Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

A Locus at 5q33.3 Confers Resistance to Tuberculosis in Highly Susceptible Individuals

(2016) Rafal S. Sobota et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease

(2016) Duo Jiang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetics and Pathogenesis of Inflammatory Bowel Disease

(2016) Ta-Chiang Liu et al.   Annual Review of Pathology-Mechanisms of Disease

Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci

(2016) André Lacour et al.   BIOINFORMATICS

Genetic Complexity of Crohn’s Disease in Two Large Ashkenazi Jewish Families

(2016) Adam P. Levine et al.   GASTROENTEROLOGY

A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF

(2016) Ling-Shiang Chuang et al.   GASTROENTEROLOGY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

(2016) David Ellinghaus et al.   NATURE GENETICS

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

ATG16L1: A multifunctional susceptibility factor in Crohn disease

(2015) Mohammad Salem et al.   Autophagy

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

Interleukin-34 sustains inflammatory pathways in the gut

(2015) Eleonora Franzè et al.   CLINICAL SCIENCE

Interleukin 34: a new modulator of human and experimental inflammatory bowel disease

(2015) Stephanie Zwicker et al.   CLINICAL SCIENCE

CYLD-Mediated Signaling and Diseases

(2015) Bryan Mathis et al.   CURRENT DRUG TARGETS

Optineurin deficiency in mice contributes to impaired cytokine secretion and neutrophil recruitment in bacteria-driven colitis

(2015) T. S. Chew et al.   Disease Models & Mechanisms

Genetics of Inflammatory Bowel Diseases

(2015) Dermot P.B. McGovern et al.   GASTROENTEROLOGY

A dualcis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages

(2015) Alessandra Mancino et al.   GENES & DEVELOPMENT

Improved integrative framework combining association data with gene expression features to prioritize Crohn's disease genes

(2015) Kaida Ning et al.   HUMAN MOLECULAR GENETICS

Respiratory syncytial virus infection of primary human mast cells induces the selective production of type I interferons, CXCL10, and CCL4

(2015) Ayham Al-Afif et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Functional regulation of Zfp36l1 and Zfp36l2 in response to lipopolysaccharide in mouse RAW264.7 macrophages

(2015) Kuan-Ting Wang et al.   Journal of Inflammation-London

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

(2015) Anagha Joshi et al.   JOURNAL OF LEUKOCYTE BIOLOGY

High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

(2015) Philippe Goyette et al.   NATURE GENETICS

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

(2015) Natalie J. Prescott et al.   PLoS Genetics

PARP-14 combines with tristetraprolin in the selective posttranscriptional control of macrophage tissue factor expression

(2014) M. B. Iqbal et al.   BLOOD

Transcription and enhancer profiling in human monocyte subsets

(2014) C. Schmidl et al.   BLOOD

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

The monocyte-macrophage axis in the intestine

(2014) Calum C. Bain et al.   CELLULAR IMMUNOLOGY

Akirin2 is critical for inducing inflammatory genes by bridging I B-  and the SWI/SNF complex

(2014) S. Tartey et al.   EMBO JOURNAL

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

The Diagnostic Approach to Monogenic Very Early Onset Inflammatory Bowel Disease

(2014) Holm H. Uhlig et al.   GASTROENTEROLOGY

Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus

(2014) S N Kariuki et al.   GENES AND IMMUNITY

SHIP-1 deficiency in the myeloid compartment is insufficient to induce myeloid expansion or chronic inflammation

(2014) M J Maxwell et al.   GENES AND IMMUNITY

Macrophage-Restricted Interleukin-10 Receptor Deficiency, but Not IL-10 Deficiency, Causes Severe Spontaneous Colitis

(2014) Ehud Zigmond et al.   IMMUNITY

Activation of Gpr109a, Receptor for Niacin and the Commensal Metabolite Butyrate, Suppresses Colonic Inflammation and Carcinogenesis

(2014) Nagendra Singh et al.   IMMUNITY

NOD1 and NOD2: Signaling, Host Defense, and Inflammatory Disease

(2014) Roberta Caruso et al.   IMMUNITY

Macrophages in intestinal homeostasis and inflammation

(2014) Calum C. Bain et al.   IMMUNOLOGICAL REVIEWS

Transcriptomic analysis of mononuclear phagocyte differentiation and activation

(2014) David A. Hume et al.   IMMUNOLOGICAL REVIEWS

Kruppel-like Transcription Factor 6 Regulates Inflammatory Macrophage Polarization

