The immune niche of the liver

Highly multiplexed 2-dimensional imaging mass cytometry analysis of HBV-infected liver

(2021) Daniel Traum et al.   JCI Insight

MATISSE: a method for improved single cell segmentation in imaging mass cytometry

(2021) Matthijs J. D. Baars et al.   BMC BIOLOGY

Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver

(2021) Alice Bertocchi et al.   CANCER CELL

Group‐2 Innate Lymphoid Cells Promote Hepatocellular Carcinoma Progression via CXCL2‐Neutrophil Induced Immunosuppression

(2021) Xingyuan Xu et al.   HEPATOLOGY

Topological analysis of hepatocellular carcinoma tumour microenvironment based on imaging mass cytometry reveals cellular neighbourhood regulated reversely by macrophages with different ontogeny

(2021) Jianpeng Sheng et al.   GUT

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels

(2020) Wenliang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VISTA is a checkpoint regulator for naïve T cell quiescence and peripheral tolerance

(2020) Mohamed A. ElTanbouly et al.   SCIENCE

Hepatic ILC2 activity is regulated by liver inflammation-induced cytokines and effector CD4+ T cells

(2020) Silja Steinmann et al.   Scientific Reports

The liver as an immunological barrier redefined by single‐cell analysis

(2020) Zania Stamataki et al.   IMMUNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis

(2020) Prakash Ramachandran et al.   Nature Reviews Gastroenterology & Hepatology

Longevity and replenishment of human liver-resident memory T cells and mononuclear phagocytes

(2020) Laura J. Pallett et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

(2020) Daniele Corridoni et al.   NATURE MEDICINE

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver

(2020) Anneleen Remmerie et al.   IMMUNITY

Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling

(2020) Manuel Winkler et al.   JOURNAL OF HEPATOLOGY

Acute liver failure is regulated by MYC- and microbiome-dependent programs

(2020) Aleksandra A. Kolodziejczyk et al.   NATURE MEDICINE

Intrahepatic TH17/TReg Cells in Homeostasis and Disease—It’s All About the Balance

(2020) Hannah K. Drescher et al.   Frontiers in Pharmacology

A single cell atlas of the human liver tumor microenvironment

(2020) Hassan Massalha et al.   Molecular Systems Biology

Commensal-driven immune zonation of the liver promotes host defence

(2020) Anita Gola et al.   NATURE

Laser capture microdissection: techniques and applications in liver diseases

(2019) Beatriz Aguilar-Bravo et al.   Hepatology International

Liver-Resident NK Cells Control Antiviral Activity of Hepatic T Cells via the PD-1-PD-L1 Axis

(2019) Jing Zhou et al.   IMMUNITY

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

(2019) Brian J. Pepe-Mooney et al.   Cell Stem Cell

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Spatial heterogeneity in the mammalian liver

(2019) Shani Ben-Moshe et al.   Nature Reviews Gastroenterology & Hepatology

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity

(2019) Anastasia Minervina et al.   TRANSPLANT INTERNATIONAL

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

(2019) Jellert T. Gaublomme et al.   Nature Communications

Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors

(2019) Joe M. Segal et al.   Nature Communications

Hepatic Natural Killer Cells: Organ-Specific Sentinels of Liver Immune Homeostasis and Physiopathology

(2019) Joanna Mikulak et al.   Frontiers in Immunology

Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements

(2019) Gi Bum Kim et al.   CELL

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

(2019) Johnny Bonnardel et al.   IMMUNITY

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity

(2019) Mashito Sakai et al.   IMMUNITY

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies

(2019) Heeva Baharlou et al.   Frontiers in Immunology

Lifting the veil on macrophage diversity in tissue regeneration and fibrosis

(2019) Catia T. Perciani et al.   Science Immunology

Interleukin-36γ–producing macrophages drive IL-17–mediated fibrosis

(2019) Sven D. Sommerfeld et al.   Science Immunology

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

(2019) Ian Setliff et al.   CELL

Immune monitoring using mass cytometry and related high-dimensional imaging approaches

(2019) Felix J. Hartmann et al.   Nature Reviews Rheumatology

Wnt/β-Catenin Signaling in Liver Development, Homeostasis, and Pathobiology

(2018) Jacquelyn O. Russell et al.   Annual Review of Pathology-Mechanisms of Disease

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Transcriptional and epigenetic regulation of innate-like T lymphocyte development

(2018) Mihalis Verykokakis et al.   CURRENT OPINION IN IMMUNOLOGY

Identification of chromatin-accessible domains in non-alcoholic steatohepatitis-derived hepatocellular carcinoma

