are rare drivers of cancer that can be targeted with histology-agnostic inhibitors. This study aimed to determine the nationwide landscape of NTRK/TRK testing in the Netherlands and the usage of pan-TRK immunohistochemistry (IHC) as a preselection tool to detect NTRK fusions. All pathology reports in 2017–2020 containing the search term ‘TRK’ were retrieved from the Dutch Pathology Registry (PALGA). Patient characteristics, tumor histology, NTRK/TRK testing methods, and reported results were extracted. NTRK/TRK testing was reported for 7457 tumors. Absolute testing rates increased from 815 (2017) to 3380 (2020). Tumors were tested with DNA/RNA-based molecular assay(s) (48%), IHC (47%), or in combination (5%). A total of 69 fusions involving NTRK1 (n = 22), NTRK2 (n = 6) and NTRK3 (n = 41) were identified in tumors from adult (n = 51) and pediatric (n = 18) patients. In patients tested with both IHC and a molecular assay (n = 327, of which 29 NTRK fusion-positive), pan-TRK IHC had a sensitivity of 77% (95% confidence interval (CI), 56–91) and a specificity of 84% (95% CI, 78–88%). These results showed that pan-TRK IHC has a low sensitivity in current routine practice and warrants the introduction of quality guidelines regarding the implementation and interpretation of pan-TRK IHC.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | | | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands;
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
- Correspondence: ; Tel.: +31-50-361-5129
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de Vries M, Nwozor KO, Muizer K, Wisman M, Timens W, van den Berge M, Faiz A, Hackett TL, Heijink IH, Brandsma CA. The relation between age and airway epithelial barrier function. Respir Res 2022; 23:43. [PMID: 35241091 PMCID: PMC8892715 DOI: 10.1186/s12931-022-01961-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 10/22/2021] [Accepted: 02/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background The prevalence of age-associated diseases, such as chronic obstructive pulmonary disease (COPD), is increasing as the average life expectancy increases around the world. We previously identified a gene signature for ageing in the human lung which included genes involved in apical and tight junction assembly, suggesting a role for airway epithelial barrier dysfunction with ageing. Aim To investigate the association between genes involved in epithelial barrier function and age both in silico and in vitro in the airway epithelium. Methods We curated a gene signature of 274 genes for epithelial barrier function and tested the association with age in two independent cohorts of bronchial brushings from healthy individuals with no respiratory disease, using linear regression analysis (FDR < 0.05). Protein–protein interactions were identified using STRING©. The barrier function of primary bronchial epithelial cells at air–liquid interface and CRISPR–Cas9-induced knock-down of target genes in human bronchial 16HBE14o-cells was assessed using Trans epithelial resistance (TER) measurement and Electric cell-surface impedance sensing (ECIS) respectively. Results In bronchial brushings, we found 55 genes involved in barrier function to be significantly associated with age (FDR < 0.05). EPCAM was most significantly associated with increasing age and TRPV4 with decreasing age. Protein interaction analysis identified CDH1, that was negatively associated with higher age, as potential key regulator of age-related epithelial barrier function changes. In vitro, barrier function was lower in bronchial epithelial cells from subjects > 45 years of age and significantly reduced in CDH1-deficient 16HBE14o-cells. Conclusion The significant association between genes involved in epithelial barrier function and age, supported by functional studies in vitro, suggest a role for epithelial barrier dysfunction in age-related airway disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-01961-7.
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Affiliation(s)
- M de Vries
- University Medical Center Groningen, University of Groningen, Department of Epidemiology, Hanzeplein 1, 9713, Groningen, The Netherlands. .,University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.
