1
|
Yang Y, McCullough CG, Seninge L, Guo L, Kwon WJ, Zhang Y, Li NY, Gaddam S, Pan C, Zhen H, Torkelson J, Glass IA, Charville GW, Que J, Stuart JM, Ding H, Oro AE. A spatiotemporal and machine-learning platform facilitates the manufacturing of hPSC-derived esophageal mucosa. Dev Cell 2025; 60:1359-1376.e10. [PMID: 39798574 PMCID: PMC12055484 DOI: 10.1016/j.devcel.2024.12.030] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/12/2024] [Indexed: 01/15/2025]
Abstract
Human pluripotent stem cell-derived tissue engineering offers great promise for designer cell-based personalized therapeutics, but harnessing such potential requires a deeper understanding of tissue-level interactions. We previously developed a cell replacement manufacturing method for ectoderm-derived skin epithelium. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium despite possessing a similar stratified epithelial structure. Here, we employ single-cell and spatial technologies to generate a spatiotemporal multi-omics cell census for human esophageal development. We identify the cellular diversity, dynamics, and signal communications for the developing esophageal epithelium and stroma. Using Manatee, a machine-learning algorithm, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of Manatee predictions leads to a clinically compatible system for manufacturing human esophageal mucosa.
Collapse
Affiliation(s)
- Ying Yang
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Carmel Grace McCullough
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Lucas Seninge
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lihao Guo
- Department of Pharmacy Practice and Science, University of Arizona, Tucson, AZ, USA
| | - Woo-Joo Kwon
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Yongchun Zhang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nancy Yanzhe Li
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Sadhana Gaddam
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Cory Pan
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Hanson Zhen
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Jessica Torkelson
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA
| | - Ian A Glass
- Birth Defect Research Laboratory Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Jianwen Que
- Department of Medicine, Columbia University, New York, NY, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hongxu Ding
- Department of Pharmacy Practice and Science, University of Arizona, Tucson, AZ, USA.
| | - Anthony E Oro
- Program in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Mazzilli SA, Rahal Z, Rouhani MJ, Janes SM, Kadara H, Dubinett SM, Spira AE. Translating premalignant biology to accelerate non-small-cell lung cancer interception. Nat Rev Cancer 2025; 25:379-392. [PMID: 39994467 DOI: 10.1038/s41568-025-00791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 02/26/2025]
Abstract
Over the past decade, substantial progress has been made in the development of targeted and immune-based therapies for patients with advanced non-small-cell lung cancer. To further improve outcomes for patients with lung cancer, identifying and intercepting disease at the earliest and most curable stages are crucial next steps. With the recent implementation of low-dose computed tomography scan screening in populations at high risk, there is an emerging unmet need for new diagnostic, prognostic and therapeutic tools to help treat patients suspected of harbouring premalignant lesions and minimally invasive non-small-cell lung cancer. Continued advances in the identification of the earliest drivers of lung carcinogenesis are poised to address these unmet needs. Employing multimodal approaches to chart the temporal and spatial maps of the molecular events driving lung premalignant lesion progression will refine our understanding of early carcinogenesis. Elucidating the molecular drivers of premalignancy is critical to the development of biomarkers to detect those incubating a premalignant lesion, to stratify risk for progression to invasive cancer and to identify novel therapeutic targets to intercept that process. In this Review, we summarize emerging insights into the earliest cellular and molecular events associated with lung squamous and adenocarcinoma carcinogenesis and highlight the growing opportunity for translating these insights into clinical tools for early detection and disease interception to transform the outcomes for those at risk for lung cancer.
Collapse
Affiliation(s)
- Sarah A Mazzilli
- Sectional Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
| | - Zahraa Rahal
- Division of Pathology-Lab Medicine, Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Maral J Rouhani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Humam Kadara
- Division of Pathology-Lab Medicine, Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Dubinett
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, and Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Avrum E Spira
- Sectional Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Johnson & Johnson Innovative Medicine, Boston, MA, USA.
| |
Collapse
|
3
|
Gómez-López S, Alhendi ASN, Przybilla MJ, Bordeu I, Whiteman ZE, Butler T, Rouhani MJ, Kalinke L, Uddin I, Otter KEJ, Chandrasekharan DP, Lebrusant-Fernandez M, Shurr AYL, Durrenberger PF, Moore DA, Falzon M, Reading JL, Martincorena I, Simons BD, Campbell PJ, Janes SM. Aberrant basal cell clonal dynamics shape early lung carcinogenesis. Science 2025:eads9145. [PMID: 40310937 DOI: 10.1126/science.ads9145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 04/10/2025] [Indexed: 05/03/2025]
Abstract
Preinvasive squamous lung lesions are precursors of lung squamous cell carcinoma (LUSC). The cellular events underlying lesion formation are unknown. Using a carcinogen-induced model of LUSC with no added genetic hits or cell type bias, we find that carcinogen exposure leads to non-neutral competition among basal cells, aberrant clonal expansions, and basal cell mobilization along the airways. Ultimately, preinvasive lesions develop from a few highly mutated clones that dominate most of the bronchial tree. Multi-site sequencing in human patients confirms the presence of clonally related preinvasive lesions across distinct airway regions. Our work identifies a transition in basal cell clonal dynamics, and an associated shift in basal cell fate, as drivers of field cancerization in the lung.
Collapse
Affiliation(s)
- Sandra Gómez-López
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Ahmed S N Alhendi
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Moritz J Przybilla
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Ignacio Bordeu
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Zoe E Whiteman
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Timothy Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Maral J Rouhani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Lukas Kalinke
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Imran Uddin
- Cancer Research UK City of London Centre Single Cell Genomics Facility, UCL Cancer Institute, University College London, London, UK
- Genomics Translational Technology Platform, UCL Cancer Institute, University College London, London, UK
| | - Kate E J Otter
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Marta Lebrusant-Fernandez
- Pre-Cancer Immunology Laboratory, UCL Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Y L Shurr
- Pre-Cancer Immunology Laboratory, UCL Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Pascal F Durrenberger
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals NHS Trust, London, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals NHS Trust, London, UK
| | - James L Reading
- Pre-Cancer Immunology Laboratory, UCL Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Benjamin D Simons
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| |
Collapse
|
4
|
Murthy S, Seabold DA, Gautam LK, Caceres AM, Sease R, Calvert BA, Busch SM, Neely A, Marconett CN, Ryan AL. Culture conditions differentially regulate the inflammatory niche and cellular phenotype of tracheobronchial basal stem cells. Am J Physiol Lung Cell Mol Physiol 2025; 328:L538-L553. [PMID: 39982813 DOI: 10.1152/ajplung.00293.2024] [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: 09/06/2024] [Revised: 10/08/2024] [Accepted: 02/07/2025] [Indexed: 02/23/2025] Open
Abstract
Bronchial epithelial cells derived from the tracheobronchial regions of human airways (HBECs) provide a valuable in vitro model for studying pathological mechanisms and evaluating therapeutics. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media: airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and PneumaCult Ex plus (PEx+). Analysis through RNA sequencing, immune assays, and impedance measurements revealed that PEx+ media significantly drove cell proliferation and a broad proinflammatory phenotype in BCs. In contrast, BCs expanded in AECGM and displayed increased expression of structural and extracellular matrix components at higher passage. AECGM increased expression of some cytokines at high passage, whereas DSI suppressed inflammation implicating the involvement TGF-β in BC inflammatory processes. Differentiation capacity of BCs declined with time in culture irrespective of expansion media. This was associated with an increase in PLUNC expressing secretory cells in AECGM and PEx+ media consistent with the known immune modulatory role of PLUNC in the airways. These findings highlight the profound impact of media conditions on inflammatory niche established by, and function of, in vitro expanded BCs. The broad proinflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic applications.NEW & NOTEWORTHY Airway basal cells, vital for airway regeneration and potential therapies, show significant changes based on culture conditions. Our study reveals that media composition and culture duration greatly affect basal cell properties with profound changes in the proinflammatory phenotype and extracellular matrix deposition driven by changes in growth conditions. These results underscore the critical impact of culture conditions on BC phenotype, influencing cell-based models for airway disease research and therapy.
Collapse
Affiliation(s)
- Shubha Murthy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Denise A Seabold
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Lalit K Gautam
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Adrian M Caceres
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Rosemary Sease
- Department of Medicine, Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California, United States
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California, United States
| | - Ben A Calvert
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
- Department of Medicine, Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California, United States
| | - Shana M Busch
- Department of Medicine, Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California, United States
| | - Aaron Neely
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States
| | - Crystal N Marconett
- Department of Medicine, Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California, United States
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California, United States
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States
| | - Amy L Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
- Department of Medicine, Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California, United States
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California, United States
| |
Collapse
|
5
|
Breugem TI, Riesebosch S, Zhang J, Mykytyn AZ, Krabbendam L, Groen N, Baptista Varela S, Schipper D, van den Doel PB, van Acker R, Stadhouders R, Lamers MM, Haagmans BL. Variable DPP4 expression in multiciliated cells of the human nasal epithelium as a determinant for MERS-CoV tropism. Proc Natl Acad Sci U S A 2025; 122:e2410630122. [PMID: 40048293 PMCID: PMC11929475 DOI: 10.1073/pnas.2410630122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 12/21/2024] [Indexed: 03/25/2025] Open
Abstract
Transmissibility of respiratory viruses is a complex viral trait that is intricately linked to tropism. Several highly transmissible viruses, including severe acute respiratory syndrome coronavirus 2 and Influenza viruses, specifically target multiciliated cells in the upper respiratory tract to facilitate efficient human-to-human transmission. In contrast, the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) generally transmits poorly between humans, which is largely attributed to the absence of its receptor dipeptidyl peptidase 4 (DPP4) in the upper respiratory tract. At the same time, MERS-CoV epidemiology is characterized by occasional superspreading events, suggesting that some individuals can disseminate this virus effectively. Here, we utilized well-differentiated human pulmonary and nasal airway organoid-derived cultures to further delineate the respiratory tropism of MERS-CoV. We find that MERS-CoV replicated to high titers in both pulmonary and nasal airway cultures. Using single-cell messenger-RNA sequencing, immunofluorescence, and immunohistochemistry, we show that MERS-CoV preferentially targeted multiciliated cells, leading to loss of ciliary coverage. MERS-CoV cellular tropism was dependent on the differentiation of the organoid-derived cultures, and replication efficiency varied considerably between donors. Similarly, variable and focal expression of DPP4 was revealed in human nose tissues. This study indicates that the upper respiratory tract tropism of MERS-CoV may vary between individuals due to differences in DPP4 expression, providing an explanation for the unpredictable transmission pattern of MERS-CoV.
Collapse
Affiliation(s)
- Tim I. Breugem
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Jingshu Zhang
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Anna Z. Mykytyn
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Lisette Krabbendam
- Pulmonary Medicine Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Nathalie Groen
- Single Cell Discoveries, Utrecht3584 BW, The Netherlands
| | - Sivana Baptista Varela
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Petra B. van den Doel
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Romy van Acker
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Ralph Stadhouders
- Pulmonary Medicine Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Bart L. Haagmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam3015 GD, The Netherlands
| |
Collapse
|
6
|
Roe T, Talbot T, Terrington I, Johal J, Kemp I, Saeed K, Webb E, Cusack R, Grocott MPW, Dushianthan A. Physiology and pathophysiology of mucus and mucolytic use in critically ill patients. Crit Care 2025; 29:68. [PMID: 39920835 PMCID: PMC11806889 DOI: 10.1186/s13054-025-05286-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 01/18/2025] [Indexed: 02/09/2025] Open
Abstract
Airway mucus is a highly specialised secretory fluid which functions as a physical and immunological barrier to pathogens whilst lubricating the airways and humifying atmospheric air. Dysfunction is common during critical illness and is characterised by changes in production rate, chemical composition, physical properties, and inflammatory phenotype. Mucociliary clearance, which is determined in part by mucus characteristics and in part by ciliary function, is also dysfunctional in critical illness via disease related and iatrogenic mechanisms. The consequences of mucus dysfunction are potentially devastating, contributing to prolonged ventilator dependency, increased risk of secondary pneumonia, and worsened lung injury. Mucolytic therapies are designed to decrease viscosity, improve expectoration/suctioning, and thereby promote mucus removal. Mucolytics, including hypertonic saline, dornase alfa/rhDNase, nebulised heparin, carbocisteine/N-Acetyl cysteine, are commonly used in critically ill patients. This review summarises the physiology and pathophysiology of mucus and the existing evidence for the use of mucolytics in critically ill patients and speculates on journey to individualised mucolytic therapy.