(2014) Dipali Date et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CD137 Induces Proliferation of Murine Hematopoietic Progenitor Cells and Differentiation to Macrophages

(2014) D. Jiang et al.   JOURNAL OF IMMUNOLOGY

Phosphatase Holoenzyme PP1/GADD34 Negatively Regulates TLR Response by Inhibiting TAK1 Serine 412 Phosphorylation

(2014) M. Gu et al.   JOURNAL OF IMMUNOLOGY

The Transcriptional Repressor BLIMP1 Curbs Host Defenses by Suppressing Expression of the Chemokine CCL8

(2014) M. Severa et al.   JOURNAL OF IMMUNOLOGY

An essential role for IFN-β in the induction of IFN-stimulated gene expression by LPS in macrophages

(2014) Faruk Sheikh et al.   JOURNAL OF LEUKOCYTE BIOLOGY

DTX3L and ARTD9 inhibit IRF1 expression and mediate in cooperation with ARTD8 survival and proliferation of metastatic prostate cancer cells

(2014) Samia B Bachmann et al.   Molecular Cancer

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Advances in IBD genetics

(2014) Johan Van Limbergen et al.   Nature Reviews Gastroenterology & Hepatology

Myocyte enhancer factor 2C regulation of hepatocellular carcinoma via vascular endothelial growth factor and Wnt/β-catenin signaling

(2014) X L Bai et al.   ONCOGENE

Accounting for eXentricities: Analysis of the X Chromosome in GWAS Reveals X-Linked Genes Implicated in Autoimmune Diseases

(2014) Diana Chang et al.   PLoS One

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

(2014) S. Saeed et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced NF- B Signaling

(2014) M.-H. Sung et al.   Science Signaling

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcriptional Control of Inflammatory Responses

(2014) S. T. Smale et al.   Cold Spring Harbor Perspectives in Biology

Microbial Sensing by Toll-Like Receptors and Intracellular Nucleic Acid Sensors

(2014) Surya Pandey et al.   Cold Spring Harbor Perspectives in Biology

Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation

(2014) Johanna Schott et al.   PLoS Genetics

Architecture and Expression of the Nfatc1 Gene in Lymphocytes

(2014) Ronald Rudolf et al.   Frontiers in Immunology

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Association Between Variants of PRDM1 and NDP52 and Crohn's Disease, Based on Exome Sequencing and Functional Studies

(2013) David Ellinghaus et al.   GASTROENTEROLOGY

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

Gene–gene and gene–environment interactions in ulcerative colitis

(2013) Ming-Hsi Wang et al.   HUMAN GENETICS

Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling

(2013) Yu Qiao et al.   IMMUNITY

Contributions of dendritic cells and macrophages to intestinal homeostasis and immune defense

(2013) Julia Farache et al.   IMMUNOLOGY AND CELL BIOLOGY

Two Phases of Inflammatory Mediator Production Defined by the Study of IRAK2 and IRAK1 Knock-in Mice

(2013) E. Pauls et al.   JOURNAL OF IMMUNOLOGY

Interferon-Stimulated Poly(ADP-Ribose) Polymerases Are Potent Inhibitors of Cellular Translation and Virus Replication

(2013) S. Atasheva et al.   JOURNAL OF VIROLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

CSF-1 Receptor-Dependent Colon Development, Homeostasis and Inflammatory Stress Response

(2013) Duy Huynh et al.   PLoS One

EBI2 Is a Negative Regulator of Type I Interferons in Plasmacytoid and Myeloid Dendritic Cells

(2013) Eugene Y. Chiang et al.   PLoS One

Intestinal macrophages: well educated exceptions from the rule

(2013) Ehud Zigmond et al.   TRENDS IN IMMUNOLOGY

Regulation of NF-κB signalling by the mono-ADP-ribosyltransferase ARTD10

(2013) Patricia Verheugd et al.   Nature Communications

ZIP8 Regulates Host Defense through Zinc-Mediated Inhibition of NF-κB

(2013) Ming-Jie Liu et al.   Cell Reports

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

(2013) Mélissa Beaudoin et al.   PLoS Genetics

Association of two independent functional risk haplotypes inTNIP1with systemic lupus erythematosus

(2012) Indra Adrianto et al.   ARTHRITIS AND RHEUMATISM

The small MAF transcription factors MAFF, MAFG and MAFK: Current knowledge and perspectives

(2012) Meenakshi B. Kannan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states

(2012) T.-H. Pham et al.   BLOOD

The interferon signature in autoimmune diseases

(2012) Lars Rönnblom et al.   CURRENT OPINION IN RHEUMATOLOGY

LRRK2 as a negative regulator of NFAT: implications for the pathogenesis of inflammatory bowel disease

(2012) Puja Vora et al.   Expert Review of Clinical Immunology

Hypothesis-free analysis of ATG16L1 demonstrates gene-wide extent of association with Crohn's disease susceptibility: Table 1

(2012) Johan Van Limbergen et al.   GUT

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

IL-34 is a tissue-restricted ligand of CSF1R required for the development of Langerhans cells and microglia

(2012) Yaming Wang et al.   NATURE IMMUNOLOGY

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

(2012) Irina Rusinova et al.   NUCLEIC ACIDS RESEARCH

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

(2012) K. Schroder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting negative regulation of Toll-like receptor signaling

(2012) Takeshi Kondo et al.   TRENDS IN IMMUNOLOGY

Emerging patterns of genetic overlap across autoimmune disorders

(2012) Corinne Richard-Miceli et al.   Genome Medicine

Dissecting the Genetics of Complex Inheritance: Linkage Disequilibrium Mapping Provides Insight into Crohn Disease

(2011) Heather Elding et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Suppressor of Cytokine Signaling (SOCS) 1 Inhibits Type I Interferon (IFN) Signaling via the Interferon α Receptor (IFNAR1)-associated Tyrosine Kinase Tyk2

(2011) Rebecca A. R. Piganis et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Krüppel-like factor 4 regulates macrophage polarization

(2011) Xudong Liao et al.   JOURNAL OF CLINICAL INVESTIGATION

Mucosal Macrophages in Intestinal Homeostasis and Inflammation

(2011) Allan McI Mowat et al.   Journal of Innate Immunity

Selective Inhibition of a Regulatory Subunit of Protein Phosphatase 1 Restores Proteostasis

(2011) P. Tsaytler et al.   SCIENCE

Dual roles for MEF2A and MEF2D during human macrophage terminal differentiation and c-Jun expression

(2010) Catherine Aude-Garcia et al.   BIOCHEMICAL JOURNAL

An antibody against the colony-stimulating factor 1 receptor depletes the resident subset of monocytes and tissue- and tumor-associated macrophages but does not inhibit inflammation

(2010) K. P. A. MacDonald et al.   BLOOD

Pattern Recognition Receptors and Inflammation

(2010) Osamu Takeuchi et al.   CELL

Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages

(2010) A. L. Sullivan et al.   MOLECULAR AND CELLULAR BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

Genome-wide association study identifies variants at CSF1, OPTN and TNFRSF11A as genetic risk factors for Paget's disease of bone

(2010) Omar M E Albagha et al.   NATURE GENETICS

TLR activation of the transcription factor XBP1 regulates innate immune responses in macrophages

(2010) Fabio Martinon et al.   NATURE IMMUNOLOGY

A Novel Mouse Model of Inflammatory Bowel Disease Links Mammalian Target of Rapamycin-Dependent Hyperproliferation of Colonic Epithelium to Inflammation-Associated Tumorigenesis

(2009) Lin Deng et al.   AMERICAN JOURNAL OF PATHOLOGY

On the level: IRGM gene function is all about expression

(2009) Alan Huett et al.   Autophagy

Elevated Mitochondrial Reactive Oxygen Species Generation Affects the Immune Response via Hypoxia-Inducible Factor-1  in Long-Lived Mclk1+/- Mouse Mutants

(2009) D. Wang et al.   JOURNAL OF IMMUNOLOGY

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

(2009) Kazufumi Matsushita et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Peli1 facilitates TRIF-dependent Toll-like receptor signaling and proinflammatory cytokine production

(2009) Mikyoung Chang et al.   NATURE IMMUNOLOGY

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

Intestinal macrophages: differentiation and involvement in intestinal immunopathologies

(2009) Benjamin Weber et al.   Seminars in Immunopathology

SLIC-1/sorting nexin 20: A novel sorting nexin that directs subcellular distribution of PSGL-1

(2008) Ulrich Y. Schaff et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophages

(2008) K. M. Irvine et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Differentiation and heterogeneity in the mononuclear phagocyte system

(2008) D A Hume   Mucosal Immunology

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

(2008) Steven A McCarroll et al.   NATURE GENETICS

TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon–response genes

(2008) Anna Yarilina et al.   NATURE IMMUNOLOGY