Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy

  1. Sierra M Barone
  2. Alberta GA Paul
  3. Lyndsey M Muehling
  4. Joanne A Lannigan
  5. William W Kwok
  6. Ronald B Turner
  7. Judith A Woodfolk
  8. Jonathan M Irish  Is a corresponding author
  1. Vanderbilt University, United States
  2. University of Virginia School of Medicine, United States
  3. Benaroya Research Institute at Virginia Mason, United States

Abstract

For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders Expanding (T-REX) was created to identify changes in both very rare and common cells in diverse human immune monitoring settings. T-REX identified cells that were highly similar in phenotype and localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized reagents used to detect the rhinovirus-specific CD4+ cells, MHCII tetramers, were not used during unsupervised analysis and instead 'left out' to serve as a test of whether T-REX identified biologically significant cells. In the rhinovirus challenge study, T-REX identified virus-specific CD4+ T cells based on these cells being a distinct phenotype that expanded by ≥95% following infection. T-REX successfully identified hotspots containing virus-specific T cells using pairs of samples comparing Day 7 of infection to samples taken either prior to infection (Day 0) or after clearing the infection (Day 28). Mapping pairwise comparisons in samples according to both the direction and degree of change provided a framework to compare systems level immune changes during infectious disease or therapy response. This revealed that the magnitude and direction of systemic immune change in some COVID-19 patients was comparable to that of blast crisis acute myeloid leukemia patients undergoing induction chemotherapy and characterized the identity of the immune cells that changed the most. Other COVID-19 patients instead matched an immune trajectory like that of individuals with rhinovirus infection or melanoma patients receiving checkpoint inhibitor therapy. T-REX analysis of paired blood samples provides an approach to rapidly identify and characterize mechanistically significant cells and to place emerging diseases into a systems immunology context.

Data availability

Datasets analyzed in this manuscript are available online, including at FlowRepository. COVID-19 Dataset 2 (https://ki.app.box.com/s/sby0jesyu23a65cbgv51vpbzqjdmipr1), melanoma Dataset 3 (https://flowrepository.org/id/FR-FCM-ZYDG), and AML Dataset 4 (https://flowrepository.org/id/FR-FCM-ZZMC) were described and shared online in the associated manuscripts. Rhinovirus Dataset 1 is a newly generated dataset created at the University of Virginia available on FlowRepository (FR-FCM-Z2VX available at: https://flowrepository.org/id/FR-FCM-Z2VX). Transparent analysis scripts for all four datasets and all presented results are publicly available on the CytoLab Github page for T-REX (https://github.com/cytolab/T-REX) and include open source code and commented Rmarkdown analysis walkthroughs.

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

Article and author information

Author details

  1. Sierra M Barone

    Department of Cell and Developmental Biology; Vanderbilt-Ingram Cancer Center,, Vanderbilt University, Nashville, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5944-750X
  2. Alberta GA Paul

    Allergy Division, University of Virginia School of Medicine, Charlottesville, United States
    Competing interests
    Alberta GA Paul, became an employee of Cytek Biosciences, Inc. after performing this research at University of Virginia..
  3. Lyndsey M Muehling

    Allergy Division; Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
    Competing interests
    No competing interests declared.
  4. Joanne A Lannigan

    Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
    Competing interests
    Joanne A Lannigan, became a paid consultant of Cytek Biosciences, Inc. after performing this research at University of Virginia..
  5. William W Kwok

    N/A, Benaroya Research Institute at Virginia Mason, Seattle, United States
    Competing interests
    No competing interests declared.
  6. Ronald B Turner

    Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, United States
    Competing interests
    No competing interests declared.
  7. Judith A Woodfolk

    Allergy Division; Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
    Competing interests
    No competing interests declared.
  8. Jonathan M Irish

    Department of Cell and Developmental Biology; Vanderbilt-Ingram Cancer Center; Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, United States
    For correspondence
    jonathan.irish@vanderbilt.edu
    Competing interests
    Jonathan M Irish, was a co-founder and a board member of Cytobank Inc. and received unrelated research support from Incyte Corp, Janssen, and Pharmacyclics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9428-8866

Funding

National Institutes of Health (U01 AI125056)

  • Sierra M Barone
  • Alberta GA Paul
  • Lyndsey M Muehling
  • Ronald B Turner
  • Judith A Woodfolk
  • Jonathan M Irish

National Institutes of Health (R01 CA226833)

  • Sierra M Barone
  • Jonathan M Irish

National Institutes of Health (U54 CA217450)

  • Jonathan M Irish

National Institutes of Health (T32 AI007496)

  • Lyndsey M Muehling

Vanderbilt-Ingram Cancer Center (P30 CA68485)

  • Sierra M Barone
  • Jonathan M Irish

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

Ethics

Human subjects: Dataset 1 was a newly generated dataset of PBMCs obtained by longitudinal sampling of healthy volunteers who were challenged intranasally with RV-A16. The study was approved by the University of Virginia Human Investigations Committee, performed in accordance with the Declaration of Helsinki, and registered with ClinicalTrials.gov (NCT02796001). Informed consent was obtained from all study participants. Data were collected and processed at the University of Virginia.

Copyright

© 2021, Barone 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. Sierra M Barone
  2. Alberta GA Paul
  3. Lyndsey M Muehling
  4. Joanne A Lannigan
  5. William W Kwok
  6. Ronald B Turner
  7. Judith A Woodfolk
  8. Jonathan M Irish
(2021)
Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
eLife 10:e64653.
https://doi.org/10.7554/eLife.64653

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https://doi.org/10.7554/eLife.64653

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