| | - K O Nwozor
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,Department of Anesthesiology, Pharmacology & Therapeutics, Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - K Muizer
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - M Wisman
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - W Timens
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - M van den Berge
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pulmonary Diseases, Groningen, The Netherlands
| | - A Faiz
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pulmonary Diseases, Groningen, The Netherlands
| | - T-L Hackett
- Department of Anesthesiology, Pharmacology & Therapeutics, Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - I H Heijink
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pulmonary Diseases, Groningen, The Netherlands
| | - C A Brandsma
- University Medical Center Groningen, University of Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
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40
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Hermans BCM, Derks JL, Hillen LM, van der Baan I, van den Broek EC, von der Thüsen JH, van Suylen R, Atmodimedjo PN, den Toom TD, Coumans‐Stallinga C, Timens W, Dinjens WNM, Dubbink HJ, Speel EM, Dingemans AC. In-depth molecular analysis of combined and co-primary pulmonary large cell neuroendocrine carcinoma and adenocarcinoma. Int J Cancer 2022; 150:802-815. [PMID: 34674268 PMCID: PMC9298697 DOI: 10.1002/ijc.33853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/31/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 01/09/2023]
Abstract
Up to 14% of large cell neuroendocrine carcinomas (LCNECs) are diagnosed in continuity with nonsmall cell lung carcinoma. In addition to these combined lesions, 1% to 7% of lung tumors present as co-primary tumors with multiple synchronous lesions. We evaluated molecular and clinicopathological characteristics of combined and co-primary LCNEC-adenocarcinoma (ADC) tumors. Ten patients with LCNEC-ADC (combined) and five patients with multiple synchronous ipsilateral LCNEC and ADC tumors (co-primary) were included. DNA was isolated from distinct tumor parts, and 65 cancer genes were analyzed by next generation sequencing. Immunohistochemistry was performed including neuroendocrine markers, pRb, Ascl1 and Rest. Pure ADC (N = 37) and LCNEC (N = 17) cases were used for reference. At least 1 shared mutation, indicating tumor clonality, was found in LCNEC- and ADC-parts of 10/10 combined tumors but only in 1/5 co-primary tumors. A range of identical mutations was observed in both parts of combined tumors: 8/10 contained ADC-related (EGFR/KRAS/STK11 and/or KEAP1), 4/10 RB1 and 9/10 TP53 mutations. Loss of pRb IHC was observed in 6/10 LCNEC- and 4/10 ADC-parts. The number and intensity of expression of Ascl1 and neuroendocrine markers increased from pure ADC (low) to combined ADC (intermediate) and combined and pure LCNEC (high). The opposite was true for Rest expression. In conclusion, all combined LCNEC-ADC tumors were clonally related indicating a common origin. A relatively high frequency of pRb inactivation was observed in both LCNEC- and ADC-parts, suggesting an underlying role in LCNEC-ADC development. Furthermore, neuroendocrine differentiation might be modulated by Ascl1(+) and Rest(-) expression.
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Affiliation(s)
- Bregtje C. M. Hermans
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Jules L. Derks
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Lisa M. Hillen
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Irene van der Baan
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | | | - Jan H. von der Thüsen
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | | | - Peggy N. Atmodimedjo
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - T. Dorine den Toom
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Cecile Coumans‐Stallinga
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Winand N. M. Dinjens
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Hendrikus J. Dubbink
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Ernst‐Jan M. Speel
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Anne‐Marie C. Dingemans
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PulmonologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
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41
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van Velthuysen MLF, van Eeden S, le Cessie S, de Boer M, van Boven H, Koomen BM, Roozekrans F, Bart J, Timens W, Voorham QJM. Impact of COVID-19 pandemic on diagnostic pathology in the Netherlands. BMC Health Serv Res 2022; 22:166. [PMID: 35139847 PMCID: PMC8826665 DOI: 10.1186/s12913-022-07546-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 06/13/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic has a huge impact on healthcare provided. The nationwide pathology registry of the Netherlands, PALGA, offers an outstanding opportunity to measure this impact for diseases in which pathology examinations are involved. METHODS Pathology specimen numbers in 2020 were compared with specimen numbers in 2019 for 5 periods of 4 weeks, representing two lockdowns and the periods in between, taking into account localization, procedure and benign versus malignant diagnosis. RESULTS The largest decrease was seen during the first lockdown (spring 2020), when numbers of pathology reports declined up to 88% and almost all specimen types were affected. Afterwards each specimen type showed its own dynamics with a decrease during the second lockdown for some, while for others numbers remained relatively low during the whole year. Generally, for most tissue types resections, cytology and malignant diagnoses showed less decrease than biopsies and benign diagnoses. A significant but small catch-up (up to 17%) was seen for benign cervical cytology, benign resections of the lower gastro-intestinal tract, malignant skin resections and gallbladder resections. CONCLUSION The COVID-19 pandemic has had a significant effect on pathology diagnostics in 2020. This effect was most pronounced during the first lockdown, diverse for different anatomical sites and for cytology compared with histology. The data presented here can help to assess the consequences on (public) health and provide a starting point in the discussion on how to make the best choices in times of scarce healthcare resources, considering the impact of both benign and malignant disease on quality of life.
