Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
- Vanderbilt University, United States
- University of Virginia School of Medicine, United States
- 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.
Article and author information
Author details
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.
Reviewing Editor
- Grégoire Altan-Bonnet, Memorial Sloan-Kettering Cancer Center, United States
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.
Version history
- Received: December 9, 2020
- Accepted: August 2, 2021
- Accepted Manuscript published: August 5, 2021 (version 1)
- Version of Record published: August 17, 2021 (version 2)
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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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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