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Interferon Regulatory Factors (IRF) 1 and 8 in the Context of Pathogen Challenge by Chip on Chip and Genome Wide Transcription Profiling

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The identification of transcriptional targets of Interferon Regulatory Factors (IRF) 1 and 8 in the context of pathogen challenge by ChIP on Chip and genome wide transcription profiling Oxana Kapoustina August 2009 A thesis submitted for the fulfillment of the Master of Science degree, Dept. of Biochemistry Acknowledgments: I sincerely thank Dr. Philippe Gros for giving me the opportunity to complete my degree in his laboratory and for providing support and advice. Thank you Gundula and Joanne for showing me the ropes (in the lab and outside) and your friendship. I would like to extend my thanks to Susan and Norm for keeping our lab running smoothly, Michel for always having advice and the right solutions, Anne for showing me how to work in TC, the rest of the ladies in the Gros lab, Charles and JF. Abstract: Interferon regulatory factors (IRFs) is a family of transcriptional regulators that are essential for cell differentiation and growth, oncogenesis and the regulation of immunity. IRF1 and IRF8 play a crucial role in immunity by regulating the differentiation of the cells of myeloid lineage, particularly the development of immune cells including macrophages, NK and dendritic cells. Both transcription factors are essential for the resistance to viral and bacterial infections. We optimized the chromatin immunoprecipitation (ChIP) technique to be used with IRF8 and IRF1 antibodies in a J774 line stimulated with IFNγ/CpG. Using ChIP coupled to an exon promoter 244K microarray (ChIP on Chip) we identified 201 and 303 binding sites of high confidence for IRF1 and IRF8 respectively. Previously known IRF1 and IRF8 transcription targets (OAS1b for IRF1 and IFNb for IRF8) as well as novel transcriptional control loci were identified. One of the major gene ontology (GO) functional categories in the two gene lists was “immune response”. The overlap of IRF1 and IRF8 transcription target genes from ChIP on Chip revealed an overlap of 19 genes most of which belonged to the “immune regulation” GO pathway and included targets of high confidence: Gbp6, Mx2, Tnfsf13b, H2-T24, and Ifit1. A parallel microarray transcription profiling study on mouse bone marrow macrophages (BMDMs) from an F2 generation of Balb/C IRF8-wildtype and BXH2 IRF8-mutant cross was performed. The BMDMs possessing the wildtype and the mutant IRF8 alleles were infected with Legionella pneumophila or stimulated with IFNγ/CpG to identify genes regulated by IRF8 in the context of infection. 1171 and 852 differentially regulated genes were differentially regulated in the infection and stimulation experiments respectively. Genes that displayed interaction between IRF8 allele and the infection conditions were isolated to yield high confidence gene lists of 31 and 129 genes for the Legionella and IFNγ/CpG experiments respectively. The overlap of the two gene lists revealed 7 genes in common, two of which belong to the JAK-STAT signalling pathway (IL10 and Ccd1). The comparison of the IFNγ/CpG microarray experiment gene list with the gene list from IRF8 ChIP on Chip revealed 15 genes in common. 2 of the 15 genes (Gbp6 and H2-T24) were also identified as potential targets common to IRF1 and IRF8 by ChIP on Chip. Gbp2 and H2-T24 represent interesting target genes for study and validation as high confidence targets of IRF8 and possibly, IRF1. Taken together, our data provides a set of novel IRF8 and IRF1 targets that may be studied to further our understanding of the regulatory networks controlled by IRF1 and IRF8 in the context of immunity. Résumé: Les facteurs régulateurs interférons (IRFs) sont une famille de régulateurs transcriptionnels essentiels à la différenciation et la croissance cellulaire, à l’oncogénèse et au bon maintien du système immunitaire. IRF1 et IRF8 jouent un role clé dans l’immunité de l’organisme par la régulation de la différenciation des lignées cellulaires myéloïdes, nottament le développement de cellules immunitaires comme les macrophages, les cellules tueuses naturelles (NK) et les cellules dendritiques. Ces deux facteurs de transcription sont indispensables pour la résistance aux infections virales et bactériennes. Nous avons optimisé une technique d’immunoprécipitation de la chromatine (ChIP) afin d’y utiliser des anticorps ciblant IRF1 et IRF8, et ce à partir d’une lignée cellulaire J774 suivant un stimulation par interféron gamma et par oligonucléotides CpG (IFNγ/CpG). En combinant cette technique ChIP à un microarray 244K comprenant exons et promoteurs (ChIP on Chip), nous avons identifiés respectivement 201 et 303 sites d’ancrages pour chacun de IRF1 et IRF8. Certaines cibles transcriptionnelles déjà connues pour IRF1 (OAS1b) et IRF8 (IFNb) ainsi que de nouveaux loci de control transcriptionel ont été identifiés. Parmi les catégories par fonction relevées par Ontologie de gène (GO), une des catégories majeures des deux listes de gènes générées fut pour les gènes reliés à la ‘‘réponse immunitaire’’. La comparaison entre les gènes cibles de transcription pour IRF1 et IRF8 par ‘‘ChIP on Chip’’ a révélé 19 gènes représentés dans les deux cas. La majeure partie de ces gènes sont reliés à la ‘‘réponse immunitaire’’ par GO et ils incluent les cibles suivantes avec détection très significative: Gbp6, Mx2, Tnfsf13b, H2-T24, et Ifit1. En parallèle, des macrophages dérivés de la moëlle osseuse de souris (BMDMs) furent utilisés pour l’étude du profile transcriptionel par microarray d’une génération F2 générée avec des souris Balb/C (IRF8-wildtype) et des souris BXH2 (IRF8-mutant). Ces BMDMs comprenant les allèles normale et mutante d’IRF8 ont été infectés avec Legionella pneumophila ou stimulés avec IFNγ/CpG pour identifer les gènes dépendant d’IRF8 dans le cadre d’une infection. Pour chaque traitement, l’expression de respectivement 1171 et 852 gènes furent observés comme étant modifiés selon la situation relative à IRF8 dans les expériences d’infections et de stimulations. Selon leur intéraction avec les allèles d’IRF8 et pour chaque traitement des BMDBs, une liste de gènes fut établie avec haut niveau de confiance comprenant 31 et 129 gènes pour chacun des types de stimulation par Legionelle et par IFNγ/CpG, respectivement. Ces deux listes de gènes comprennent 7 gènes en commun, deux appartenant à la voie de signalement JAK-STAT (IL10 et Ccd1). La comparaison en les listes de gènes générées dans les expériences de stimulation IFNγ/CpG par microarray ainsi que celles générées par les expériences ‘‘ChIP on Chip’’ avec IRF8 ont révélés 15 gènes en commun. Deux de ces 15 gènes (Gbp6 et H2-T24) ont aussi été identifiés comme cibles potentielles pour IRF1 en plus de IRF8 par ‘‘ChIP on Chip’’. Gpb2 et H2-T24 représentent des gènes cibles intéressants pour d’autres séries d’études et de validations comme étant des cibles à haut niveau de confiance pour IRF8 et possiblement, IRF1. En somme, ces résultats fournissent un nouveau répertoire de cibles pour IRF1 et IRF8 qui pourront être étudiées pour approfondir nos connaissances sur les réseaux de régulation controlés par IRF1 et IRF8 dans le maintien de l’immunité de l’organisme. Table of Contents 1. Introduction 4 1.1 Rationale .................................................................................................................. 4 1.2 Specific aims of the project ...................................................................................... 5 1.3 Interferons ................................................................................................................ 5 1.3.1 Interferons as a family ...................................................................................... 5 1.3.2 Interferon receptors and interferon signalling .................................................. 6 1.3.3 IFNγ-IL12 signalling axis ................................................................................ 8 1.2 Interferon Regulatory Factors .................................................................................. 9 1.2.1. IRFs as a family of structurally related transcription factors ......................... 9 1.2.1. IRF8 (ICSBP) ................................................................................................ 10 1.2.2. IRF8 induction ............................................................................................... 11 1.2.3. Transcription targets of IRF8 ........................................................................ 11 1.2.4. IRF8 in immune response ............................................................................. 12 1.2.5. IRF8 in myelopoiesis .................................................................................... 12 1.2.6. IRF8 in cancer .............................................................................................. 13 1.3. IRF1 ...................................................................................................................... 14 1.3.1 IRF1 expression and induction .................................................................. 14 1.3.2. IRF1 in immunity .......................................................................................... 16 1.3.3. IRF1 in oncogenesis ...................................................................................... 17 2. Results 20 2.1 Materials and methods ........................................................................................... 20 2.2 Overview ........................................................................................................... 31 2.3. Optimization of the ChIP technique .....................................................................
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  • 140503 IPF Signatures Supplement Withfigs Thorax

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    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.