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Karp T, Faiz A, van Nijnatten J, Kerstjens HAM, Boudewijn I, Kraft M, Vonk JM, Nawijn MC, Heijink IH, Beghé B, Rabe KF, Papi A, Brightling C, Singh D, van der Molen T, Siddiqui S, Christenson S, Guryev V, van den Berge M. Nasal epithelial gene expression identifies relevant asthma endotypes in the ATLANTIS study. Thorax 2024:thorax-2023-221230. [PMID: 39009441 DOI: 10.1136/thorax-2023-221230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/18/2024] [Indexed: 07/17/2024]
Abstract
INTRODUCTION Asthma is an inflammatory airways disease encompassing multiple phenotypes and endotypes. Several studies suggested gene expression in nasal epithelium to serve as a proxy for bronchial epithelium, being a non-invasive approach to investigate lung diseases. We hypothesised that molecular differences in upper airway epithelium reflect asthma-associated differences in the lower airways and are associated with clinical expression of asthma. METHODS We analysed nasal epithelial gene expression data from 369 patients with asthma and 58 non-asthmatic controls from the Assessment of Small Airways Involvement in Asthma study. Unsupervised hierarchical clustering was performed on asthma-associated genes. Asthma-associated gene signatures were replicated in independent cohorts with nasal and bronchial brushes data by comparing Gene Set Variation Analysis scores between asthma patients and non-asthmatic controls. RESULTS We identified 67 higher expressed and 59 lower expressed genes in nasal epithelium from asthma patients compared with controls (false discovery rate<0.05), including CLCA1, CST1 and POSTN, genes well known to reflect asthma in bronchial airway epithelium. Hierarchical clustering revealed several molecular asthma endotypes with distinct clinical characteristics, including an endotype with higher blood and sputum eosinophils, high fractional exhaled nitric oxide, and more severe small airway dysfunction, as reflected by lower forced expiratory flow at 50%. In an independent cohort, we demonstrated that genes higher expressed in the nasal epithelium reflect asthma-associated changes in the lower airways. CONCLUSION Our results show that the nasal epithelial gene expression profile reflects asthma-related processes in the lower airways. We suggest that nasal epithelium may be a useful non-invasive tool to identify asthma endotypes and may advance personalised management of the disease.
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Affiliation(s)
- Tatiana Karp
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Jos van Nijnatten
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Huib A M Kerstjens
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Ilse Boudewijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Monica Kraft
- Samuel Bronfman Department of Medicine, Icahn School of Medicine, Mount Sinai Medical Center, New York, New York, USA
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Irene H Heijink
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Bianca Beghé
- Department of Respiratory Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and LungenClinic, Grosshansdorf, Germany
| | - Alberto Papi
- Section of Respiratory Medicine, Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Chris Brightling
- The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dave Singh
- Centre for Respiratory Medicine and Allergy, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Thys van der Molen
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of General Practice and Elderly Care Medicine, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Salman Siddiqui
- Imperial College London National Heart and Lung Institute, London, UK
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, San Francisco, California, USA
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
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Hoyer A, Chakraborty S, Lilienthal I, Konradsen JR, Katayama S, Söderhäll C. The functional role of CST1 and CCL26 in asthma development. Immun Inflamm Dis 2024; 12:e1162. [PMID: 38270326 PMCID: PMC10797655 DOI: 10.1002/iid3.1162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Asthma is the most common chronic disease in children with an increasing prevalence. Its development is caused by genetic and environmental factors and allergic sensitization is a known trigger. Dog allergens affect up to 30% of all children and dog dander-sensitized children show increased expression of cystatin-1 (CST1) and eotaxin-3 (CCL26) in nasal epithelium. The aim of our study was to investigate the functional mechanism of CST1 and CCL26 in the alveolar basal epithelial cell line A549. METHODS A549 cells were transfected with individual overexpression vectors for CST1 and CCL26 and RNA sequencing was performed to examine the transcriptomics. edgeR was used to identify differentially expressed genes (= DEG, |log2 FC | ≥ 2, FDR < 0.01). The protein expression levels of A549 cells overexpressing CST1 and CCL26 were analyzed using the Target 96 inflammation panel from OLINK (antibody-mediated proximity extension-based assay; OLINK Proteomics). Differentially expressed proteins were considered with a |log2 FC| ≥ 1, p < .05. RESULTS The overexpression of CST1 resulted in a total of 27 DEG (1 upregulated and 26 downregulated) and the overexpression of CCL26 in a total of 137 DEG (0 upregulated and 137 downregulated). The gene ontology enrichment analysis showed a significant downregulation of type I and III interferon signaling pathway genes as well as interferon-stimulated genes. At the protein level, overexpression of CST1 induced a significantly increased expression of CCL3, whereas CCL26 overexpression led to increased expression of HGF, and a decrease of CXCL11, CCL20, CCL3 and CXCL10. CONCLUSION Our results indicate that an overexpression of CST1 and CCL26 cause a downregulation of interferon related genes and inflammatory proteins. It might cause a higher disease susceptibility, mainly for allergic asthma, as CCL26 is an agonist for CCR-3-carrying cells, such as eosinophils and Th2 lymphocytes, mostly active in allergic asthma.
