COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.
Xianwen Ren,Wen Wen,Xiaoying Fan,Wenhong Hou,Bin Su,Pengfei Cai,Jiesheng Li,Yang Liu,Fei Tang,Fan Zhang,Yu Yang,Jiangping He,Wenji Ma,Jingjing He,Pingping Wang,Qiqi Cao,Fangjin Chen,Yuqing Chen,Xuelian Cheng,Guohong Deng,Xilong Deng,Wenyu Ding,Wenyu Ding,Yingmei Feng,Rui Gan,Chuang Guo,Weiqiang Guo,Shuai He,Chen Jiang,Juanran Liang,Yimin Li,Jun Lin,Yun Ling,Haofei Liu,Jianwei Liu,Nianping Liu,Shu-Qiang Liu,Meng Luo,Qiang Ma,Qibing Song,Wujianan Sun,Gaoxiang Wang,Feng Wang,Ying Wang,Xiaofeng Wen,Qian Wu,Gang Xu,Xiaowei Xie,Xinxin Xiong,Xudong Xing,Hao Xu,Chonghai Yin,Dongdong Yu,Kezhuo Yu,Jin Yuan,Biao Zhang,Peipei Zhang,Peipei Zhang,Peipei Zhang,Tong Zhang,Jincun Zhao,Peidong Zhao,Jianfeng Zhou,Wei Zhou,Sujuan Zhong,Xiaosong Zhong,Shuye Zhang,Lin Zhu,Ping Zhu,Bin Zou,Jiahua Zou,Zengtao Zuo,Fan Bai,Xi Huang,Penghui Zhou,Qinghua Jiang,Zhiwei Huang,Jin-Xin Bei,Lai Wei,Xiu-Wu Bian,Xiu-Wu Bian,Xindong Liu,Xindong Liu,Tao Cheng,Xiangpan Li,Pingsen Zhao,Fu-Sheng Wang,Hongyang Wang,Bing Su,Zheng Zhang,Kun Qu,Xiaoqun Wang,Jiekai Chen,Ronghua Jin,Zemin Zhang +94 more
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TLDR
In this article, the authors applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells.About:
This article is published in Cell.The article was published on 2021-04-01 and is currently open access. It has received 385 citations till now. The article focuses on the topics: Immune system & Cytokine storm.read more
Citations
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Multiple early factors anticipate post-acute COVID-19 sequelae
Yapeng Su,Dan Yuan,Daniel G. Chen,Rachel Ng,Kai Wang,Jongchan Choi,Sarah Li,Sunga Hong,Rongyu Zhang,Jingyi Xie,Sergey A. Kornilov,Kelsey Scherler,A.-J. Pavlovitch-Bedzyk,Shen Dong,Christopher Lausted,Inyoul Lee,Shannon Fallen,Chengzhen L. Dai,Priyanka Baloni,Brett Smith,Venkata R. Duvvuri,Kristin G. Anderson,Jing Wei Li,Fan Yang,Caroline J. Duncombe,Denise J. McCulloch,Clifford Rostomily,Pamela Troisch,Jing Zhou,Sean Mackay,Quinn DeGottardi,Damon May,Ruth T. Taniguchi,Rachel M. Gittelman,Mark Klinger,Thomas M. Snyder,Ryan Roper,Gladys Wojciechowska,Kim Murray,Rick Edmark,Simon Evans,Lesley Jones,Yon-gan Zhou,Lee Rowen,Rachel Xia-Ying Liu,William Chour,Heather Algren,William R. Berrington,Julie A. Wallick,Rebecca Cochran,Mary Micikas,Christos J. Petropoulos,Hunter Cole,Trevan D Fischer,Wei Wei,Dave S.B. Hoon,Nathan D. Price,Naeha Subramanian,Joshua A. Hill,Jenn J. Hadlock,Andrew T. Magis,Antoni Ribas,Lewis L. Lanier,Scott D. Boyd,Jeffrey A. Bluestone,Helen Y. Chu,Leroy Hood,Raphael Gottardo,Philip D. Greenberg,Mark M. Davis,Jason D Goldman,James R. Heath +71 more
TL;DR: Huang et al. as discussed by the authors performed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data and patient-reported symptoms.
Journal ArticleDOI
Single-cell multi-omics analysis of the immune response in COVID-19.
