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Milross L, Hunter B, McDonald D, Merces G, Thomson A, Hilkens CMU, Wills J, Rees P, Jiwa K, Cooper N, Majo J, Ashwin H, Duncan CJA, Kaye PM, Bayraktar OA, Filby A, Fisher AJ. Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19. EBioMedicine 2024; 99:104945. [PMID: 38142637 PMCID: PMC10788437 DOI: 10.1016/j.ebiom.2023.104945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Lung damage in severe COVID-19 is highly heterogeneous however studies with dedicated spatial distinction of discrete temporal phases of diffuse alveolar damage (DAD) and alternate lung injury patterns are lacking. Existing studies have also not accounted for progressive airspace obliteration in cellularity estimates. We used an imaging mass cytometry (IMC) analysis with an airspace correction step to more accurately identify the cellular immune response that underpins the heterogeneity of severe COVID-19 lung disease. METHODS Lung tissue was obtained at post-mortem from severe COVID-19 deaths. Pathologist-selected regions of interest (ROIs) were chosen by light microscopy representing the patho-evolutionary spectrum of DAD and alternate disease phenotypes were selected for comparison. Architecturally normal SARS-CoV-2-positive lung tissue and tissue from SARS-CoV-2-negative donors served as controls. ROIs were stained for 40 cellular protein markers and ablated using IMC before segmented cells were classified. Cell populations corrected by ROI airspace and their spatial relationships were compared across lung injury patterns. FINDINGS Forty patients (32M:8F, age: 22-98), 345 ROIs and >900k single cells were analysed. DAD progression was marked by airspace obliteration and significant increases in mononuclear phagocytes (MnPs), T and B lymphocytes and significant decreases in alveolar epithelial and endothelial cells. Neutrophil populations proved stable overall although several interferon-responding subsets demonstrated expansion. Spatial analysis revealed immune cell interactions occur prior to microscopically appreciable tissue injury. INTERPRETATION The immunopathogenesis of severe DAD in COVID-19 lung disease is characterised by sustained increases in MnPs and lymphocytes with key interactions occurring even prior to lung injury is established. FUNDING UK Research and Innovation/Medical Research Council through the UK Coronavirus Immunology Consortium, Barbour Foundation, General Sir John Monash Foundation, Newcastle University, JGW Patterson Foundation, Wellcome Trust.
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Affiliation(s)
- Luke Milross
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Bethany Hunter
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - David McDonald
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - George Merces
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amanda Thomson
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Catharien M U Hilkens
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - John Wills
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul Rees
- Department of Biomedical Engineering, Swansea University, Wales, UK; Imaging Platform, Broad Institute of MIT and Harvard, 415 Main Street, Boston, Cambridge, MA, USA
| | - Kasim Jiwa
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nigel Cooper
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Joaquim Majo
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Helen Ashwin
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Christopher J A Duncan
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Paul M Kaye
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | | | - Andrew Filby
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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Hunter B, Nicorescu I, Foster E, McDonald D, Hulme G, Fuller A, Thomson A, Goldsborough T, Hilkens CMU, Majo J, Milross L, Fisher A, Bankhead P, Wills J, Rees P, Filby A, Merces G. OPTIMAL: An OPTimized Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data exploration. Cytometry A 2024; 105:36-53. [PMID: 37750225 PMCID: PMC10952805 DOI: 10.1002/cyto.a.24803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Analysis of imaging mass cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single-cell segmentation and suboptimal approaches for data visualization and exploration. This can lead to inaccurate identification of cell phenotypes, states, or spatial relationships compared to reference data from single-cell suspension technologies. To this end we have developed the "OPTimized Imaging Mass cytometry AnaLysis (OPTIMAL)" framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualization/clustering, and spatial neighborhood analysis. Using a panel of 27 metal-tagged antibodies recognizing well-characterized phenotypic and functional markers to stain the same Formalin-Fixed Paraffin Embedded (FFPE) human tonsil sample tissue microarray over 12 temporally distinct batches we tested several cell segmentation models, a range of different arcsinh cofactor parameter transformation values, 5 different dimensionality reduction algorithms, and 2 clustering methods. Finally, we assessed the optimal approach for performing neighborhood analysis. We found that single-cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using "classical" bivariate data display techniques. The optimal arcsinh cofactor for parameter transformation was 1 as it maximized the statistical separation between negative and positive signal distributions and a simple Z-score normalization step after arcsinh transformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing phenograph in terms of cell type identification. We also found that neighborhood analysis was influenced by the method used for finding neighboring cells with a "disc" pixel expansion outperforming a "bounding box" approach combined with the need for filtering objects based on size and image-edge location. Importantly, OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output and allows for single-cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.
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Affiliation(s)
- Bethany Hunter
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Ioana Nicorescu
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Emma Foster
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - David McDonald
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Gillian Hulme
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fuller
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Amanda Thomson
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Catharien M. U. Hilkens
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joaquim Majo
- Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Luke Milross
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fisher
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Peter Bankhead
- Centre for Genomic and Experimental Medicine, CRUK Scotland Centre, and Edinburgh PathologyUniversity of EdinburghEdinburghUK
| | - John Wills
- Department of Veterinary MedicineCambridge UniversityCambridgeUK
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
| | - Paul Rees
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
- Imaging PlatformBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Andrew Filby
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - George Merces
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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Pelliciari S, Bodet-Lefèvre S, Fenyk S, Stevens D, Winterhalter C, Schramm FD, Pintar S, Burnham DR, Merces G, Richardson TT, Tashiro Y, Hubbard J, Yardimci H, Ilangovan A, Murray H. The bacterial replication origin BUS promotes nucleobase capture. Nat Commun 2023; 14:8339. [PMID: 38097584 PMCID: PMC10721633 DOI: 10.1038/s41467-023-43823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaAATP assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).
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Affiliation(s)
- Simone Pelliciari
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Salomé Bodet-Lefèvre
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK
| | - Stepan Fenyk
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Daniel Stevens
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Frederic D Schramm
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Sara Pintar
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Daniel R Burnham
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - George Merces
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Tomas T Richardson
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Yumiko Tashiro
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK
| | - Julia Hubbard
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Hasan Yardimci
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Aravindan Ilangovan
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK.
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK.
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