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Affiliation(s)
- Angela Hoyer
- Department of Women's and Children's HealthKarolinska InstitutetSolnaSweden
- Astrid Lindgren Children's HospitalKarolinska University HospitalSolnaSweden
| | - Sandip Chakraborty
- Department of Women's and Children's HealthKarolinska InstitutetSolnaSweden
- Astrid Lindgren Children's HospitalKarolinska University HospitalSolnaSweden
| | - Ingrid Lilienthal
- Childhood Cancer Research Unit, Department of Women's and Children's HealthKarolinska InstitutetSolnaSweden
| | - Jon R. Konradsen
- Department of Women's and Children's HealthKarolinska InstitutetSolnaSweden
- Astrid Lindgren Children's HospitalKarolinska University HospitalSolnaSweden
| | - Shintaro Katayama
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Stem Cells and Metabolism Research ProgramUniversity of HelsinkiHelsinkiFinland
- Folkhälsan Research CenterHelsinkiFinland
| | - Cilla Söderhäll
- Department of Women's and Children's HealthKarolinska InstitutetSolnaSweden
- Astrid Lindgren Children's HospitalKarolinska University HospitalSolnaSweden
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El-Husseini ZW, Khalenkow D, Lan A, van der Molen T, Brightling C, Papi A, Rabe KF, Siddiqui S, Singh D, Kraft M, Beghe B, van den Berge M, van Gosliga D, Nawijn MC, Rose-John S, Koppelman GH, Gosens R. An epithelial gene signature of trans-IL-6 signaling defines a subgroup of type 2-low asthma. Respir Res 2023; 24:308. [PMID: 38062491 PMCID: PMC10704725 DOI: 10.1186/s12931-023-02617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Asthma is stratified into type 2-high and type 2-low inflammatory phenotypes. Limited success has been achieved in developing drugs that target type 2-low inflammation. Previous studies have linked IL-6 signaling to severe asthma. IL-6 cooperates with soluble-IL-6Rα to activate cell signaling in airway epithelium. OBJECTIVE We sought to study the role of sIL-6Rα amplified IL-6 signaling in airway epithelium and to develop an IL-6+ sIL-6Rα gene signature that may be used to select asthma patients who potentially respond to anti-IL-6 therapy. METHODS Human airway epithelial cells were stimulated with combinations of IL-6, sIL-6Rα, and inhibitors, sgp130 (Olamkicept), and anti-IL-6R (Tocilizumab), to assess effects on pathway activation, epithelial barrier integrity, and gene expression. A gene signature was generated to identify IL-6 high patients using bronchial biopsies and nasal brushes. RESULTS Soluble-IL-6Rα amplified the activation of the IL-6 pathway, shown by the increase of STAT3 phosphorylation and stronger gene induction in airway epithelial cells compared to IL-6 alone. Olamkicept and Tocilizumab inhibited the effect of IL-6 + sIL-6Rα on gene expression. We developed an IL-6 + sIL-6Rα gene signature and observed enrichment of this signature in bronchial biopsies but not nasal brushes from asthma patients compared to healthy controls. An IL-6 + sIL-6Rα gene signature score was associated with lower levels of sputum eosinophils in asthma. CONCLUSION sIL-6Rα amplifies IL-6 signaling in bronchial epithelial cells. Higher local airway IL-6 + sIL-6Rα signaling is observed in asthma patients with low sputum eosinophils.
