ImmunoCluster provides a computational framework for the non-specialist to profile high- dimensional cytometry data

Abstract

High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a non-specialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users' needs. The protocol consists of three core computational stages: 1, data import and quality control; 2, dimensionality reduction and unsupervised clustering; and 3, annotation and differential testing, all contained within an R-based open-source framework.

Data availability

The liquid mass cytometry dataset is avaiable from FlowRepository (http://flowrepository.org/id/FR-FCM-Z244).Imaging and flow cytometry datasets have been deposited to Dryad under the following DOIs: 10.5061/dryad.gf1vhhmpr, 10.5061/dryad.4b8gthtcf, 10.5061/dryad.3n5tb2rhd

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. James W Opzoomer

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  2. Jessica A Timms

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3687-9312
  3. Kevin Blighe

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  4. Thanos P Mourikis

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  5. Nicolas Chapuis

    Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université, Université Paris Descartes, Paris, France
    Competing interests
    No competing interests declared.
  6. Richard Bekoe

    UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  7. Sedigeh Kareemaghay

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  8. Paola Nocerino

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  9. Benedetta Apollonio

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  10. Alan G Ramsay

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0452-0420
  11. Mahvash Tavassoli

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  12. Claire Harrison

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine; Haematology Department, Guy's Hospital, London, SE1 1UL, United Kingdom, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  13. Francesca D Ciccarelli

    Comprehensive Cancer Centre, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  14. Peter Parker

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine; Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom, King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  15. Michaela Fontenay

    Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université, Université Paris Descartes, Paris, France
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5492-6349
  16. Paul R Barber

    Molecular Oncology Group, UCL Cancer Institute, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8595-1141
  17. James N Arnold

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    For correspondence
    james.n.arnold@kcl.ac.uk
    Competing interests
    No competing interests declared.
  18. Shahram Kordasti

    School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine,, King's College London, London, United Kingdom
    For correspondence
    shahram.kordasti@kcl.ac.uk
    Competing interests
    Shahram Kordasti, Honoraria: Beckman Coulter, GWT-TUD, Alexion. Consulting or Advisory Role: Syneos Health.Research Funding: Celgene, Novartis pharmaceutical.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0347-4207

Funding

Cancer Research UK (A29283)

  • Jessica A Timms
  • Shahram Kordasti

Aplastic Anemia and MDS International Foundation

  • Jessica A Timms
  • Shahram Kordasti

Blood Cancer UK

  • Jessica A Timms
  • Shahram Kordasti

H2020 European Research Council (335326)

  • James W Opzoomer
  • James N Arnold

Medical Research Council (MR/N013700/1)

  • James W Opzoomer

Medical Research Council (Doctoral Training Partnership in Biomedical Sciences)

  • James W Opzoomer

Rosetrees Trust (M117-F2)

  • Sedigeh Kareemaghay
  • Mahvash Tavassoli

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

Ethics

Human subjects: Formalin-fixed paraffin-embedded (FFPE) DLBCL tumor tissue was obtained from King's College Hospital, in accordance with the Declaration of Helsinki and approved by the UK National Research Ethics Committee (reference 13/NW/0040).Head and neck squamous cell carcinoma (HNSCC) tissue was obtained from King's College Hospital, consent was attained by the King Guy's & St Thomas' Research Biobank, within King's Health Partners Integrated Cancer Centre.The non-interventional study which collected bone marrow samples from elderly healthy donors was approved by the ethical committee of Cochin-Port Royal Hospital (Paris, France) (CLEP Decision N{degree sign}: AAA-2020-08039).

Reviewing Editor

  1. Simon Yona, The Hebrew University of Jerusalem, Israel

Publication history

  1. Received: September 8, 2020
  2. Accepted: April 22, 2021
  3. Accepted Manuscript published: April 30, 2021 (version 1)
  4. Version of Record published: May 11, 2021 (version 2)

Copyright

© 2021, Opzoomer 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.

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  1. James W Opzoomer
  2. Jessica A Timms
  3. Kevin Blighe
  4. Thanos P Mourikis
  5. Nicolas Chapuis
  6. Richard Bekoe
  7. Sedigeh Kareemaghay
  8. Paola Nocerino
  9. Benedetta Apollonio
  10. Alan G Ramsay
  11. Mahvash Tavassoli
  12. Claire Harrison
  13. Francesca D Ciccarelli
  14. Peter Parker
  15. Michaela Fontenay
  16. Paul R Barber
  17. James N Arnold
  18. Shahram Kordasti
(2021)
ImmunoCluster provides a computational framework for the non-specialist to profile high- dimensional cytometry data
eLife 10:e62915.
https://doi.org/10.7554/eLife.62915

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