(2018) Mekonnen L. Dechassa et al.   MOLECULAR CARCINOGENESIS

Liver sinusoidal endothelial cells — gatekeepers of hepatic immunity

(2018) Shishir Shetty et al.   Nature Reviews Gastroenterology & Hepatology

Hepatic Dendritic Cells, the Tolerogenic Liver Environment, and Liver Disease

(2018) Lei Dou et al.   SEMINARS IN LIVER DISEASE

The Contribution of Non-Professional Antigen-Presenting Cells to Immunity and Tolerance in the Liver

(2018) Christina Mehrfeld et al.   Frontiers in Immunology

Regulatory T Cell Metabolism in the Hepatic Microenvironment

(2018) Rebecca Ellen Wawman et al.   Frontiers in Immunology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Burden of Liver Diseases in the World

(2018) Sumeet K. Asrani et al.   JOURNAL OF HEPATOLOGY

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

Impaired endothelial autophagy promotes liver fibrosis by aggravating the oxidative stress response during acute liver injury

(2018) Maria Ruart et al.   JOURNAL OF HEPATOLOGY

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Liver sinusoidal endothelial cells: Physiology and role in liver diseases

(2017) Johanne Poisson et al.   JOURNAL OF HEPATOLOGY

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

CD1d-Restricted pathways in hepatocytes control local natural killer T cell homeostasis and hepatic inflammation

(2017) Sebastian Zeissig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunofluorescence identifies distinct subsets of endothelial cells in the human liver

(2017) Otto Strauss et al.   Scientific Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets

(2016) David Dao et al.   BIOINFORMATICS

A Reservoir of Mature Cavity Macrophages that Can Rapidly Invade Visceral Organs to Affect Tissue Repair

(2016) Jing Wang et al.   CELL

Liver immunology and its role in inflammation and homeostasis

(2016) Mark W Robinson et al.   Cellular & Molecular Immunology

Hepatic macrophages in homeostasis and liver diseases: from pathogenesis to novel therapeutic strategies

(2016) Cynthia Ju et al.   Cellular & Molecular Immunology

Mouse and Human Liver Contain Immunoglobulin A–Secreting Cells Originating From Peyer's Patches and Directed Against Intestinal Antigens

(2016) Ludovic Moro-Sibilot et al.   GASTROENTEROLOGY

Subcapsular Hepatic Dendritic Cells: Hiding in Plain Sight

(2016) D. Radika Soysa et al.   GASTROENTEROLOGY

Combination of Mass Cytometry and Imaging Analysis Reveals Origin, Location, and Functional Repopulation of Liver Myeloid Cells in Mice

(2016) Bruna Araujo David et al.   GASTROENTEROLOGY

Tissue-Resident Macrophage Ontogeny and Homeostasis

(2016) Florent Ginhoux et al.   IMMUNITY

Human liver-resident CD56bright/CD16neg NK cells are retained within hepatic sinusoids via the engagement of CCR5 and CXCR6 pathways

(2016) Kelly Hudspeth et al.   JOURNAL OF AUTOIMMUNITY

IL-6 pathway in the liver: From physiopathology to therapy

(2016) Dirk Schmidt-Arras et al.   JOURNAL OF HEPATOLOGY

Macrophage autophagy limits acute toxic liver injury in mice through down regulation of interleukin-1β

(2016) Ghulam Ilyas et al.   JOURNAL OF HEPATOLOGY

Biliary epithelium and liver B cells exposed to bacteria activate intrahepatic MAIT cells through MR1

(2016) Hannah C. Jeffery et al.   JOURNAL OF HEPATOLOGY

Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst γδ T, Innate Lymphoid, and Th Cells

(2016) You Jeong Lee et al.   JOURNAL OF IMMUNOLOGY

Murine liver-resident group 1 innate lymphoid cells regulate optimal priming of anti-viral CD8 + T cells

(2016) Peter D. Krueger et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

(2016) Isaac Engel et al.   NATURE IMMUNOLOGY

Immunology in the liver — from homeostasis to disease

(2016) Felix Heymann et al.   Nature Reviews Gastroenterology & Hepatology

Insights into the Role and Interdependence of Oxidative Stress and Inflammation in Liver Diseases

(2016) Sha Li et al.   Oxidative Medicine and Cellular Longevity

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Developing a pro-regenerative biomaterial scaffold microenvironment requires T helper 2 cells

(2016) K. Sadtler et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

(2016) Charlotte L. Scott et al.   Nature Communications

Clinical Potential of Regulatory T Cell Therapy in Liver Diseases: An Overview and Current Perspectives