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Affiliation(s)
- Zaid W El-Husseini
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Dmitry Khalenkow
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Andy Lan
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Thys van der Molen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Chris Brightling
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Alberto Papi
- Department of Respiratory Medicine, University of Ferrara, Ferrara, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and Lungen Clinic Grosshansdorf (Members of the German Center for Lung Research (DZL)), Grosshansdorf, Germany
| | - Salman Siddiqui
- National Heart and Lung Institute, Imperial College and Imperial NIHR Biomedical Research Centre, London, UK
| | - Dave Singh
- Medicines Evaluation Unit, Manchester University NHS Foundation Hospital Trust, University of Manchester, Manchester, UK
| | - Monica Kraft
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bianca Beghe
- University of Modena and Reggio Emilia, AOU of Modena, Modena, Italy
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Djoke van Gosliga
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Reinoud Gosens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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4
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Rodenburg LW, Metzemaekers M, van der Windt IS, Smits SMA, den Hertog-Oosterhoff LA, Kruisselbrink E, Brunsveld JE, Michel S, de Winter-de Groot KM, van der Ent CK, Stadhouders R, Beekman JM, Amatngalim GD. Exploring intrinsic variability between cultured nasal and bronchial epithelia in cystic fibrosis. Sci Rep 2023; 13:18573. [PMID: 37903789 PMCID: PMC10616285 DOI: 10.1038/s41598-023-45201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
The nasal and bronchial epithelium are unified parts of the respiratory tract that are affected in the monogenic disorder cystic fibrosis (CF). Recent studies have uncovered that nasal and bronchial tissues exhibit intrinsic variability, including differences in mucociliary cell composition and expression of unique transcriptional regulatory proteins which relate to germ layer origin. In the present study, we explored whether intrinsic differences between nasal and bronchial epithelial cells persist in cell cultures and affect epithelial cell functioning in CF. Comparison of air-liquid interface (ALI) differentiated epithelial cells from subjects with CF revealed distinct mucociliary differentiation states of nasal and bronchial cultures. Moreover, using RNA sequencing we identified cell type-specific signature transcription factors in differentiated nasal and bronchial epithelial cells, some of which were already poised for expression in basal progenitor cells as evidenced by ATAC sequencing. Analysis of differentiated nasal and bronchial epithelial 3D organoids revealed distinct capacities for fluid secretion, which was linked to differences in ciliated cell differentiation. In conclusion, we show that unique phenotypical and functional features of nasal and bronchial epithelial cells persist in cell culture models, which can be further used to investigate the effects of tissue-specific features on upper and lower respiratory disease development in CF.
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Affiliation(s)
- Lisa W Rodenburg
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands.
| | - Mieke Metzemaekers
- Department of Pulmonary Medicine, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Isabelle S van der Windt
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Shannon M A Smits
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Loes A den Hertog-Oosterhoff
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Sabine Michel
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Gimano D Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT, Utrecht, The Netherlands
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5
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George PM, Reed A, Desai SR, Devaraj A, Faiez TS, Laverty S, Kanwal A, Esneau C, Liu MKC, Kamal F, Man WDC, Kaul S, Singh S, Lamb G, Faizi FK, Schuliga M, Read J, Burgoyne T, Pinto AL, Micallef J, Bauwens E, Candiracci J, Bougoussa M, Herzog M, Raman L, Ahmetaj-Shala B, Turville S, Aggarwal A, Farne HA, Dalla Pria A, Aswani AD, Patella F, Borek WE, Mitchell JA, Bartlett NW, Dokal A, Xu XN, Kelleher P, Shah A, Singanayagam A. A persistent neutrophil-associated immune signature characterizes post-COVID-19 pulmonary sequelae. Sci Transl Med 2022; 14:eabo5795. [PMID: 36383686 DOI: 10.1126/scitranslmed.abo5795] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Interstitial lung disease and associated fibrosis occur in a proportion of individuals who have recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through unknown mechanisms. We studied individuals with severe coronavirus disease 2019 (COVID-19) after recovery from acute illness. Individuals with evidence of interstitial lung changes at 3 to 6 months after recovery had an up-regulated neutrophil-associated immune signature including increased chemokines, proteases, and markers of neutrophil extracellular traps that were detectable in the blood. Similar pathways were enriched in the upper airway with a concomitant increase in antiviral type I interferon signaling. Interaction analysis of the peripheral phosphoproteome identified enriched kinases critical for neutrophil inflammatory pathways. Evaluation of these individuals at 12 months after recovery indicated that a subset of the individuals had not yet achieved full normalization of radiological and functional changes. These data provide insight into mechanisms driving development of pulmonary sequelae during and after COVID-19 and provide a rational basis for development of targeted approaches to prevent long-term complications.
