The Experts below are selected from a list of 4497 Experts worldwide ranked by ideXlab platform
Herbert C Morse - One of the best experts on this subject based on the ideXlab platform.
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the transcription factor IRF8 epigenetically regulates early dendritic cell specification
Experimental Hematology, 2019Co-Authors: Wataru Kawase, Akira Nishiyama, Daisuke Kurotaki, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Tomohiko TamuraAbstract:Dendritic cells (DCs) are vital for immune responses to pathogens. These cells are produced from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). Recently, DC lineage fate decisions occurring at stages much earlier than CDPs have been recognized, yet the mechanism remains unknown. In this study, we demonstrate that IRF8 regulates chromatin at the LMPP stage to induce early commitment towards DCs. Single-cell RNA-seq revealed that the expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. By in vivo transfer experiments, we showed that these IRF8 expressing LMPP (IRF8+ LMPPs) were derived from IRF8- LMPPs and predominantly produced DCs, especially classical DC1s (cDC1s). On the other hand, IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils or lymphocytes. RNA-seq and an assay for transposase-accessible chromatin (ATAC)-seq revealed that IRF8- and IRF8+ LMPPs displayed very similar global gene expression patterns; however, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8- LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs and cDC1s. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, thereby biasing their fate decision towards DCs.
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epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice
Blood, 2019Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Wataru Kawase, Tomohiko TamuraAbstract:Dendritic cells (DCs), which are vital for immune responses, are derived from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). DC lineage fate decisions occurring at stages much earlier than CDPs have recently been recognized, yet the mechanism remains elusive. By single-cell RNA-sequencing, in vivo cell transfer experiments, and an assay for transposase-accessible chromatin sequencing using wild-type, IRF8-GFP chimera knock-in or IRF8-knockout mice, we demonstrate that IRF8 regulates chromatin at the lymphoid-primed multipotent progenitor (LMPP) stage to induce early commitment toward DCs. A low but significant expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. These IRF8 + LMPPs were derived from IRF8 – LMPPs and predominantly produced DCs, especially classical DC1s, potentially via known progenitors, such as monocyte-DC progenitors, CDPs, and preclassical DCs. IRF8 + LMPPs did not generate significant numbers of monocytes, neutrophils, or lymphocytes. Although IRF8 – and IRF8 + LMPPs displayed very similar global gene expression patterns, the chromatin of enhancers near DC lineage genes was more accessible in IRF8 + LMPPs than in IRF8 – LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, biasing their fate decision toward DCs.
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cutting edge expression of IRF8 in gastric epithelial cells confers protective innate immunity against helicobacter pylori infection
Journal of Immunology, 2016Co-Authors: Hongsheng Wang, Peng Li, Sadia Abbasi, Alexander L Kovalchuk, Wei Liao, Chengfu Xu, Nonghua Lv, Warren J Leonard, Herbert C MorseAbstract:IFN regulatory factor 8 (IRF8) is expressed in many types of blood cells and plays critical roles in cellular differentiation and function. However, the role of IRF8 in nonhematopoietic systems remains poorly understood. In this study, we provide evidence that IRF8 is a transcriptional modulator of the gastric mucosa necessary for limiting Helicobacter pylori colonization. H. pylori infection significantly upregulated expression of IRF8, which, in turn, promoted IFN-γ expression by gastric epithelial cells. Mice deficient in IRF8 exhibited increased H. pylori colonization and aborted induction of mucosal IFN-γ. Genome-wide analyses of IFN-γ–treated gastric epithelial cells by chromatin immunoprecipitation sequencing and RNA sequencing led to the identification of IRF8 target genes, with many belonging to the IFN-regulated gene family that was observed previously in immune cells. Our results identify the IRF8–IFN-γ circuit as a novel gastric innate immune mechanism in the host defense against infection with H. pylori .
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dual function of the IRF8 transcription factor in autoimmune uveitis loss of IRF8 in t cells exacerbates uveitis whereas IRF8 deletion in the retina confers protection
Journal of Immunology, 2015Co-Authors: Jenna Burton, Hongsheng Wang, Herbert C Morse, Chengrong Yu, Chang He, Charles E EgwuaguAbstract:IFN regulatory factor 8 (IRF8) is constitutively expressed in monocytes and B cells and plays a critical role in the functional maturation of microglia cells. It is induced in T cells following Ag stimulation, but its functions are less well understood. However, recent studies in mice with T cell–specific IRF8 disruption under direction of the Lck promoter (LCK-IRF8KO) suggest that IRF8 directs a silencing program for Th17 differentiation, and IL-17 production is markedly increased in IRF8-deficient T cells. Paradoxically, loss of IRF8 in T cells has no effect on the development or severity of experimental autoimmune encephalomyelitis (EAE), although exacerbating colitis in a mouse colitis model. In contrast, mice with a macrophage/microglia-specific IRF8 disruption are resistant to EAE, further confounding our understanding of the roles of IRF8 in host immunity and autoimmunity. To clarify the role of IRF8 in autoimmune diseases, we have generated two mouse strains with targeted deletion of IRF8 in retinal cells, including microglial cells and a third mouse strain with targeted IRF8 deletion in T cells under direction of the nonpromiscuous, CD4 promoter (CD4-IRF8KO). In contrast to the report that IRF8 deletion in T cells has no effect on EAE, experimental autoimmune uveitis is exacerbated in CD4-IRF8KO mice and disease enhancement correlates with significant expansion of Th17 cells and a reduction in T regulatory cells. In contrast to CD4-IRF8KO mice, IRF8 deletion in retinal cells confers protection from uveitis, underscoring divergent and tissue-specific roles of IRF8 in host immunity. These results raise a cautionary note in the context of therapeutic targeting of IRF8.
