Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.
Mingfeng Liao,Yang Liu,Jing Yuan,Yanling Wen,Gang Xu,Juanjuan Zhao,Lin Cheng,Jinxiu Li,Xin Wang,Fuxiang Wang,Lei Liu,Ido Amit,Shuye Zhang,Zheng Zhang +13 more
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.read more
Citations
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Single-cell landscape of immunological responses in patients with COVID-19.
Ji Yuan Zhang,Xiang Ming Wang,Xudong Xing,Zhe Xu,Chao Zhang,Jin-Wen Song,Xing Fan,Peng Xia,Jun Liang Fu,Si Yu Wang,Ruo Nan Xu,Xiao Peng Dai,Lei Shi,Lei Huang,Tian Jun Jiang,Ming Shi,Yuxia Zhang,Alimuddin Zumla,Alimuddin Zumla,Markus Maeurer,Fan Bai,Fu-Sheng Wang +21 more
TL;DR: The single-cell transcriptional landscape of moderate, severe and convalescent cases of patients with COVID-19 describes the dynamic nature of immune responses during disease progression, and shows a deranged interferon response, profound immune exhaustion with skewed T cell receptor repertoire and broad T cell expansion.
Journal ArticleDOI
The hypercoagulable state in COVID-19: Incidence, pathophysiology, and management.
Mouhamed Yazan Abou-Ismail,Mouhamed Yazan Abou-Ismail,Akiva Diamond,Sargam Kapoor,Yasmin Arafah,Lalitha Nayak,Lalitha Nayak +6 more
TL;DR: Of concern, is the observation that anticoagulation may be inadequate in many circumstances, highlighting the need for alternative or additional therapies.
Journal ArticleDOI
COVID-19 and the human innate immune system.
TL;DR: In this article, a conceptual framework for the interaction of the human innate immune system with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was provided to link the clinical observations with experimental findings that have been made during the first year of the pandemic.
Journal ArticleDOI
Immunity, endothelial injury and complement-induced coagulopathy in COVID-19.
Luca Perico,Ariela Benigni,Federica Casiraghi,Lisa F. P. Ng,Lisa F. P. Ng,Laurent Rénia,Giuseppe Remuzzi,Giuseppe Remuzzi +7 more
TL;DR: Current understanding of the pathogenic mechanisms involved in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the progression of coronav virus disease 2019 (COVID-19) is described, focusing on the immunological hyper-response and the induction of widespread endothelial damage, complement-associated blood clotting and systemic microangiopathy, as well as the effects of these processes on the kidney.
Journal ArticleDOI
Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.
Rogan A. Grant,Luisa Morales-Nebreda,Nikolay S. Markov,Suchitra Swaminathan,Melissa Querrey,Estefany R Guzman,Darryl A. Abbott,Helen K. Donnelly,Alvaro Donayre,Isaac Goldberg,Zasu M Klug,Nicole Borkowski,Ziyan Lu,Hermon Kihshen,Yuliya Politanska,Lango Sichizya,Mengjia Kang,Ali Shilatifard,Chao Qi,Jon W. Lomasney,A. Christine Argento,Jacqueline M. Kruser,Elizabeth S. Malsin,Chiagozie O Pickens,Sean B. Smith,James M. Walter,Anna Pawlowski,Daniel Schneider,Prasanth Nannapaneni,Hiam Abdala-Valencia,Ankit Bharat,Cara J. Gottardi,G. R. Scott Budinger,Alexander V. Misharin,Benjamin D. Singer,Richard G Wunderink,NU Script Study Investigators +36 more
TL;DR: In this paper, the authors investigated SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus, and they collected bronchoalveolar lavage fluid samples from 88 patients with severe acute respiratory syndrome coronavirus 2 (SARSCoV2)induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analyzed them using flow cytometry and bulk transcriptomic profiling.
References
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Journal ArticleDOI
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
Chaolin Huang,Yeming Wang,Xingwang Li,Lili Ren,Jianping Zhao,Yi Hu,Li Zhang,Guohui Fan,Jiuyang Xu,Xiaoying Gu,Zhenshun Cheng,Ting Yu,Jia'an Xia,Yuan Wei,Wenjuan Wu,Xuelei Xie,Wen Yin,Li Hui,Min Liu,Yan Xiao,Hong Gao,Li Guo,Jungang Xie,Guang-Fa Wang,Rongmeng Jiang,Zhancheng Gao,Qi Jin,Jianwei Wang,Bin Cao +28 more
TL;DR: The epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of patients with laboratory-confirmed 2019-nCoV infection in Wuhan, China, were reported.
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
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.
Tim Stuart,Andrew Butler,Paul J. Hoffman,Christoph Hafemeister,Efthymia Papalexi,William M. Mauck,Yuhan Hao,Marlon Stoeckius,Peter Smibert,Rahul Satija +9 more
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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