3d virtual pathohistology of lung tissue from COVID-19 patients based on phase contrast x-ray tomography

  1. Marina Eckermann
  2. Jasper Frohn
  3. Marius Reichardt
  4. Markus Osterhoff
  5. Michael Sprung
  6. Fabian Westermeier
  7. Alexandar Tzankov
  8. Christopher Werlein
  9. Mark Kühnel
  10. Danny Jonigk  Is a corresponding author
  11. Tim Salditt  Is a corresponding author
  1. Georg-August-Universität Göttingen, Germany
  2. Deutsches Elektronen-Synchrotron (DESY), Germany
  3. Universitätsspital Basel, Switzerland
  4. Medizinische Hochschule Hannover (MHH), Germany

Abstract

We present a three-dimensional (3d) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3d visualisation of the DAD with its prominent hyaline membrane formation, by mapping the 3d distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.

Data availability

All datasets were uploaded to zenodo: 10.5281/zenodo.3892637

The following data sets were generated

Article and author information

Author details

  1. Marina Eckermann

    Institute for x-ray physics, Georg-August-Universität Göttingen, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Jasper Frohn

    Institute for x-ray physics, Georg-August-Universität Göttingen, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Marius Reichardt

    Institute for x-ray physics, Georg-August-Universität Göttingen, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Markus Osterhoff

    Institute for x-ray physics, Georg-August-Universität Göttingen, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Michael Sprung

    Petra III, P10, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Fabian Westermeier

    Petra III, P10, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Alexandar Tzankov

    Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Christopher Werlein

    Medizinische Hochschule Hannover (MHH), Hannover, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Mark Kühnel

    Medizinische Hochschule Hannover (MHH), Hannover, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Danny Jonigk

    Medizinische Hochschule Hannover (MHH), Hannover, Germany
    For correspondence
    Jonigk.Danny@mh-hannover.de
    Competing interests
    The authors declare that no competing interests exist.
  11. Tim Salditt

    Institute for x-ray physics, Georg-August-Universität Göttingen, Göttingen, Germany
    For correspondence
    tsaldit@gwdg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4636-0813

Funding

Bundesministerium für Bildung und Forschung (05K19MG2)

  • Tim Salditt

H2020 European Research Council (771883)

  • Danny Jonigk

Max-Planck School (Matter to Life)

  • Marius Reichardt
  • Tim Salditt

Deutsche Forschungsgemeinschaft (-EXC 2067/1-390729940)

  • Tim Salditt

Botnar Research Center of Child Health (BRCCH)

  • Alexandar Tzankov

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: The study was approved by and conducted according to requirements of the ethics committees at the Hannover Medical School (vote Nr. 9022 BO K 2020).

Copyright

© 2020, Eckermann et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 5,579
    views
  • 611
    downloads
  • 43
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Marina Eckermann
  2. Jasper Frohn
  3. Marius Reichardt
  4. Markus Osterhoff
  5. Michael Sprung
  6. Fabian Westermeier
  7. Alexandar Tzankov
  8. Christopher Werlein
  9. Mark Kühnel
  10. Danny Jonigk
  11. Tim Salditt
(2020)
3d virtual pathohistology of lung tissue from COVID-19 patients based on phase contrast x-ray tomography
eLife 9:e60408.
https://doi.org/10.7554/eLife.60408

Share this article

https://doi.org/10.7554/eLife.60408

Further reading

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Malika Hale, Kennidy K Takehara ... Marion Pepper
    Research Article

    Pseudomonas aeruginosa (PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here, we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across three donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.

    1. Cell Biology
    2. Immunology and Inflammation
    Alejandro Rosell, Agata Adelajda Krygowska ... Esther Castellano Sanchez
    Research Article

    Macrophages are crucial in the body’s inflammatory response, with tightly regulated functions for optimal immune system performance. Our study reveals that the RAS–p110α signalling pathway, known for its involvement in various biological processes and tumourigenesis, regulates two vital aspects of the inflammatory response in macrophages: the initial monocyte movement and later-stage lysosomal function. Disrupting this pathway, either in a mouse model or through drug intervention, hampers the inflammatory response, leading to delayed resolution and the development of more severe acute inflammatory reactions in live models. This discovery uncovers a previously unknown role of the p110α isoform in immune regulation within macrophages, offering insight into the complex mechanisms governing their function during inflammation and opening new avenues for modulating inflammatory responses.