Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal.
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/COVID-19). 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) novel 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.
['Jin|Kang|K|', 'Bardes|Eric E|EE|', 'Mitelpunkt|Alexis|A|', 'Wang|Jake Y|JY|', 'Bhatnagar|Surbhi|S|', 'Sengupta|Soma|S|', 'Krummel|Daniel Pomeranz|DP|', 'Rothenberg|Marc E|ME|', 'Aronow|Bruce J|BJ|']
COVID-19 SARS-CoV-2 bronchoalveolar lavage platelets antiviral host defense autoimmune disorder host-pathogen cell atlas inflammatory thrombosis interactive datamining single-cell RNA-seq systems biology