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Affiliation(s)
- Peter M George
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Anna Reed
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Sujal R Desai
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Anand Devaraj
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Tasnim Shahridan Faiez
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Sarah Laverty
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Amama Kanwal
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Camille Esneau
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Michael K C Liu
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | - William D-C Man
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
- Faculty of Life Sciences and Medicine, King's College London, London WC2R 2LS, UK
| | - Sundeep Kaul
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Suveer Singh
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Georgia Lamb
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Fatima K Faizi
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Michael Schuliga
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jane Read
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Thomas Burgoyne
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andreia L Pinto
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Jake Micallef
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Emilie Bauwens
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Julie Candiracci
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Mhammed Bougoussa
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Marielle Herzog
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Lavanya Raman
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - Stuart Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hugo A Farne
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
- Chest and Allergy Department, St Mary's Hospital, Imperial College NHS Trust, London W2 1NY, UK
| | - Alessia Dalla Pria
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
- Department of HIV and Genitourinary Medicine, Chelsea and Westminster NHS Foundation Trust, London SW10 9NH, UK
| | - Andrew D Aswani
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London SE1 7EH, UK
- Santersus AG, Buckhauserstrasse 34, Zurich 8048, Switzerland
| | - Francesca Patella
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Weronika E Borek
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Jane A Mitchell
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Nathan W Bartlett
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Arran Dokal
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Xiao-Ning Xu
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Peter Kelleher
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- Department of HIV and Genitourinary Medicine, Chelsea and Westminster NHS Foundation Trust, London SW10 9NH, UK
- Immunology of Infection Section, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
- Department of Infection and Immunity Sciences, North West London Pathology NHS Trust, London W2 1NY, UK
| | - Anand Shah
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- MRC Centre of Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Aran Singanayagam
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
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6
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Bernal V, Soancatl-Aguilar V, Bulthuis J, Guryev V, Horvatovich P, Grzegorczyk M. GeneNetTools: tests for Gaussian graphical models with shrinkage. Bioinformatics 2022; 38:5049-5054. [PMID: 36179082 PMCID: PMC9665865 DOI: 10.1093/bioinformatics/btac657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Gaussian graphical models (GGMs) are network representations of random variables (as nodes) and their partial correlations (as edges). GGMs overcome the challenges of high-dimensional data analysis by using shrinkage methodologies. Therefore, they have become useful to reconstruct gene regulatory networks from gene-expression profiles. However, it is often ignored that the partial correlations are 'shrunk' and that they cannot be compared/assessed directly. Therefore, accurate (differential) network analyses need to account for the number of variables, the sample size, and also the shrinkage value, otherwise, the analysis and its biological interpretation would turn biased. To date, there are no appropriate methods to account for these factors and address these issues. RESULTS We derive the statistical properties of the partial correlation obtained with the Ledoit-Wolf shrinkage. Our result provides a toolbox for (differential) network analyses as (i) confidence intervals, (ii) a test for zero partial correlation (null-effects) and (iii) a test to compare partial correlations. Our novel (parametric) methods account for the number of variables, the sample size and the shrinkage values. Additionally, they are computationally fast, simple to implement and require only basic statistical knowledge. Our simulations show that the novel tests perform better than DiffNetFDR-a recently published alternative-in terms of the trade-off between true and false positives. The methods are demonstrated on synthetic data and two gene-expression datasets from Escherichia coli and Mus musculus. AVAILABILITY AND IMPLEMENTATION The R package with the methods and the R script with the analysis are available in https://github.com/V-Bernal/GeneNetTools. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victor Bernal
- Center of Information Technology, University of Groningen, Groningen 9747 AJ, The Netherlands,Department of Mathematics, Bernoulli Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | | | - Jonas Bulthuis
- Center of Information Technology, University of Groningen, Groningen 9747 AJ, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
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7