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loss of IRF8 inhibits the growth of diffuse large b cell lymphoma
Journal of Cancer, 2015Co-Authors: Yulian Xu, Herbert C Morse, Lei Jiang, Jianchen Fang, Rong Fang, Guifang Ouyang, Jeff X ZhouAbstract:IRF8 is a transcription factor with a critical role in B lymphocyte development and functions. Its role in human diffuse large B-cell lymphoma (DLBCL), however, remained elusive. In this study, using shRNA-mediated knockdown of IRF8 expression, we found that the loss of IRF8 significantly reduced the proliferation of DLBCL cells (P<0.05). Mechanistically, decreasing the levels of IRF8 led to a suppression of the phosphorylation of p38 and ERK, molecules critical for B cell proliferation. Furthermore, using a xenograft lymphoma mouse model, we found that the loss of IRF8 significantly inhibited the growth of lymphomas in vivo (P<0.05). Immunohistochemical analysis of human DLBCL tissues revealed that the levels of IRF8 were significantly greater in non-germinal center B-cell-like (non-GCB) subtype than that in GCB subtype (P<0.05). Analysis of public available data also suggested that the expression levels of IRF8 mRNA in human DLBCL tissues were inversely correlated with patients' overall survival time. Taken together, this study suggested that IRF8 may play an oncogenic role in human DLBCL by promoting cell proliferation.
Keiko Ozato - One of the best experts on this subject based on the ideXlab platform.
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the transcription factor IRF8 epigenetically regulates early dendritic cell specification
Experimental Hematology, 2019Co-Authors: Wataru Kawase, Akira Nishiyama, Daisuke Kurotaki, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Tomohiko TamuraAbstract:Dendritic cells (DCs) are vital for immune responses to pathogens. These cells are produced from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). Recently, DC lineage fate decisions occurring at stages much earlier than CDPs have been recognized, yet the mechanism remains unknown. In this study, we demonstrate that IRF8 regulates chromatin at the LMPP stage to induce early commitment towards DCs. Single-cell RNA-seq revealed that the expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. By in vivo transfer experiments, we showed that these IRF8 expressing LMPP (IRF8+ LMPPs) were derived from IRF8- LMPPs and predominantly produced DCs, especially classical DC1s (cDC1s). On the other hand, IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils or lymphocytes. RNA-seq and an assay for transposase-accessible chromatin (ATAC)-seq revealed that IRF8- and IRF8+ LMPPs displayed very similar global gene expression patterns; however, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8- LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs and cDC1s. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, thereby biasing their fate decision towards DCs.
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epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice
Blood, 2019Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Wataru Kawase, Tomohiko TamuraAbstract:Dendritic cells (DCs), which are vital for immune responses, are derived from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). DC lineage fate decisions occurring at stages much earlier than CDPs have recently been recognized, yet the mechanism remains elusive. By single-cell RNA-sequencing, in vivo cell transfer experiments, and an assay for transposase-accessible chromatin sequencing using wild-type, IRF8-GFP chimera knock-in or IRF8-knockout mice, we demonstrate that IRF8 regulates chromatin at the lymphoid-primed multipotent progenitor (LMPP) stage to induce early commitment toward DCs. A low but significant expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. These IRF8 + LMPPs were derived from IRF8 – LMPPs and predominantly produced DCs, especially classical DC1s, potentially via known progenitors, such as monocyte-DC progenitors, CDPs, and preclassical DCs. IRF8 + LMPPs did not generate significant numbers of monocytes, neutrophils, or lymphocytes. Although IRF8 – and IRF8 + LMPPs displayed very similar global gene expression patterns, the chromatin of enhancers near DC lineage genes was more accessible in IRF8 + LMPPs than in IRF8 – LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, biasing their fate decision toward DCs.
