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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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COVID-19: Complement, Coagulation, and Collateral Damage.

TL;DR: A summary of CO VID-19 is provided and complement’s role in COVID-19 acute respiratory distress syndrome and coagulopathy is reviewed, suggesting that the complement system plays a key role in this inflammatory reaction.
Journal ArticleDOI

Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies.

TL;DR: The current understanding of how NK cells respond in both early and late coronavirus infections, and the implication for ongoing COVID-19 clinical trials are summarized and recommendations for therapeutic strategies are outlined.
Journal ArticleDOI

Chemokines and chemokine receptors during COVID-19 infection

TL;DR: In this paper, the role of chemokines and their receptors in COVID-19 pathogenesis was reviewed to better understand the disease immunopathology which may aid in developing possible therapeutic targets for the infection.
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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