A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses

Jin, K.; Bardes, E. E.; Mitelpunkt, A.; Wang, Y. J.; Bhatnagar, S.; Sengupta, S.; Krummel, D. P.; Rothenberg, M. E.; Aronow, B. J.

doi:10.1101/2021.06.07.447287

bioRxiv · 10.1101/2021.06.07.447287

A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses

Jin, K.·Bardes, E. E.·Mitelpunkt, A.·Wang, Y. J.·Bhatnagar, S.·Sengupta, S.·Krummel, D. P.·Rothenberg, M. E.·Aronow, B. J.

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Abstract

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.

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Jin, K., Bardes, E. E., Mitelpunkt, A., Wang, Y. J., Bhatnagar, S., Sengupta, S., Krummel, D. P., Rothenberg, M. E., Aronow, B. J.. 2021-06-07. A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses. https://doi.org/10.1101/2021.06.07.447287

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