Summary
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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
↵9 Lead contact
This version improves the figure descriptions (legends) and also distinguishes more succinctly the description of the web resource itself versus how users can develop hypotheses through the use of the system versus the specifics of the three principle hypotheses that we develop as examples of using the system.
https://toppcell.cchmc.org/biosystems/go/index3/COVID-19%20Atlas