Collapse
Affiliation(s)
- Thomas Roe
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK
| | - Thomas Talbot
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
| | - Isis Terrington
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK
| | - Jayant Johal
- Integrative Physiology and Critical Illness Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Ivan Kemp
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
| | - Kordo Saeed
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK
- Integrative Physiology and Critical Illness Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Elizabeth Webb
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
| | - Rebecca Cusack
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK
- Integrative Physiology and Critical Illness Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Michael P W Grocott
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK
- Integrative Physiology and Critical Illness Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Ahilanandan Dushianthan
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6YD, UK.
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton/University of Southampton, Southampton, SO16 6YD, UK.
- Integrative Physiology and Critical Illness Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.
| |
Collapse
|
7
|
Chen H, Chen X, Ding J, Xue H, Tang X, Li X, Xie Y. Single nuclear RNA sequencing and analysis of basal cells in pulmonary acute respiratory distress syndrome. Gene 2025; 936:149131. [PMID: 39622393 DOI: 10.1016/j.gene.2024.149131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 11/25/2024] [Accepted: 11/27/2024] [Indexed: 12/12/2024]
Abstract
OBJECTIVE This study aims to find the gene expression profile specifically in basal cells from pulmonary acute respiratory distress syndrome (ARDSp) patients using single-cell level analysis. METHODS Single nuclear RNA sequencing (snRNA-seq) data of lung samples, including 18 ARDSp participants and 7 healthy participants, were sourced from the GEO database (GSE171524). The differentially expressed genes (DEGs) were screened by | log2FC | >1 and P < 0.05. Functional enrichment was constructed via Gene Ontology (GO) analysis. Pathway enrichment was conducted via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The protein-protein interaction (PPI) network of the DEGs was performed via the STRING database. Cytoscape software was employed to find hub genes. The hub genes were sequenced and validated via data set after constructing the rat model of ARDSp. RESULTS Using DESeq2 package, 299 genes were disclosed to be downregulated, while 228 were upregulated in ARDSp participants. GO analysis disclosed DEGs were enriched in processes like actin filament organization, regulation of small GTPase-mediated signal transduction, response to unfolded protein, wound healing, and response to oxygen levels. Meanwhile, KEGG analysis disclosed DEGs were involved in protein digestion and absorption, Th17 cell differentiation, iron death, and other biological effects. Ten hub genes, including FN1, HIF1A, HSP90AA1, SMAD3, FOS, CDKN2A, COL1A1, HSPA8, FLNA, and NFKBIA were highlighted based on their network centrality and biological significance. HIF1A, HSPA8, NFKBIA, and CDKN2A were differentially expressed in the validation dataset. CONCLUSIONS Basal cells in ARDSp exhibit significant changes in gene expression, with ten hub genes identified. Among them, four (HIF1A, HSPA8, NFKBIA, CDKN2A) were validated experimentally using RNA-Seq data from an ARDSp rat model. This study emphasizes the role of basal cells in ARDSp, highlighting the altered gene networks involved in repair and inflammatory responses, providing potential targets for further therapeutic exploration. These findings suggest that alterations in these hub genes may be crucial to basal cell-driven inflammatory and reparative responses in ARDSp.
Collapse
Affiliation(s)
- Haoran Chen
- Kangda College of Nanjing Medical University, Lianyungang City, Jiangsu Province Zip Code 222000, China
| | - Xiaobing Chen
- The Institute of Emergency Medicine of Lianyungang, Lianyungang City, Jiangsu Province Zip Code 222000, China
| | - Jinqiu Ding
- The Institute of Emergency Medicine of Lianyungang, Lianyungang City, Jiangsu Province Zip Code 222000, China
| | - Haoyue Xue
- The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang City, Jiangsu Province Zip Code 222000, China
| | - Xinyi Tang
- Lianyungang Clinical College of Nanjing Medical University, Lianyungang City, Jiangsu Province Zip Code 222000, China
| | - Xiaomin Li
- The Institute of Emergency Medicine of Lianyungang, Lianyungang City, Jiangsu Province Zip Code 222000, China; Department of Emergency and Critical Care Medicine, the First pepple's Hospital of Lianyungang, Jiangsu Province Zip Code 222000, China.
| | - Yongpeng Xie
- The Institute of Emergency Medicine of Lianyungang, Lianyungang City, Jiangsu Province Zip Code 222000, China; Department of Emergency and Critical Care Medicine, the First pepple's Hospital of Lianyungang, Jiangsu Province Zip Code 222000, China.
| |
Collapse
|
8
|
Walsh JML, Miao VN, Owings AH, Tang Y, Bromley JD, Kazer SW, Kimler K, Asare C, Ziegler CGK, Ibrahim S, Jivanjee T, George M, Navia AW, Drake RS, Parker A, Billingsley BC, Dotherow P, Tarugu S, Kota SK, Laird H, Wichman TG, Davis YT, Dhaliwal NS, Pride Y, Guo Y, Senitko M, Harvey J, Bates JT, Diamond G, Garrett MR, Robinson DA, Frame IJ, Lyons JJ, Robinson TO, Shalek AK, Horwitz BH, Glover SC, Ordovas-Montanes J. Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2. Nat Immunol 2025; 26:294-307. [PMID: 39833605 DOI: 10.1038/s41590-024-02052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 12/05/2024] [Indexed: 01/22/2025]
Abstract
Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2hi cell subsets, which was distinct from that of ancestral cases. Delta-infected samples had a marked increase in viral RNA, and a subset of PER2+EGR1+GDF15+ epithelial cells was enriched in SARS-CoV-2 RNA+ cells in all variants. Prior vaccination was associated with increased frequency and activation of nasal macrophages. Expression of interferon-stimulated genes negatively correlated with coronavirus disease 2019 (COVID-19) severity in patients with ancestral and Delta but not Omicron variants. Our study defines nasal cell responses and signatures of disease severity across SARS-CoV-2 variants and vaccination.
Collapse
Affiliation(s)
- Jaclyn M L Walsh
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vincent N Miao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School and MIT, Boston, MA, USA
| | - Anna H Owings
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ying Tang
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Joshua D Bromley
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samuel W Kazer
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kyle Kimler
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Chelsea Asare
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carly G K Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School and MIT, Boston, MA, USA
- Harvard Graduate Program in Biophysics, Cambridge, MA, USA
| | - Samira Ibrahim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tasneem Jivanjee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Micayla George
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew W Navia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Riley S Drake
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam Parker
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Paul Dotherow
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Spurthi Tarugu
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sai K Kota
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Hannah Laird
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - T Grant Wichman
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yesenia T Davis
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Neha S Dhaliwal
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yilianys Pride
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yanglin Guo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michal Senitko
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jessie Harvey
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - John T Bates
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Gill Diamond
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA
| | - Michael R Garrett
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - I J Frame
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jonathan J Lyons
- Division of Allergy and Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Tanya O Robinson
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Alex K Shalek
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School and MIT, Boston, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bruce H Horwitz
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Division of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sarah C Glover
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Medicine, Section of Gastroenterology and Hepatology, Tulane University, New Orleans, LA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
- Program in Immunology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| |
Collapse
|
9
|
Khoury Damaa M, Serizay J, Balagué R, Boudjema AR, Faucourt M, Delgehyr N, Goh KJ, Lu H, Tan EK, James CT, Faucon C, Mitri R, Bracht DC, Bingle CD, Dunn NR, Arnold SJ, Zaragosi LE, Barbry P, Koszul R, Omran H, Gil-Gómez G, Escudier E, Legendre M, Roy S, Spassky N, Meunier A. Cyclin O controls entry into the cell-cycle variant required for multiciliated cell differentiation. Cell Rep 2025; 44:115117. [PMID: 39740663 DOI: 10.1016/j.celrep.2024.115117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 11/21/2024] [Accepted: 12/05/2024] [Indexed: 01/02/2025] Open
Abstract
Multiciliated cells (MCCs) ensure fluid circulation in various organs. Their differentiation is marked by the amplification of cilia-nucleating centrioles, driven by a genuine cell-cycle variant, which is characterized by wave-like expression of canonical and non-canonical cyclins such as Cyclin O (CCNO). Patients with CCNO mutations exhibit a subtype of primary ciliary dyskinesia called reduced generation of motile cilia (RGMC). Here, we show that Ccno is activated at the crossroads of the onset of MCC differentiation, the entry into the MCC cell-cycle variant, and the activation of the centriole biogenesis program. Its absence blocks the G1/S-like transition of the cell-cycle variant, interrupts the centriologenesis transcription program, and compromises the production of centrioles and cilia in mouse brain and human respiratory MCCs. Altogether, our study identifies CCNO as a core regulator of entry into the MCC cell-cycle variant and the interruption of this variant as one etiology of RGMC.
Collapse
Affiliation(s)
- Michella Khoury Damaa
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Jacques Serizay
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France; Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Rémi Balagué
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Amélie-Rose Boudjema
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Marion Faucourt
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Nathalie Delgehyr
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Kim Jee Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | - Hao Lu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Ee Kim Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | - Cameron T James
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore; Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2RX, UK; Singapore-MIT Association for Research and Technology, Critical Analytics for Manufacturing Personalised-Medicine (SMART CAMP), 1 CREATE Way, Singapore 138602, Singapore
| | - Catherine Faucon
- Centre Hospitalier Intercommunal de Créteil, Laboratoire de Microscopie Électronique, Service d'Anatomopathologie, 94010 Créteil, France
| | - Rana Mitri
- Centre Hospitalier Intercommunal de Créteil, Laboratoire de Microscopie Électronique, Service d'Anatomopathologie, 94010 Créteil, France
| | - Diana Carolin Bracht
- Department of General Pediatrics, University Hospital Muenster, 48149 Muenster, Germany
| | - Colin D Bingle
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Norris Ray Dunn
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore; Skin Research Institute of Singapore, 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore 308232, Singapore
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany
| | - Laure-Emmanuelle Zaragosi
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Sophia Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Sophia Antipolis, France; 3IA Côte d'Azur, 06560 Sophia Antipolis, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, 48149 Muenster, Germany
| | - Gabriel Gil-Gómez
- Hospital del Mar Research Institute, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Estelle Escudier
- Sorbonne Université, Inserm, Childhood genetic diseases UMR_S933, Hôpital Armand-Trousseau, 75012 Paris, France; AP-HP, Sorbonne Université, Hôpital Armand-Trousseau, 75012 Paris, France
| | - Marie Legendre
- Sorbonne Université, Inserm, Childhood genetic diseases UMR_S933, Hôpital Armand-Trousseau, 75012 Paris, France; AP-HP, Sorbonne Université, Hôpital Armand-Trousseau, 75012 Paris, France
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119288, Singapore
| | - Nathalie Spassky
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Alice Meunier
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France.
| |
Collapse
|
10
|
Serizay J, Khoury Damaa M, Boudjema AR, Balagué R, Faucourt M, Delgehyr N, Noûs C, Zaragosi LE, Barbry P, Spassky N, Koszul R, Meunier A. Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis. Cell Rep 2025; 44:115103. [PMID: 39740664 DOI: 10.1016/j.celrep.2024.115103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 11/19/2024] [Accepted: 12/03/2024] [Indexed: 01/02/2025] Open
Abstract
Meiosis, endoreplication, and asynthetic fissions are variations of the canonical cell cycle where either replication or mitotic divisions are muted. Here, we identify a cell cycle variantconserved across organs and mammals, where both replication and mitosis are muted, and that orchestrates the differentiation of post-mitotic progenitors into multiciliated cells (MCCs). MCC progenitors reactivate most of the cell cycle transcriptional program but replace the temporal expression of cyclins E2 and A2 with non-canonical cyclins O and A1. In addition, the primary APC/C inhibitor Emi1 is silenced. Re-expressing cyclins E2 and A2 and/or Emi1 can induce partial replication or mitosis. This shows that a cell can co-opt the cell cycle genetic program and regulate only certain elements to qualitatively and quantitatively divert CDK activity toward differentiation rather than division. We propose this cell cycle variant to exploit the existence of a cytoplasmic-or centriolar-CDK threshold lower than the S-phase threshold.
Collapse
Affiliation(s)
- Jacques Serizay
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France; Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
| | - Michella Khoury Damaa
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Amélie-Rose Boudjema
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Rémi Balagué
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Marion Faucourt
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Nathalie Delgehyr
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Camille Noûs
- Cogitamus Laboratory, PSL University, Paris, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Sophia Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Sophia Antipolis, France
| | - Nathalie Spassky
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Alice Meunier
- Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, École Normale Supérieure, PSL Research University, Paris, France.
| |
Collapse
|
11
|
Petit LM, Saber Cherif L, Devilliers MA, Hatoum S, Ancel J, Delepine G, Durlach A, Dubernard X, Mérol JC, Ruaux C, Polette M, Deslée G, Perotin JM, Dormoy V. Glypican-3 is a key tuner of the Hedgehog pathway in COPD. Heliyon 2025; 11:e41564. [PMID: 39844999 PMCID: PMC11751517 DOI: 10.1016/j.heliyon.2024.e41564] [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: 09/13/2024] [Revised: 12/12/2024] [Accepted: 12/27/2024] [Indexed: 01/24/2025] Open
Abstract
Hedgehog (HH) pathway is involved in pulmonary development and lung homeostasis. It orchestrates airway epithelial cell (AEC) differentiation and contributes to respiratory pathogenesis. The core elements Gli2, Smo, and Shh were found altered in the bronchial epithelium of patients with chronic obstructive pulmonary disease (COPD). Here, we investigated the co-receptors to fully decipher the complex machinery of airway HH pathway activation in health and COPD. The core elements and co-receptors of HH signalling were investigated in lung cell populations using single-cell RNAseq analysis. The transcript levels of the principal co-receptor GPC3 were investigated on public RNAseq datasets and by RT-qPCR. The localisation of GPC3 was evaluated through immunofluorescent stainings on isolated bronchial AEC and tissues from non-COPD and COPD patients. GPC3 pharmacological modulation was achieved with Codrituzumab during AEC differentiation. We demonstrated that the core elements were not abundant in pulmonary cell populations. Focusing on co-receptors, GPC3 was the most expressed transcript in tracheobronchial epithelial cells. The decrease in GPC3 transcript levels correlated with the severity of airway obstrution in COPD patients. Finally, interfering with GPC3 signalling during AEC differentiation induced downregulation of the HH pathway attested by a decrease of Gli2 leading to reduced ciliogenesis and altered mucin production. GPC3 appears as a crucial co-receptor for the HH pathway in the respiratory context. The modulation of GPC3 may represent a novel experimental strategy to tune HH signalling in therapeutic perspectives.
Collapse
Affiliation(s)
- Laure M.G. Petit
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Lynda Saber Cherif
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Maëva A. Devilliers
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Sarah Hatoum
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Julien Ancel
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, P3Cell UMR-S1250, Reims, France
| | - Gonzague Delepine
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Anne Durlach
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Xavier Dubernard
- Université de Reims Champagne-Ardenne, CHU de Reims, Reims, France
| | - Jean-Claude Mérol
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| | - Christophe Ruaux
- Clinique Mutualiste La Sagesse, Département d’Otorhinolaryngologie, Rennes, France
| | - Myriam Polette
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, P3Cell UMR-S1250, Reims, France
| | - Gaëtan Deslée
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, P3Cell UMR-S1250, Reims, France
| | - Jeanne-Marie Perotin
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, P3Cell UMR-S1250, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, Reims, France
| |
Collapse
|
12
|
Watkinson RL, Bochkov YA, Gern JE, Iosifidis T, Looi K, Laing IA, Kicic A. Investigation of Differentiated Nasal Epithelial Responses to Infection with Clinical Isolates of Rhinovirus A and C. Methods Mol Biol 2025; 2903:113-139. [PMID: 40016462 DOI: 10.1007/978-1-0716-4410-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2025]
Abstract
The nasal epithelium is the primary point of contact for inhaled respiratory viruses such as rhinovirus, respiratory syncytial virus, influenza, and coronavirus, among others. In order to establish infection, these viruses must engage their respective receptors located on host epithelial cells and begin replication. However, the nasal epithelium is also a pivotal orchestrator of both structural and innate immune defenses against these pathogens and thus mounts a broad antiviral response to halt the progression of the infection into the lower airways. Of note, the most common virus found in the airways of children presenting to the hospital emergency department with acute wheezing and asthma is rhinovirus C (RV-C), followed by rhinovirus A (RV-A). Here, we illustrate infection of a preclinical differentiated nasal epithelial model with clinical isolates of RV-A and -C, in conjunction with several methods utilized for characterization of epithelial responses post-infection in vitro.
Collapse
Affiliation(s)
- Rebecca L Watkinson
- Division of Paediatrics, School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Nedlands, WA, Australia
| | - Yury A Bochkov
- Department of Paediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - James E Gern
- Department of Paediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Thomas Iosifidis
- Division of Paediatrics, School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Nedlands, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Kevin Looi
- Division of Paediatrics, School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Nedlands, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
| | - Ingrid A Laing
- Division of Paediatrics, School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Nedlands, WA, Australia
- Division of Cardiovascular and Respiratory Sciences, School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Nedlands, WA, Australia.
- School of Population Health, Curtin University, Bentley, WA, Australia.
- Centre for Cell Therapy and Regenerative Medicine, The University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
13
|
Bao Y, Ma Q, Chen L, Feng K, Guo W, Huang T, Cai YD. Recognizing SARS-CoV-2 infection of nasopharyngeal tissue at the single-cell level by machine learning method. Mol Immunol 2025; 177:44-61. [PMID: 39700903 DOI: 10.1016/j.molimm.2024.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 11/27/2024] [Accepted: 12/13/2024] [Indexed: 12/21/2024]
Abstract
SARS-CoV-2 has posed serious global health challenges not only because of the high degree of virus transmissibility but also due to its severe effects on the respiratory system, such as inducing changes in multiple organs through the ACE2 receptor. This virus makes changes to gene expression at the single-cell level and thus to cellular functions and immune responses in a variety of cell types. Previous studies have not been able to resolve these mechanisms fully, and so our study tries to bridge knowledge gaps about the cellular responses under conditions of infection. We performed single-cell RNA-sequencing of nasopharyngeal swabs from COVID-19 patients and healthy controls. We assembled a dataset of 32,588 cells for 58 subjects for analysis. The data were sorted into eight cell types: ciliated, basal, deuterosomal, goblet, myeloid, secretory, squamous, and T cells. Using machine learning, including nine feature ranking algorithms and two classification algorithms, we classified the infection status of single cells and analyzed gene expression to pinpoint critical markers of SARS-CoV-2 infection. Our findings show distinct gene expression profiles between infected and uninfected cells across diverse cell types, with key indicators such as FKBP4, IFITM1, SLC35E1, CD200R1, MT-ATP6, KRT13, RBM15, and FTH1 illuminating unique immune responses and potential pathways for viral spread and immune evasion. The machine learning methods effectively differentiated between infected and non-infected cells, shedding light on the cellular heterogeneity of SARS-CoV-2 infection. The findings will improve our knowledge of the cellular dynamics of SARS-CoV-2.
Collapse
Affiliation(s)
- YuSheng Bao
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China.
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China.
| | - Wei Guo
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| |
Collapse
|
14
|
Jurkowska RZ. Role of epigenetic mechanisms in the pathogenesis of chronic respiratory diseases and response to inhaled exposures: From basic concepts to clinical applications. Pharmacol Ther 2024; 264:108732. [PMID: 39426605 DOI: 10.1016/j.pharmthera.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 10/11/2024] [Indexed: 10/21/2024]
Abstract
Epigenetic modifications are chemical groups in our DNA (and chromatin) that determine which genes are active and which are shut off. Importantly, they integrate environmental signals to direct cellular function. Upon chronic environmental exposures, the epigenetic signature of lung cells gets altered, triggering aberrant gene expression programs that can lead to the development of chronic lung diseases. In addition to driving disease, epigenetic marks can serve as attractive lung disease biomarkers, due to early onset, disease specificity, and stability, warranting the need for more epigenetic research in the lung field. Despite substantial progress in mapping epigenetic alterations (mostly DNA methylation) in chronic lung diseases, the molecular mechanisms leading to their establishment are largely unknown. This review is meant as a guide for clinicians and lung researchers interested in epigenetic regulation with a focus on DNA methylation. It provides a short introduction to the main epigenetic mechanisms (DNA methylation, histone modifications and non-coding RNA) and the machinery responsible for their establishment and removal. It presents examples of epigenetic dysregulation across a spectrum of chronic lung diseases and discusses the current state of epigenetic therapies. Finally, it introduces the concept of epigenetic editing, an exciting novel approach to dissecting the functional role of epigenetic modifications. The promise of this emerging technology for the functional study of epigenetic mechanisms in cells and its potential future use in the clinic is further discussed.
Collapse
Affiliation(s)
- Renata Z Jurkowska
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK.
| |
Collapse
|
15
|
Koo MS, Moon S, Rha MS. Mucosal Inflammatory Memory in Chronic Rhinosinusitis. Cells 2024; 13:1947. [PMID: 39682698 PMCID: PMC11639807 DOI: 10.3390/cells13231947] [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: 09/28/2024] [Revised: 11/20/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
Recent advancements in medical management, endoscopic sinus surgery, and biologics have significantly improved outcomes for patients with chronic rhinosinusitis (CRS). However, long-term recurrence is frequently observed following endoscopic sinus surgery, with symptoms worsening after biologics are discontinued. Consequently, refractory or recurrent CRS remains a significant challenge, causing a substantial healthcare burden. In this review, we provide current insights into mucosal inflammatory memory, a potential mechanism leading to CRS recurrence. Given that both immune and non-immune cells in the sinonasal mucosa play critical roles in the pathophysiology of CRS, a deeper understanding of the mechanisms underlying mucosal inflammatory memory in various cellular components of sinonasal tissue could aid in the management of refractory CRS. We describe and discuss the latest knowledge regarding the novel concept of inflammatory memory, including both adaptive immune memory and trained immunity. Additionally, we summarize the pathogenic memory features of the sinonasal mucosa cellular components in the context of CRS.
Collapse
Affiliation(s)
| | | | - Min-Seok Rha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (M.-S.K.); (S.M.)
| |
Collapse
|
16
|
McKenzie CW, Wilcox RM, Isaiah OJ, Kareta MS, Lee L. Airway ciliary microenvironment responses in mice with primary ciliary dyskinesia and central pair apparatus defects. Sci Rep 2024; 14:28437. [PMID: 39558053 PMCID: PMC11574124 DOI: 10.1038/s41598-024-79877-z] [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: 09/20/2024] [Accepted: 11/13/2024] [Indexed: 11/20/2024] Open
Abstract
Dysfunction of motile cilia can impair mucociliary clearance in the airway and result in primary ciliary dyskinesia (PCD). We previously showed that mutations in central pair apparatus (CPA) genes perturb ciliary motility and result in PCD in mouse models. However, little is known about how epithelial cell types in the ciliary microenvironment of the upper airway respond to defects in ciliary motility and mucociliary clearance. Here, we have used single-cell RNA sequencing to investigate responses in tracheal epithelial cells from mice with mutations in CPA genes Cfap221/ Pcdp1, Cfap54, and Spef2. Expected cell types were identified, along with an unidentified cell type not expressing markers of typical airway cells. Deuterosomal cells were found to exist in two states that differ largely in expression of genes involved in differentiation into ciliated cells. Functional enrichment analysis of differentially expressed genes (DEGs) revealed important cellular functions and molecular pathways for each cell type that are altered in mutant mice. Overlapping DEGs shed light on general responses to cilia dysfunction, while unique DEGs indicate that some responses may be specific to the individual mutation and ciliary defect.
Collapse
Affiliation(s)
- Casey W McKenzie
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th St. N., Sioux Falls, Sioux Falls, SD, 57104, USA
| | - Reesa M Wilcox
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th St. N., Sioux Falls, Sioux Falls, SD, 57104, USA
| | - Oduduabasi J Isaiah
- Functional Genomics and Bioinformatics Core, Sanford Research, 2301 E. 60th St. N., Sioux Falls, SD, 57104, USA
| | - Michael S Kareta
- Genetics and Genomics Group, Sanford Research, 2301 E. 60th St. N., Sioux Falls, SD, 57104, USA
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22nd Street, Sioux Falls, SD, 57105, USA
| | - Lance Lee
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th St. N., Sioux Falls, Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22nd Street, Sioux Falls, SD, 57105, USA.
| |
Collapse
|
17
|
Patel MB, Griffin PJ, Olson SF, Dai J, Hou Y, Malik T, Das P, Zhang G, Zhao W, Witman GB, Lechtreck KF. Distribution and bulk flow analyses of the intraflagellar transport (IFT) motor kinesin-2 support an "on-demand" model for Chlamydomonas ciliary length control. Cytoskeleton (Hoboken) 2024; 81:586-604. [PMID: 38456596 PMCID: PMC11380706 DOI: 10.1002/cm.21851] [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: 10/30/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Most cells tightly control the length of their cilia. The regulation likely involves intraflagellar transport (IFT), a bidirectional motility of multi-subunit particles organized into trains that deliver building blocks into the organelle. In Chlamydomonas, the anterograde IFT motor kinesin-2 consists of the motor subunits FLA8 and FLA10 and the nonmotor subunit KAP. KAP dissociates from IFT at the ciliary tip and diffuses back to the cell body. This observation led to the diffusion-as-a-ruler model of ciliary length control, which postulates that KAP is progressively sequestered into elongating cilia because its return to the cell body will require increasingly more time, limiting motor availability at the ciliary base, train assembly, building block supply, and ciliary growth. Here, we show that Chlamydomonas FLA8 also returns to the cell body by diffusion. However, more than 95% of KAP and FLA8 are present in the cell body and, at a given time, just ~1% of the motor participates in IFT. After repeated photobleaching of both cilia, IFT of fluorescent kinesin subunits continued indicating that kinesin-2 cycles from the large cell-body pool through the cilia and back. Furthermore, growing and full-length cilia contained similar amounts of kinesin-2 subunits and the size of the motor pool at the base changed only slightly with ciliary length. These observations are incompatible with the diffusion-as-a-ruler model, but rather support an "on-demand model," in which the cargo load of the trains is regulated to assemble cilia of the desired length.
Collapse
Affiliation(s)
- Mansi B Patel
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Paul J Griffin
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Spencer F Olson
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Jin Dai
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Yuqing Hou
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Tara Malik
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Gui Zhang
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Winston Zhao
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - George B Witman
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
18
|
Pion A, Kavanagh E, Joynt AT, Raraigh KS, Vanscoy L, Langfelder-Schwind E, McNamara J, Moore B, Patel S, Merlo K, Temme R, Capurro V, Pesce E, Merlo C, Pedemonte N, Cutting GR, Sharma N. Investigation of CFTR Function in Human Nasal Epithelial Cells Informs Personalized Medicine. Am J Respir Cell Mol Biol 2024; 71:577-588. [PMID: 39012815 PMCID: PMC11568479 DOI: 10.1165/rcmb.2023-0398oc] [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: 11/15/2023] [Accepted: 07/16/2024] [Indexed: 07/18/2024] Open
Abstract
We broaden the clinical versatility of human nasal epithelial (HNE) cells. HNEs were isolated from 10 participants harboring cystic fibrosis transmembrane conductance regulator (CFTR) variants: 9 with rare variants (Q359R [n = 2], G480S, R334W [n = 5], and R560T) and 1 harboring R117H;7T;TG10/5T;TG12. Cultures were differentiated at the air-liquid interface. CFTR function was measured in Ussing chambers at three conditions: baseline, ivacaftor, and elexacaftor + tezacaftor + ivacaftor (ETI). Four participants initiated modulators. Q359R HNEs had 5.4% (% wild-type) baseline CFTR function and 25.5% with ivacaftor. With therapy, sweat [Cl-] decreased and symptoms resolved. G480S HNEs had 4.1% baseline and 32.1% CFTR function with ETI. Clinically, forced expiratory volume in 1 second increased and sweat [Cl-] decreased (119 to 46 mmol/L) with ETI. In vitro cultures derived from 5 participants harboring R334W showed a moderate increase in CFTR function with exposure to modulators. For one of these participants, ETI was begun in vivo; symptoms and forced expiratory volume in 1 second improved. The c.1679G>C (R560T) HNEs had less than 4% baseline CFTR function and no modulator response. RNA analysis confirmed that c.1679G>C completely missplices. A symptomatic patient harboring R117H;7T;TG10/5T;TG12 exhibited reduced CFTR function (17.5%) in HNEs, facilitating a diagnosis of mild CF. HNEs responded to modulators (ivacaftor: 32.8%, ETI: 55.5%), and, since beginning therapy, lung function improved. We reaffirm HNE use for guiding therapeutic approaches, inform predictions on modulator response (e.g., R334W), and closely assess variants that affect splicing (e.g., c.1679G>C). Notably, functional studies in HNEs harboring R117H;7T;TG10/5T;TG12 facilitated a diagnosis of mild CF, suggesting the use for HNE functional studies as a clinical diagnostic test.
Collapse
Affiliation(s)
| | | | | | | | | | | | - John McNamara
- Children’s Respiratory and Critical Care Specialists, Minneapolis, Minnesota
| | - Brooke Moore
- Children’s Respiratory and Critical Care Specialists, Minneapolis, Minnesota
| | - Shivani Patel
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Renee Temme
- Genetics Department, Children’s Minnesota, Minneapolis, Minnesota
| | - Valeria Capurro
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | |
Collapse
|
19
|
Branch MC, Weber M, Li MY, Flora P, Ezhkova E. Overview of chromatin regulatory processes during surface ectodermal development and homeostasis. Dev Biol 2024; 515:30-45. [PMID: 38971398 PMCID: PMC11317222 DOI: 10.1016/j.ydbio.2024.07.001] [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: 11/15/2023] [Revised: 05/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The ectoderm is the outermost of the three germ layers of the early embryo that arise during gastrulation. Once the germ layers are established, the complex interplay of cellular proliferation, differentiation, and migration results in organogenesis. The ectoderm is the progenitor of both the surface ectoderm and the neural ectoderm. Notably, the surface ectoderm develops into the epidermis and its associated appendages, nails, external exocrine glands, olfactory epithelium, and the anterior pituitary. Specification, development, and homeostasis of these organs demand a tightly orchestrated gene expression program that is often dictated by epigenetic regulation. In this review, we discuss the recent discoveries that have highlighted the importance of chromatin regulatory mechanisms mediated by transcription factors, histone and DNA modifications that aid in the development of surface ectodermal organs and maintain their homeostasis post-development.
Collapse
Affiliation(s)
- Meagan C Branch
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madison Weber
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng-Yen Li
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pooja Flora
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
20
|
Wang W, Liu R, Zhong Q, Cao Y, Qi J, Li Y, Yang Q. Single-cell analysis of nasal epithelial cell development in domestic pigs. Vet Res 2024; 55:140. [PMID: 39478588 PMCID: PMC11523856 DOI: 10.1186/s13567-024-01403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/28/2024] [Indexed: 11/03/2024] Open
Abstract
The nasal mucosa forms a critical barrier against the invasion of respiratory pathogens. Composed of a heterogeneous assortment of cell types, the nasal mucosa relies on the unique characteristics and complex intercellular dynamics of these cells to maintain their structural integrity and functional efficacy. In this study, single-cell RNA sequencing (scRNA-seq) of porcine nasal mucosa was performed, and nineteen distinct nasal cell types, including nine epithelial cell types, five stromal cell types, and five immune cell types, were identified. The distribution patterns of three representative types of epithelial cells (basal cells, goblet cells, and ciliated cells) were subsequently detected by immunofluorescence. We conducted a comparative analysis of these data with published human single-cell data, revealing consistent differentiation trajectories among porcine and human nasal epithelial cells. Specifically, basal cells serve as the initial stage in the differentiation process of nasal epithelial cells, which then epithelial cells. This research not only enhances our understanding of the composition and transcriptional signature of porcine nasal mucosal cells but also offers a theoretical foundation for developing alternative models for human respiratory diseases.
Collapse
Affiliation(s)
- Wenqian Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ruiling Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qiu Zhong
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yunlei Cao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiaxin Qi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuchen Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Qian Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| |
Collapse
|
21
|
Wesselman HM, Arceri L, Nguyen TK, Lara CM, Wingert RA. Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models. FEBS J 2024; 291:4159-4192. [PMID: 37997009 DOI: 10.1111/febs.17012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.
Collapse
Affiliation(s)
| | - Liana Arceri
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Caroline M Lara
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, IN, USA
| |
Collapse
|
22
|
Orr JC, Laali A, Durrenberger PF, Lazarus KA, El Mdawar MB, Janes SM, Hynds RE. A lentiviral toolkit to monitor airway epithelial cell differentiation using bioluminescence. Am J Physiol Lung Cell Mol Physiol 2024; 327:L587-L599. [PMID: 39137525 PMCID: PMC11482462 DOI: 10.1152/ajplung.00047.2024] [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: 02/09/2024] [Revised: 07/26/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024] Open
Abstract
Basal cells are adult stem cells in the airway epithelium and regenerate differentiated cell populations, including the mucosecretory and ciliated cells that enact mucociliary clearance. Human basal cells can proliferate and produce differentiated epithelium in vitro. However, studies of airway epithelial differentiation mostly rely on immunohistochemical or immunofluorescence-based staining approaches, meaning that a dynamic approach is lacking, and quantitative data are limited. Here, we use a lentiviral reporter gene approach to transduce primary human basal cells with bioluminescence reporter constructs to monitor airway epithelial differentiation longitudinally. We generated three constructs driven by promoter sequences from the TP63, MUC5AC, and FOXJ1 genes to quantitatively assess basal cell, mucosecretory cell, and ciliated cell abundance, respectively. We validated these constructs by tracking differentiation of basal cells in air-liquid interface and organoid ("bronchosphere") cultures. Transduced cells also responded appropriately to stimulation with interleukin 13 (IL-13; to increase mucosecretory differentiation and mucus production) and IL-6 (to increase ciliated cell differentiation). These constructs represent a new tool for monitoring airway epithelial cell differentiation in primary epithelial and/or induced pluripotent stem cell (iPSC)-derived cell cultures.NEW & NOTEWORTHY Orr et al. generated and validated new lentiviral vectors to monitor the differentiation of airway basal cells, goblet cells, or multiciliated cells using bioluminescence.
Collapse
Affiliation(s)
- Jessica C Orr
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, United Kingdom
| | - Asma Laali
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, United Kingdom
| | - Pascal F Durrenberger
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Kyren A Lazarus
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Marie-Belle El Mdawar
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| |
Collapse
|
23
|
Roe K. The epithelial cell types and their multi-phased defenses against fungi and other pathogens. Clin Chim Acta 2024; 563:119889. [PMID: 39117034 DOI: 10.1016/j.cca.2024.119889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
Abstract
Mucus and its movements are essential to epithelial tissue immune defenses against pathogens, including fungal pathogens, which can infect respiratory, gastrointestinal or the genito-urinary tracts. Several epithelial cell types contribute to their immune defense. This review focuses on the respiratory tract because of its paramount importance, but the observations will apply to epithelial cell defenses of other mucosal tissue, including the gastrointestinal and genito-urinary tracts. Mucus and its movements can enhance or degrade the immune defenses of the respiratory tract, particularly the lungs. The enhancements include inhaled pathogen entrapments, including fungal pathogens, pollutants and particulates, for their removal. The detriments include smaller lung airway obstructions by mucus, impairing the physical removal of pathogens and impairing vital transfers of oxygen and carbon dioxide between the alveolar circulatory system and the pulmonary air. Inflammation, edema and/or alveolar cellular damage can also reduce vital transfers of oxygen and carbon dioxide between the lung alveolar circulatory system and the pulmonary air. Furthermore, respiratory tract defenses are affected by several fatty acid mediators which activate cellular receptors to manipulate neutrophils, macrophages, dendritic cells, various innate lymphoid cells including the natural killer cells, T cells, γδ T cells, mucosal-associated invariant T cells, NKT cells and mast cells. These mediators include the inflammatory and frequently immunosuppressive prostaglandins and leukotrienes, and the special pro-resolving mediators, which normally resolve inflammation and immunosuppression. The total effects on the various epithelial cell and immune cell types, after exposures to pathogens, pollutants or particulates, will determine respiratory tract health or disease.
Collapse
Affiliation(s)
- Kevin Roe
- Retired United States Patent and Trademark Office, San Jose, CA, United States.
| |
Collapse
|
24
|
Cheng C, Katoch P, Zhong YP, Higgins CT, Moredock M, Chang MEK, Flory MR, Randell SH, Streeter PR. Identification of a Novel Subset of Human Airway Epithelial Basal Stem Cells. Int J Mol Sci 2024; 25:9863. [PMID: 39337350 PMCID: PMC11432080 DOI: 10.3390/ijms25189863] [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: 08/16/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
The basal cell maintains the airway's respiratory epithelium as the putative resident stem cell. Basal cells are known to self-renew and differentiate into airway ciliated and secretory cells. However, it is not clear if every basal cell functions as a stem cell. To address functional heterogeneity amongst the basal cell population, we developed a novel monoclonal antibody, HLO1-6H5, that identifies a subset of KRT5+ (cytokeratin 5) basal cells. We used HLO1-6H5 and other known basal cell-reactive reagents to isolate viable airway subsets from primary human airway epithelium by Fluorescence Activated Cell Sorting. Isolated primary cell subsets were assessed for the stem cell capabilities of self-renewal and differentiation in the bronchosphere assay, which revealed that bipotent stem cells were, at minimum 3-fold enriched in the HLO1-6H5+ cell subset. Crosslinking-mass spectrometry identified the HLO1-6H5 target as a glycosylated TFRC/CD71 (transferrin receptor) proteoform. The HLO1-6H5 antibody provides a valuable new tool for identifying and isolating a subset of primary human airway basal cells that are substantially enriched for bipotent stem/progenitor cells and reveals TFRC as a defining surface marker for this novel cell subset.
Collapse
Affiliation(s)
- Christopher Cheng
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Parul Katoch
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Yong-Ping Zhong
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Claire T. Higgins
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Maria Moredock
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Scott H. Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Philip R. Streeter
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| |
Collapse
|
25
|
Murthy S, Seabold DA, Gautam LK, Caceres AM, Sease R, Calvert BA, Busch S, Neely A, Marconett CN, Ryan AL. Culture Conditions Differentially Regulate the Inflammatory Niche and Cellular Phenotype of Tracheo-Bronchial Basal Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611264. [PMID: 39282256 PMCID: PMC11398510 DOI: 10.1101/2024.09.04.611264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Human bronchial epithelial cells (HBECs) derived from the tracheo-bronchial regions of human airways provide an excellent in vitro model for studying pathological mechanisms and evaluating therapeutics in human airway cells. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media, airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and Pneumacult Ex plus (PEx+). Extensive RNA sequencing, immune assays and electrical measurements revealed that PEx+ media significantly drove cell proliferation and a broad pro-inflammatory phenotype in BCs. In contrast, BCs expanded in AECGM, displayed increased expression of structural and extracellular matrix components at high passage. Whereas culture in AECGM increased expression of some cytokines at high passage, DSI suppressed inflammation altogether thus implicating TGF-β in BC inflammatory processes. Differentiation capacity declined with time in culture irrespective of expansion media except for PLUNC expressing secretory cells that were elevated at high passage in AECGM and PEx+ suggestive of an immune modulatory role of PLUNC in BCs. These findings underscore the profound impact of media conditions on inflammatory niche and function of in vitro expanded BCs. The broad pro-inflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic application.
Collapse
Affiliation(s)
- Shubha Murthy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Denise A. Seabold
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Lalit K. Gautam
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Adrian M. Caceres
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
| | - Rosemary Sease
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
| | - Ben A. Calvert
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
| | - Shana Busch
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Neely
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Crystal N. Marconett
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Amy L. Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA
| |
Collapse
|
26
|
Liu Y, Ye SY, He S, Chi DM, Wang XZ, Wen YF, Ma D, Nie RC, Xiang P, Zhou Y, Ruan ZH, Peng RJ, Luo CL, Wei PP, Lin GW, Zheng J, Cui Q, Cai MY, Yun JP, Dong J, Mai HQ, Xia X, Bei JX. Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinoma. Nat Commun 2024; 15:7713. [PMID: 39231979 PMCID: PMC11375053 DOI: 10.1038/s41467-024-52153-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/22/2024] [Indexed: 09/06/2024] Open
Abstract
Tertiary lymphoid structures are immune cell aggregates linked with cancer outcomes, but their interactions with tumour cell aggregates are unclear. Using nasopharyngeal carcinoma as a model, here we analyse single-cell transcriptomes of 343,829 cells from 77 biopsy and blood samples and spatially-resolved transcriptomes of 31,316 spots from 15 tumours to decipher their components and interactions with tumour cell aggregates. We identify essential cell populations in tertiary lymphoid structure, including CXCL13+ cancer-associated fibroblasts, stem-like CXCL13+CD8+ T cells, and B and T follicular helper cells. Our study shows that germinal centre reaction matures plasma cells. These plasma cells intersperse with tumour cell aggregates, promoting apoptosis of EBV-related malignant cells and enhancing immunotherapy response. CXCL13+ cancer-associated fibroblasts promote B cell adhesion and antibody production, activating CXCL13+CD8+ T cells that become exhausted in tumour cell aggregates. Tertiary lymphoid structure-related cell signatures correlate with prognosis and PD-1 blockade response, offering insights for therapeutic strategies in cancers.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Shuang-Yan Ye
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, P. R. China
| | - Shuai He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Dong-Mei Chi
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Xiu-Zhi Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yue-Feng Wen
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510000, P. R. China
| | - Dong Ma
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Run-Cong Nie
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Pu Xiang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - You Zhou
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Zhao-Hui Ruan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Rou-Jun Peng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Chun-Ling Luo
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Pan-Pan Wei
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Guo-Wang Lin
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Qian Cui
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, P. R. China
| | - Mu-Yan Cai
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Jing-Ping Yun
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Hai-Qiang Mai
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
- Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211103, P. R. China.
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, 168583, Singapore, Singapore.
| |
Collapse
|
27
|
Redman E, Fierville M, Cavard A, Plaisant M, Arguel MJ, Ruiz Garcia S, McAndrew EM, Girard-Riboulleau C, Lebrigand K, Magnone V, Ponzio G, Gras D, Chanez P, Abelanet S, Barbry P, Marcet B, Zaragosi LE. Cell Culture Differentiation and Proliferation Conditions Influence the In Vitro Regeneration of the Human Airway Epithelium. Am J Respir Cell Mol Biol 2024; 71:267-281. [PMID: 38843491 PMCID: PMC11376247 DOI: 10.1165/rcmb.2023-0356ma] [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: 10/09/2023] [Accepted: 06/06/2024] [Indexed: 07/06/2024] Open
Abstract
The human airway mucociliary epithelium can be recapitulated in vitro using primary cells cultured in an air-liquid interface (ALI), a reliable surrogate to perform pathophysiological studies. As tremendous variations exist among media used for ALI-cultured human airway epithelial cells, the aim of our study was to evaluate the impact of several media (BEGM, PneumaCult, Half & Half, and Clancy) on cell type distribution using single-cell RNA sequencing and imaging. Our work revealed the impact of these media on cell composition, gene expression profile, cell signaling, and epithelial morphology. We found higher proportions of multiciliated cells in PneumaCult-ALI and Half & Half, stronger EGF signaling from basal cells in BEGM-ALI, differential expression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry factor ACE2, and distinct secretome transcripts depending on the media used. We also established that proliferation in PneumaCult-Ex Plus favored secretory cell fate, showing the key influence of proliferation media on late differentiation epithelial characteristics. Altogether, our data offer a comprehensive repertoire for evaluating the effects of culture conditions on airway epithelial differentiation and will aid in choosing the most relevant medium according to the processes to be investigated, such as cilia, mucus biology, or viral infection. We detail useful parameters that should be explored to document airway epithelial cell fate and morphology.
Collapse
Affiliation(s)
- Elisa Redman
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Morgane Fierville
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
- Interdisciplinary Institute for Artificial Intelligence (3IA Côte d'Azur), Université Côte d'Azur, Sophia Antipolis, France; and
| | - Amélie Cavard
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
| | - Magali Plaisant
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Sandra Ruiz Garcia
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
| | - Eamon M McAndrew
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Cédric Girard-Riboulleau
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Virginie Magnone
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Gilles Ponzio
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Delphine Gras
- Centre de Recherche en Cardiovasculaire et Nutrition, Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de Recherche pour L'agriculture, L'alimentation et L'environnement (INRAE), Université Aix-Marseille, Marseille, France
| | - Pascal Chanez
- Centre de Recherche en Cardiovasculaire et Nutrition, Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de Recherche pour L'agriculture, L'alimentation et L'environnement (INRAE), Université Aix-Marseille, Marseille, France
| | - Sophie Abelanet
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
- Interdisciplinary Institute for Artificial Intelligence (3IA Côte d'Azur), Université Côte d'Azur, Sophia Antipolis, France; and
| | - Brice Marcet
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur
- IHU RespirERA, and
| |
Collapse
|
28
|
Gay ACA, Banchero M, Carpaij O, Kole TM, Apperloo L, van Gosliga D, Fajar PA, Koppelman GH, Bont L, Hendriks RW, van den Berge M, Nawijn MC. Airway epithelial cell response to RSV is mostly impaired in goblet and multiciliated cells in asthma. Thorax 2024; 79:811-821. [PMID: 38373824 PMCID: PMC11347251 DOI: 10.1136/thorax-2023-220230] [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: 03/10/2023] [Accepted: 11/27/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND In patients with asthma, respiratory syncytial virus (RSV) infections can cause disease exacerbation by infecting the epithelial layer of the airways, inducing subsequent immune response. The type I interferon antiviral response of epithelial cells upon RSV infection is found to be reduced in asthma in most-but not all-studies. Moreover, the molecular mechanisms causing the differences in the asthmatic bronchial epithelium in response to viral infection are poorly understood. METHODS Here, we investigated the transcriptional response to RSV infection of primary bronchial epithelial cells (pBECs) from patients with asthma (n=8) and healthy donors (n=8). The pBECs obtained from bronchial brushes were differentiated in air-liquid interface conditions and infected with RSV. After 3 days, cells were processed for single-cell RNA sequencing. RESULTS A strong antiviral response to RSV was observed for all cell types, for all samples (p<1e-48). Most (1045) differentially regulated genes following RSV infection were found in cells transitioning to secretory cells. Goblet cells from patients with asthma showed lower expression of genes involved in the interferon response (false discovery rate <0.05), including OASL, ICAM1 and TNFAIP3. In multiciliated cells, an impairment of the signalling pathways involved in the response to RSV in asthma was observed. CONCLUSION Our results highlight that the response to RSV infection of the bronchial epithelium in asthma and healthy airways was largely similar. However, in asthma, the response of goblet and multiciliated cells is impaired, highlighting the need for studying airway epithelial cells at high resolution in the context of asthma exacerbation.
Collapse
Affiliation(s)
- Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Orestes Carpaij
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tessa M Kole
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Leonie Apperloo
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Djoke van Gosliga
- GRIAC research institute, 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
| | - Putri Ayu Fajar
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard H Koppelman
- GRIAC research institute, 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
| | - Louis Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
- Division of Infectious Diseases, Department of Pediatrics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maarten van den Berge
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
29
|
Sun L, Walls SA, Dang H, Quinney NL, Sears PR, Sadritabrizi T, Hasegawa K, Okuda K, Asakura T, Chang X, Zheng M, Mikami Y, Dizmond FU, Danilova D, Zhou L, Deshmukh A, Cholon DM, Radicioni G, Rogers TD, Kissner WJ, Markovetz MR, Guhr Lee TN, Gutay MI, Esther CR, Chua M, Grubb BR, Ehre C, Kesimer M, Hill DB, Ostrowski LE, Button B, Gentzsch M, Robinson C, Olivier KN, Freeman AF, Randell SH, O'Neal WK, Boucher RC, Chen G. Dysregulated Airway Host Defense in Hyper IgE Syndrome due to STAT3 Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607930. [PMID: 39211176 PMCID: PMC11361074 DOI: 10.1101/2024.08.14.607930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Rationale Hyper IgE syndrome (STAT3-HIES), also known as Job's syndrome, is a rare immunodeficiency disease typically caused by dominant-negative STAT3 mutations. STAT3-HIES syndrome is characterized by chronic pulmonary infection and inflammation, suggesting impairment of pulmonary innate host defense. Objectives To identify airway epithelial host defense defects consequent to STAT3 mutations that, in addition to reported mutant STAT3 immunologic abnormalities, produce pulmonary infection. Methods STAT3-HIES sputum was evaluated for biochemical/biophysical properties. STAT3-HIES excised lungs were harvested for histology; bronchial brush samples were collected for RNA sequencing and in vitro culture. A STAT3-HIES-specific mutation (R382W), expressed by lentiviruses, and a STAT3 knockout, generated by CRISPR/Cas9, were maintained in normal human bronchial epithelia under basal or inflammatory (IL1β) conditions. Effects of STAT3 deficiency on transcriptomics, and epithelial ion channel, secretory, antimicrobial, and ciliary functions were assessed. Measurements and Main Results Mucus concentrations and viscoelasticity were increased in STAT3-HIES sputum. STAT3-HIES excised lungs exhibited mucus obstruction and elevated IL1β expression. STAT3 deficiency impaired CFTR-dependent fluid and mucin secretion, inhibited expression of antimicrobial peptides, cytokines, and chemokines, and acidified airway surface liquid at baseline and post-IL1β exposure in vitro. Notably, mutant STAT3 suppressed IL1R1 expression. STAT3 mutations also inhibited ciliogenesis in vivo and impaired mucociliary transport in vitro, a process mediated via HES6 suppression. Administration of a γ-secretase inhibitor increased HES6 expression and improved ciliogenesis in STAT3 R382W mutant cells. Conclusions STAT3 dysfunction leads to multi-component defects in airway epithelial innate defense, which, in conjunction with STAT3-HIES immune deficiency, contributes to chronic pulmonary infection.
Collapse
|
30
|
Koenitzer JR, Gupta DK, Twan WK, Xu H, Hadas N, Hawkins FJ, Beermann ML, Penny GM, Wamsley NT, Berical A, Major MB, Dutcher SK, Brody SL, Horani A. Transcriptional analysis of primary ciliary dyskinesia airway cells reveals a dedicated cilia glutathione pathway. JCI Insight 2024; 9:e180198. [PMID: 39042459 PMCID: PMC11385084 DOI: 10.1172/jci.insight.180198] [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: 03/01/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetic condition that results in dysmotile cilia. The repercussions of cilia dysmotility and gene variants on the multiciliated cell remain poorly understood. We used single-cell RNA-Seq, proteomics, and advanced microscopy to compare primary culture epithelial cells from patients with PCD, their heterozygous mothers, and healthy individuals, and we induced pluripotent stem cells (iPScs) generated from a patient with PCD. Transcriptomic analysis revealed unique signatures in PCD airway cells compared with their mothers' cells and the cells of healthy individuals. Gene expression in heterozygous mothers' cells diverged from both control and PCD cells, marked by increased inflammatory and cellular stress signatures. Primary and iPS-derived PCD multiciliated cells had increased expression of glutathione-S-transferases GSTA2 and GSTA1, as well as NRF2 target genes, accompanied by elevated levels of reactive oxygen species (ROS). Immunogold labeling in human cilia and proteomic analysis of the ciliated organism Chlamydomonas reinhardtii demonstrated that GSTA2 localizes to motile cilia. Loss of human GSTA2 and C. reinhardtii GSTA resulted in slowed cilia motility, pointing to local cilia regulatory roles. Our findings identify cellular responses unique to PCD variants and independent of environmental stress and uncover a dedicated ciliary GSTA2 pathway essential for normal motility that may be a therapeutic target.
Collapse
Affiliation(s)
| | - Deepesh Kumar Gupta
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Wang Kyaw Twan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Huihui Xu
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas Hadas
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine and
- The Pulmonary Center, Department of Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | | | | | - Nathan T Wamsley
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew Berical
- Center for Regenerative Medicine and
- The Pulmonary Center, Department of Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Susan K Dutcher
- Department of Genetics and
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
31
|
Quach H, Farrell S, Wu MJM, Kanagarajah K, Leung JWH, Xu X, Kallurkar P, Turinsky AL, Bear CE, Ratjen F, Kalish B, Goyal S, Moraes TJ, Wong AP. Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity. Nat Commun 2024; 15:5898. [PMID: 39003323 PMCID: PMC11246468 DOI: 10.1038/s41467-024-50281-5] [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: 11/16/2023] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
Collapse
Affiliation(s)
- Henry Quach
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer Farrell
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Jia Michael Wu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kayshani Kanagarajah
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Wai-Hin Leung
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoqiao Xu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prajkta Kallurkar
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine E Bear
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Felix Ratjen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Kalish
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy P Wong
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
32
|
Yamada K, St Croix C, Stolz DB, Tyurina YY, Tyurin VA, Bradley LR, Kapralov AA, Deng Y, Zhou X, Wei Q, Liao B, Fukuda N, Sullivan M, Trudeau J, Ray A, Kagan VE, Zhao J, Wenzel SE. Compartmentalized mitochondrial ferroptosis converges with optineurin-mediated mitophagy to impact airway epithelial cell phenotypes and asthma outcomes. Nat Commun 2024; 15:5818. [PMID: 38987265 PMCID: PMC11237105 DOI: 10.1038/s41467-024-50222-2] [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: 07/11/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
A stable mitochondrial pool is crucial for healthy cell function and survival. Altered redox biology can adversely affect mitochondria through induction of a variety of cell death and survival pathways, yet the understanding of mitochondria and their dysfunction in primary human cells and in specific disease states, including asthma, is modest. Ferroptosis is traditionally considered an iron dependent, hydroperoxy-phospholipid executed process, which induces cytosolic and mitochondrial damage to drive programmed cell death. However, in this report we identify a lipoxygenase orchestrated, compartmentally-targeted ferroptosis-associated peroxidation process which occurs in a subpopulation of dysfunctional mitochondria, without promoting cell death. Rather, this mitochondrial peroxidation process tightly couples with PTEN-induced kinase (PINK)-1(PINK1)-Parkin-Optineurin mediated mitophagy in an effort to preserve the pool of functional mitochondria and prevent cell death. These combined peroxidation processes lead to altered epithelial cell phenotypes and loss of ciliated cells which associate with worsened asthma severity. Ferroptosis-targeted interventions of this process could preserve healthy mitochondria, reverse cell phenotypic changes and improve disease outcomes.
Collapse
Affiliation(s)
- Kazuhiro Yamada
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Claudette St Croix
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Laura R Bradley
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Alexander A Kapralov
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yanhan Deng
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Rheumatology and Immunology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiuxia Zhou
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Qi Wei
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Bo Liao
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Otolaryngology-Head & Neck Surgery, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Nobuhiko Fukuda
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Mara Sullivan
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - John Trudeau
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Anuradha Ray
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jinming Zhao
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| |
Collapse
|
33
|
Swart AL, Laventie BJ, Sütterlin R, Junne T, Lauer L, Manfredi P, Jakonia S, Yu X, Karagkiozi E, Okujava R, Jenal U. Pseudomonas aeruginosa breaches respiratory epithelia through goblet cell invasion in a microtissue model. Nat Microbiol 2024; 9:1725-1737. [PMID: 38858595 DOI: 10.1038/s41564-024-01718-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/29/2024] [Indexed: 06/12/2024]
Abstract
Pseudomonas aeruginosa, a leading cause of severe hospital-acquired pneumonia, causes infections with up to 50% mortality rates in mechanically ventilated patients. Despite some knowledge of virulence factors involved, it remains unclear how P. aeruginosa disseminates on mucosal surfaces and invades the tissue barrier. Using infection of human respiratory epithelium organoids, here we observed that P. aeruginosa colonization of apical surfaces is promoted by cyclic di-GMP-dependent asymmetric division. Infection with mutant strains revealed that Type 6 Secretion System activities promote preferential invasion of goblet cells. Type 3 Secretion System activity by intracellular bacteria induced goblet cell death and expulsion, leading to epithelial rupture which increased bacterial translocation and dissemination to the basolateral epithelium. These findings show that under physiological conditions, P. aeruginosa uses coordinated activity of a specific combination of virulence factors and behaviours to invade goblet cells and breach the epithelial barrier from within, revealing mechanistic insight into lung infection dynamics.
Collapse
Affiliation(s)
| | | | | | - Tina Junne
- Biozentrum, University of Basel, Basel, Switzerland
| | - Luisa Lauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Xiao Yu
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Evdoxia Karagkiozi
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Rusudan Okujava
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
34
|
Chang JJY, Grimley SL, Tran BM, Deliyannis G, Tumpach C, Nguyen AN, Steinig E, Zhang J, Schröder J, Caly L, McAuley J, Wong SL, Waters SA, Stinear TP, Pitt ME, Purcell D, Vincan E, Coin LJ. Uncovering strain- and age-dependent innate immune responses to SARS-CoV-2 infection in air-liquid-interface cultured nasal epithelia. iScience 2024; 27:110009. [PMID: 38868206 PMCID: PMC11166695 DOI: 10.1016/j.isci.2024.110009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 04/03/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Continuous assessment of the impact of SARS-CoV-2 on the host at the cell-type level is crucial for understanding key mechanisms involved in host defense responses to viral infection. We investigated host response to ancestral-strain and Alpha-variant SARS-CoV-2 infections within air-liquid-interface human nasal epithelial cells from younger adults (26-32 Y) and older children (12-14 Y) using single-cell RNA-sequencing. Ciliated and secretory-ciliated cells formed the majority of highly infected cell-types, with the latter derived from ciliated lineages. Strong innate immune responses were observed across lowly infected and uninfected bystander cells and heightened in Alpha-infection. Alpha highly infected cells showed increased expression of protein-refolding genes compared with ancestral-strain-infected cells in children. Furthermore, oxidative phosphorylation-related genes were down-regulated in bystander cells versus infected and mock-control cells, underscoring the importance of these biological functions for viral replication. Overall, this study highlights the complexity of cell-type-, age- and viral strain-dependent host epithelial responses to SARS-CoV-2.
Collapse
Affiliation(s)
- Jessie J.-Y. Chang
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Samantha L. Grimley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Bang M. Tran
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Georgia Deliyannis
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Carolin Tumpach
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - An N.T. Nguyen
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Eike Steinig
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - JianShu Zhang
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jan Schröder
- Computational Sciences Initiative (CSI), The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sharon L. Wong
- Molecular and Integrative Cystic Fibrosis Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shafagh A. Waters
- Molecular and Integrative Cystic Fibrosis Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Respiratory Medicine, Sydney Children’s Hospital, Sydney, NSW 2031, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Miranda E. Pitt
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Damian Purcell
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Lachlan J.M. Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia
| |
Collapse
|
35
|
Choksi SP, Byrnes LE, Konjikusic MJ, Tsai BWH, Deleon R, Lu Q, Westlake CJ, Reiter JF. An alternative cell cycle coordinates multiciliated cell differentiation. Nature 2024; 630:214-221. [PMID: 38811726 PMCID: PMC11996048 DOI: 10.1038/s41586-024-07476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
Collapse
Affiliation(s)
- Semil P Choksi
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Lauren E Byrnes
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mia J Konjikusic
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict W H Tsai
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Deleon
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Quanlong Lu
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
36
|
Stoleriu MG, Ansari M, Strunz M, Schamberger A, Heydarian M, Ding Y, Voss C, Schneider JJ, Gerckens M, Burgstaller G, Castelblanco A, Kauke T, Fertmann J, Schneider C, Behr J, Lindner M, Stacher-Priehse E, Irmler M, Beckers J, Eickelberg O, Schubert B, Hauck SM, Schmid O, Hatz RA, Stoeger T, Schiller HB, Hilgendorff A. COPD basal cells are primed towards secretory to multiciliated cell imbalance driving increased resilience to environmental stressors. Thorax 2024; 79:524-537. [PMID: 38286613 PMCID: PMC11137452 DOI: 10.1136/thorax-2022-219958] [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: 12/18/2022] [Accepted: 01/03/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Environmental pollutants injure the mucociliary elevator, thereby provoking disease progression in chronic obstructive pulmonary disease (COPD). Epithelial resilience mechanisms to environmental nanoparticles in health and disease are poorly characterised. METHODS We delineated the impact of prevalent pollutants such as carbon and zinc oxide nanoparticles, on cellular function and progeny in primary human bronchial epithelial cells (pHBECs) from end-stage COPD (COPD-IV, n=4), early disease (COPD-II, n=3) and pulmonary healthy individuals (n=4). After nanoparticle exposure of pHBECs at air-liquid interface, cell cultures were characterised by functional assays, transcriptome and protein analysis, complemented by single-cell analysis in serial samples of pHBEC cultures focusing on basal cell differentiation. RESULTS COPD-IV was characterised by a prosecretory phenotype (twofold increase in MUC5AC+) at the expense of the multiciliated epithelium (threefold reduction in Ac-Tub+), resulting in an increased resilience towards particle-induced cell damage (fivefold reduction in transepithelial electrical resistance), as exemplified by environmentally abundant doses of zinc oxide nanoparticles. Exposure of COPD-II cultures to cigarette smoke extract provoked the COPD-IV characteristic, prosecretory phenotype. Time-resolved single-cell transcriptomics revealed an underlying COPD-IV unique basal cell state characterised by a twofold increase in KRT5+ (P=0.018) and LAMB3+ (P=0.050) expression, as well as a significant activation of Wnt-specific (P=0.014) and Notch-specific (P=0.021) genes, especially in precursors of suprabasal and secretory cells. CONCLUSION We identified COPD stage-specific gene alterations in basal cells that affect the cellular composition of the bronchial elevator and may control disease-specific epithelial resilience mechanisms in response to environmental nanoparticles. The identified phenomena likely inform treatment and prevention strategies.
Collapse
Affiliation(s)
- Mircea Gabriel Stoleriu
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Meshal Ansari
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Maximilian Strunz
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Andrea Schamberger
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Motaharehsadat Heydarian
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Yaobo Ding
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Carola Voss
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Juliane Josephine Schneider
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Michael Gerckens
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine V, University Hospital, LMU Munich and Asklepios Medical Center, Munich, Germany
| | - Gerald Burgstaller
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Alejandra Castelblanco
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Teresa Kauke
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Jan Fertmann
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Christian Schneider
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Juergen Behr
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine V, University Hospital, LMU Munich and Asklepios Medical Center, Munich, Germany
| | - Michael Lindner
- Department of Visceral and Thoracic Surgery Salzburg, Paracelsus Medical University, Salzburg, Austria
| | | | - Martin Irmler
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Experimental Genetics, Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Experimental Genetics, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Life Sciences, Chair of Experimental Genetics, Technical University Munich, Freising, Germany
| | - Oliver Eickelberg
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine, Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Benjamin Schubert
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Mathematics, Technische Universität München, Garching bei München, München, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Otmar Schmid
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Rudolf A Hatz
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Tobias Stoeger
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Herbert B Schiller
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Anne Hilgendorff
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Center for Comprehensive Developmental Care at the iSPZ Hauner, Dr. von Haunersches Children's University Hospital, Ludwig-Maximilians-University of Munich (LMU); Member of the German Lung Research Center (DZL), Munich, Germany
| |
Collapse
|
37
|
Ambrogi M, Vezina CM. Roles of airway and intestinal epithelia in responding to pathogens and maintaining tissue homeostasis. Front Cell Infect Microbiol 2024; 14:1346087. [PMID: 38736751 PMCID: PMC11082347 DOI: 10.3389/fcimb.2024.1346087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/10/2024] [Indexed: 05/14/2024] Open
Abstract
Epithelial cells form a resilient barrier and orchestrate defensive and reparative mechanisms to maintain tissue stability. This review focuses on gut and airway epithelia, which are positioned where the body interfaces with the outside world. We review the many signaling pathways and mechanisms by which epithelial cells at the interface respond to invading pathogens to mount an innate immune response and initiate adaptive immunity and communicate with other cells, including resident microbiota, to heal damaged tissue and maintain homeostasis. We compare and contrast how airway and gut epithelial cells detect pathogens, release antimicrobial effectors, collaborate with macrophages, Tregs and epithelial stem cells to mount an immune response and orchestrate tissue repair. We also describe advanced research models for studying epithelial communication and behaviors during inflammation, tissue injury and disease.
Collapse
Affiliation(s)
| | - Chad M. Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
38
|
McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
39
|
Liu Y, Lv W, Wang W. Uncovering the Cellular Microenvironment in Chronic Rhinosinusitis via Single-Cell RNA Sequencing: Application and Future Directions. Clin Rev Allergy Immunol 2024; 66:210-222. [PMID: 38687404 DOI: 10.1007/s12016-024-08992-6] [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] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Chronic rhinosinusitis (CRS) is a heterogenic disease characterized by persistent mucosal inflammation of the upper airway. Researches of CRS have progressed from phenotype-based to endotype-based, looking more deeply into molecular biomarkers, signaling pathways, and immune microenvironment. Single-cell RNA sequencing is an effective tool in analyzing composition, function, and interaction of cells in disease microenvironment at transcriptome level, showing great advantage in analyzing potential biomarkers, pathogenesis, and heterogeneity of chronic airway inflammation in an unbiased manner. In this article, we will review the latest advances in scRNA-seq studies of CRS to provide new perspectives for the diagnosis and treatment of this heterogeneous disease.
Collapse
Affiliation(s)
- Yuzhuo Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
| | - Wei Lv
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China.
| | - Weiqing Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
40
|
Vaidyanathan S, Kerschner JL, Paranjapye A, Sinha V, Lin B, Bedrosian TA, Thrasher AJ, Turchiano G, Harris A, Porteus MH. Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102134. [PMID: 38384445 PMCID: PMC10879780 DOI: 10.1016/j.omtn.2024.102134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
A "universal strategy" replacing the full-length CFTR cDNA may treat >99% of people with cystic fibrosis (pwCF), regardless of their specific mutations. Cas9-based gene editing was used to insert the CFTR cDNA and a truncated CD19 (tCD19) enrichment tag at the CFTR locus in airway basal stem cells. This strategy restores CFTR function to non-CF levels. Here, we investigate the safety of this approach by assessing genomic and regulatory changes after CFTR cDNA insertion. Safety was first assessed by quantifying genetic rearrangements using CAST-seq. After validating restored CFTR function in edited and enriched airway cells, the CFTR locus open chromatin profile was characterized using ATAC-seq. The regenerative potential and differential gene expression in edited cells was assessed using scRNA-seq. CAST-seq revealed a translocation in ∼0.01% of alleles primarily occurring at a nononcogenic off-target site and large indels in 1% of alleles. The open chromatin profile of differentiated airway epithelial cells showed no appreciable changes, except in the region corresponding to the CFTR cDNA and tCD19 cassette, indicating no detectable changes in gene regulation. Edited stem cells produced the same types of airway cells as controls with minimal alternations in gene expression. Overall, the universal strategy showed minor undesirable genomic changes.
Collapse
Affiliation(s)
- Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny L. Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vrishti Sinha
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Brian Lin
- Department of Developmental, Molecular, and Chemical Biology, Tufts University, Boston, MA 02111, USA
| | - Tracy A. Bedrosian
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Adrian J. Thrasher
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Giandomenico Turchiano
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | |
Collapse
|
41
|
Martins LR, Sieverling L, Michelhans M, Schiller C, Erkut C, Grünewald TGP, Triana S, Fröhling S, Velten L, Glimm H, Scholl C. Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung. Nat Commun 2024; 15:2246. [PMID: 38472236 DOI: 10.1038/s41467-024-46469-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.
Collapse
Affiliation(s)
- Leila R Martins
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| | - Lina Sieverling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
| | - Michelle Michelhans
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Chiara Schiller
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | - Cihan Erkut
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas G P Grünewald
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, DKFZ, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sergio Triana
- Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Broad Institute of Harvard and MIT, Cambridge, USA
- Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
- DKTK, partner site Dresden, Dresden, Germany
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|
42
|
Barrera-Lopez JF, Cumplido-Laso G, Olivera-Gomez M, Garrido-Jimenez S, Diaz-Chamorro S, Mateos-Quiros CM, Benitez DA, Centeno F, Mulero-Navarro S, Roman AC, Carvajal-Gonzalez JM. Early Atf4 activity drives airway club and goblet cell differentiation. Life Sci Alliance 2024; 7:e202302284. [PMID: 38176727 PMCID: PMC10766780 DOI: 10.26508/lsa.202302284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
Activating transcription factor 4 (Atf4), which is modulated by the protein kinase RNA-like ER kinase (PERK), is a stress-induced transcription factor responsible for controlling the expression of a wide range of adaptive genes, enabling cells to withstand stressful conditions. However, the impact of the Atf4 signaling pathway on airway regeneration remains poorly understood. In this study, we used mouse airway epithelial cell culture models to investigate the role of PERK/Atf4 in respiratory tract differentiation. Through pharmacological inhibition and silencing of ATF4, we uncovered the crucial involvement of PERK/Atf4 in the differentiation of basal stem cells, leading to a reduction in the number of secretory cells. ChIP-seq analysis revealed direct binding of ATF4 to regulatory elements of genes associated with osteoblast differentiation and secretory cell function. Our findings provide valuable insights into the role of ATF4 in airway epithelial differentiation and its potential involvement in innate immune responses and cellular adaptation to stress.
Collapse
Affiliation(s)
- Juan F Barrera-Lopez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Guadalupe Cumplido-Laso
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Marcos Olivera-Gomez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sergio Garrido-Jimenez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Selene Diaz-Chamorro
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Clara M Mateos-Quiros
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Dixan A Benitez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Francisco Centeno
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Angel C Roman
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Jose M Carvajal-Gonzalez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| |
Collapse
|
43
|
Rouhani MJ, Janes SM, Kim CF. Epithelial stem and progenitor cells of the upper airway. Cells Dev 2024; 177:203905. [PMID: 38355015 DOI: 10.1016/j.cdev.2024.203905] [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: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The upper airway acts as a conduit for the passage of air to the respiratory system and is implicated in several chronic diseases. Whilst the cell biology of the distal respiratory system has been described in great detail, less is known about the proximal upper airway. In this review, we describe the relevant anatomy of the upper airway and discuss the literature detailing the identification and roles of the progenitor cells of these regions.
Collapse
Affiliation(s)
- Maral J Rouhani
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Carla F Kim
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
44
|
Shiratsuchi G, Konishi S, Yano T, Yanagihashi Y, Nakayama S, Katsuno T, Kashihara H, Tanaka H, Tsukita K, Suzuki K, Herawati E, Watanabe H, Hirai T, Yagi T, Kondoh G, Gotoh S, Tamura A, Tsukita S. Dual-color live imaging unveils stepwise organization of multiple basal body arrays by cytoskeletons. EMBO Rep 2024; 25:1176-1207. [PMID: 38316902 PMCID: PMC10933483 DOI: 10.1038/s44319-024-00066-0] [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: 05/03/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 02/07/2024] Open
Abstract
For mucociliary clearance of pathogens, tracheal multiciliated epithelial cells (MCCs) organize coordinated beating of cilia, which originate from basal bodies (BBs) with basal feet (BFs) on one side. To clarify the self-organizing mechanism of coordinated intracellular BB-arrays composed of a well-ordered BB-alignment and unidirectional BB-orientation, determined by the direction of BB to BF, we generated double transgenic mice with GFP-centrin2-labeled BBs and mRuby3-Cep128-labeled BFs for long-term, high-resolution, dual-color live-cell imaging in primary-cultured tracheal MCCs. At early timepoints of MCC differentiation, BB-orientation and BB-local alignment antecedently coordinated in an apical microtubule-dependent manner. Later during MCC differentiation, fluctuations in BB-orientation were restricted, and locally aligned BB-arrays were further coordinated to align across the entire cell (BB-global alignment), mainly in an apical intermediate-sized filament-lattice-dependent manner. Thus, the high coordination of the BB-array was established for efficient mucociliary clearance as the primary defense against pathogen infection, identifying apical cytoskeletons as potential therapeutic targets.
