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Open AccessJournal ArticleDOI

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.

TLDR
Single-cell transcriptome and T cell receptor analysis of bronchoalveolar lavage fluid suggests enrichment of proinflammatory macrophages in patients with severe COVID-19 and the presence of clonally expanded CD8 + T cells in Patients with moderate CO VID-19.
Abstract
Respiratory immune characteristics associated with Coronavirus Disease 2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people by using single-cell RNA sequencing. Proinflammatory monocyte-derived macrophages were abundant in the bronchoalveolar lavage fluid from patients with severe COVID-9. Moderate cases were characterized by the presence of highly clonally expanded CD8+ T cells. This atlas of the bronchoalveolar immune microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.

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Journal ArticleDOI

Innate Immune Response to SARS-CoV-2 Infection: From Cells to Soluble Mediators.

TL;DR: In this article, a review of the innate immune response to SARS-CoV-2 infection is described not only in light of its capacity to influence the adaptive immune response towards a protective phenotype but also with the intent to point out the multiple strategies exploited by SARS CoV2 to antagonize host antiviral response and, finally, to outline inborn errors predisposing individuals to COVID-19 disease severity.
Posted ContentDOI

In plain sight: the role of alpha-1-antitrypsin in COVID-19 pathogenesis and therapeutics.

TL;DR: It is argued that the anti-inflammatory and coagulation regulatory activity of AAT have implications for coronavirus disease 2019 (COVID-19) pathogenicity, SARS-CoV-2 tissue restriction, convalescent plasma therapies, and even potentially AAT therapy.
Posted ContentDOI

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients

TL;DR: A model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19 is proposed and found that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells.
Journal ArticleDOI

SARS-CoV-2 Infection of Airway Epithelial Cells

TL;DR: In this paper, the authors reviewed cellular entry, host-viral interactions, immune responses to SARS-CoV-2 in airway epithelial cells, and discussed therapeutic options related to epithelial immune reactions.
Journal ArticleDOI

Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing.

TL;DR: Wang et al. as discussed by the authors used single-cell V(D)J sequencing to conduct comparative analyses of TCR repertoire between 12 COVID-19 patients and 6 healthy controls, as well as other virus-infected samples.
References
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Journal ArticleDOI

STAR: ultrafast universal RNA-seq aligner

TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.
Journal ArticleDOI

Comprehensive Integration of Single-Cell Data.

TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
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