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Luengen AE, Cheremkhina M, Gonzalez-Rubio J, Weckauf J, Kniebs C, Uebner H, Buhl EM, Taube C, Cornelissen CG, Schmitz-Rode T, Jockenhoevel S, Thiebes AL. Bone Marrow Derived Mesenchymal Stromal Cells Promote Vascularization and Ciliation in Airway Mucosa Tri-Culture Models in Vitro. Front Bioeng Biotechnol 2022; 10:872275. [PMID: 35782511 PMCID: PMC9247357 DOI: 10.3389/fbioe.2022.872275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Patients suffering from irresectable tracheal stenosis often face limited treatment options associated with low quality of life. To date, an optimal tracheal replacement strategy does not exist. A tissue-engineered tracheal substitute promises to overcome limitations such as implant vascularization, functional mucociliary clearance and mechanical stability. In order to advance a tracheal mucosa model recently developed by our group, we examined different supporting cell types in fibrin-based tri-culture with primary human umbilical vein endothelial cells (HUVEC) and primary human respiratory epithelial cells (HRE). Bone marrow-derived mesenchymal stromal cells (BM-MSC), adipose-derived mesenchymal stromal cells (ASC) and human nasal fibroblasts (HNF) were compared regarding their ability to promote mucociliary differentiation and vascularization in vitro. Three-dimensional co-cultures of the supporting cell types with either HRE or HUVEC were used as controls. Mucociliary differentiation and formation of vascular-like structures were analyzed by scanning electron microscopy (SEM), periodic acid Schiff’s reaction (PAS reaction), two-photon laser scanning microscopy (TPLSM) and immunohistochemistry. Cytokine levels of vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), interleukin-6 (IL6), interleukin-8 (IL8), angiopoietin 1, angiopoietin 2, fibroblast growth factor basic (FGF-b) and placenta growth factor (PIGF) in media supernatant were investigated using LEGENDplex™ bead-based immunoassay. Epithelial morphology of tri-cultures with BM-MSC most closely resembled native respiratory epithelium with respect to ciliation, mucus production as well as expression and localization of epithelial cell markers pan-cytokeratin, claudin-1, α-tubulin and mucin5AC. This was followed by tri-cultures with HNF, while ASC-supported tri-cultures lacked mucociliary differentiation. For all supporting cell types, a reduced ciliation was observed in tri-cultures compared to the corresponding co-cultures. Although formation of vascular-like structures was confirmed in all cultures, vascular networks in BM-MSC-tri-cultures were found to be more branched and extended. Concentrations of pro-angiogenic and inflammatory cytokines, in particular VEGF and angiopoietin 2, revealed to be reduced in tri-cultures compared to co-cultures. With these results, our study provides an important step towards a vascularized and ciliated tissue-engineered tracheal replacement. Additionally, our tri-culture model may in the future contribute to an improved understanding of cell-cell interactions in diseases associated with impaired mucosal function.
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Affiliation(s)
- Anja E. Luengen
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
| | - Maria Cheremkhina
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
| | - Julian Gonzalez-Rubio
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
| | - Jan Weckauf
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
| | - Caroline Kniebs
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
| | - Hendrik Uebner
- Department of Pulmonary Medicine, University Medical Center Essen—Ruhrlandklinik, Essen, Germany
| | - E. Miriam Buhl
- Institute of Pathology, Electron Microscopy Facility, RWTH Aachen University Hospital, Aachen, Germany
| | - Christian Taube
- Department of Pulmonary Medicine, University Medical Center Essen—Ruhrlandklinik, Essen, Germany
| | - Christian G. Cornelissen
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Clinic for Pneumology and Internal Intensive Care Medicine (Medical Clinic V), RWTH Aachen University Hospital, Aachen, Germany
| | - Thomas Schmitz-Rode
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
| | - Stefan Jockenhoevel
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
- *Correspondence: Stefan Jockenhoevel, ; Anja Lena Thiebes,
| | - Anja Lena Thiebes
- Department of Biohybrid and Medical Textiles (BioTex), AME - Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Brightlands Chemelot Campus, Geleen, Netherlands
- *Correspondence: Stefan Jockenhoevel, ; Anja Lena Thiebes,
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8
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Nakamura M, Kamiya K, Furuhata A, Ikeda K, Niyonsaba F. S100A7 Co-localization and Up-regulation of Filaggrin in Human Sinonasal Epithelial Cells. Curr Med Sci 2021; 41:863-868. [PMID: 34643881 DOI: 10.1007/s11596-021-2431-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Filaggrin (FLG) is a protein expressed in the epidermis and involved in the maintenance of the epidermal barrier. However, the expression and localization of FLG in the upper airway remain controversial. The present study aimed to determine the significance of FLG and the effect of S100A7 on FLG expression in the upper respiratory mucosa. METHODS Human nasal epithelial cells (HNECs) were cultured and examined for FLG expression and S100A7 effects by real-time polymerase chain reaction and Western blotting. The localization and distribution of FLG were assessed using sinonasal mucosa. RESULTS A significant expression of FLG was detected at the mRNA and protein levels in HNECs. A moderate FLG immunoreactivity was observed in the epithelial cells, but no staining was seen in epithelial goblet cells. S100A7 increased the FLG mRNA level in HNECs in a dose-dependent manner and also up-regulated the FLG protein in a dose-dependent manner. CONCLUSION This study significantly contributes to a better understanding of the role of FLG in the pathogenesis of airway inflammation from the viewpoint of the epithelial barrier function. FLG-related events in response to S100A7 protein may represent novel therapeutic targets for the treatment of upper airway inflammation.
