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Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs

Author

Listed:
  • Praveen Weeratunga

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Laura Denney

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Joshua A. Bull

    (University of Oxford)

  • Emmanouela Repapi

    (MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Martin Sergeant

    (MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Rachel Etherington

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Chaitanya Vuppussetty

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Gareth D. H. Turner

    (Oxford University Hospitals NHS Foundation Trust)

  • Colin Clelland

    (Anatomic Pathology, Weill Cornell Medical College)

  • Jeongmin Woo

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Amy Cross

    (University of Oxford)

  • Fadi Issa

    (University of Oxford)

  • Carlos Eduardo Andrea

    (Navarra Institute for Health Research)

  • Ignacio Melero Bermejo

    (Navarra Institute for Health Research)

  • David Sims

    (MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Simon McGowan

    (MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Yasemin-Xiomara Zurke

    (Kennedy Institute for Rheumatology, University of Oxford)

  • David J. Ahern

    (Kennedy Institute for Rheumatology, University of Oxford)

  • Eddie C. Gamez

    (Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford)

  • Justin Whalley

    (Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford)

  • Duncan Richards

    (University of Oxford)

  • Paul Klenerman

    (University of Oxford)

  • Claudia Monaco

    (Kennedy Institute for Rheumatology, University of Oxford)

  • Irina A. Udalova

    (Kennedy Institute for Rheumatology, University of Oxford)

  • Tao Dong

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford
    University of Oxford)

  • Agne Antanaviciute

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford)

  • Graham Ogg

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford
    University of Oxford)

  • Julian C. Knight

    (Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford
    University of Oxford)

  • Helen M. Byrne

    (University of Oxford
    University of Oxford)

  • Stephen Taylor

    (MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford
    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford)

  • Ling-Pei Ho

    (MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford
    University of Oxford
    University of Oxford)

Abstract

Single cell spatial interrogation of the immune-structural interactions in COVID −19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.

Suggested Citation

  • Praveen Weeratunga & Laura Denney & Joshua A. Bull & Emmanouela Repapi & Martin Sergeant & Rachel Etherington & Chaitanya Vuppussetty & Gareth D. H. Turner & Colin Clelland & Jeongmin Woo & Amy Cross , 2023. "Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42421-0
    DOI: 10.1038/s41467-023-42421-0
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    References listed on IDEAS

    as
    1. Johannes C. Melms & Jana Biermann & Huachao Huang & Yiping Wang & Ajay Nair & Somnath Tagore & Igor Katsyv & André F. Rendeiro & Amit Dipak Amin & Denis Schapiro & Chris J. Frangieh & Adrienne M. Luom, 2021. "Author Correction: A molecular single-cell lung atlas of lethal COVID-19," Nature, Nature, vol. 598(7882), pages 2-2, October.
    2. William J. Zacharias & David B. Frank & Jarod A. Zepp & Michael P. Morley & Farrah A. Alkhaleel & Jun Kong & Su Zhou & Edward Cantu & Edward E. Morrisey, 2018. "Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor," Nature, Nature, vol. 555(7695), pages 251-255, March.
    3. André F. Rendeiro & Hiranmayi Ravichandran & Yaron Bram & Vasuretha Chandar & Junbum Kim & Cem Meydan & Jiwoon Park & Jonathan Foox & Tyler Hether & Sarah Warren & Youngmi Kim & Jason Reeves & Steven , 2021. "The spatial landscape of lung pathology during COVID-19 progression," Nature, Nature, vol. 593(7860), pages 564-569, May.
    4. Toni M. Delorey & Carly G. K. Ziegler & Graham Heimberg & Rachelly Normand & Yiming Yang & Åsa Segerstolpe & Domenic Abbondanza & Stephen J. Fleming & Ayshwarya Subramanian & Daniel T. Montoro & Karth, 2021. "COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets," Nature, Nature, vol. 595(7865), pages 107-113, July.
    5. Avraham Unterman & Tomokazu S. Sumida & Nima Nouri & Xiting Yan & Amy Y. Zhao & Victor Gasque & Jonas C. Schupp & Hiromitsu Asashima & Yunqing Liu & Carlos Cosme & Wenxuan Deng & Ming Chen & Micha Sam, 2022. "Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    6. M. Büttner & J. Ostner & C. L. Müller & F. J. Theis & B. Schubert, 2021. "scCODA is a Bayesian model for compositional single-cell data analysis," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    7. Johannes C. Melms & Jana Biermann & Huachao Huang & Yiping Wang & Ajay Nair & Somnath Tagore & Igor Katsyv & André F. Rendeiro & Amit Dipak Amin & Denis Schapiro & Chris J. Frangieh & Adrienne M. Luom, 2021. "A molecular single-cell lung atlas of lethal COVID-19," Nature, Nature, vol. 595(7865), pages 114-119, July.
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