Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Christopher Smillie,Moshe Biton,Jose Ordovas-Montanes,Keri M. Sullivan,Grace Burgin,Daniel B. Graham,Rebecca H. Herbst,Rebecca H. Herbst,Noga Rogel,Michal Slyper,Julia Waldman,Malika Sud,Elizabeth Andrews,Gabriella Velonias,Adam L. Haber,Karthik A. Jagadeesh,Sanja Vickovic,Junmei Yao,Christine Stevens,Danielle Dionne,Lan T. Nguyen,Alexandra-Chloé Villani,Matan Hofree,Elizabeth A. Creasey,Hailiang Huang,Orit Rozenblatt-Rosen,John J. Garber,Hamed Khalili,A. Nicole Desch,Mark J. Daly,Mark J. Daly,Ashwin N. Ananthakrishnan,Alex K. Shalek,Ramnik J. Xavier,Aviv Regev,Aviv Regev +35 more
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TLDR
An atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals is generated, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4+ enterocytes, microfold-like cells, and IL13RA2+IL11+ inflammatory fibroblasts, which are associated with resistance to anti-TNF treatment.About:
This article is published in Cell.The article was published on 2019-07-25 and is currently open access. It has received 680 citations till now. The article focuses on the topics: Stromal cell & Cell type.read more
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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
Waradon Sungnak,Ni Huang,Christophe Bécavin,Marijn Berg,Rachel Queen,Monika Litvinukova,Monika Litvinukova,Carlos Talavera-López,Henrike Maatz,Daniel Reichart,Fotios Sampaziotis,Kaylee B Worlock,Masahiro Yoshida,Josephine Barnes +13 more
TL;DR: In this paper, the expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors was investigated, and co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission.
Journal ArticleDOI
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
Carly G. K. Ziegler,Samuel J. Allon,Sarah K. Nyquist,Ian M. Mbano,Vincent N. Miao,Constantine N. Tzouanas,Yuming Cao,Ashraf S. Yousif,Julia Bals,Blake M. Hauser,Blake M. Hauser,Jared Feldman,Jared Feldman,Christoph Muus,Christoph Muus,Marc H. Wadsworth,Samuel W. Kazer,Travis K. Hughes,Benjamin Doran,G. James Gatter,G. James Gatter,G. James Gatter,Marko Vukovic,Faith Taliaferro,Faith Taliaferro,Benjamin E. Mead,Zhiru Guo,Jennifer P. Wang,Delphine Gras,Magali Plaisant,Meshal Ansari,Ilias Angelidis,Heiko Adler,Jennifer M.S. Sucre,Chase J. Taylor,Brian M. Lin,Avinash Waghray,Vanessa Mitsialis,Vanessa Mitsialis,Daniel F. Dwyer,Kathleen M. Buchheit,Joshua A. Boyce,Nora A. Barrett,Tanya M. Laidlaw,Shaina L. Carroll,Lucrezia Colonna,Victor Tkachev,Victor Tkachev,Christopher W. Peterson,Christopher W. Peterson,Alison Yu,Alison Yu,Hengqi Betty Zheng,Hengqi Betty Zheng,Hannah P. Gideon,Caylin G. Winchell,Philana Ling Lin,Philana Ling Lin,Colin D. Bingle,Scott B. Snapper,Scott B. Snapper,Jonathan A. Kropski,Jonathan A. Kropski,Fabian J. Theis,Herbert B. Schiller,Laure-Emmanuelle Zaragosi,Pascal Barbry,Alasdair Leslie,Alasdair Leslie,Hans-Peter Kiem,Hans-Peter Kiem,JoAnne L. Flynn,Sarah M. Fortune,Sarah M. Fortune,Sarah M. Fortune,Bonnie Berger,Robert W. Finberg,Leslie S. Kean,Leslie S. Kean,Manuel Garber,Aaron G. Schmidt,Aaron G. Schmidt,Daniel Lingwood,Alex K. Shalek,Jose Ordovas-Montanes,Nicholas E. Banovich,Alvis Brazma,Tushar J. Desai,Thu Elizabeth Duong,Oliver Eickelberg,Christine S. Falk,Michael Farzan,Ian A. Glass,Muzlifah Haniffa,Peter Horvath,Deborah T. Hung,Naftali Kaminski,Mark A. Krasnow,Malte Kühnemund,Robert Lafyatis,Haeock Lee,Sylvie Leroy,Sten Linnarson,Joakim Lundeberg,Kerstin B. Meyer,Alexander V. Misharin,Martijn C. Nawijn,Marko Nikolic,Dana Pe'er,Joseph E. Powell,Stephen R. Quake,Jay Rajagopal,Purushothama Rao Tata,Emma L. Rawlins,Aviv Regev,Paul A. Reyfman,Mauricio Rojas,Orit Rosen,Kourosh Saeb-Parsy,Christos Samakovlis,Herbert B. Schiller,Joachim L. Schultze,Max A. Seibold,Douglas P. Shepherd,Jason R. Spence,Avrum Spira,Xin Sun,Sarah A. Teichmann,Fabian J. Theis,Alexander M. Tsankov,Maarten van den Berge,Michael von Papen,Jeffrey A. Whitsett,Ramnik J. Xavier,Yan Xu,Kun Zhang +135 more
TL;DR: The data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.
Journal ArticleDOI
SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways
TL;DR: Analysis of the compendium of data points to a particularly relevant role for nasal goblet and ciliated cells as early viral targets and potential reservoirs of SARS-CoV-2 infection and underscores the importance of the availability of the Human Cell Atlas as a reference dataset.
Journal ArticleDOI
Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
Lei Zhang,Ziyi Li,Katarzyna M. Skrzypczynska,Qiao Fang,Wei Zhang,Sarah A. O’Brien,Yao He,Lynn Wang,Qiming Zhang,Aeryon Kim,Ranran Gao,Jessica Orf,Tao Wang,Deepali V. Sawant,Jiajinlong Kang,Dev Bhatt,Daniel Lu,Chi-Ming Li,Aaron S. Rapaport,Kristy Perez,Yingjiang Ye,Shan Wang,Xueda Hu,Xianwen Ren,Wenjun Ouyang,Zhanlong Shen,Jackson G. Egen,Zemin Zhang,Xin Yu +28 more
TL;DR: This comprehensive analysis of key myeloid subsets in human and mouse identifies critical cellular interactions regulating tumor immunity and defines mechanisms underlying myeloids-targeted immunotherapies currently undergoing clinical testing.
Posted ContentDOI
The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes
Hao Zhang,Zijian Kang,Haiyi Gong,Da Xu,Jing Wang,Zifu Li,Xingang Cui,Jianru Xiao,Tong Meng,Wang Zhou,Jianmin Liu,Huji Xu,Huji Xu +12 more
TL;DR: The bioinformatics evidence of the potential route for infection of 2019-nCov in digestive system along with respiratory tract is provided and may have significant impact for the authors' healthy policy setting regards to prevention of2019-nCoV infection.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
NIH Image to ImageJ: 25 years of image analysis
TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal Article
Visualizing Data using t-SNE
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Proceedings Article
Gephi: An Open Source Software for Exploring and Manipulating Networks
TL;DR: This work presents several key features of Gephi in the context of interactive exploration and interpretation of networks, and highlights key aspects of dynamic network visualization.
Journal ArticleDOI
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.