Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut

Evidence for gastrointestinal infection of SARS-CoV-2

(2020) Fei Xiao et al.   GASTROENTEROLOGY

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

(2020) Furong Qi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

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SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients

(2020) Zhuo Zhou et al.   Cell Host & Microbe

Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure

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Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19

(2020) Annsea Park et al.   Cell Host & Microbe

SARS ‐CoV‐2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells

(2020) Soeren Lukassen et al.   EMBO JOURNAL

Retinoic Acid and Lymphotoxin Signaling Promote Differentiation of Human Intestinal M Cells

(2020) Siyuan Ding et al.   GASTROENTEROLOGY

Clinical and immunological features of severe and moderate coronavirus disease 2019

(2020) Guang Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Prolonged viral shedding in feces of pediatric patients with coronavirus disease 2019

(2020) Yu-Han Xing et al.   JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION

COVID-19: consider cytokine storm syndromes and immunosuppression

(2020) Puja Mehta et al.   LANCET

Virological assessment of hospitalized patients with COVID-2019

(2020) Roman Wölfel et al.   NATURE

Infection of bat and human intestinal organoids by SARS-CoV-2

(2020) Jie Zhou et al.   NATURE MEDICINE

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

Targeted Perturb-seq enables genome-scale genetic screens in single cells

(2020) Daniel Schraivogel et al.   NATURE METHODS

SARS-CoV-2 productively infects human gut enterocytes

(2020) Mart M. Lamers et al.   SCIENCE

Prolonged presence of SARS-CoV-2 viral RNA in faecal samples

(2020) Yongjian Wu et al.   Lancet Gastroenterology & Hepatology

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes

(2020) Ruochen Zang et al.   Science Immunology

Single-cell RNA Expression Profiling of ACE2, The Receptor of SARS-CoV-2

(2020) Yu Zhao et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium

(2020) Ozge Kayisoglu et al.   GUT

Longitudinal analyses reveal immunological misfiring in severe COVID-19

(2020) Carolina Lucas et al.   NATURE

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

Extrapulmonary manifestations of COVID-19

(2020) Aakriti Gupta et al.   NATURE MEDICINE

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients

(2020) Jérôme Hadjadj et al.   SCIENCE

Intestinal organoids as tools for enriching and studying specific and rare cell types: advances and future directions

(2020) Kim E Boonekamp et al.   Journal of Molecular Cell Biology

Activation and evasion of type I interferon responses by SARS-CoV-2

(2020) Xiaobo Lei et al.   Nature Communications

Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells

(2020) Megan L. Stanifer et al.   Cell Reports

Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading?

(2020) Ashish Prasad et al.   Frontiers in Medicine

TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells

(2020) Dorothea Bestle et al.   Life Science Alliance

Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor

(2020) Olusegun O. Onabajo et al.   NATURE GENETICS

A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors

(2020) Manvendra Singh et al.   Cell Reports

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

(2020) Mirko Cortese et al.   Cell Host & Microbe

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

(2020) Steffen Klein et al.   Nature Communications

Importance of Type I and III Interferons at Respiratory and Intestinal Barrier Surfaces

(2020) Megan L. Stanifer et al.   Frontiers in Immunology

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Differential Regulation of Type I and Type III Interferon Signaling

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Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape

(2019) Abimbola O. Kolawole et al.   PLoS Pathogens

Asymmetric distribution of TLR3 leads to a polarized immune response in human intestinal epithelial cells

(2019) Megan L. Stanifer et al.   Nature Microbiology

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Early Growth Response Gene-1 Suppresses Foot-and-Mouth Disease Virus Replication by Enhancing Type I Interferon Pathway Signal Transduction

(2018) Zixiang Zhu et al.   Frontiers in Microbiology

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition

(2018) Masayuki Fujii et al.   Cell Stem Cell

Type I and Type III Interferons Display Different Dependency on Mitogen-Activated Protein Kinases to Mount an Antiviral State in the Human Gut

(2017) Kalliopi Pervolaraki et al.   Frontiers in Immunology

Reovirus intermediate subviral particles constitute a strategy to infect intestinal epithelial cells by exploiting TGF-β dependent pro-survival signaling

(2016) Megan L. Stanifer et al.   CELLULAR MICROBIOLOGY

Replication of human noroviruses in stem cell-derived human enteroids

(2016) K. Ettayebi et al.   SCIENCE

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY