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Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality

View ORCID ProfileDario Bressan, View ORCID ProfileClaire M. Mulvey, Fatime Qosaj, Robert Becker, Flaminia Grimaldi, Suvi Coffey, Sara Lisa Vogl, Laura Kuett, View ORCID ProfileRaul Catena, Ali Dariush, Carlos Gonzalez-Fernandez, Eduardo A. Gonzalez-Solares, Mohammad Al Sa’d, Aybüke Küpcü Yoldaş, Tristan Whitmarsh, Ilaria Falciatori, View ORCID ProfileSpencer S. Watson, CRUK IMAXT Grand Challenge Team, Johanna A. Joyce, Nicholas Walton, View ORCID ProfileBernd Bodenmiller, Owen Harris, View ORCID ProfileGregory J. Hannon
doi: https://doi.org/10.1101/2021.06.28.448342
Dario Bressan
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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  • For correspondence: Dario.Bressan@cruk.cam.ac.uk Greg.Hannon@cruk.cam.ac.uk
Claire M. Mulvey
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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  • ORCID record for Claire M. Mulvey
Fatime Qosaj
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Robert Becker
2Suil Interactive Ltd, Dublin, Ireland
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Flaminia Grimaldi
2Suil Interactive Ltd, Dublin, Ireland
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Suvi Coffey
2Suil Interactive Ltd, Dublin, Ireland
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Sara Lisa Vogl
2Suil Interactive Ltd, Dublin, Ireland
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Laura Kuett
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
4Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Raul Catena
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
4Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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  • ORCID record for Raul Catena
Ali Dariush
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Carlos Gonzalez-Fernandez
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Eduardo A. Gonzalez-Solares
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Mohammad Al Sa’d
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Aybüke Küpcü Yoldaş
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Tristan Whitmarsh
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Ilaria Falciatori
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Spencer S. Watson
6Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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7A list of members and affiliations is provided as a supplement
Johanna A. Joyce
6Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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Nicholas Walton
5Institute of Astronomy, University of Cambridge, Cambridge, UK
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Bernd Bodenmiller
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
4Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Owen Harris
2Suil Interactive Ltd, Dublin, Ireland
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Gregory J. Hannon
1CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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  • ORCID record for Gregory J. Hannon
  • For correspondence: Dario.Bressan@cruk.cam.ac.uk Greg.Hannon@cruk.cam.ac.uk
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ABSTRACT

A set of increasingly powerful approaches are enabling spatially resolved measurements of growing numbers of molecular features in biological samples. While important insights can be derived from the two-dimensional data that many of these technologies generate, it is clear that extending these approaches into the third and fourth dimensions will magnify their impact. Realizing biological insights from datasets where thousands to millions of cells are annotated with tens to hundreds of parameters in space will require the development of new computational and visualization strategies. Here, we describe Theia, a virtual reality-based platform, which enables exploration and analysis of either volumetric or segmented, molecularly-annotated, three-dimensional datasets, with the option to extend the analysis to time-series data. We also describe our pipeline for generating annotated 3D models of breast cancer and supply several datasets to enable users to explore the utility of Theia for understanding cancer biology in three dimensions.

Competing Interest Statement

Dario Bressan, Robert Becker, Flaminia Grimaldi, and Gregory J. Hannon are shareholders of Suil Interactive Ltd, the commercial entity which produced the VR software described in this manuscript. No other author has competing interests to declare.

Footnotes

  • https://imaxt.ast.cam.ac.uk/release/docs/dr1/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 29, 2021.
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Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality
Dario Bressan, Claire M. Mulvey, Fatime Qosaj, Robert Becker, Flaminia Grimaldi, Suvi Coffey, Sara Lisa Vogl, Laura Kuett, Raul Catena, Ali Dariush, Carlos Gonzalez-Fernandez, Eduardo A. Gonzalez-Solares, Mohammad Al Sa’d, Aybüke Küpcü Yoldaş, Tristan Whitmarsh, Ilaria Falciatori, Spencer S. Watson, CRUK IMAXT Grand Challenge Team, Johanna A. Joyce, Nicholas Walton, Bernd Bodenmiller, Owen Harris, Gregory J. Hannon
bioRxiv 2021.06.28.448342; doi: https://doi.org/10.1101/2021.06.28.448342
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Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality
Dario Bressan, Claire M. Mulvey, Fatime Qosaj, Robert Becker, Flaminia Grimaldi, Suvi Coffey, Sara Lisa Vogl, Laura Kuett, Raul Catena, Ali Dariush, Carlos Gonzalez-Fernandez, Eduardo A. Gonzalez-Solares, Mohammad Al Sa’d, Aybüke Küpcü Yoldaş, Tristan Whitmarsh, Ilaria Falciatori, Spencer S. Watson, CRUK IMAXT Grand Challenge Team, Johanna A. Joyce, Nicholas Walton, Bernd Bodenmiller, Owen Harris, Gregory J. Hannon
bioRxiv 2021.06.28.448342; doi: https://doi.org/10.1101/2021.06.28.448342

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