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abstract 4682 IRF8 controls t cell development and survival to regulate t cell antitumor activity
Cancer Research, 2018Co-Authors: John D Klement, Mohammed L. Ibrahim, Mary Zimmerman, Amy V Paschall, Priscilla S Redd, Chunwan Lu, Hussein Sultan, Esteban Celis, Keiko OzatoAbstract:Interferon Regulatory Factor 8 (IRF8, or ICSBP1) is a member of the Interferon Regulatory transcription factor family, and functions as a key hematopoietic transcription factor. Loss of IRF8 leads to defective antigen-presenting cell activity, perturbations in B cell development and, in mouse models, an accumulation of CD11b + Gr1 + immature myeloid cells. However, the role of IRF8 in T cell development and antitumor activity remains unclear. Whole body and chimeric IRF8-knockout mice (IRF8-KO) demonstrate increased susceptibility to both allogenic transplant and carcinogen-induced tumor models. T cell function is crucial for the immune system9s endogenous antitumor response. Analysis of the T cell compartment of IRF8-KO mice demonstrated a deficiency in both naive T cell percentages and total number. Despite this peripheral decrease in T cell numbers, early T cell progenitors in both the bone marrow and thymus were significantly increased in IRF8-KO mice compared to wild-type. To further investigate the role of IRF8 in T cell development and survival, IRF8-KO:WT mixed chimera mice were generated by lethal irradiation of CD45.1 + CD45.2 + recipient mice, followed by transfer of CD45.2 + IRF8-KO and CD45.1 + WT bone marrow (BM). Surprisingly, analysis of blood obtained from reconstituted mice demonstrated preferential engraftment and survival of T cells derived from WT, rather than IRF8-KO BM. This imbalanced phenotype was not rescued by increasing the proportion of IRF8-KO BM administered to mice, suggesting the effect was not due to failure of IRF8-KO BM engraftment. Furthermore, analysis of T cell populations in both primary (thymus) and secondary (spleen) lymphoid organs showed a progressive loss of IRF8-KO T cells during their maturation and development process, while WT T cells remained unaltered. Given that IRF8 has been shown in tumor cells to regulate a variety of pro- and anti-apoptotic molecules, we hypothesized that IRF8 controls the peripheral survival of T cells. To test this hypothesis, resting T cells were isolated from the spleen of mixed chimera mice and viability was measured by Annexin V/PI staining. Resting IRF8-KO cells, but not WT, demonstrated a pro-apoptotic phenotype, as shown by increased Annexin V staining. Accordingly, upon in vitro stimulation and activation, IRF8-KO T cells demonstrated increased apoptosis. Our data determine that IRF8 controls both T cell development and peripheral survival, and that loss of IRF8 impairs the T cell antitumor immune response. Citation Format: John D. Klement, Amy V. Paschall, Mary A. Zimmerman, Mohammed L. Ibrahim, Priscilla S. Redd, Chunwan Lu, Hussein Sultan, Esteban Celis, Keiko Ozato, Kebin Liu. IRF8 controls T cell development and survival to regulate T cell antitumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4682.
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interferon regulatory factor 8 IRF8 impairs induction of interferon induced with tetratricopeptide repeat motif ifit gene family members
Journal of Biological Chemistry, 2016Co-Authors: Christine L White, Patricia M Kessler, Benjamin K Dickerman, Keiko OzatoAbstract:Abstract The chromosomally clustered interferon-induced with tetratricopeptide repeat motif (IFIT) gene family members share structural features at the gene and protein levels. Despite these similarities, different IFIT genes have distinct inducer- and cell type-specific induction patterns. Here, we investigated the mechanism for the observed differential induction of the mouse Ifit1, Ifit2, and Ifit3 genes in B cells and demonstrated that the repressive effect of the transcription factor interferon regulatory factor 8 (IRF8), which is highly expressed in B cells, played an essential role in this regulation. Although IRF8 could impair induction of all three IFIT genes following stimulation of retinoic acid-inducible gene I (RIG-I), it could selectively impair the induction of the Ifit1 gene following IFN stimulation. The above properties could be imparted to IRF8-non-expressing cells by ectopic expression of the protein. Induction of reporter genes, driven by truncated Ifit1 promoters, identified the regions that mediate the repression, and a chromatin immunoprecipitation assay revealed that more IRF8 bound to the IFN-stimulated response element of the Ifit1 gene than to those of the Ifit2 and the Ifit3 genes. Mutational analyses of IRF8 showed that its ability to bind DNA, interact with other proteins, and undergo sumoylation were all necessary to selectively repress Ifit1 gene induction in response to IFN. Our study revealed a new role for IRFs in differentially regulating the induction patterns of closely related IFN-stimulated genes that are located adjacent to one another in the mouse genome.