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Affiliation(s)
- Masahiro Nakamura
- Department of Otorhinolaryngology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.,Atopy (Allergy) Research Center, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Kazusaku Kamiya
- Department of Otorhinolaryngology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Atsushi Furuhata
- Biomedical Research Center, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Katsuhisa Ikeda
- Department of Otorhinolaryngology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.
| | - François Niyonsaba
- Atopy (Allergy) Research Center, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.,Faculty of International Liberal Arts, Laboratory of Morphology and Image Analysis, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
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9
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Fransen LFH, Leonard MO. Small Airway Susceptibility to Chemical and Particle Injury. Respiration 2021; 101:321-333. [PMID: 34649249 DOI: 10.1159/000519344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022] Open
Abstract
Small airways (SA) in humans are commonly defined as those conducting airways <2 mm in diameter. They are susceptible to particle- and chemical-induced injury and play a major role in the development of airway disease such as COPD and asthma. Susceptibility to injury can be attributed in part to structural features including airflow dynamics and tissue architecture, but recent evidence may indicate a more prominent role for cellular composition in directing toxicological responses. Animal studies support the hypothesis that inherent cellular differences across the tracheobronchial tree, including metabolic CYP450 expression in the distal conducting airways, can influence SA susceptibility to injury. Currently, there is insufficient information in humans to make similar conclusions, prompting further necessary work in this area. An understanding of why the SA are more susceptible to certain chemical and particle exposures than other airway regions is fundamental to our ability to identify hazardous materials, their properties, and accompanying exposure scenarios that compromise lung function. It is also important for the ability to develop appropriate models for toxicity testing. Moreover, it is central to our understanding of SA disease aetiology and how interventional strategies for treatment may be developed. In this review, we will document the structural and cellular airway regional differences that are likely to influence airway susceptibility to injury, including the role of secretory club cells. We will also describe recent advances in single-cell sequencing of human airways, which have provided unprecedented details of cell phenotype, likely to impact airway chemical and particle injury.
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Affiliation(s)
| | - Martin Oliver Leonard
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Didcot, United Kingdom
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10
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Abstract
Lung cancer represents the world's leading cause of cancer deaths. Sex differences in the incidence and mortality rates for various types of lung cancers have been identified, but the biological and endocrine mechanisms implicated in these disparities have not yet been determined. While some cancers such as lung adenocarcinoma are more commonly found among women than men, others like squamous cell carcinoma display the opposite pattern or show no sex differences. Associations of tobacco product use rates, susceptibility to carcinogens, occupational exposures, and indoor and outdoor air pollution have also been linked to differential rates of lung cancer occurrence and mortality between sexes. While roles for sex hormones in other types of cancers affecting women or men have been identified and described, little is known about the influence of sex hormones in lung cancer. One potential mechanism identified to date is the synergism between estrogen and some tobacco compounds, and oncogene mutations, in inducing the expression of metabolic enzymes, leading to enhanced formation of reactive oxygen species and DNA adducts, and subsequent lung carcinogenesis. In this review, we present the literature available regarding sex differences in cancer rates, associations of male and female sex hormones with lung cancer, the influence of exogenous hormone therapy in women, and potential mechanisms mediated by male and female sex hormone receptors in lung carcinogenesis. The influence of biological sex on lung disease has recently been established, thus new research incorporating this variable will shed light on the mechanisms behind the observed disparities in lung cancer rates, and potentially lead to the development of new therapeutics to treat this devastating disease.
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Affiliation(s)
- Nathalie Fuentes
- National Institute of Allergy and Infectious Diseases, Bethesda, MD 20852, USA
| | - Miguel Silva Rodriguez
- Department of Environmental and Occupational Health, Indiana University, School of Public Health, Bloomington, IN 47405, USA
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, Indiana University, School of Public Health, Bloomington, IN 47405, USA
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11
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Bernal V, Bischoff R, Horvatovich P, Guryev V, Grzegorczyk M. The 'un-shrunk' partial correlation in Gaussian graphical models. BMC Bioinformatics 2021; 22:424. [PMID: 34493207 PMCID: PMC8424921 DOI: 10.1186/s12859-021-04313-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In systems biology, it is important to reconstruct regulatory networks from quantitative molecular profiles. Gaussian graphical models (GGMs) are one of the most popular methods to this end. A GGM consists of nodes (representing the transcripts, metabolites or proteins) inter-connected by edges (reflecting their partial correlations). Learning the edges from quantitative molecular profiles is statistically challenging, as there are usually fewer samples than nodes ('high dimensional problem'). Shrinkage methods address this issue by learning a regularized GGM. However, it remains open to study how the shrinkage affects the final result and its interpretation. RESULTS We show that the shrinkage biases the partial correlation in a non-linear way. This bias does not only change the magnitudes of the partial correlations but also affects their order. Furthermore, it makes networks obtained from different experiments incomparable and hinders their biological interpretation. We propose a method, referred to as 'un-shrinking' the partial correlation, which corrects for this non-linear bias. Unlike traditional methods, which use a fixed shrinkage value, the new approach provides partial correlations that are closer to the actual (population) values and that are easier to interpret. This is demonstrated on two gene expression datasets from Escherichia coli and Mus musculus. CONCLUSIONS GGMs are popular undirected graphical models based on partial correlations. The application of GGMs to reconstruct regulatory networks is commonly performed using shrinkage to overcome the 'high-dimensional problem'. Besides it advantages, we have identified that the shrinkage introduces a non-linear bias in the partial correlations. Ignoring this type of effects caused by the shrinkage can obscure the interpretation of the network, and impede the validation of earlier reported results.
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Affiliation(s)
- Victor Bernal
- Bernoulli Institute, University of Groningen, Groningen, 9747 AG, The Netherlands.,Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands.
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, 9713 AV, The Netherlands.
| | - Marco Grzegorczyk
- Bernoulli Institute, University of Groningen, Groningen, 9747 AG, The Netherlands.
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12
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Banerjee P, Balraj P, Ambhore NS, Wicher SA, Britt RD, Pabelick CM, Prakash YS, Sathish V. Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma. Sci Rep 2021; 11:14386. [PMID: 34257337 PMCID: PMC8277837 DOI: 10.1038/s41598-021-93845-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relationship between ASM genes to uncover the putative mechanism underlying asthma in humans. To this end, the gene expression from human ASM was measured with RNA-Seq in non-asthmatic and asthmatic groups. The gene network for the asthmatic and non-asthmatic group was constructed by prioritizing differentially expressed genes (DEGs) (121) and transcription factors (TFs) (116). Furthermore, we identified differentially connected or co-expressed genes in each group. The asthmatic group showed a loss of gene connectivity due to the rewiring of major regulators. Notably, TFs such as ZNF792, SMAD1, and SMAD7 were differentially correlated in the asthmatic ASM. Additionally, the DEGs, TFs, and differentially connected genes over-represented in the pathways involved with herpes simplex virus infection, Hippo and TGF-β signaling, adherens junctions, gap junctions, and ferroptosis. The rewiring of major regulators unveiled in this study likely modulates the expression of gene-targets as an adaptive response to asthma. These multiple gene interactions pointed out novel targets and pathways for asthma exacerbations.
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Affiliation(s)
- Priyanka Banerjee
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA
| | - Premanand Balraj
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA
| | | | - Sarah A Wicher
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Rodney D Britt
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Christina M Pabelick
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Y S Prakash
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Venkatachalem Sathish
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Sudro 108A, Fargo, ND, 58108-6050, USA.
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13
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Deprez M, Zaragosi LE, Truchi M, Becavin C, Ruiz García S, Arguel MJ, Plaisant M, Magnone V, Lebrigand K, Abelanet S, Brau F, Paquet A, Pe'er D, Marquette CH, Leroy S, Barbry P. A Single-Cell Atlas of the Human Healthy Airways. Am J Respir Crit Care Med 2021; 202:1636-1645. [PMID: 32726565 DOI: 10.1164/rccm.201911-2199oc] [Citation(s) in RCA: 223] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rationale: The respiratory tract constitutes an elaborate line of defense that is based on a unique cellular ecosystem.Objectives: We aimed to investigate cell population distributions and transcriptional changes along the airways by using single-cell RNA profiling.Methods: We have explored the cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. A total of 77,969 cells were collected at 35 distinct locations, from the nose to the 12th division of the airway tree.Measurements and Main Results: The resulting atlas is composed of a high percentage of epithelial cells (89.1%) but also immune (6.2%) and stromal (4.7%) cells with distinct cellular proportions in different regions of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type-specific gene expression is stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuroendocrine cells, and brush cells and identifies a related population of NREP-positive cells. We also report the association of KRT13 with dividing cells that are reminiscent of previously described mouse "hillock" cells and with squamous cells expressing SCEL and SPRR1A/B.Conclusions: Robust characterization of a single-cell cohort in healthy airways establishes a valuable resource for future investigations. The precise description of the continuum existing from the nasal epithelium to successive divisions of the airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.
