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

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About: Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
Creator	Turner, Ronald Kwok, William Irish, Jonathan Affiliations, ¥ Barone, Sierra Lannigan, Joanne Muehling, Lyndsey Paul, Alberta Woodfolk, Judith
Source	BioRxiv; Medline; PMC
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. MHC tetramers were not used during unsupervised analysis and instead ‘left out’ to serve as a test of whether T-REX identifies 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 with virus-specific T cells using pairs of samples comparing Day 7 of infection to samples taken either after clearing the infection (Day 28) or samples taken prior to infection (Day 0). 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.
has issue date	2020-08-01(xsd:dateTime)
bibo:doi	10.1101/2020.07.31.190454
bibo:pmid	32766581
has license	cc-by-nc-nd
sha1sum (hex)	288ade468da8259eae2df0f2df5f63cdaaf09f29
schema:url	https://doi.org/10.1101/2020.07.31.190454
resource representing a document's title	Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
has PubMed Central identifier	PMC7402038
has PubMed identifier	32766581
schema:publication	bioRxiv
resource representing a document's body	covid:288ade468da8259eae2df0f2df5f63cdaaf09f29#body_text
is schema:about of	named entity 'identified' named entity 'clearing' named entity 'T-REX' named entity 'subsets' named entity 'immune cell' named entity 'machine learning' named entity 'EITHER' named entity 'IDENTIFIED' named entity 'IMMUNOLOGY' named entity 'THERAPY' named entity 'cells' named entity 'T cells' named entity 'pairwise comparisons' named entity 'infection' named entity 'However' named entity 'melanoma' named entity 'diseases' named entity 'Day' named entity 'With' named entity 'settings' named entity 'infection' named entity 'comparing' named entity 'phenotype' named entity 'repeated' named entity 'virus-specific' named entity 'rare' named entity 'tools' named entity 'patients' named entity 'CD4' named entity 'infection' named entity 'direction' named entity 'cells' named entity 'induction chemotherapy' named entity 'rhinovirus' named entity 'COVID-19' named entity 'acute myeloid leukemia' named entity 'T-REX' named entity 'infection' named entity 'virus' named entity 'melanoma' named entity 'T-REX' named entity 'T-REX' named entity 'infection' named entity 'immune cell' named entity 'infection' named entity 'Unsupervised machine learning' named entity 'cells' named entity 'immune' named entity 'based' named entity 'CD147' named entity 'KNN' named entity 'phenotype' named entity 'cellular immune responses' named entity 'CXCR5' named entity 'CD147' named entity 'University of Virginia' named entity 'infection' named entity 'T-REX' named entity 'phenotypic' named entity 'mononuclear cells' named entity 'COVID-19' named entity 'computational analysis' named entity 'KNN' named entity 'peer review' named entity 'CD55' named entity 'T-REX' named entity 'virus' named entity 'variance' named entity 'phenotypic' named entity 'viruses' named entity 'Dataset' named entity 'MHC II' named entity 'memory cells'

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