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| 1 | Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages显示文摘How the innate and adaptive host immune system miscommunicate to worsen COVID-19 immunopathology has not been fully elucidated.Here,we perform single-cell deep-immune profiling of bronchoalveolar lavage(BAL)samples from 5 patients with mild and 26 with critical COVID-19 in comparison to BALs from non-COVID-19 pneumonia and normal lung.We use pseudotime inference to build T-cell and monocyte-to-macrophage trajectories and model gene expression changes along them.In mild COVID-19,CD8^(+)resident-memory(TRM)and CD4^(+)T-helper-17(T_(H17))cells undergo active(presumably antigen-driven)expansion towards the end of the trajectory,and are characterized by good effector functions,while in critical COVID-19 they remain more naïve.Vice versa,CD4^(+)T-cells with T-helper-1 characteristics(TH1-like)and CD8^(+)T-cells expressing exhaustion markers(T_(EX)-like)are enriched halfway their trajectories in mild COVID-19,where they also exhibit good effector functions,while in critical COVID-19 they show evidence of inflammation-associated stress at the end of their trajectories.Monocyte-to-macrophage trajectories show that chronic hyperinflammatory monocytes are enriched in critical COVID-19,while alveolar macrophages,otherwise characterized by anti-inflammatory and antigen-presenting characteristics,are depleted.In critical COVID-19,monocytes contribute to an ATP-purinergic signaling-inflammasome footprint that could enable COVID-19 associated fibrosis and worsen disease-severity.Finally,viral RNA-tracking reveals infected lung epithelial cells,and a significant proportion of neutrophils and macrophages that are involved in viral clearance. | Els Wauters Pierre Van Mol Abhishek Dinkarnath Garg Sander Jansen Yannick Van Herck Lore Vanderbeke Ayse Bassez Bram Boeckx Bert Malengier-Devlies Anna Timmerman Thomas Van Brussel Tina Van Buyten Rogier Schepers Elisabeth Heylen Dieter Dauwe Christophe Dooms Jan Gunst Greet Hermans Philippe Meersseman Dries Testelmans Jonas Yserbyt Sabine Tejpar Walter De Wever Patrick Matthys CONTAGIOUS collaborators Johan Neyts Joost Wauters Junbin Qian Diether Lambrechts | 2021 | Cell Research2021，31，3： | 11 |
| 2 | A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling显示文摘The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells,which are profoundly moulded by cancer cells.An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs.Here,we profile 233,591 single cells from patients with lung,colorectal,ovary and breast cancer(n=36)and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies.We identify 68 stromal cell populations,of which 46 are shared between cancer types and 22 are unique.We also characterise each population phenotypically by highlighting its marker genes,transcription factors,metabolic activities and tissue-specific expression differences.Resident cell types are characterised by substantial tissue specificity,while tumor-infiltrating cell types are largely shared across cancer types.Finally,by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naive CD4+T-cell phenotype predictive of response to checkpoint immunotherapy,we illustrate how it can serve as a guide to interpret scRNA-seq data.In conclusion,by providing a comprehensive blueprint through an interactive web server,we generate the first panoramic view on the shared complexity of stromal cells in different cancers. | Junbin Qian Siel Olbrecht Bram Boeckx Hanne Vos Damya Laoui Emre Etlioglu Els Wauters Valentina Pomella Sara Verbandt Pieter Busschaert Ayse Bassez Amelie Franken Marlies Vanden Bempt Jieyi Xiong Birgit Weynand Yannick van Herck Asier Antoranz Francesca Maria Bosisio Bernard Thienpont Giuseppe Floris Ignace Vergote Ann Smeets Sabine Tejpar Diether Lambrechts | 2020 | Cell Research2020，30，9： | 11 |
| 3 | microRNAs in colon cancer: A roadmap for discovery显示文摘 | Simona Rossi Antonio Fabio Di Narzo Pieter Mestdagh Bart Jacobs Fredrik T. Bosman Bengt Gustavsson Bernard Majoie Arnaud Roth Jo Vandesompele Isidore Rigoutsos Mauro Delorenzi Sabine Tejpar | 2012 | FEBS Letters2012，，19： | 3 |
| 4 | KRAS , BRAF , PIK3CA , and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer显示文摘 | Wendy De Roock Veerle De Vriendt Nicola Normanno Fortunato Ciardiello Sabine Tejpar | 2011 | Lancet Oncology2011，，6： | 3 |
| 5 | Antitumor activity of pimasertib, a selective MEK 1/2 inhibitor, in combination with PI3K/mTOR inhibitors or with multi‐targeted kinase inhibitors in pimasertib‐resistant human lung and colorectal cancer cells显示文摘 | Erika Martinelli Teresa Troiani Elena D’Aiuto Floriana Morgillo Donata Vitagliano Anna Capasso Sarah Costantino Loreta Pia Ciuffreda Francesco Merolla Loredana Vecchione Veerle Vriendt Sabine Tejpar Anna Nappi Vincenzo Sforza Giulia Martini Liberato Berri | 2013 | Int J Cancer2013，，9： | 2 |
| 6 | Magnesium wasting associated with epidermal-growth-factor receptor-targeting antibodies in colorectal cancer: a prospective study显示文摘 | Sabine Tejpar Hubert Piessevaux Kathleen Claes Patricia Piront Joost GJ Hoenderop Chris Verslype Eric Van Cutsem | 2007 | Lancet Oncology2007，，5： | 2 |
| 7 | Molecular Markers Identify Subtypes of Stage III Colon Cancer Associated with Patient Outcomes显示文摘 | Frank A. Sinicrope Qian Shi Thomas C. Smyrk Stephen N. Thibodeau Rodrigo Dienstmann Justin Guinney Brian M. Bot Sabine Tejpar Mauro Delorenzi Richard M. Goldberg Michelle Mahoney Daniel J. Sargent Steven R. Alberts | 2014 | Gastroenterology2014，，： | 2 |
| 8 | KRAS , BRAF , PIK3CA , and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer显示文摘 | Wendy De Roock Veerle De Vriendt Nicola Normanno Fortunato Ciardiello Sabine Tejpar | 2011 | Lancet Oncology2011，，6： | 1 |
| 9 | VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials显示文摘 | Diether Lambrechts Bart Claes Paul Delmar Joke Reumers Massimiliano Mazzone Betül T Yesilyurt Roland Devlieger Chris Verslype Sabine Tejpar Hans Wildiers Sanne de Haas Peter Carmeliet Stefan J Scherer Eric Van Cutsem | 2012 | Lancet Oncology2012，，7： | 1 |
| 10 | KRAS , BRAF , PIK3CA , and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer显示文摘 | Wendy De Roock Veerle De Vriendt Nicola Normanno Fortunato Ciardiello Sabine Tejpar | 2011 | Lancet Oncology2011，，6： | 1 |
| 11 | A combined syndrome of juvenile polyposis and hereditary haemorrhagic telangiectasia associated with mutations in MADH4 ( SMAD4)显示文摘 | Carol J Gallione Gabriela M Repetto Eric Legius Anil K Rustgi Susan L Schelley Sabine Tejpar Grant Mitchell éric Drouin Cornelius JJ Westermann Douglas A Marchuk | 2004 | The Lancet2004，，9412： | 1 |
| 12 | Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer显示文摘 | Eva Budinska Vlad Popovici Sabine Tejpar Giovanni D’Ario Nicolas Lapique Katarzyna Otylia Sikora Antonio Fabio Di Narzo Pu Yan John Graeme Hodgson Scott Weinrich Fred Bosman Arnaud Roth Mauro Delorenzi | 2013 | J. Pathol2013，，1： | 1 |
| 13 | ZIC1 gene expression is controlled by DNA and histone methylation in mesenchymal proliferations显示文摘 | Rasoul Pourebrahim Kim Van Dam Marijke Bauters Ivo De Wever Raf Sciot Jean-Jacques Cassiman Sabine Tejpar | 2007 | FEBS Letters2007，，26： | 1 |
| 14 | Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer显示文摘 | Eva Budinska Vlad Popovici Sabine Tejpar Giovanni D’Ario Nicolas Lapique Katarzyna Otylia Sikora Antonio Fabio Di Narzo Pu Yan John Graeme Hodgson Scott Weinrich Fred Bosman Arnaud Roth Mauro Delorenzi | 2013 | J Pathol2013，，1： | 1 |
| 15 | KRAS , BRAF , PIK3CA , and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer显示文摘 | Wendy De Roock Veerle De Vriendt Nicola Normanno Fortunato Ciardiello Sabine Tejpar | 2011 | Lancet Oncology2011，，6： | 1 |
| 16 | ZIC1 gene expression is controlled by DNA and histone methylation in mesenchymal proliferations显示文摘 | Rasoul Pourebrahim Kim Van Dam Marijke Bauters Ivo De Wever Raf Sciot Jean-Jacques Cassiman Sabine Tejpar | 2007 | FEBS Letters2007，，26： | 1 |
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