An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses
| Autor: | Eric E. Bardes, Soma Sengupta, Daniel Pomeranz Krummel, Bruce J. Aronow, Surbhi Bhatnagar, Kang Jin, Jake Y. Wang, Alexis Mitelpunkt, Marc E. Rothenberg |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Cell type
T cell Systems biology Science interactive datamining Cell AI/ML Bionetworks Systems Immunobiology Omics inflammatory thrombosis Computational biology Biology Article Transcriptome Virology medicine host-pathogen cell atlas bronchoalveolar lavage Compartment (development) Transcriptomics Gene single-cell RNA-seq Multidisciplinary SARS-CoV-2 COVID-19 systems biology Gene signature medicine.anatomical_structure platelets autoimmune disorder antiviral host defense |
| Zdroj: | iScience, Vol 24, Iss 10, Pp 103115-(2021) bioRxiv article-version (status) pre article-version (number) 2 iScience |
| ISSN: | 2589-0042 |
| Popis: | Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (http://toppcell.cchmc.org/). As examples, we develop three hypotheses: (1) a multicellular signaling cascade among alternatively differentiated monocyte-derived macrophages whose tasks include T cell recruitment and activation; (2) platelet subtypes with drastically modulated expression of genes responsible for adhesion, coagulation and thrombosis; and (3) a multilineage cell activator network able to drive extrafollicular B maturation via an ensemble of genes strongly associated with risk for developing post-viral autoimmunity. Graphical Abstract |
| Databáze: | OpenAIRE |
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