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enhancer landscape dynamics and the role of IRF8 in mononuclear phagocyte development
Blood, 2015Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Naofumi Kaneko, Shinichi Koizumi, Yutaka Suzuki, Tomohiko TamuraAbstract:Monocytes and dendritic cells (DCs) are critical mononuclear phagocytes that regulate innate and adaptive immune responses. Hematopoietic stem cells give rise to monocytes and DCs via intermediate myeloid progenitor populations, such as granulocyte-monocyte progenitors (GMPs), monocyte-DC progenitors (MDPs), and common monocyte progenitors (cMoPs) or common DC progenitors (CDPs). However, the molecular mechanism underlying their lineage determination is poorly understood. Recently, promoter-distal enhancers have been found to be key for cell fate decision. In this study, we performed chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of three histone modifications (H3K4me1, H3K27ac, and H3K4me3, representing primed enhancers, active enhancers, and transcriptional intiation, respectively) in seven myeloid populations (GMPs, MDPs, cMoPs, CDPs, monocytes, DCs, and neutrophils), and identified approximately sixty thousand putative enhancer regions. We found that a majority of monocyte- and DC-specific active enhancers were gradually established at progenitor stages prior to gene expression and terminal differentiation. Computational DNA motif analysis implicated that these enhancers were regulated by combinations of lineage-determining transcription factors such as PU.1, RUNX, C/EBP, and IRF. Indeed, ChIP-seq of PU.1 confirmed that the myeloid master regulator PU.1 was the common transcription factors bound to enhancers at all the stages examined. IRF binding motifs were enriched at the enhancer regions in MDPs, cMoPs and CDPs, but not GMPs. Among IRFs, IRF8, a partner of PU.1, has been shown to be highly expressed in MDPs and their descendants, and to be required for MDP-to-CDP and cMoP-to-monocyte transitions. Indeed, ChIP-seq analysis in IRF8 -/- progenitors demonstrated that the enhancer landscapes of IRF8 -/- GMPs, MDPs, and cMoPs all remained similar to that of wild-type GMPs. Moreover, ChIP-seq for IRF8 binding revealed that IRF8 directly promoted the priming and activation of many enhancers in MDPs and cMoPs. These results contribute to a comprehensive understanding of how transcription factors govern the enhancer landscape dynamics during mononuclear phagocyte development. Disclosures No relevant conflicts of interest to declare.
Philippe Gros - One of the best experts on this subject based on the ideXlab platform.
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role of IRF8 in immune cells functions protection against infections and susceptibility to inflammatory diseases
Human Genetics, 2020Co-Authors: Sandra Salem, David Salem, Philippe GrosAbstract:The transcription factor IRF8 (ICSBP) is required for the development and maturation of myeloid cells (dendritic cells, monocytes, macrophages), and for expression of intrinsic anti-microbial function such as antigen capture, processing and presentation to lymphoid cells, and for activation of these cells in response to cytokines and pro-inflammatory stimuli (IFN-gamma, IFN-beta, LPS). IRF8 deficiency in humans causes a severe primary immunodeficiency presenting as susceptibility to infections, complete or severe depletion of blood dendritic cells (DC) subsets, depletion of CD14(+) and CD16(+) monocytes and reduced numbers and impaired activity of NK cells. In genome-wide association studies (GWAS), sequence variants near IRF8 are significant risk factors for multiple chronic inflammatory diseases in humans including inflammatory bowel disease, lupus, rheumatoid arthritis, multiple sclerosis, and several others. Recent studies have cataloged all the genes bound by and transcriptionally activated by IRF8 in myeloid cells, either alone or in combination with other transcription factors (PU.1, IRF1, STAT1) at steady state and in response to pro-inflammatory stimuli. This IRF1/IRF8 regulome comprises immune pathways such as antigen processing and presentation pathways, expression of costimulatory molecules, cytokines and chemokines, response to stimuli such as cytokine receptors, pathogen-associated molecular pattern receptors, TLRs and nucleotide-binding oligomerization domain-like receptor signaling pathways, and small antiviral GTPases. Members of the IRF8/IRF1 regulome are over-represented amongst genes in which mutations cause primary immunodeficiencies, and are specifically enriched at GWAS loci associated with chronic inflammatory diseases in humans. These recent studies highlight a critical role of IRF8 in the activity of several immune cell types for protection against infections, but also in pathological inflammation associated with common human inflammatory conditions.
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Role of IRF8 in immune cells functions, protection against infections, and susceptibility to inflammatory diseases
Human Genetics, 2020Co-Authors: Sandra Salem, David Salem, Philippe GrosAbstract:The transcription factor IRF8 (ICSBP) is required for the development and maturation of myeloid cells (dendritic cells, monocytes, macrophages), and for expression of intrinsic anti-microbial function such as antigen capture, processing and presentation to lymphoid cells, and for activation of these cells in response to cytokines and pro-inflammatory stimuli (IFN-γ, IFN-β, LPS). IRF8 deficiency in humans causes a severe primary immunodeficiency presenting as susceptibility to infections, complete or severe depletion of blood dendritic cells (DC) subsets, depletion of CD14^+ and CD16^+ monocytes and reduced numbers and impaired activity of NK cells. In genome-wide association studies (GWAS), sequence variants near IRF8 are significant risk factors for multiple chronic inflammatory diseases in humans including inflammatory bowel disease, lupus, rheumatoid arthritis, multiple sclerosis, and several others. Recent studies have cataloged all the genes bound by and transcriptionally activated by IRF8 in myeloid cells, either alone or in combination with other transcription factors (PU.1, IRF1, STAT1) at steady state and in response to pro-inflammatory stimuli. This IRF1/IRF8 regulome comprises immune pathways such as antigen processing and presentation pathways, expression of costimulatory molecules, cytokines and chemokines, response to stimuli such as cytokine receptors, pathogen-associated molecular pattern receptors, TLRs and nucleotide-binding oligomerization domain-like receptor signaling pathways, and small antiviral GTPases. Members of the IRF8/IRF1 regulome are over-represented amongst genes in which mutations cause primary immunodeficiencies, and are specifically enriched at GWAS loci associated with chronic inflammatory diseases in humans. These recent studies highlight a critical role of IRF8 in the activity of several immune cell types for protection against infections, but also in pathological inflammation associated with common human inflammatory conditions.