(2016) Hannah C. Jeffery et al.   Frontiers in Immunology

CXCR6 marks a novel subset of T-betloEomeshi natural killer cells residing in human liver

(2016) Kerstin A. Stegmann et al.   Scientific Reports

Biodistribution of cisplatin revealed by imaging mass cytometry identifies extensive collagen binding in tumor and normal tissues

(2016) Qing Chang et al.   Scientific Reports

Immunosurveillance of the Liver by Intravascular Effector CD8 + T Cells

(2015) Luca G. Guidotti et al.   CELL

Quantifying Memory CD8 T Cells Reveals Regionalization of Immunosurveillance

(2015) Elizabeth M. Steinert et al.   CELL

Liver sinusoidal endothelial cells induce immunosuppressive IL-10-producing Th1 cells via the Notch pathway

(2015) Katrin Neumann et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The biliary epithelium presents antigens to and activates natural killer T cells

(2015) Elisabeth Schrumpf et al.   HEPATOLOGY

Liver inflammation abrogates immunological tolerance induced by Kupffer cells

(2015) Felix Heymann et al.   HEPATOLOGY

Most Tissue-Resident Macrophages Except Microglia Are Derived from Fetal Hematopoietic Stem Cells

(2015) Jianpeng Sheng et al.   IMMUNITY

C-Myb+ Erythro-Myeloid Progenitor-Derived Fetal Monocytes Give Rise to Adult Tissue-Resident Macrophages

(2015) Guillaume Hoeffel et al.   IMMUNITY

Barcoding of Live Human Peripheral Blood Mononuclear Cells for Multiplexed Mass Cytometry

(2015) Henrik E. Mei et al.   JOURNAL OF IMMUNOLOGY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

The Complex Myeloid Network of the Liver with Diverse Functional Capacity at Steady State and in Inflammation

(2015) Christoph Eckert et al.   Frontiers in Immunology

The role of neutrophils in the development of liver diseases

(2014) Ruonan Xu et al.   Cellular & Molecular Immunology

Roles for Chemokines in Liver Disease

(2014) Fabio Marra et al.   GASTROENTEROLOGY

Immune tolerance in liver disease

(2014) Ian N. Crispe   HEPATOLOGY

Macrophage heterogeneity in tissues: phenotypic diversity and functions

(2014) Siamon Gordon et al.   IMMUNOLOGICAL REVIEWS

TGF-β-dependent induction of CD4+CD25+Foxp3+ Tregs by liver sinusoidal endothelial cells

(2014) Antonella Carambia et al.   JOURNAL OF HEPATOLOGY

Cutting Edge: Activation by Innate Cytokines or Microbial Antigens Can Cause Arrest of Natural Killer T Cell Patrolling of Liver Sinusoids

(2014) P. Velazquez et al.   JOURNAL OF IMMUNOLOGY

Intrahepatic Innate Lymphoid Cells Secrete IL-17A and IL-17F That Are Crucial for T Cell Priming in Viral Infection

(2014) Z. Jie et al.   JOURNAL OF IMMUNOLOGY

Viral expression and molecular profiling in liver tissue versus microdissected hepatocytes in hepatitis B virus - associated hepatocellular carcinoma

(2014) Marta Melis et al.   Journal of Translational Medicine

Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors

(2014) Elisa Gomez Perdiguero et al.   NATURE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Epigenetic Control of Immunity

(2014) M. Busslinger et al.   Cold Spring Harbor Perspectives in Biology

Use of Laser Capture Microdissection to Map Hepatitis C Virus–Positive Hepatocytes in Human Liver

(2013) Abraham J. Kandathil et al.   GASTROENTEROLOGY

Regulatory dendritic cell therapy: From rodents to clinical application

(2013) Dalia Raïch-Regué et al.   IMMUNOLOGY LETTERS

Chemokine Receptor CXCR6-Dependent Hepatic NK T Cell Accumulation Promotes Inflammation and Liver Fibrosis

(2013) A. Wehr et al.   JOURNAL OF IMMUNOLOGY

Hepatic Stellate Cells Preferentially Induce Foxp3+ Regulatory T Cells by Production of Retinoic Acid

(2013) R. M. Dunham et al.   JOURNAL OF IMMUNOLOGY

Ex vivoanalysis of resident hepatic pro-inflammatory CD1d-reactive T cells and hepatocyte surface CD1d expression in hepatitis C

(2013) K. Yanagisawa et al.   JOURNAL OF VIRAL HEPATITIS

In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration

(2013) Meritxell Huch et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Pathogenic Mouse Hepatitis Virus or Poly(I:C) Induce IL-33 in Hepatocytes in Murine Models of Hepatitis

(2013) Muhammad Imran Arshad et al.   PLoS One

Autophagy Releases Lipid That Promotes Fibrogenesis by Activated Hepatic Stellate Cells in Mice and in Human Tissues

(2012) Virginia Hernández–Gea et al.   GASTROENTEROLOGY

Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users

(2012) Supriya Munshaw et al.   HEPATOLOGY

Source and characterization of hepatic macrophages in acetaminophen-induced acute liver failure in humans

(2012) Charalambos Gustav Antoniades et al.   HEPATOLOGY

Protective role of V-set and immunoglobulin domain-containing 4 expressed on kupffer cells during immune-mediated liver injury by inducing tolerance of liver T- and natural killer T-cells

(2012) Keunok Jung et al.   HEPATOLOGY

Fate Mapping Reveals Origins and Dynamics of Monocytes and Tissue Macrophages under Homeostasis

(2012) Simon Yona et al.   IMMUNITY

Up-regulation of a death receptor renders antiviral T cells susceptible to NK cell–mediated deletion

(2012) Dimitra Peppa et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CXCR3-dependent recruitment and CCR6-mediated positioning of Th-17 cells in the inflamed liver

(2012) Ye Htun Oo et al.   JOURNAL OF HEPATOLOGY

Inhibition of inflammatory CD4 T cell activity by murine liver sinusoidal endothelial cells

(2012) Antonella Carambia et al.   JOURNAL OF HEPATOLOGY

Reduced Il17a Expression Distinguishes a Ly6c lo MHCII hi Macrophage Population Promoting Wound Healing

(2012) Mathieu P. Rodero et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

NK cells from HCV-infected patients effectively induce apoptosis of activated primary human hepatic stellate cells in a TRAIL-, FasL- and NKG2D-dependent manner

(2012) Andreas Glässner et al.   LABORATORY INVESTIGATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Hepatitis B virus–induced lipid alterations contribute to natural killer T cell–dependent protective immunity

(2012) Sebastian Zeissig et al.   NATURE MEDICINE

Differential Ly-6C expression identifies the recruited macrophage phenotype, which orchestrates the regression of murine liver fibrosis

(2012) P. Ramachandran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ly6ChiMonocytes Direct Alternatively Activated Profibrotic Macrophage Regulation of Lung Fibrosis

(2011) Michael A. Gibbons et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Innate or Adaptive Immunity? The Example of Natural Killer Cells

(2011) E. Vivier et al.   SCIENCE

Human MAIT cells are xenobiotic-resistant, tissue-targeted, CD161hi IL-17-secreting T cells

(2010) M. Dusseaux et al.   BLOOD

The Role of Chemokines in the Recruitment of Lymphocytes to the Liver

(2010) Ye H. Oo et al.   DIGESTIVE DISEASES

Characterization of two F4/80-positive Kupffer cell subsets by their function and phenotype in mice

(2010) Manabu Kinoshita et al.   JOURNAL OF HEPATOLOGY

Distinct Roles for CCR4 and CXCR3 in the Recruitment and Positioning of Regulatory T Cells in the Inflamed Human Liver

(2010) Y. H. Oo et al.   JOURNAL OF IMMUNOLOGY

Dynamic Regulation of CD8 T Cell Tolerance Induction by Liver Sinusoidal Endothelial Cells

(2010) A. Schurich et al.   JOURNAL OF IMMUNOLOGY

Contribution of Gut Bacteria to Liver Pathobiology

(2010) Gakuhei Son et al.   Gastroenterology Research and Practice

The Liver as a Lymphoid Organ

(2009) Ian Nicholas Crispe   Annual Review of Immunology

Priming of CD4+ T cells by liver sinusoidal endothelial cells induces CD25low forkhead box protein 3− regulatory T cells suppressing autoimmune hepatitis

(2009) Nils Kruse et al.   HEPATOLOGY

Hepatic regulatory T cells and Kupffer cells are crucial mediators of systemic T cell tolerance to antigens targeting murine liver

(2009) Ekaterina Breous et al.   HEPATOLOGY

CX3CR1+CD115+CD135+common macrophage/DC precursors and the role of CX3CR1 in their response to inflammation

(2009) Cedric Auffray et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Autophagy regulates lipid metabolism

(2009) Rajat Singh et al.   NATURE

Intrahepatic Murine CD8 T-Cell Activation Associates With a Distinct Phenotype Leading to Bim-Dependent Death

(2008) Lauren E. Holz et al.   GASTROENTEROLOGY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS