Epigenetic memory of coronavirus infection in innate immune cells and their progenitors

[1]  O. Elemento,et al.  Sensing of SARS-CoV-2 by pDCs and their subsequent production of IFN-I contribute to macrophage-induced cytokine storm during COVID-19 , 2022, Science Immunology.

[2]  Liliang Jin,et al.  Regulation of emergency granulopoiesis during infection , 2022, Frontiers in Immunology.

[3]  N. Kenyon,et al.  Long-Term Sequelae of COVID-19 in Experimental Mice , 2022, Molecular Neurobiology.

[4]  D. Sedding,et al.  The IL-1β, IL-6, and TNF cytokine triad is associated with post-acute sequelae of COVID-19 , 2022, Cell Reports Medicine.

[5]  E. Pearce,et al.  Trained immunity of alveolar macrophages requires metabolic rewiring and type 1 interferon signaling , 2022, Mucosal Immunology.

[6]  A. Iwasaki,et al.  Unexplained post-acute infection syndromes , 2022, Nature Medicine.

[7]  M. Netea,et al.  Maladaptive innate immune training of myelopoiesis links inflammatory comorbidities , 2022, Cell.

[8]  I. Douglas,et al.  Tocilizumab in patients hospitalised with COVID-19 pneumonia: Efficacy, safety, viral clearance, and antibody response from a randomised controlled trial (COVACTA) , 2022, eClinicalMedicine.

[9]  N. Dean,et al.  The changing epidemiology of SARS-CoV-2 , 2022, Science.

[10]  G. Guyatt,et al.  Use of tocilizumab and sarilumab alone or in combination with corticosteroids for covid-19: systematic review and network meta-analysis , 2022, BMJ medicine.

[11]  M. Merad,et al.  Pathological sequelae of long-haul COVID , 2022, Nature Immunology.

[12]  Vivek V. Thacker,et al.  The cGAS–STING pathway drives type I IFN immunopathology in COVID-19 , 2022, Nature.

[13]  D. Perl,et al.  Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain , 2022, bioRxiv.

[14]  A. Dopazo,et al.  Trained immunity induction by the inactivated mucosal vaccine MV130 protects against experimental viral respiratory infections , 2022, Cell reports.

[15]  C. Lareau,et al.  Single-cell chromatin state analysis with Signac , 2021, Nature Methods.

[16]  R. Xavier,et al.  Single-cell transcriptomic profiles reveal changes associated with BCG-induced trained immunity and protective effects in circulating monocytes. , 2021, Cell reports.

[17]  L. Joosten,et al.  Trained innate immunity, long-lasting epigenetic modulation, and skewed myelopoiesis by heme , 2021, Proceedings of the National Academy of Sciences.

[18]  J. Lieberman,et al.  Inflammasome activation in infected macrophages drives COVID-19 pathology , 2021, Nature.

[19]  Yan Li,et al.  Vaccination induces rapid protection against bacterial pneumonia via training alveolar macrophage in mice , 2021, eLife.

[20]  Zev J. Gartner,et al.  AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data , 2021, Genome Biology.

[21]  H. Cameron,et al.  Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring , 2021, Science.

[22]  F. Apple,et al.  Rapid, robust, and sustainable antibody responses to mRNA COVID-19 vaccine in convalescent COVID-19 individuals , 2021, medRxiv.

[23]  F. Ginhoux,et al.  Dysregulated hematopoiesis in bone marrow marks severe COVID-19 , 2021, Cell discovery.

[24]  Konrad U. Förstner,et al.  6th European Congress of Immunology, 1-4 September 2021, Virtual meeting. , 2021, European journal of immunology.

[25]  Jason D. Buenrostro,et al.  Functional inference of gene regulation using single-cell multi-omics , 2021, bioRxiv.

[26]  E. Fuchs,et al.  Establishment, maintenance, and recall of inflammatory memory. , 2021, Cell stem cell.

[27]  M. VanElzakker,et al.  Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms , 2021, Frontiers in Microbiology.

[28]  Mark M. Davis,et al.  The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination , 2021, Cell.

[29]  S. Kent,et al.  Immunological dysfunction persists for 8 months following initial mild-moderate SARS-CoV-2 infection , 2021, medRxiv.

[30]  A. Rudensky,et al.  Inflammatory adaptation in barrier tissues , 2021, Cell.

[31]  Mark M. Davis,et al.  Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19 , 2021, Nature Cell Biology.

[32]  Benjamin Bowe,et al.  High-dimensional characterization of post-acute sequelae of COVID-19 , 2021, Nature.

[33]  Y. Klimentidis,et al.  Post-acute sequelae of COVID-19 in a non-hospitalized cohort: Results from the Arizona CoVHORT , 2021, medRxiv.

[34]  V. Pascual,et al.  Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28 , 2021, Frontiers in Immunology.

[35]  David A. Drew,et al.  Attributes and predictors of long COVID , 2021, Nature Medicine.

[36]  L. Joosten,et al.  Trained Immunity: Reprogramming Innate Immunity in Health and Disease. , 2021, Annual review of immunology.

[37]  I. Douglas,et al.  Tocilizumab in Hospitalized Patients with Severe Covid-19 Pneumonia , 2021, The New England journal of medicine.

[38]  Howard Y. Chang,et al.  ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis , 2021, Nature Genetics.

[39]  Sven Rahmann,et al.  Sustainable data analysis with Snakemake , 2021, F1000Research.

[40]  Christopher M. Horvat,et al.  Interleukin-6 Receptor Antagonists in Critically Ill Patients with Covid-19 - Preliminary report , 2021, medRxiv.

[41]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[42]  C. Newton-Cheh,et al.  Case Series of Multisystem Inflammatory Syndrome in Adults Associated with SARS-CoV-2 Infection — United Kingdom and United States, March–August 2020 , 2020, MMWR. Morbidity and mortality weekly report.

[43]  C. del Rio,et al.  Long-term Health Consequences of COVID-19. , 2020, JAMA.

[44]  M. Netea,et al.  Innate Immune Training of Granulopoiesis Promotes Anti-tumor Activity , 2020, Cell.

[45]  José Alquicira-Hernández,et al.  Nebulosa recovers single cell gene expression signals by kernel density estimation , 2020, bioRxiv.

[46]  Jacques Fellay,et al.  Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 , 2020, Science.

[47]  K. Wilson,et al.  Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C) , 2020, Cell.

[48]  M. Malim,et al.  Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection , 2020, Nature Medicine.

[49]  Madeleine K. D. Scott,et al.  Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans , 2020, Science.

[50]  I. Amit,et al.  Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19 , 2020, Cell.

[51]  A. Iwasaki,et al.  Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling , 2020, The Journal of experimental medicine.

[52]  Eric Song,et al.  Longitudinal analyses reveal immunological misfiring in severe COVID-19 , 2020, Nature.

[53]  Nicolas Carlier,et al.  Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients , 2020, Science.

[54]  P. Palma,et al.  The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19 , 2020, Cell.

[55]  Jian-Piao Cai,et al.  Attenuated Interferon and Proinflammatory Response in SARS-CoV-2–Infected Human Dendritic Cells Is Associated With Viral Antagonism of STAT1 Phosphorylation , 2020, The Journal of infectious diseases.

[56]  Aviv Regev,et al.  Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin , 2020, Cell.

[57]  L. Montaner,et al.  Cytokine storm and leukocyte changes in mild versus severe SARS-CoV-2 infection: Review of 3939 COVID-19 patients in China and emerging pathogenesis and therapy concepts , 2020, Journal of leukocyte biology.

[58]  M. Oosting,et al.  BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment , 2020, Cell Host & Microbe.

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

[60]  O. Tsang,et al.  Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses , 2020, Immunity.

[61]  D. Acharya,et al.  Dysregulation of type I interferon responses in COVID-19 , 2020, Nature Reviews Immunology.

[62]  D. McGonagle,et al.  The Role of Cytokines including Interleukin-6 in COVID-19 induced Pneumonia and Macrophage Activation Syndrome-Like Disease , 2020, Autoimmunity Reviews.

[63]  R. Xavier,et al.  Defining trained immunity and its role in health and disease , 2020, Nature Reviews Immunology.

[64]  M. Shi,et al.  Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients , 2020, Emerging microbes & infections.

[65]  Howard Y. Chang,et al.  Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia , 2019, Nature Biotechnology.

[66]  F. Ginhoux,et al.  Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells. , 2019, Immunity.

[67]  M. Oosting,et al.  β-Glucan-Induced Trained Immunity Protects against Leishmania braziliensis Infection: a Crucial Role for IL-32. , 2019, Cell reports.

[68]  H. Ellingsgaard,et al.  Exercise and health — emerging roles of IL-6 , 2019, Current Opinion in Physiology.

[69]  M. Fullwood,et al.  Identification of a novel enhancer of CEBPE essential for granulocytic differentiation. , 2019, Blood.

[70]  Samuel L. Wolock,et al.  A comprehensive single cell transcriptional landscape of human hematopoietic progenitors , 2019, Nature Communications.

[71]  Fan Zhang,et al.  Fast, sensitive, and accurate integration of single cell data with Harmony , 2018, bioRxiv.

[72]  J. Schertzer,et al.  Induction of Autonomous Memory Alveolar Macrophages Requires T Cell Help and Is Critical to Trained Immunity , 2018, Cell.

[73]  M. Guilliams,et al.  Niche signals and transcription factors involved in tissue-resident macrophage development , 2018, Cellular immunology.

[74]  Samuel L. Wolock,et al.  Scrublet: computational identification of cell doublets in single-cell transcriptomic data , 2018, bioRxiv.

[75]  Martin J. Aryee,et al.  Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation , 2018, Cell.

[76]  Marcel H. Schulz,et al.  Identification of transcription factor binding sites using ATAC-seq , 2018, bioRxiv.

[77]  S. Rose-John Interleukin-6 Family Cytokines. , 2018, Cold Spring Harbor perspectives in biology.

[78]  L. Joosten,et al.  Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity , 2018, Cell.

[79]  Irah L. King,et al.  BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis , 2018, Cell.

[80]  M. Oosting,et al.  Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming , 2018, Cell.

[81]  T. Yoshimoto,et al.  Regulation of myelopoiesis by proinflammatory cytokines in infectious diseases , 2017, Cellular and Molecular Life Sciences.

[82]  H. Hammad,et al.  A gammaherpesvirus provides protection against allergic asthma by inducing the replacement of resident alveolar macrophages with regulatory monocytes , 2017, Nature Immunology.

[83]  E. Fuchs,et al.  Inflammatory Memory Sensitizes Skin Epithelial Stem Cells to Tissue Damage , 2017, Nature.

[84]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[85]  C. Macaubas,et al.  The MHC class II antigen presentation pathway in human monocytes differs by subset and is regulated by cytokines , 2017, PloS one.

[86]  William J. Greenleaf,et al.  chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data , 2017, Nature Methods.

[87]  Amit A. Patel,et al.  The fate and lifespan of human monocyte subsets in steady state and systemic inflammation , 2017, The Journal of experimental medicine.

[88]  M. Manz,et al.  Sensing and translation of pathogen signals into demand-adapted myelopoiesis , 2016, Current opinion in hematology.

[89]  F. Schaper,et al.  Interleukin-6: Biology, signaling and strategies of blockade. , 2015, Cytokine & growth factor reviews.

[90]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[91]  C. Hunter,et al.  IL-6 as a keystone cytokine in health and disease , 2015, Nature Immunology.

[92]  R. Xavier,et al.  BCG-induced trained immunity in NK cells: Role for non-specific protection to infection. , 2014, Clinical immunology.

[93]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[94]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[95]  Markus G. Manz,et al.  Emergency granulopoiesis , 2014, Nature Reviews Immunology.

[96]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[97]  B. Pedersen,et al.  Interleukin‐6 myokine signaling in skeletal muscle: a double‐edged sword? , 2013, The FEBS journal.

[98]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[99]  R. Xavier,et al.  Bacille Calmette-Guérin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes , 2012, Proceedings of the National Academy of Sciences.

[100]  R. Xavier,et al.  Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. , 2012, Cell host & microbe.

[101]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[102]  I. Ellis,et al.  Differential oestrogen receptor binding is associated with clinical outcome in breast cancer , 2011, Nature.

[103]  Wing-Cheong Wong,et al.  Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets. , 2011, Blood.

[104]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[105]  Jun Seita,et al.  Hematopoietic stem cell: self‐renewal versus differentiation , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[106]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[107]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[108]  D. Meyerholz,et al.  Protective and Pathologic Roles of the Immune Response to Mouse Hepatitis Virus Type 1: Implications for Severe Acute Respiratory Syndrome , 2009, Journal of Virology.

[109]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[110]  M. Karin,et al.  IL-6 and Stat3 are required for survival of intestinal epithelial cells and development of colitis-associated cancer. , 2009, Cancer cell.

[111]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[112]  G. Downey,et al.  MurineHepatitis Virus Strain 1 Produces a Clinically Relevant Model of Severe Acute Respiratory Syndrome in A/J Mice , 2006, Journal of Virology.

[113]  K. Akashi,et al.  C/EBPβ is required for 'emergency' granulopoiesis , 2006, Nature Immunology.

[114]  S. Akira,et al.  A nuclear factor for IL‐6 expression (NF‐IL6) is a member of a C/EBP family. , 1990, The EMBO journal.

[115]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[116]  J. J. Gordon,et al.  Bioinformatics Original Paper Improved Prediction of Bacterial Transcription Start Sites , 2022 .