A bioinformatics pipeline to uncover regulatory modules and their condition-specific regulators in human monocyte-to-macrophages differentiation and polarization

Abstract

Event Abstract Back to Event A bioinformatics pipeline to uncover regulatory modules and their condition-specific regulators in human monocyte-to-macrophages differentiation and polarization Emilia Maria Cristina Mazza1*, Paola Italiani2, Sara Valsoni1, Ingrid Cifola3, Diana Boraschi2, Cristina Battaglia3, 4 and Silvio Bicciato1 1 University of Modena and Reggio Emilia, Center for Genome Research, Department of Life Sciences, Italy 2 National Research Council (CNR), Pisa, Institute of Biomedical Technologies (ITB), Italy 3 National Research Council (CNR), Milan, Institute of Biomedical Technologies (ITB), Italy 4 University of Milan, Department of Medical Biotechnology and Translational Medicine, Italy In healthy organisms, inflammation is the first line of defense against infections and other damage. Monocytes and macrophages are key players of this process. Since a deregulation of the activity of these cells is at the basis of several pathological conditions, elucidating the molecular mechanisms of monocyte/macrophage activation represents a major step to study inflammatory disorders and, eventually, develop new therapeutic strategies. However, these mechanisms and their interplay during monocyte/macrophage activation and M1/M2 polarization remain poorly characterized. Here we report the application of computational methods to reconstruct gene regulatory networks and decipher transcriptional modules in an in vitro model of physiological inflammation. Specifically, gene expression profiles of human blood monocytes, from normal healthy donors and exposed to combinations of factors reproducing normal inflammatory conditions, have been monitored during a time course of 48 hours and transcriptional data analyzed using an ad-hoc bioinformatics pipeline aimed at reconstructing gene regulatory modules. The computational process starts with the identification of clusters of co-regulated genes whose expression changes during the time course. Through enrichment analysis and scanning analysis of transcription factor (TF) binding site motifs, we identified subsets of inflammation related genes and TFs that can be considered as process controllers and, thus, further used as candidates to reconstruct regulatory modules. The bioinformatics analysis identified several member of the interleukin-1 family as master regulators of specific regulatory modules linked to the inflammation process. Keywords: Gene Regulatory Networks, Transcriptional regulation, physiological inflammation, Macrophages, Macrophage Differentiation and Polarization Conference: 15th International Congress of Immunology (ICI), Milan, Italy, 22 Aug - 27 Aug, 2013. Presentation Type: Abstract Topic: Innate immunity Citation: Mazza E, Italiani P, Valsoni S, Cifola I, Boraschi D, Battaglia C and Bicciato S (2013). A bioinformatics pipeline to uncover regulatory modules and their condition-specific regulators in human monocyte-to-macrophages differentiation and polarization. Front. Immunol. Conference Abstract: 15th International Congress of Immunology (ICI). doi: 10.3389/conf.fimmu.2013.02.01058 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 30 Jun 2013; Published Online: 22 Aug 2013. * Correspondence: Dr. Emilia Maria Cristina Mazza, University of Modena and Reggio Emilia, Center for Genome Research, Department of Life Sciences, Modena, Italy, emilia.mazza@unimore.it Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Emilia Maria Cristina Mazza Paola Italiani Sara Valsoni Ingrid Cifola Diana Boraschi Cristina Battaglia Silvio Bicciato Google Emilia Maria Cristina Mazza Paola Italiani Sara Valsoni Ingrid Cifola Diana Boraschi Cristina Battaglia Silvio Bicciato Google Scholar Emilia Maria Cristina Mazza Paola Italiani Sara Valsoni Ingrid Cifola Diana Boraschi Cristina Battaglia Silvio Bicciato PubMed Emilia Maria Cristina Mazza Paola Italiani Sara Valsoni Ingrid Cifola Diana Boraschi Cristina Battaglia Silvio Bicciato Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.