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Affiliation(s)
| | - S van Eeden
- Department of Pathology, Erasmus Medical Center, Rotterdam, Netherlands
| | - S le Cessie
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - M de Boer
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - H van Boven
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - B M Koomen
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - F Roozekrans
- Laboratory of Pathology Oost Nederland (LABPON), Hengelo, Netherlands
| | - J Bart
- Dutch Society of Pathology (NVVP), Leiden, Netherlands.,Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - W Timens
- Dutch Society of Pathology (NVVP), Leiden, Netherlands.,Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Q J M Voorham
- Pathologisch Anatomisch Landelijk Geautomatiseerd Archief (PALGA), Houten, Netherlands
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42
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Ditz B, Boekhoudt J, Couto N, Brandsma CA, Hiemstra PS, Tew GW, Neighbors M, Grimbaldeston MA, Timens W, Kerstjens HAM, Rossen JWA, Guryev V, van den Berge M, Faiz A. The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach. COPD 2022; 19:81-87. [PMID: 35118915 DOI: 10.1080/15412555.2022.2033193] [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: 10/19/2022]
Abstract
Current knowledge about the respiratory microbiome is mainly based on 16S ribosomal RNA gene sequencing. Newer sequencing approaches, such as metatranscriptomics, offer the technical ability to measure the viable microbiome response to environmental conditions such as smoking as well as to explore its functional role by investigating host-microbiome interactions. However, knowledge about its feasibility in respiratory microbiome research, especially in lung biopsies, is still very limited. RNA sequencing was performed in bronchial biopsies from clinically stable smokers (n = 5) and ex-smokers (n = 6) with COPD not using (inhaled) steroids. The Trinity assembler was used to assemble non-human reads in order to allow unbiased taxonomical and microbial transcriptional analyses. Subsequently, host-microbiome interactions were analyzed based on associations with host transcriptomic data. Ultra-low levels of microbial mass (0.009%) were identified in the RNA-seq data. Overall, no differences were identified in microbiome diversity or transcriptional profiles of microbial communities or individual microbes between COPD smokers and ex-smokers in the initial test dataset as well as a larger replication dataset. We identified an upregulated host gene set, related to the simultaneous presence of Bradyrhizobium, Roseomonas, Brevibacterium.spp., which were related to PERK-mediated unfolded protein response (UPR) and expression of the microRNA-155-5p. Our results show that metatranscriptomic profiling in bronchial biopsy samples from stable COPD patients yields ultra-low levels of microbial mass. Further, this study illustrates the potential of using transcriptional profiling of the host and microbiome to gain more insight into their interaction in the airways.
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Affiliation(s)
- B Ditz
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - J Boekhoudt
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - N Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - C A Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - G W Tew
- OMNI-Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | - M Neighbors
- OMNI-Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | - M A Grimbaldeston
- OMNI-Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | - W Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - H A M Kerstjens
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - J W A Rossen
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,IDbyDNA Inc, Salt Lake City, UT, USA.,University of Utah School of Medicine, Department of Pathology, Salt Lake City, UT, USA
| | - V Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - A Faiz
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.,Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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43
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Aliee H, Massip F, Qi C, Stella de Biase M, Nijnatten J, Kersten ETG, Kermani NZ, Khuder B, Vonk JM, Vermeulen RCH, Neighbors M, Tew GW, Grimbaldeston MA, Hacken NHT, Hu S, Guo Y, Zhang X, Sun K, Hiemstra PS, Ponder BA, Mäkelä MJ, Malmström K, Rintoul RC, Reyfman PA, Theis FJ, Brandsma C, Adcock IM, Timens W, Xu C, Berge M, Schwarz RF, Koppelman GH, Nawijn M, Faiz A. Determinants of expression of SARS-CoV-2 entry-related genes in upper and lower airways. Allergy 2022; 77:690-694. [PMID: 34698405 PMCID: PMC8652715 DOI: 10.1111/all.15152] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/19/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022]
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44
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Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J 2022; 60:13993003.02057-2021. [PMID: 35086829 PMCID: PMC9386332 DOI: 10.1183/13993003.02057-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions. The discovAIR project contributes to the Human Cell Atlas Lung Biological Network by establishing a first draft of the Human Lung Cell Atlas, advancing our insight into the cellular complexity and spatial organisation of the lung in health and diseasehttps://bit.ly/3zX4cad
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Affiliation(s)
- Malte D Luecken
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Laure-Emmanuelle Zaragozi
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.,These authors made an equal contribution to this manuscript
| | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,These authors made an equal contribution to this manuscript
| | - Lisa Sikkema
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Alexandra B Firsova
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Louis Kümmerle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Janine Schniering
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Christoph H Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Sarah Teichmann
- Wellcome Sanger Institute, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK
| | - Karen van Eunen
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,UMCG Research BV, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Sylvie Leroy
- Département de Pneumologie, Université Côte d'Azur and CHU Nice, FHU-OncoAge, Nice, France
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Maarten van den Berge
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Peter Horváth
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Joachim Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Herbert B Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Pascal Barbry
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Ilya Petoukhov
- A Beta World (former Principal at MIcompany), Amsterdam, the Netherlands
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ian Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Christos Samakovlis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands .,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
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45
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Weber S, van der Leest P, Donker HC, Schlange T, Timens W, Tamminga M, Hasenleithner SO, Graf R, Moser T, Spiegl B, Yaspo ML, Terstappen LWMM, Sidorenkov G, Hiltermann TJN, Speicher MR, Schuuring E, Heitzer E, Groen HJM. Dynamic Changes of Circulating Tumor DNA Predict Clinical Outcome in Patients With Advanced Non-Small-Cell Lung Cancer Treated With Immune Checkpoint Inhibitors. JCO Precis Oncol 2022; 5:1540-1553. [PMID: 34994642 DOI: 10.1200/po.21.00182] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PURPOSE Immune checkpoint inhibitors (ICIs) are increasingly being used in non-small-cell lung cancer (NSCLC), yet biomarkers predicting their benefit are lacking. We evaluated if on-treatment changes of circulating tumor DNA (ctDNA) from ICI start (t0) to after two cycles (t1) assessed with a commercial panel could identify patients with NSCLC who would benefit from ICI. PATIENTS AND METHODS The molecular ctDNA response was evaluated as a predictor of radiographic tumor response and long-term survival benefit of ICI. To maximize the yield of ctDNA detection, de novo mutation calling was performed. Furthermore, the impact of clonal hematopoiesis (CH)-related variants as a source of biologic noise was investigated. RESULTS After correction for CH-related variants, which were detected in 75 patients (44.9%), ctDNA was detected in 152 of 167 (91.0%) patients. We observed only a fair agreement of the molecular and radiographic response, which was even more impaired by the inclusion of CH-related variants. After exclusion of those, a ≥ 50% molecular response improved progression-free survival (10 v 2 months; hazard ratio [HR], 0.55; 95% CI, 0.39 to 0.77; P = .0011) and overall survival (18.4 v 5.9 months; HR, 0.44; 95% CI, 0.31 to 0.62; P < .0001) compared with patients not achieving this end point. After adjusting for clinical variables, ctDNA response and STK11/KEAP1 mutations (HR, 2.08; 95% CI, 1.4 to 3.0; P < .001) remained independent predictors for overall survival, irrespective of programmed death ligand-1 expression. A landmark survival analysis at 2 months (n = 129) provided similar results. CONCLUSION On-treatment changes of ctDNA in plasma reveal predictive information for long-term clinical benefit in ICI-treated patients with NSCLC. A broader NSCLC patient coverage through de novo mutation calling and the use of a variant call set excluding CH-related variants improved the classification of molecular responders, but had no significant impact on survival.
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Affiliation(s)
- Sabrina Weber
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Paul van der Leest
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Hylke C Donker
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Menno Tamminga
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | - Samantha O Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Benjamin Spiegl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Marie-Laure Yaspo
- Max Plank Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Berlin, Germany
| | | | - Grigory Sidorenkov
- Department of Epidemiology, University Medical Center Groningen, Groningen, the Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Harry J M Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
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46
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van der Leest P, Hiddinga B, Miedema A, Aguirre Azpurua ML, Rifaela N, ter Elst A, Timens W, Groen HJM, van Kempen LC, Hiltermann TJN, Schuuring E. Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors. Mol Oncol 2021; 15:2910-2922. [PMID: 34449963 PMCID: PMC8564646 DOI: 10.1002/1878-0261.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/07/2022] Open
Abstract
Immunotherapy for metastasized non-small-cell lung cancer (NSCLC) can show long-lasting clinical responses. Selection of patients based on programmed death-ligand 1 (PD-L1) expression shows limited predictive value for durable clinical benefit (DCB). We investigated whether early treatment effects as measured by a change in circulating tumor DNA (ctDNA) level is a proxy of early tumor response to immunotherapy according to response evaluation criteria in solid tumors v1.1 criteria, progression-free survival (PFS), DCB, and overall survival (OS). To this aim, blood tubes were collected from advanced-stage lung adenocarcinoma patients (n = 100) receiving immune checkpoint inhibitors (ICI) at baseline (t0 ) and prior to first treatment evaluation (4-6 weeks; t1 ). Nontargetable (driver) mutations detected in the pretreatment tumor biopsy were used to quantify tumor-specific ctDNA levels using droplet digital PCR. We found that changes in ctDNA levels were strongly associated with tumor response. A > 30% decrease in ctDNA at t1 correlated with a longer PFS and OS. In total, 80% of patients with a DCB of ≥ 26 weeks displayed a > 30% decrease in ctDNA levels. For patients with a PD-L1 tumor proportion score of ≥ 1%, decreasing ctDNA levels were associated with a higher frequency a DCB (80%) and a prolonged median PFS (85 weeks) and OS (101 weeks) compared with patients with no decrease in ctDNA (34%; 11 and 39 weeks, respectively). This study shows that monitoring of ctDNA dynamics is an easy-to-use and promising tool for assessing PFS, DCB, and OS for ICI-treated NSCLC patients.
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Affiliation(s)
- Paul van der Leest
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Birgitta Hiddinga
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Anneke Miedema
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Maria L. Aguirre Azpurua
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Naomi Rifaela
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Arja ter Elst
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Wim Timens
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Harry J. M. Groen
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Léon C. van Kempen
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Ed Schuuring
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
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47
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Gijtenbeek RG, Van Noort V, Aerts J, Staal - Van Den Brekel J, Smit E, Krouwels F, Wilschut F, Hilterman T, Timens W, Schuuring E, Janssen J, Goosens M, Van De Berg P, De Langen A, Stigt J, Van Den Borne B, Groen H, Van Geffen W, Van Der Wekken A. Late Breaking Abstract - Randomized phase III study of erlotinib compared to intercalated erlotinib with cisplatin and pemetrexed as first-line therapy for advanced EGFR mutated non-small cell lung cancer, the NVALT 17 study. Lung Cancer 2021. [DOI: 10.1183/13993003.congress-2021.oa4324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Roffel MP, Boudewijn IM, van Nijnatten JLL, Faiz A, Vermeulen CJ, van Oosterhout AJ, Affleck K, Timens W, Bracke KR, Maes T, Heijink IH, Brandsma CA, van den Berge M. Identification of asthma associated microRNAs in bronchial biopsies. Eur Respir J 2021; 59:13993003.01294-2021. [PMID: 34446467 DOI: 10.1183/13993003.01294-2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/30/2021] [Indexed: 11/05/2022]
Abstract
Changes in microRNA (miRNA) expression can contribute to the pathogenesis of many diseases, including asthma. We aimed to identify miRNAs that are differentially expressed between asthma patients and healthy controls and explored their association with clinical and inflammatory parameters of asthma.Differentially expressed miRNAs were determined by small RNA sequencing on bronchial biopsies of 79 asthma patients and 82 healthy controls using linear regression models. Differentially expressed miRNAs were associated with clinical and inflammatory asthma features. Potential miRNA-mRNA interactions were analysed using mRNA data available from the same bronchial biopsies and enrichment of pathways was identified with Enrichr and g:Profiler.In total 78 differentially expressed miRNAs were identified in bronchial biopsies of asthma patients compared to controls, of which 60 remained differentially expressed after controlling for smoke and inhaled corticosteroid treatment. We identified several asthma associated miRNAs, including miR-125b-5p and miR-223-3p, based on a significant association with multiple clinical and inflammatory asthma features and their negative correlation with genes associated with the presence of asthma. The most enriched biological pathway(s) affected by miR-125b-5p and miR-223-3p were inflammatory response and cilium assembly and organisation. Of interest, we identified that lower expression of miR-26a-5p was linked to more severe eosinophilic inflammation as measured in blood, sputum as well as bronchial biopsies. Collectively, we identified miR-125b-5p, miR-223-3p and miR-26a-5p, as potential regulators that could contribute to the pathogenesis of asthma.
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Affiliation(s)
- Mirjam P Roffel
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Respiratory Medicine, Ghent University, University Hospital Ghent, Laboratory for Translational Research in Obstructive Pulmonary Diseases, Ghent, Belgium
| | - Ilse M Boudewijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jos L L van Nijnatten
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Faculty of Science, Respiratory Bioinformatics and Molecular Biology (RBMB), University of Technology Sydney, Sydney, Australia
| | - Alen Faiz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Faculty of Science, Respiratory Bioinformatics and Molecular Biology (RBMB), University of Technology Sydney, Sydney, Australia
| | - Corneel J Vermeulen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Antoon J van Oosterhout
- Allergic Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Karen Affleck
- Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Ken R Bracke
- Department of Respiratory Medicine, Ghent University, University Hospital Ghent, Laboratory for Translational Research in Obstructive Pulmonary Diseases, Ghent, Belgium
| | - Tania Maes
- Department of Respiratory Medicine, Ghent University, University Hospital Ghent, Laboratory for Translational Research in Obstructive Pulmonary Diseases, Ghent, Belgium
| | - Irene H Heijink
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Both senior authors contributed equally
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands .,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Both senior authors contributed equally
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49
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Thunnissen E, Motoi N, Minami Y, Matsubara D, Timens W, Nakatani Y, Ishikawa Y, Baez-Navarro X, Radonic T, Blaauwgeers H, Borczuk AC, Noguchi M. Elastin in pulmonary pathology: relevance in tumors with lepidic or papillary appearance. A comprehensive understanding from a morphological viewpoint. Histopathology 2021; 80:457-467. [PMID: 34355407 PMCID: PMC9293161 DOI: 10.1111/his.14537] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 10/14/2020] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Elastin and collagen are the main components of the lung connective tissue network, and together provide the lung with elasticity and tensile strength. In pulmonary pathology, elastin staining is used to variable extents in different countries. These uses include evaluation of the pleura in staging, and the distinction of invasion from collapse of alveoli after surgery (iatrogenic collapse). In the latter, elastin staining is used to highlight distorted but pre‐existing alveolar architecture from true invasion. In addition to variable levels of use and experience, the interpretation of elastin staining in some adenocarcinomas leads to interpretative differences between collapsed lepidic patterns and true papillary patterns. This review aims to summarise the existing data on the use of elastin staining in pulmonary pathology, on the basis of literature data and morphological characteristics. The effect of iatrogenic collapse and the interpretation of elastin staining in pulmonary adenocarcinomas is discussed in detail, especially for the distinction between lepidic patterns and papillary carcinoma.