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the macrophage IRF8 irf1 regulome is required for protection against infections and is associated with chronic inflammation
Journal of Experimental Medicine, 2016Co-Authors: David Langlais, Luis B Barreiro, Philippe GrosAbstract:IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by proinflammatory signals such as interferon-γ (IFN-γ). Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all of the genes bound by (cistromes) and transcriptionally activated by (regulomes) IRF8, IRF1, PU.1, and STAT1, including modulation of epigenetic histone marks. Of the seven binding combinations identified, two (cluster 1 [IRF8/IRF1/STAT1/PU.1] and cluster 5 [IRF1/STAT1/PU.1]) were found to have a major role in controlling macrophage transcriptional programs both at the basal level and after IFN-γ activation. They direct the expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and antimicrobial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immunodeficiencies and with loci associated with several inflammatory diseases in humans.
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The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation
Journal of Experimental Medicine, 2016Co-Authors: David Langlais, Luis B Barreiro, Philippe GrosAbstract:IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by proinflammatory signals such as interferon-γ (IFN-γ). Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all of the genes bound by (cistromes) and transcriptionally activated by (regulomes) IRF8, IRF1, PU.1, and STAT1, including modulation of epigenetic histone marks. Of the seven binding combinations identified, two (cluster 1 [IRF8/IRF1/STAT1/PU.1] and cluster 5 [IRF1/STAT1/PU.1]) were found to have a major role in controlling macrophage transcriptional programs both at the basal level and after IFN-γ activation. They direct the expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and antimicrobial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immunodeficiencies and with loci associated with several inflammatory diseases in humans.
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155 : IRF8 and IRF1: Genomic regulators of innate immunity
Cytokine, 2013Co-Authors: David Langlais, Philippe GrosAbstract:IRF8 transcription factor is essential for proper macrophage and dendritic cell (DC) differentiation, activation and function. We recently identified IRF8 mutations that are associated with a novel primary myeloid immunodeficiency, coupled with mycobacterial infections susceptibility (MSMD). Interestingly, mice bearing IRF8R294C loss-of-function alleles exhibit a similar phenotype; i.e. development of a chronic myelogenous leukemia-like syndrome characterized by a severe loss of dendritic cells and expansion of immature myeloid precursors, concomitant with susceptibility to intracellular infections. Recent GWAS and eQTL mapping studies associated IRF8 locus with various inflammatory diseases. Our objective is to define transcriptional networks controlled by these important inflammatory checkpoints (IRF8 and its binding partners IRF1 and PU.1), in order to identify novel genes implicated in MSMD and in susceptibility to Mycobacterium tuberculosis infection. To identify these networks, we used a combination high-throughput sequencing techniques. Primary macrophages, prior and after IFNγ activation, were subjected to (1) RNA-seq to identify IFNγ-regulated genes and (2) chromatin immunoprecipitation (ChIP-seq) to localize IRF8, IRF1 and PU.1 genomic binding sites. The comparison of ChIP-seq results for these well-known binding partners confirmed their co-recruitment to regulatory elements. Interestingly however, they are not obligate partners as we uncovered many different binding schemes. Furthermore, IFNγ triggers de novo IRF1 DNA binding, but had limited influence on IRF8 and PU.1 that are already occupying their binding sites. The overlap of ChIP-seq and RNA-seq data revealed that IFNγ-upregulated genes are strongly associated with IRF binding sites, as opposed to repressed genes. ChIP-qPCR and RNA-seq in IRF8R294C and IRF1−/− primary macrophages confirmed the interdependence of IRF8 and IRF1 co-recruitment and their respective importance for IFNγ-regulated genes subsets. Genes identified in these transcriptional pathways represent the “core myeloid transcriptome” and are likely to play critical roles in macrophage function and may represent valuable candidates for myeloid immunodeficiencies and susceptibility to mycobacterial infections.
Tomohiko Tamura - One of the best experts on this subject based on the ideXlab platform.
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Decrypting DC development
Nature Immunology, 2019Co-Authors: Martin Guilliams, Tomohiko TamuraAbstract:The NFIL3–ZEB2–ID2 transcription-factor regulatory circuit switches the E protein–dependent +41 kb IRF8 enhancer in DC progenitors to the BATF3-dependent +32 kb IRF8 enhancer in mature cDC1s. Deletion of the cryptic +41 kb IRF8 enhancer impedes cDC1 development.