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Affiliation(s)
- Marie Deprez
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Christophe Becavin
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Sandra Ruiz García
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Marie-Jeanne Arguel
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Virginie Magnone
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Sophie Abelanet
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Frédéric Brau
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Dana Pe'er
- Memorial Sloan Kettering Cancer Center, New York, New York; and
| | - Charles-Hugo Marquette
- Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Fédération Hospitalo-Universitaire OncoAge, CNRS, Inserm, Institute for Research on Cancer and Aging Nice Team 3, Pulmonology Department, Nice, France
| | - Sylvie Leroy
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France.,Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Fédération Hospitalo-Universitaire OncoAge, CNRS, Inserm, Institute for Research on Cancer and Aging Nice Team 3, Pulmonology Department, Nice, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
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14
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Aliee H, Massip F, Qi C, de Biase MS, van Nijnatten J, Kersten ETG, Kermani NZ, Khuder B, Vonk JM, Vermeulen RCH, Neighbors M, Tew GW, Grimbaldeston M, Ten 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 CA, Adcock IM, Timens W, Xu CJ, van den Berge M, Schwarz RF, Koppelman GH, Nawijn MC, Faiz A. Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.08.31.20169946. [PMID: 32909007 PMCID: PMC7480059 DOI: 10.1101/2020.08.31.20169946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has led to a worldwide pandemic. One week after initial symptoms develop, a subset of patients progresses to severe disease, with high mortality and limited treatment options. To design novel interventions aimed at preventing spread of the virus and reducing progression to severe disease, detailed knowledge of the cell types and regulating factors driving cellular entry is urgently needed. Here we assess the expression patterns in genes required for COVID-19 entry into cells and replication, and their regulation by genetic, epigenetic and environmental factors, throughout the respiratory tract using samples collected from the upper (nasal) and lower airways (bronchi). Matched samples from the upper and lower airways show a clear increased expression of these genes in the nose compared to the bronchi and parenchyma. Cellular deconvolution indicates a clear association of these genes with the proportion of secretory epithelial cells. Smoking status was found to increase the majority of COVID-19 related genes including ACE2 and TMPRSS2 but only in the lower airways, which was associated with a significant increase in the predicted proportion of goblet cells in bronchial samples of current smokers. Both acute and second hand smoke were found to increase ACE2 expression in the bronchus. Inhaled corticosteroids decrease ACE2 expression in the lower airways. No significant effect of genetics on ACE2 expression was observed, but a strong association of DNA- methylation with ACE2 and TMPRSS2- mRNA expression was identified in the bronchus.
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Affiliation(s)
- H Aliee
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
| | - F Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - C Qi
- 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 Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - M Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - J van Nijnatten
- 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
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
| | - E T G Kersten
- 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 Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - N Z Kermani
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - B Khuder
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA
| | - J M Vonk
- 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 epidemiology, Groningen, the Netherlands
| | - R C H Vermeulen
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute for Risk Assessment Science (IRAS), Division of Environmental Epidemiology (EEPI), Utrecht University, Utrecht, The Netherlands
| | - M Neighbors
- OMNI Biomarker Development, Genentech Inc. South San Francisco. CA, USA
| | - G W Tew
- Product Development Immunology, Infectious Disease & Opthalmology, Genentech Inc. South San Francisco. CA, USA
| | - M Grimbaldeston
- OMNI Biomarker Development, Genentech Inc. South San Francisco. CA, USA
| | - N H T Ten Hacken
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - S Hu
- Department of statistics, university of Oxford, Oxford, UK
| | - Y Guo
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - X Zhang
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - K Sun
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - B A Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, CB2 0XZ, UK
| | - M J Mäkelä
- Dept. of Allergy, University of Helsinki and Helsinki University Hospital, PO Box 160, FI-00029, Helsinki, Finland
| | - K Malmström
- Dept. of Allergy, University of Helsinki and Helsinki University Hospital, PO Box 160, FI-00029, Helsinki, Finland
| | - R C Rintoul
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, CB2 0XZ, UK
- Royal Papworth Hospital, Cambridge, Papworth Road, Cambridge Biomedical Campus, CB2 0AY, UK
| | - P A Reyfman
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA
| | - F J Theis
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
- Department of Mathematics, Technical University of Munich, Germany
| | - C A Brandsma
- 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
| | - I M Adcock
- National Heart and Lung Institute, London, UK
| | - W 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
| | - C J Xu
- Research group Bioinformatics and Computational Genomics, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M 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
| | - R F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - G H Koppelman
- 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 Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - M C Nawijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- National Heart and Lung Institute, London, UK
| | - A Faiz
- 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
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
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