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Affiliation(s)
- Erik Thunnissen
- Department of Pathology, Amsterdam University Medical Center, location VUmc, Amsterdam, the Netherlands
| | - Noriko Motoi
- Dept. of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuko Minami
- National Organization Hospital Ibarakihigashi National Hospital, The Center of Chest Diseases and Severe Motor & Intellectual Disabilities, Pathology Department, Tokai-mura, Naka-gun, Ibaraki, Japan
| | - Daisuke Matsubara
- Division of Integrative Pathology, Jichi Medical University, Tochigi, Japan
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Yukio Nakatani
- Department of Pathology, Yokosuka Kyosai Hospital, Yokosuka, Japan
| | - Yuichi Ishikawa
- Department of Pathology, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | | | - Teodora Radonic
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Hans Blaauwgeers
- Department of Pathology, OLVG LAB BV, Amsterdam, the Netherlands
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Masayuki Noguchi
- Department of Pathology, Institute of Basic Medical Sciences, University of Tsukuba, Tsukuba, Japan
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50
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Koopman B, Groen HJ, Ligtenberg MJ, Grünberg K, Monkhorst K, de Langen AJ, Boelens MC, Paats MS, von der Thüsen JH, Dinjens WN, Solleveld N, van Wezel T, Gelderblom H, Hendriks LE, Speel EM, Theunissen TE, Kroeze LI, Mehra N, Piet B, van der Wekken AJ, ter Elst A, Timens W, Willems SM, Meijers RW, de Leng WW, van Lindert AS, Radonic T, Hashemi SM, Heideman DA, Schuuring E, van Kempen LC. Multicenter Comparison of Molecular Tumor Boards in The Netherlands: Definition, Composition, Methods, and Targeted Therapy Recommendations. Oncologist 2021; 26:e1347-e1358. [PMID: 33111480 PMCID: PMC8342588 DOI: 10.1002/onco.13580] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 05/26/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Molecular tumor boards (MTBs) provide rational, genomics-driven, patient-tailored treatment recommendations. Worldwide, MTBs differ in terms of scope, composition, methods, and recommendations. This study aimed to assess differences in methods and agreement in treatment recommendations among MTBs from tertiary cancer referral centers in The Netherlands. MATERIALS AND METHODS MTBs from all tertiary cancer referral centers in The Netherlands were invited to participate. A survey assessing scope, value, logistics, composition, decision-making method, reporting, and registration of the MTBs was completed through on-site interviews with members from each MTB. Targeted therapy recommendations were compared using 10 anonymized cases. Participating MTBs were asked to provide a treatment recommendation in accordance with their own methods. Agreement was based on which molecular alteration(s) was considered actionable with the next line of targeted therapy. RESULTS Interviews with 24 members of eight MTBs revealed that all participating MTBs focused on rare or complex mutational cancer profiles, operated independently of cancer type-specific multidisciplinary teams, and consisted of at least (thoracic and/or medical) oncologists, pathologists, and clinical scientists in molecular pathology. Differences were the types of cancer discussed and the methods used to achieve a recommendation. Nevertheless, agreement among MTB recommendations, based on identified actionable molecular alteration(s), was high for the 10 evaluated cases (86%). CONCLUSION MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational cancer profiles. We propose a "Dutch MTB model" for an optimal, collaborative, and nationally aligned MTB workflow. IMPLICATIONS FOR PRACTICE Interpretation of genomic analyses for optimal choice of target therapy for patients with cancer is becoming increasingly complex. A molecular tumor board (MTB) supports oncologists in rationalizing therapy options. However, there is no consensus on the most optimal setup for an MTB, which can affect the quality of recommendations. This study reveals that the eight MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational profiles. The Dutch MTB model is based on a collaborative and nationally aligned workflow with interinstitutional collaboration and data sharing.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Harry J.M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marjolijn J.L. Ligtenberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
- Department of Human Genetics, Radboud University Medical CenterNijmegenThe Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Adrianus J. de Langen
- Department of Thoracic Oncology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mirjam C. Boelens
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Marthe S. Paats
- Department of Pulmonary Medicine, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Jan H. von der Thüsen
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Winand N.M. Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Nienke Solleveld
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Tom van Wezel
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical CenterLeidenThe Netherlands
| | - Lizza E. Hendriks
- Department of Pulmonary Diseases, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Ernst‐Jan M. Speel
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Tom E. Theunissen
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical CenterNijmegenThe Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Ruud W.J. Meijers
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Wendy W.J. de Leng
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | | | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sayed M.S. Hashemi
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Daniëlle A.M. Heideman
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
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