SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells

[1]  C. Conrad,et al.  Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells , 2021, Nature.

[2]  Konrad U. Förstner,et al.  Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19 , 2021, Immunity.

[3]  M. Nöthen,et al.  New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations , 2021, medRxiv.

[4]  H. Ljunggren,et al.  Natural killer cells in antiviral immunity , 2021, Nature reviews. Immunology.

[5]  J. Liu,et al.  The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι , 2021, Proceedings of the National Academy of Sciences.

[6]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[7]  Avital Lev,et al.  Viral infection modulates Qa-1b in infected and bystander cells to properly direct NK cell killing , 2021, The Journal of experimental medicine.

[8]  F. Borrego,et al.  T Cell Activation, Highly Armed Cytotoxic Cells and a Shift in Monocytes CD300 Receptors Expression Is Characteristic of Patients With Severe COVID-19 , 2021, Frontiers in Immunology.

[9]  J. Schultze,et al.  COVID-19 and the human innate immune system , 2021, Cell.

[10]  Xiandong Tao,et al.  Natural killer cells associated with SARS-CoV-2 viral RNA shedding, antibody response and mortality in COVID-19 patients , 2021, Experimental Hematology & Oncology.

[11]  A. Sette,et al.  Adaptive immunity to SARS-CoV-2 and COVID-19 , 2021, Cell.

[12]  Aaron J. Wilk,et al.  Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19 , 2020, bioRxiv.

[13]  V. Thiel,et al.  Coronavirus biology and replication: implications for SARS-CoV-2 , 2020, Nature Reviews Microbiology.

[14]  J. C. Cohen Tervaert,et al.  Impaired natural killer cell counts and cytolytic activity in patients with severe COVID-19 , 2020, Blood Advances.

[15]  D. Sahoo,et al.  AI-guided discovery of the invariant host response to viral pandemics , 2020, bioRxiv.

[16]  André F. Rendeiro,et al.  Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression , 2020, medRxiv.

[17]  D. Cummings,et al.  Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries , 2020, medRxiv.

[18]  B. Reinius,et al.  Natural killer cell immunotypes related to COVID-19 disease severity , 2020, Science Immunology.

[19]  Bijal A. Parikh,et al.  Control of Viral Infection by Natural Killer Cell Inhibitory Receptors , 2020, Cell reports.

[20]  J. Erdmann,et al.  Genomewide Association Study of Severe Covid-19 with Respiratory Failure , 2020, The New England journal of medicine.

[21]  Aaron J. Wilk,et al.  A single-cell atlas of the peripheral immune response in patients with severe COVID-19 , 2020, Nature Medicine.

[22]  L. Cosmi,et al.  Impaired immune cell cytotoxicity in severe COVID-19 is IL-6 dependent. , 2020, The Journal of clinical investigation.

[23]  I. Amit,et al.  Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 , 2020, Nature Medicine.

[24]  Aaron J. Wilk,et al.  A single-cell atlas of the peripheral immune response to severe COVID-19 , 2020, medRxiv.

[25]  R. Bruno,et al.  Unique immunological profile in patients with COVID-19 , 2020, Cellular & Molecular Immunology.

[26]  Z. Tian,et al.  Functional exhaustion of antiviral lymphocytes in COVID-19 patients , 2020, Cellular & Molecular Immunology.

[27]  K. Yuen,et al.  Clinical Characteristics of Coronavirus Disease 2019 in China , 2020, The New England journal of medicine.

[28]  J. Verbsky,et al.  Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome , 2019, Nature Communications.

[29]  Jeff E. Mold,et al.  Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells , 2019, Nature Communications.

[30]  Simon C. Potter,et al.  The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..

[31]  J. Aurelius,et al.  The HLA-B -21 dimorphism impacts on NK cell education and clinical outcome of immunotherapy in acute myeloid leukemia. , 2019, Blood.

[32]  Vincent A. Traag,et al.  From Louvain to Leiden: guaranteeing well-connected communities , 2018, Scientific Reports.

[33]  C. Romagnani,et al.  Natural killer cell specificity for viral infections , 2018, Nature Immunology.

[34]  J. Walter,et al.  Peptide-specific recognition of human cytomegalovirus strains controls adaptive natural killer cells , 2018, Nature Immunology.

[35]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[36]  M. Veldhoen Guidelines for the use of flow cytometry , 2017, Immunity, inflammation and disease.

[37]  J. Paul Robinson,et al.  Guidelines for the use of flow cytometry and cell sorting in immunological studies. , 2017, European journal of immunology.

[38]  P. Parham,et al.  Class I HLA haplotypes form two schools that educate NK cells in different ways , 2016, Science Immunology.

[39]  M. Altfeld,et al.  Sequence variations in HCV core-derived epitopes alter binding of KIR2DL3 to HLA-C∗03:04 and modulate NK cell function. , 2016, Journal of hepatology.

[40]  M. Uhrberg,et al.  Age-related changes in natural killer cell repertoires: impact on NK cell function and immune surveillance , 2016, Cancer Immunology, Immunotherapy.

[41]  Morten Nielsen,et al.  Gapped sequence alignment using artificial neural networks: application to the MHC class I system , 2016, Bioinform..

[42]  S. Le Gall,et al.  A Conserved HIV-1-Derived Peptide Presented by HLA-E Renders Infected T-cells Highly Susceptible to Attack by NKG2A/CD94-Bearing Natural Killer Cells , 2016, PLoS pathogens.

[43]  Jaclyn K. Mann,et al.  Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa , 2015, PLoS medicine.

[44]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[45]  J. Orange Natural killer cell deficiency. , 2013, Journal of Allergy and Clinical Immunology.

[46]  P. Nordlund,et al.  Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay , 2013, Science.

[47]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[48]  Holger Gohlke,et al.  MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[49]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[50]  Todd M. Allen,et al.  HIV-1 adaptation to NK cell mediated immune pressure , 2011, Nature.

[51]  S. Jonjić,et al.  Cytomegalovirus immunoevasin reveals the physiological role of “missing self” recognition in natural killer cell dependent virus control in vivo , 2010, The Journal of experimental medicine.

[52]  Wolfgang Viechtbauer,et al.  Conducting Meta-Analyses in R with the metafor Package , 2010 .

[53]  H. Ljunggren,et al.  Estimation of the Size of the Alloreactive NK Cell Repertoire: Studies in Individuals Homozygous for the Group A KIR Haplotype1 , 2008, The Journal of Immunology.

[54]  K. Kärre Natural killer cell recognition of missing self , 2008, Nature Immunology.

[55]  J. Dowd,et al.  Socioeconomic disparities in the seroprevalence of cytomegalovirus infection in the US population: NHANES III , 2008, Epidemiology and Infection.

[56]  T. Beddoe,et al.  CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence , 2008, The Journal of experimental medicine.

[57]  Bjoern Peters,et al.  Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries , 2008, Immunome research.

[58]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[59]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Alessandro Sette,et al.  Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method , 2005, BMC Bioinformatics.

[61]  G. Ahlenstiel,et al.  The HLA-A2 restricted T cell epitope HCV core 35-44 stabilizes HLA-E expression and inhibits cytolysis mediated by natural killer cells. , 2005, The American journal of pathology.

[62]  B. Honig,et al.  A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.

[63]  O. Lund,et al.  novel sequence representations Reliable prediction of T-cell epitopes using neural networks with , 2003 .

[64]  J. Ellwart,et al.  Cutting Edge: The Human Cytomegalovirus UL40 Gene Product Contains a Ligand for HLA-E and Prevents NK Cell-Mediated Lysis1 , 2000, The Journal of Immunology.

[65]  A. McMichael,et al.  Surface expression of HLA-E, an inhibitor of natural killer cells, enhanced by human cytomegalovirus gpUL40. , 2000, Science.

[66]  M. Llano,et al.  HLA‐E‐bound peptides influence recognition by inhibitory and triggering CD94/NKG2 receptors: preferential response to an HLA‐G‐derived nonamer , 1998, European journal of immunology.

[67]  D. Goodlett,et al.  HLA-E surface expression depends on binding of TAP-dependent peptides derived from certain HLA class I signal sequences. , 1998, Journal of immunology.

[68]  M. Llano,et al.  HLA-E is a major ligand for the natural killer inhibitory receptor CD94/NKG2A. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[69]  J. Bell,et al.  HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C , 1998, Nature.

[70]  C. Romagnani,et al.  About Training and Memory: NK-Cell Adaptation to Viral Infections. , 2017, Advances in immunology.

[71]  E. Reefman,et al.  of Cytotoxic Granules in NK Cells Cytokine Secretion Is Distinct from Secretion , 2010 .

[72]  L. Lanier,et al.  NK cell recognition of mouse cytomegalovirus-infected cells. , 2006, Current topics in microbiology and immunology.

[73]  Lewis L Lanier,et al.  NK cell recognition. , 2005, Annual review of immunology.

[74]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[75]  K. Kärre How to recognize a foreign submarine. , 1997, Immunological reviews.

[76]  H. Ljunggren,et al.  In search of the 'missing self': MHC molecules and NK cell recognition. , 1990, Immunology today.