Emily Stephenson,Gary Reynolds,Rachel A. Botting,Fernando J Calero-Nieto,Michael D Morgan,Michael D Morgan,Zewen K. Tuong,Zewen K. Tuong,Karsten Bach,Karsten Bach,Waradon Sungnak,Kaylee B Worlock,Masahiro Yoshida,Natsuhiko Kumasaka,Katarzyna D. Kania,Justin Engelbert,Bayanne Olabi,Jarmila Stremenova Spegarova,Nicola K. Wilson,Nicole Mende,Laura Jardine,Louis C.S. Gardner,Issac Goh,Dave Horsfall,Jim McGrath,Simone Webb,Michael W. Mather,Rik G.H. Lindeboom,Emma Dann,Ni Huang,Krzysztof Polanski,Elena Prigmore,Florian Gothe,Florian Gothe,Jonathan M. Scott,Rebecca Payne,Kenneth F Baker,Kenneth F Baker,Aidan T Hanrath,Aidan T Hanrath,Ina Schim van der Loeff,Andrew Barr,Amada Sanchez-Gonzalez,Laura Bergamaschi,Federica Mescia,Josephine Barnes,Eliz Kilich,Angus de Wilton,A Saigal,Aarash Saleh,Sam M. Janes,Sam M. Janes,Claire Smith,Nusayhah Gopee,Caroline Wilson,Caroline Wilson,Paul Coupland,Jonathan Coxhead +57 more
TL;DR: In this article, the authors performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19.
Journal ArticleDOI
Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies.
Florian A. Lempp,Leah Soriaga,Martin Montiel-Ruiz,Fabio Benigni,Julia Noack,Young-Jun Park,Siro Bianchi,Alexandra C. Walls,John E. Bowen,Jiayi Zhou,Hannah Kaiser,Anshu Joshi,Maria De Agostini,Marcel Meury,Exequiel Dellota,Stefano Jaconi,Elisabetta Cameroni,Javier Martinez-Picado,Javier Martinez-Picado,Júlia Vergara-Alert,Nuria Izquierdo-Useros,Herbert W. Virgin,Herbert W. Virgin,Antonio Lanzavecchia,David Veesler,Lisa A. Purcell,Amalio Telenti,Davide Corti +27 more
TL;DR: In this article, C-type lectins and SIGLEC1 function as attachment-receptors for SARS-CoV-2 infection and reveal distinct mechanisms of neutralization by different classes of spike-specific antibodies.
Journal ArticleDOI
Inflammasome activation at the crux of severe COVID-19.
TL;DR: In this article, the authors review evidence that SARS-CoV-2 directly or indirectly activates inflammasomes, which are large multiprotein assemblies that are broadly responsive to pathogen-associated and stress-associated cellular insults, leading to secretion of the pleiotropic IL-1 family cytokines (IL-1β and IL-18), and pyroptosis, an inflammatory form of cell death.
Journal ArticleDOI
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19.
Carly G. K. Ziegler,Vincent N. Miao,Anna H. Owings,Andrew W. Navia,Ying Tang,Joshua D. Bromley,Peter Lotfy,Peter Lotfy,Meredith Sloan,Hannah Laird,Haley B. Williams,Micayla George,Micayla George,Micayla George,Riley S. Drake,Riley S. Drake,Riley S. Drake,Taylor Christian,Adam M. Parker,Campbell B Sindel,Molly W. Burger,Yilianys Pride,Mohammad H. Hasan,George E. Abraham,Michal Senitko,Tanya O. Robinson,Alex K. Shalek,Sarah C. Glover,Bruce H. Horwitz,Bruce H. Horwitz,Jose Ordovas-Montanes +30 more
TL;DR: In this article, the authors performed scRNA-seq on nasopharyngeal swabs from 58 healthy and COVID-19 participants, and identified genes associated with susceptibility, resistance, or infection response.
References
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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.
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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
Markus Hoffmann,Hannah Kleine-Weber,Simon Schroeder,Nadine Krüger,Tanja Herrler,Sandra Erichsen,Tobias S. Schiergens,Georg Herrler,Nai Huei Wu,Andreas Nitsche,Marcel A. Müller,Christian Drosten,Christian Drosten,Stefan Pöhlmann +13 more
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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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