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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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Hyper/neuroinflammation in COVID-19 and suicide etiopathogenesis: Hypothesis for a nefarious collision?

TL;DR: In this article , the authors provide a summary of current knowledge on the molecular and cellular mechanisms of COVID-19-associated hyper/neuroinflammation with focus on their relevance to the inflammatory hypothesis of suicide development.
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deCS: A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues

TL;DR: Wang et al. as mentioned in this paper presented deCS (decoding Cell type-Specificity), an automatic cell type annotation method based on a comprehensive collection of human cell type expression profiles or a list of marker genes.
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Transcriptome network analyses in human coronavirus infections suggest a rational use of immunomodulatory drugs for COVID-19 therapy.

TL;DR: In this article, the ΔORF6 mutant of SARS-CoV was used as a surrogate for SARS CoV-2, since both lack the moiety responsible for interferon antagonistic effects.
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Purinergic signaling elements are correlated with coagulation players in peripheral blood and leukocyte samples from COVID-19 patients

TL;DR: In this article , the authors compared the purinergic profile of the total leukocyte population and evaluated the levels of these soluble biomolecules in the blood, and their correlation with coagulation components in COVID-19 patients, in comparison to healthy people or non-COVID-2019 patients.
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A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options

TL;DR: In this paper, the authors presented a comprehensively humanized mouse COVID-19 model that faithfully recapitulates the innate and adaptive human immune responses during infection with SARS-CoV-2 by adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver human ACE2 to the lungs 1 of MISTRG6 mice.
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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