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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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Can iron, zinc, copper and selenium status be a prognostic determinant in COVID-19 patients?

TL;DR: In severe COVID-19, the levels of iron (Fe), copper (Cu), zinc (Zn), and selenium (Se) do not only regulate host immune responses but modify the viral genome, as well as discussed by the authors .
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Triple jeopardy in ageing: COVID-19, co-morbidities and inflamm-ageing

TL;DR: In the older and oldest age groups and in people with co-morbidities such as diabetes, heart disease and obesity, COVID-19 endangers lives, has disrupted normal life, changed the way medicine is practised and is likely to alter our world for the foreseeable future as discussed by the authors .
Journal ArticleDOI

Endothelial cell, myeloid, and adaptive immune responses in SARS-CoV-2 infection.

TL;DR: In this article, the authors reviewed endothelial cell responses in inflammation and infection due to SARS-CoV-2 together with phenotypic and functional alterations of monocytes, T and B lymphocytes with which they interact and surmise that endothelial cells function as an integrative and active platform for the various cells recruited.
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Aging whole blood transcriptome reveals candidate genes for SARS-CoV-2-related vascular and immune alterations.

TL;DR: In this article, the authors investigated the whole transcriptome from the Genotype-Tissue Expression (GTEx) database to explore differentially expressed genes translated into proteins interacting with viral proteins during aging.
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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