Collapse
Affiliation(s)
- Gen Shiratsuchi
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Satoshi Konishi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Tomoki Yano
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | | | - Shogo Nakayama
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Tatsuya Katsuno
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Center for Anatomical Studies, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroo Tanaka
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- School of Medicine, Teikyo University, Tokyo, Japan
| | - Kazuto Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koya Suzuki
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Elisa Herawati
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Surakarta, Central Java, Indonesia
| | - Hitomi Watanabe
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Yagi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Gen Kondoh
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shimpei Gotoh
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Atsushi Tamura
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
- School of Medicine, Teikyo University, Tokyo, Japan.
| | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
| |
Collapse
|
45
|
Turan G, Olgun ÇE, Ayten H, Toker P, Ashyralyyev A, Savaş B, Karaca E, Muyan M. Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance. Protein Sci 2024; 33:e4859. [PMID: 38145972 PMCID: PMC10804680 DOI: 10.1002/pro.4859] [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: 08/17/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/27/2023]
Abstract
YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is largely unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner in response to internal and external stimuli. Here, we explored interaction partners of YPEL2 by using dynamic TurboID-coupled mass spectrometry analyses to infer a function for the protein. Our results using inducible transgene expressions in COS7 cells indicate that proximity interaction partners of YPEL2 are mainly involved in RNA and mRNA metabolic processes, ribonucleoprotein complex biogenesis, regulation of gene silencing by miRNA, and cellular responses to stress. We showed that YPEL2 interacts with the RNA-binding protein ELAVL1 and the selective autophagy receptor SQSTM1. We also found that YPEL2 localizes stress granules in response to sodium arsenite, an oxidative stress inducer, which suggests that YPEL2 participates in stress granule-related processes. Establishing a point of departure in the delineation of structural/functional features of YPEL2, our results suggest that YPEL2 may be involved in stress surveillance mechanisms.
Collapse
Affiliation(s)
- Gizem Turan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Çağla Ece Olgun
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Hazal Ayten
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Pelin Toker
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | | | - Büşra Savaş
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Ezgi Karaca
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Mesut Muyan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
- CanSyl LaboratoriesMiddle East Technical UniversityAnkaraTürkiye
| |
Collapse
|
46
|
Hata K, Tsubouchi K, Suzuki K, Eto D, Ando H, Yanagihara T, Kan-O K, Okamoto I. Surfactant protein D prevents mucin overproduction in airway goblet cells via SIRPα. Sci Rep 2024; 14:1799. [PMID: 38245585 PMCID: PMC10799941 DOI: 10.1038/s41598-024-52328-5] [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: 10/10/2023] [Accepted: 01/17/2024] [Indexed: 01/22/2024] Open
Abstract
Mucin overproduction is a common feature of chronic airway diseases such as asthma and chronic obstructive pulmonary disease (COPD), and exacerbates their underlying respiratory condition. Surfactant protein D (SP-D) protects against airway diseases through modulation of immune reactions, but whether it also exerts direct effects on airway epithelial cells has remained unclear. Therefore, we sought to investigate the inhibitory role of SP-D on mucin production in airway epithelial cells. We prepared air-liquid interface (ALI) cultures of human primary bronchial epithelial cells (HBECs), which recapitulated a well-differentiated human airway epithelium. Benzo(a)pyrene (BaP), a key toxicant in cigarette smoke, induced mucin 5AC (MUC5AC) production in ALI-cultured HBECs, airway secretory cell lines, and airway epithelia of mice. Then, the protective effects of SP-D against the BaP-induced mucin overproduction were examined. BaP increased MUC5AC production in ALI cultures of HBECs, and this effect was attenuated by SP-D. SP-D also suppressed the BaP-induced phosphorylation of extracellular signal-regulated kinase (ERK) and MUC5AC expression in NCI-H292 goblet-like cells, but not in NCI-H441 club-like cells. Signal regulatory protein α (SIRPα) was found to be expressed in HBECs and NCI-H292 cells but absent in NCI-H441 cells. In NCI-H292 cells, SP-D activated SH2 domain-containing tyrosine phosphatase-1 (SHP-1), downstream of SIRPα, and knockdown of SIRPα abolished the suppressive effects of SP-D on BaP-induced ERK phosphorylation and MUC5AC production. Consistent with these in vitro findings, intratracheal instillation of SP-D prevented the BaP-induced phosphorylation of ERK and Muc5ac expression in airway epithelial cells in a mouse model. SP-D acts directly on airway epithelial cells to inhibit mucin secretion through ligation of SIRPα and SHP-1-mediated dephosphorylation of ERK. Targeting of SIRPα is therefore a potential new therapeutic approach to suppression of mucin hypersecretion in chronic airway diseases such as COPD and asthma.
Collapse
Affiliation(s)
- Kentaro Hata
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kazuya Tsubouchi
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Kunihiro Suzuki
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Daisuke Eto
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hiroyuki Ando
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Toyoshi Yanagihara
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Keiko Kan-O
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Isamu Okamoto
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| |
Collapse
|
47
|
Brand M, Ritzmann F, Kattler K, Milasius D, Yao Y, Herr C, Kirsch SH, Müller R, Yildiz D, Bals R, Beisswenger C. Biochemical and transcriptomic evaluation of a 3D lung organoid platform for pre-clinical testing of active substances targeting senescence. Respir Res 2024; 25:3. [PMID: 38172839 PMCID: PMC10765931 DOI: 10.1186/s12931-023-02636-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Chronic lung diseases such as chronic obstructive pulmonary disease and cystic fibrosis are incurable. Epithelial senescence, a state of dysfunctional cell cycle arrest, contributes to the progression of such diseases. Therefore, lung epithelial cells are a valuable target for therapeutic intervention. Here, we present a 3D airway lung organoid platform for the preclinical testing of active substances with regard to senescence, toxicity, and inflammation under standardized conditions in a 96 well format. Senescence was induced with doxorubicin and measured by activity of senescence associated galactosidase. Pharmaceutical compounds such as quercetin antagonized doxorubicin-induced senescence without compromising organoid integrity. Using single cell sequencing, we identified a subset of cells expressing senescence markers which was decreased by quercetin. Doxorubicin induced the expression of detoxification factors specifically in goblet cells independent of quercetin. In conclusion, our platform enables for the analysis of senescence-related processes and will allow the pre-selection of a wide range of compounds (e.g. natural products) in preclinical studies, thus reducing the need for animal testing.
Collapse
Affiliation(s)
- Michelle Brand
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Felix Ritzmann
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
- Department of Drug Delivery (DDEL), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany
| | - Deivydas Milasius
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Yiwen Yao
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Susanne H Kirsch
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Daniela Yildiz
- Experimental and Clinical Pharmacology and Toxicology, PZMS, and Center for Human and Molecular Biology (ZHMB), Saarland University, 66421, Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
- Department of Drug Delivery (DDEL), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Christoph Beisswenger
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany.
| |
Collapse
|
48
|
Zaragosi LE, Gouleau A, Delin M, Lebrigand K, Arguel MJ, Girard-Riboulleau C, Rios G, Redman E, Plaisant M, Waldmann R, Magnone V, Marcet B, Barbry P, Ponzio G. Combination of CRISPR-Cas9-RNP and Single-Cell RNAseq to Identify Cell State-Specific FOXJ1 Functions in the Human Airway Epithelium. Methods Mol Biol 2024; 2725:1-25. [PMID: 37856015 DOI: 10.1007/978-1-0716-3507-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The study of the airway epithelium in vitro is routinely performed using air-liquid culture (ALI) models from nasal or bronchial basal cells. These 3D experimental models allow to follow the regeneration steps of fully differentiated mucociliary epithelium and to study gene function by performing gene invalidation. Recent progress made with CRISPR-based techniques has overcome the experimental difficulty of this approach, by a direct transfection of ribonucleoprotein complexes combining a mix of synthetic small guide RNAs (sgRNAs) and recombinant Cas9. The approach shows more than 95% efficiency and does not require any selection step. A limitation of this approach is that it generates cell populations that contain heterogeneous deletions, which makes the evaluation of invalidation efficiency difficult. We have successfully used Flongle sequencing (Nanopore) to quantify the number of distinct deletions. We describe the use of CRISPR-Cas9 RNP in combination with single-cell RNA sequencing to functionally characterize the impact of gene invalidation in ALI cultures. The complex ecosystem of the airway epithelium, composed of many cell types, makes single-cell approaches particularly relevant to study cell type, or cell state-specific events. This protocol describes the invalidation of FOXJ1 in ALI cultures through the following steps: (1) Establishment of basal cell cultures from nasal turbinates, (2) CRISPR-Cas9 RNP invalidation of FOXJ1, (3) Quantification of FOXJ1 invalidation efficiency by Nanopore sequencing, (4) Dissociation of ALI cultures and single-cell RNAseq, (5) Analysis of single-cell RNAseq data from FOXJ1-invalidated cells.We confirm here that FOXJ1 invalidation impairs the final differentiation step of multiciliated cells and provides a framework to explore other gene functions.
Collapse
Affiliation(s)
| | - Alizé Gouleau
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Margot Delin
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | | | - Geraldine Rios
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Elisa Redman
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| |
Collapse
|
49
|
Petit LMG, Belgacemi R, Ancel J, Saber Cherif L, Polette M, Perotin JM, Spassky N, Pilette C, Al Alam D, Deslée G, Dormoy V. Airway ciliated cells in adult lung homeostasis and COPD. Eur Respir Rev 2023; 32:230106. [PMID: 38056888 PMCID: PMC10698550 DOI: 10.1183/16000617.0106-2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/07/2023] [Indexed: 12/08/2023] Open
Abstract
Cilia are organelles emanating from the cell surface, consisting of an axoneme of microtubules that extends from a basal body derived from the centrioles. They are either isolated and nonmotile (primary cilia), or grouped and motile (motile cilia). Cilia are at the centre of fundamental sensory processes and are involved in a wide range of human disorders. Pulmonary cilia include motile cilia lining the epithelial cells of the conductive airways to orchestrate mucociliary clearance, and primary cilia found on nondifferentiated epithelial and mesenchymal cells acting as sensors and cell cycle keepers. Whereas cilia are essential along the airways, their regulatory molecular mechanisms remain poorly understood, resulting in a lack of therapeutic strategies targeting their structure or functions. This review summarises the current knowledge on cilia in the context of lung homeostasis and COPD to provide a comprehensive overview of the (patho)biology of cilia in respiratory medicine with a particular emphasis on COPD.
Collapse
Affiliation(s)
- Laure M G Petit
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
| | - Randa Belgacemi
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Julien Ancel
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
- CHU Reims, Hôpital Maison Blanche, Service de Pneumologie, Reims, France
| | - Lynda Saber Cherif
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
| | - Myriam Polette
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
- CHU Reims, Hôpital Maison Blanche, Laboratoire de Biopathologie, Reims, France
| | - Jeanne-Marie Perotin
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
- CHU Reims, Hôpital Maison Blanche, Service de Pneumologie, Reims, France
| | - Nathalie Spassky
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Charles Pilette
- Université Catholique de Louvain (UCL), Institute of Experimental and Clinical Research - Pole of Pneumology, ENT, Dermatology and Pulmonology Department, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gaëtan Deslée
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
- CHU Reims, Hôpital Maison Blanche, Service de Pneumologie, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, INSERM, P3Cell UMR-S1250, SFR CAP-SANTE, Reims, France
| |
Collapse
|
50
|
Chae S, Park TJ, Kwon T. Convergent differentiation of multiciliated cells. Sci Rep 2023; 13:23028. [PMID: 38155158 PMCID: PMC10754865 DOI: 10.1038/s41598-023-50077-5] [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: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Multiciliated cells (MCCs) are epithelial cells that control body fluid flow and contribute to the clearance of pathogenic microbes and other particles from the airways, egg transport in oviducts, and circulation of cerebrospinal fluid in the central nervous system. Although MCCs have shared functions to control fluid flow via coordinated motility of multiple ciliary structures, they are found in multiple mammalian tissues originating from distinct germ layers and differentiate via distinct developmental pathways. To understand the similarities and differences of MCCs in multiple tissues, we investigated single-cell transcriptome data of nasal epithelial cells, bronchial tubes, fallopian tubes, and ependymal cells in the subventricular zone from humans and mice by cross-species data integration. Expression of cilia-associated genes was indistinguishable between these MCCs, although cell populations had unique properties by the species and tissue, demonstrating that they share the same final differentiation status for ciliary functions. We further analyzed the final differentiation step of MCCs from their distinctive progenitors and confirmed their convergent gene set expression for ciliogenesis at the final step. These results may provide new insight into understanding ciliogenesis during the developmental process.
Collapse
Affiliation(s)
- Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| |
Collapse
|