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the transcription factor IRF8 epigenetically regulates early dendritic cell specification
Experimental Hematology, 2019Co-Authors: Wataru Kawase, Akira Nishiyama, Daisuke Kurotaki, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Tomohiko TamuraAbstract:Dendritic cells (DCs) are vital for immune responses to pathogens. These cells are produced from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). Recently, DC lineage fate decisions occurring at stages much earlier than CDPs have been recognized, yet the mechanism remains unknown. In this study, we demonstrate that IRF8 regulates chromatin at the LMPP stage to induce early commitment towards DCs. Single-cell RNA-seq revealed that the expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. By in vivo transfer experiments, we showed that these IRF8 expressing LMPP (IRF8+ LMPPs) were derived from IRF8- LMPPs and predominantly produced DCs, especially classical DC1s (cDC1s). On the other hand, IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils or lymphocytes. RNA-seq and an assay for transposase-accessible chromatin (ATAC)-seq revealed that IRF8- and IRF8+ LMPPs displayed very similar global gene expression patterns; however, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8- LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs and cDC1s. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, thereby biasing their fate decision towards DCs.
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1024 - EPIGENETIC CONTROL OF MYELOID CELL DEVELOPMENT BY THE TRANSCRIPTION FACTOR IRF8
Experimental Hematology, 2019Co-Authors: Tomohiko TamuraAbstract:Differentiation of hematopoietic stem and progenitor cells to various types of blood cells is a process of establishing cell type-specific gene expression patterns. We have been investigating the mechanism of myeloid cell development from a viewpoint of gene expression control by transcription factors, particularly IRF8. In IRF8–/– mice, mononuclear phagocyte progenitors are accumulated, and these progenitors do not efficiently differentiate into monocytes (Mos) or dendritic cells (DCs) but instead, give rise to a large number of neutrophils. Accordingly, the loss of IRF8 causes immunodeficiency and chronic myeloid leukemia-like neutrophilia in mice and humans. Recently, we found that a novel 3’ enhancer is responsible for high IRF8 expression in the DC lineage. Deletion of this enhancer in vivo resulted in the loss of classical DC1s (cDC1s) and somehow surprisingly, caused a significant increase in Mo counts. Thus, the expression level of IRF8 determines the fate of myeloid progenitors; absence, low, or high expression of IRF8 promotes differentiation towards neutrophils, Mos, or DCs, respectively. We also analyzed enhancer landscape dynamics and the genome-wide behavior of IRF8 during the development of mononuclear phagocytes in vivo. While IRF8 does not immediately change the global gene expression pattern in the mononuclear phagocyte progenitors, it does establish their enhancer landscapes by cooperating or antagonizing with other transcription factors, thereby preparing for future gene expression. Furthermore, we found that IRF8 is weakly expressed in a subpopulation of lymphoid-primed multipotent progenitors and leads to early lineage specification towards cDC1s by regulating chromatin states before inducing major transcriptional changes. We are now investigating the 3D chromatin structure dynamics and the role of IRF8 during myeloid development. Collectively, these results illustrate that the epigenetic changes induced by key transcription factors such as IRF8 determine the fate of hematopoietic progenitor cells before establishing gene expression patterns.
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epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice
Blood, 2019Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Wataru Kawase, Tomohiko TamuraAbstract:Dendritic cells (DCs), which are vital for immune responses, are derived from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). DC lineage fate decisions occurring at stages much earlier than CDPs have recently been recognized, yet the mechanism remains elusive. By single-cell RNA-sequencing, in vivo cell transfer experiments, and an assay for transposase-accessible chromatin sequencing using wild-type, IRF8-GFP chimera knock-in or IRF8-knockout mice, we demonstrate that IRF8 regulates chromatin at the lymphoid-primed multipotent progenitor (LMPP) stage to induce early commitment toward DCs. A low but significant expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. These IRF8 + LMPPs were derived from IRF8 – LMPPs and predominantly produced DCs, especially classical DC1s, potentially via known progenitors, such as monocyte-DC progenitors, CDPs, and preclassical DCs. IRF8 + LMPPs did not generate significant numbers of monocytes, neutrophils, or lymphocytes. Although IRF8 – and IRF8 + LMPPs displayed very similar global gene expression patterns, the chromatin of enhancers near DC lineage genes was more accessible in IRF8 + LMPPs than in IRF8 – LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, biasing their fate decision toward DCs.
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enhancer landscape dynamics and the role of IRF8 in mononuclear phagocyte development
Blood, 2015Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Naofumi Kaneko, Shinichi Koizumi, Yutaka Suzuki, Tomohiko TamuraAbstract:Monocytes and dendritic cells (DCs) are critical mononuclear phagocytes that regulate innate and adaptive immune responses. Hematopoietic stem cells give rise to monocytes and DCs via intermediate myeloid progenitor populations, such as granulocyte-monocyte progenitors (GMPs), monocyte-DC progenitors (MDPs), and common monocyte progenitors (cMoPs) or common DC progenitors (CDPs). However, the molecular mechanism underlying their lineage determination is poorly understood. Recently, promoter-distal enhancers have been found to be key for cell fate decision. In this study, we performed chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of three histone modifications (H3K4me1, H3K27ac, and H3K4me3, representing primed enhancers, active enhancers, and transcriptional intiation, respectively) in seven myeloid populations (GMPs, MDPs, cMoPs, CDPs, monocytes, DCs, and neutrophils), and identified approximately sixty thousand putative enhancer regions. We found that a majority of monocyte- and DC-specific active enhancers were gradually established at progenitor stages prior to gene expression and terminal differentiation. Computational DNA motif analysis implicated that these enhancers were regulated by combinations of lineage-determining transcription factors such as PU.1, RUNX, C/EBP, and IRF. Indeed, ChIP-seq of PU.1 confirmed that the myeloid master regulator PU.1 was the common transcription factors bound to enhancers at all the stages examined. IRF binding motifs were enriched at the enhancer regions in MDPs, cMoPs and CDPs, but not GMPs. Among IRFs, IRF8, a partner of PU.1, has been shown to be highly expressed in MDPs and their descendants, and to be required for MDP-to-CDP and cMoP-to-monocyte transitions. Indeed, ChIP-seq analysis in IRF8 -/- progenitors demonstrated that the enhancer landscapes of IRF8 -/- GMPs, MDPs, and cMoPs all remained similar to that of wild-type GMPs. Moreover, ChIP-seq for IRF8 binding revealed that IRF8 directly promoted the priming and activation of many enhancers in MDPs and cMoPs. These results contribute to a comprehensive understanding of how transcription factors govern the enhancer landscape dynamics during mononuclear phagocyte development. Disclosures No relevant conflicts of interest to declare.
Daisuke Kurotaki - One of the best experts on this subject based on the ideXlab platform.
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the transcription factor IRF8 epigenetically regulates early dendritic cell specification
Experimental Hematology, 2019Co-Authors: Wataru Kawase, Akira Nishiyama, Daisuke Kurotaki, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Tomohiko TamuraAbstract:Dendritic cells (DCs) are vital for immune responses to pathogens. These cells are produced from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). Recently, DC lineage fate decisions occurring at stages much earlier than CDPs have been recognized, yet the mechanism remains unknown. In this study, we demonstrate that IRF8 regulates chromatin at the LMPP stage to induce early commitment towards DCs. Single-cell RNA-seq revealed that the expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. By in vivo transfer experiments, we showed that these IRF8 expressing LMPP (IRF8+ LMPPs) were derived from IRF8- LMPPs and predominantly produced DCs, especially classical DC1s (cDC1s). On the other hand, IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils or lymphocytes. RNA-seq and an assay for transposase-accessible chromatin (ATAC)-seq revealed that IRF8- and IRF8+ LMPPs displayed very similar global gene expression patterns; however, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8- LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs and cDC1s. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, thereby biasing their fate decision towards DCs.
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epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice
Blood, 2019Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Yutaka Suzuki, Herbert C Morse, Wataru Kawase, Tomohiko TamuraAbstract:Dendritic cells (DCs), which are vital for immune responses, are derived from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). DC lineage fate decisions occurring at stages much earlier than CDPs have recently been recognized, yet the mechanism remains elusive. By single-cell RNA-sequencing, in vivo cell transfer experiments, and an assay for transposase-accessible chromatin sequencing using wild-type, IRF8-GFP chimera knock-in or IRF8-knockout mice, we demonstrate that IRF8 regulates chromatin at the lymphoid-primed multipotent progenitor (LMPP) stage to induce early commitment toward DCs. A low but significant expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. These IRF8 + LMPPs were derived from IRF8 – LMPPs and predominantly produced DCs, especially classical DC1s, potentially via known progenitors, such as monocyte-DC progenitors, CDPs, and preclassical DCs. IRF8 + LMPPs did not generate significant numbers of monocytes, neutrophils, or lymphocytes. Although IRF8 – and IRF8 + LMPPs displayed very similar global gene expression patterns, the chromatin of enhancers near DC lineage genes was more accessible in IRF8 + LMPPs than in IRF8 – LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, biasing their fate decision toward DCs.
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Down-regulation of IRF8 by Lyz2-cre/loxP accelerates osteoclast differentiation in vitro
Cytotechnology, 2016Co-Authors: Emi Saito, Daisuke Kurotaki, Dai Suzuki, Ayako Mochizuki, Yoko Manome, Tetsuo Suzawa, Yoichi Toyoshima, Takahiro Ichikawa, Takahiro Funatsu, Tomio InoueAbstract:Interferon regulatory factor 8 (IRF8) is a transcription factor that negatively regulates osteoclast differentiation and IRF8 global knockout (IRF8 −/−) mice have been shown to have reduced bone volume resulting from increased osteoclast numbers. However, detailed analysis of the functions of IRF8 in osteoclast precursors with a monocyte/macrophage linage is difficult, because the population and properties of hematopoietic cells in IRF8 −/− mice are severely altered. Therefore, to clearly elucidate the functions of IRF8 during osteoclastogenesis, we established myeloid cell-specific IRF8 conditional knockout (IRF8 fl/fl ;Lyz2 cre/+) mice. We found that trabecular bone volume in the IRF8 fl/fl ;Lyz2 cre/+ mice was not significantly affected, while exposure to M-CSF and RANKL significantly increased TRAP activity in vitro in osteoclasts that underwent osteoclastogenesis from bone marrow-derived macrophages (BMMs) induced from bone marrow cells (BMCs) of those mice by addition of M-CSF. Our results also showed that expression of IRF8 mRNA and protein in BMMs obtained from IRF8 fl/fl ;Lyz2 cre/+ mice and cultured with M-CSF was reduced. These findings predicted that Lyz2/Lyz2-cre expression is induced when BMCs differentiate into BMMs in cultures with M-CSF. In osteoclast differentiation cultures, Lyz2 was gradually increased by M-CSF during the first 3 days of culture, then rapidly decreased by the addition of RANKL with M-CSF during the next 3 days. Furthermore, BMCs differentiated into osteoclasts while maintaining a low level of Lyz2 expression when cultured simultaneously with both M-CSF and RANKL from the initiation of culture. These findings suggest that Lyz2-cre expression is induced along with differentiation to BMMs by BMCs obtained from IRF8 fl/fl ;Lyz2 cre/+ mice and cultured with M-CSF. In addition, IRF8 was down-regulated by activation of the cre/loxP recombination system in BMMs and osteoclastogenesis was accelerated. Based on our results, we propose the existence in vivo of a new lineage of osteoclast precursors among BMCs, which differentiate into osteoclasts without up-regulation of Lyz2 expression.
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enhancer landscape dynamics and the role of IRF8 in mononuclear phagocyte development
Blood, 2015Co-Authors: Daisuke Kurotaki, Akira Nishiyama, Keiko Ozato, Jun Nakabayashi, Haruka Sasaki, Naofumi Kaneko, Shinichi Koizumi, Yutaka Suzuki, Tomohiko TamuraAbstract:Monocytes and dendritic cells (DCs) are critical mononuclear phagocytes that regulate innate and adaptive immune responses. Hematopoietic stem cells give rise to monocytes and DCs via intermediate myeloid progenitor populations, such as granulocyte-monocyte progenitors (GMPs), monocyte-DC progenitors (MDPs), and common monocyte progenitors (cMoPs) or common DC progenitors (CDPs). However, the molecular mechanism underlying their lineage determination is poorly understood. Recently, promoter-distal enhancers have been found to be key for cell fate decision. In this study, we performed chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of three histone modifications (H3K4me1, H3K27ac, and H3K4me3, representing primed enhancers, active enhancers, and transcriptional intiation, respectively) in seven myeloid populations (GMPs, MDPs, cMoPs, CDPs, monocytes, DCs, and neutrophils), and identified approximately sixty thousand putative enhancer regions. We found that a majority of monocyte- and DC-specific active enhancers were gradually established at progenitor stages prior to gene expression and terminal differentiation. Computational DNA motif analysis implicated that these enhancers were regulated by combinations of lineage-determining transcription factors such as PU.1, RUNX, C/EBP, and IRF. Indeed, ChIP-seq of PU.1 confirmed that the myeloid master regulator PU.1 was the common transcription factors bound to enhancers at all the stages examined. IRF binding motifs were enriched at the enhancer regions in MDPs, cMoPs and CDPs, but not GMPs. Among IRFs, IRF8, a partner of PU.1, has been shown to be highly expressed in MDPs and their descendants, and to be required for MDP-to-CDP and cMoP-to-monocyte transitions. Indeed, ChIP-seq analysis in IRF8 -/- progenitors demonstrated that the enhancer landscapes of IRF8 -/- GMPs, MDPs, and cMoPs all remained similar to that of wild-type GMPs. Moreover, ChIP-seq for IRF8 binding revealed that IRF8 directly promoted the priming and activation of many enhancers in MDPs and cMoPs. These results contribute to a comprehensive understanding of how transcription factors govern the enhancer landscape dynamics during mononuclear phagocyte development. Disclosures No relevant conflicts of interest to declare.
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regulation of myelopoiesis by the transcription factor IRF8
International Journal of Hematology, 2015Co-Authors: Tomohiko Tamura, Daisuke Kurotaki, Shinichi KoizumiAbstract:Interferon regulatory factor-8 (IRF8) is a transcription factor expressed in hematopoietic cells, particularly in mononuclear phagocytes [monocytes/macrophages and dendritic cells (DCs)] and their progenitors. Various studies have demonstrated that IRF8 is essential for the development of monocytes, DCs, eosinophils, and basophils. Conversely, IRF8 suppresses the generation of neutrophils. Accordingly, IRF8−/− mice develop immunodeficiency and a chronic myeloid leukemia (CML)-like disease. Mutations and loss of expression of the human IRF8 gene are also associated with immunodeficiency and CML, respectively. Recent findings have begun to reveal the transcription factor network and epigenetic changes governed by IRF8. For example, in mononuclear phagocyte progenitors, IRF8 cooperates with PU.1 to promote the formation of promoter-distal enhancers to induce monocyte-related genes including the critical downstream transcription factor gene Klf4. On the other hand, IRF8 blocks C/EBPα activity to suppress the neutrophil differentiation program. Indeed, IRF8−/− mononuclear phagocyte progenitors fail to efficiently generate monocytes and DCs and, instead, aberrantly give rise to neutrophils. This article provides an overview of recent advances in our understanding of the role of IRF8 in myelopoiesis and related diseases.
