IRF8 Inhibits C/EBPΑ Activity to Restrain Mononuclear Phagocyte Progenitors from Differentiating Into Neutrophils
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RBP-J Signaling − Cells Through Notch Novel IRF8-Controlled
Sca-1+Lin−CD117− Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch −RBP-J Signaling This information is current as of September 25, 2021. Xingxia Liu, Shaoda Ren, Chaozhuo Ge, Kai Cheng, Martin Zenke, Armand Keating and Robert C. H. Zhao J Immunol 2015; 194:4298-4308; Prepublished online 30 March 2015; doi: 10.4049/jimmunol.1402641 Downloaded from http://www.jimmunol.org/content/194/9/4298 Supplementary http://www.jimmunol.org/content/suppl/2015/03/28/jimmunol.140264 http://www.jimmunol.org/ Material 1.DCSupplemental References This article cites 59 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/194/9/4298.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 25, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Sca-1+Lin2CD1172 Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch–RBP-J Signaling Xingxia Liu,*,1 Shaoda Ren,*,1 Chaozhuo Ge,* Kai Cheng,* Martin Zenke,† Armand Keating,‡,x and Robert C. -
Microglia Emerge from Erythromyeloid Precursors Via Pu.1- and Irf8-Dependent Pathways
ART ic LE S Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways Katrin Kierdorf1,2, Daniel Erny1, Tobias Goldmann1, Victor Sander1, Christian Schulz3,4, Elisa Gomez Perdiguero3,4, Peter Wieghofer1,2, Annette Heinrich5, Pia Riemke6, Christoph Hölscher7,8, Dominik N Müller9, Bruno Luckow10, Thomas Brocker11, Katharina Debowski12, Günter Fritz1, Ghislain Opdenakker13, Andreas Diefenbach14, Knut Biber5,15, Mathias Heikenwalder16, Frederic Geissmann3,4, Frank Rosenbauer6 & Marco Prinz1,17 Microglia are crucial for immune responses in the brain. Although their origin from the yolk sac has been recognized for some time, their precise precursors and the transcription program that is used are not known. We found that mouse microglia were derived from primitive c-kit+ erythromyeloid precursors that were detected in the yolk sac as early as 8 d post conception. + lo − + − + These precursors developed into CD45 c-kit CX3CR1 immature (A1) cells and matured into CD45 c-kit CX3CR1 (A2) cells, as evidenced by the downregulation of CD31 and concomitant upregulation of F4/80 and macrophage colony stimulating factor receptor (MCSF-R). Proliferating A2 cells became microglia and invaded the developing brain using specific matrix metalloproteinases. Notably, microgliogenesis was not only dependent on the transcription factor Pu.1 (also known as Sfpi), but also required Irf8, which was vital for the development of the A2 population, whereas Myb, Id2, Batf3 and Klf4 were not required. Our data provide cellular and molecular insights into the origin and development of microglia. Microglia are the tissue macrophages of the brain and scavenge dying have the ability to give rise to microglia and macrophages in vitro cells, pathogens and molecules using pattern recognition receptors and in vivo under defined conditions. -
A Molecular Switch from STAT2-IRF9 to ISGF3 Underlies Interferon-Induced Gene Transcription
ARTICLE https://doi.org/10.1038/s41467-019-10970-y OPEN A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription Ekaterini Platanitis 1, Duygu Demiroz1,5, Anja Schneller1,5, Katrin Fischer1, Christophe Capelle1, Markus Hartl 1, Thomas Gossenreiter 1, Mathias Müller2, Maria Novatchkova3,4 & Thomas Decker 1 Cells maintain the balance between homeostasis and inflammation by adapting and inte- grating the activity of intracellular signaling cascades, including the JAK-STAT pathway. Our 1234567890():,; understanding of how a tailored switch from homeostasis to a strong receptor-dependent response is coordinated remains limited. Here, we use an integrated transcriptomic and proteomic approach to analyze transcription-factor binding, gene expression and in vivo proximity-dependent labelling of proteins in living cells under homeostatic and interferon (IFN)-induced conditions. We show that interferons (IFN) switch murine macrophages from resting-state to induced gene expression by alternating subunits of transcription factor ISGF3. Whereas preformed STAT2-IRF9 complexes control basal expression of IFN-induced genes (ISG), both type I IFN and IFN-γ cause promoter binding of a complete ISGF3 complex containing STAT1, STAT2 and IRF9. In contrast to the dogmatic view of ISGF3 formation in the cytoplasm, our results suggest a model wherein the assembly of the ISGF3 complex occurs on DNA. 1 Max Perutz Labs (MPL), University of Vienna, Vienna 1030, Austria. 2 Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria. 3 Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna 1030, Austria. 4 Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria. -
Comprehensive Study of Nuclear Receptor DNA Binding Provides a Revised Framework for Understanding Receptor Specificity
ARTICLE https://doi.org/10.1038/s41467-019-10264-3 OPEN Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity Ashley Penvose 1,2,4, Jessica L. Keenan 2,3,4, David Bray2,3, Vijendra Ramlall 1,2 & Trevor Siggers 1,2,3 The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous 1234567890():,; ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for under- standing NR regulatory specificity and will facilitate more accurate analyses of genomic datasets. 1 Department of Biology, Boston University, Boston, MA 02215, USA. 2 Biological Design Center, Boston University, Boston, MA 02215, USA. 3 Bioinformatics Program, Boston University, Boston, MA 02215, USA. 4These authors contributed equally: Ashley Penvose, Jessica L. Keenan. Correspondence -
IRF5 Gene Interferon Regulatory Factor 5
IRF5 gene interferon regulatory factor 5 Normal Function The protein produced from the IRF5 gene, called interferon regulatory factor 5 (IRF5), acts as a transcription factor, which means that it attaches (binds) to specific regions of DNA and helps control the activity of certain genes. When a virus is recognized in the cell, the IRF5 gene is turned on (activated), which leads to the production of IRF5 protein. The protein binds to specific regions of DNA that regulate the activity of genes that produce interferons and other cytokines. Cytokines are proteins that help fight infection by promoting inflammation and regulating the activity of immune system cells. In particular, interferons control the activity of genes that help block the replication of viruses, and they stimulate the activity of certain immune system cells known as natural killer cells. Health Conditions Related to Genetic Changes Systemic scleroderma Several normal variations in the IRF5 gene have been associated with an increased risk of developing systemic scleroderma, which is an autoimmune disorder characterized by the buildup of scar tissue (fibrosis) in the skin and internal organs. Although the IRF5 gene is known to stimulate the immune system in response to viruses, it is unknown how the gene variations contribute to the increased risk of systemic scleroderma. Researchers believe that a combination of genetic and environmental factors may play a role in development of the condition. Rheumatoid arthritis MedlinePlus Genetics provides information about Rheumatoid arthritis Systemic lupus erythematosus MedlinePlus Genetics provides information about Systemic lupus erythematosus Ulcerative colitis MedlinePlus Genetics provides information about Ulcerative colitis Reprinted from MedlinePlus Genetics (https://medlineplus.gov/genetics/) 1 Autoimmune disorders Studies have associated normal variations in the IRF5 gene with an increased risk of several autoimmune disorders. -
IFN-Α Wakes up Sleeping Hematopoietic Stem Cells
NEWS AND VIEWS calcium consumption does not seem to have without increasing the risk of coronary heart 7. Aoki, K. et al. Ann. Epidemiol. 15, 598–606 (2005). such an effect. How to optimize calcium sup- disease, which has been associated with cal- 8. Langhans, N. et al. Gastroenterology 112, 280–286 13 plements for human health deserves further cium supplementation . (1997). investigation. 9. Recker, R.R. N. Engl. J. Med. 313, 70–73 (1985). 10. Yang, Y.-X. et al. J. Am. Med. Assoc. , 2947– Maybe it’s time to determine whether low- 1. Zaidi, M. Nat. Med. 13, 791–801 (2007). 296 2. Del Fattore, A. et al. Bone 42, 19–29 (2008). 2953 (2006). fat milk–based drinks taken as an alternative 3. Sobacchi, C. et al. Hum. Mol. Genet. 10, 1767–1773 11. Collazo-Clavell, M.L., Jimenez, A., Hodgson, S.F. & to the soda so frequently consumed, especially (2001). Sarr, M.G. Endocr. Pract. 10, 195–198 (2004). 4. Amling, M. et al. Nat. Med. 15, 674–681 (2009). 12. Bo-Linn, G.W. et al. J. Clin. Invest. 73, 640–647 during the early adolescent years, can attain 5. Straub, D.A. Nutr. Clin. Pract. 22, 286–296 (2007). (1984). the noble goal of keeping bones healthy— 6. Teitelbaum, S.L. Science 289, 1504–1508 (2000). 13. Bolland, M.J. BMJ 336, 262–266 (2008). IFN-α wakes up sleeping hematopoietic stem cells Emmanuelle Passegué & Patricia Ernst The cytokine interferon-α stimulates the turnover and proliferation of hematopoietic cells in vivo (pages 696–700). -
Partner-Regulated Interaction of IFN Regulatory Factor 8 with Chromatin Visualized in Live Macrophages
Partner-regulated interaction of IFN regulatory factor 8 with chromatin visualized in live macrophages Leopoldo Laricchia-Robbio*, Tomohiko Tamura*, Tatiana Karpova†, Brian L. Sprague†, James G. McNally†, and Keiko Ozato*‡ *Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2753; and †Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055 Edited by Laurie H. Glimcher, Harvard School of Public Health, Boston, MA, and approved August 18, 2005 (received for review May 17, 2005) IFN regulatory factor (IRF) 8 is a transcription factor that directs protein–protein interactions on fluorescence recovery have not macrophage differentiation. By fluorescence recovery after pho- been extensively studied. Moreover, many FRAP studies so far tobleaching, we visualized the movement of IRF8-GFP in differen- reported are qualitative, lacking quantitative insight into the tiating macrophages. Recovery data fitted to mathematical models chromatin-binding events. More recent efforts to fit FRAP data revealed two binding states for IRF8. The majority of IRF8 was to mathematical models begin to provide a clearer knowledge on highly mobile and transiently interacted with chromatin, whereas the property of FRAP mobility (16, 17). a small fraction of IRF8 bound to chromatin more stably. IRF8 IRF8, a member of the IFN regulatory factor (IRF) family, is mutants that did not stimulate macrophage differentiation a key factor that guides the development of macrophages (18). showed a faster recovery, revealing little interaction with chro- We previously established an in vitro model system where matin. A macrophage activation signal by IFN-␥͞LPS led to a global IRF8Ϫ/Ϫ myeloid progenitor cells called Tot2 differentiate into slowdown of IRF8 movement, leading to increased chromatin macrophages upon IRF8 introduction (19). -
An Immunoevasive Strategy Through Clinically-Relevant Pan-Cancer Genomic and Transcriptomic Alterations of JAK-STAT Signaling Components
bioRxiv preprint doi: https://doi.org/10.1101/576645; this version posted March 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. An immunoevasive strategy through clinically-relevant pan-cancer genomic and transcriptomic alterations of JAK-STAT signaling components Wai Hoong Chang1 and Alvina G. Lai1, 1Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ, United Kingdom Since its discovery almost three decades ago, the Janus ki- Although cytokines are responsible for inflammation in nase (JAK)-signal transducer and activator of transcription cancer, spontaneous eradication of tumors by endoge- (STAT) pathway has paved the road for understanding inflam- nous immune processes rarely occurs. Moreover, the matory and immunity processes related to a wide range of hu- dynamic interaction between tumor cells and host immu- man pathologies including cancer. Several studies have demon- nity shields tumors from immunological ablation, which strated the importance of JAK-STAT pathway components in overall limits the efficacy of immunotherapy in the clinic. regulating tumor initiation and metastatic progression, yet, the extent of how genetic alterations influence patient outcome is far from being understood. Focusing on 133 genes involved in Cytokines can be pro- or anti-inflammatory and are inter- JAK-STAT signaling, we found that copy number alterations dependent on each other’s function to maintain immune underpin transcriptional dysregulation that differs within and homeostasis(3). -
CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: a PR Signaling to Gene Expression Independently of Its Binding to Chromatin
CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: A PR Signaling to Gene Expression Independently of Its Binding to Chromatin Griselda Vallejo1, Alejandro D. La Greca1., Inti C. Tarifa-Reischle1., Ana C. Mestre-Citrinovitz1, Cecilia Ballare´ 2, Miguel Beato2,3, Patricia Saragu¨ eta1* 1 Instituto de Biologı´a y Medicina Experimental, IByME-Conicet, Buenos Aires, Argentina, 2 Centre de Regulacio´ Geno`mica, (CRG), Barcelona, Spain, 3 University Pompeu Fabra (UPF), Barcelona, Spain Abstract Although non-genomic steroid receptor pathways have been studied over the past decade, little is known about the direct gene expression changes that take place as a consequence of their activation. Progesterone controls proliferation of rat endometrial stromal cells during the peri-implantation phase of pregnancy. We showed that picomolar concentration of progestin R5020 mimics this control in UIII endometrial stromal cells via ERK1-2 and AKT activation mediated by interaction of Progesterone Receptor (PR) with Estrogen Receptor beta (ERb) and without transcriptional activity of endogenous PR and ER. Here we identify early downstream targets of cytoplasmic PR signaling and their possible role in endometrial stromal cell proliferation. Microarray analysis of global gene expression changes in UIII cells treated for 45 min with progestin identified 97 up- and 341 down-regulated genes. The most over-represented molecular functions were transcription factors and regulatory factors associated with cell proliferation and cell cycle, a large fraction of which were repressors down-regulated by hormone. Further analysis verified that progestins regulate Ccnd1, JunD, Usf1, Gfi1, Cyr61, and Cdkn1b through PR- mediated activation of ligand-free ER, ERK1-2 or AKT, in the absence of genomic PR binding. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Genome-Wide Assessment of REST Binding Profiles Reveals Distinctions Between Human and Mouse Hippocampus
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.192229; this version posted July 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genome-wide assessment of REST binding profiles reveals distinctions between human and mouse hippocampus James C. McGann1,2#, Michael Spinner1#, Saurabh K. Garg1,3#, Karin Mullendorf1,4, Randall L. Woltjer5 and Gail Mandel1*. 1 Vollum Institute, Oregon Health and Science University, Portland, OR, USA. 2 Cancer Early Detection Advanced Research Center, Oregon Health and Science Institute, Portland, OR, USA. 3 Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. 4 Universidad San Sebastian, Puerto Montt, Chile 5 Department of Pathology, Division of Neuropathology, Oregon Health and Science University, Portland, OR, USA. *Corresponding author # These authors contributed equally Abstract Background The transcriptional repressor, RE1 Silencing Transcription Factor (REST), recognized historically as a master regulator of neuronal gene expression during mouse development, has recently been ascribed roles in human aging and neurodegenerative disorders. However, REST’s role in healthy adult human brain, and how faithfully mouse models reproduce REST function in human brain, is not known. Results Here, we present the first genome-wide binding profile for REST in both mouse and human postnatal hippocampus. We find the majority of REST-bound sites in human hippocampus are unique compared to both mouse hippocampus and to all other reported human ENCODE cell types. -
A Dual Cis-Regulatory Code Links IRF8 to Constitutive and Inducible Gene Expression in Macrophages
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages Alessandra Mancino,1,3 Alberto Termanini,1,3 Iros Barozzi,1 Serena Ghisletti,1 Renato Ostuni,1 Elena Prosperini,1 Keiko Ozato,2 and Gioacchino Natoli1 1Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy; 2Laboratory of Molecular Growth Regulation, Genomics of Differentiation Program, National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome.