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Open Access Highly Accessed Research article

Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling

Paul Lacaze1, Sobia Raza14, Garwin Sing1, David Page1, Thorsten Forster12, Petter Storm1, Marie Craigon1, Tarif Awad3, Peter Ghazal12 and Tom C Freeman14*

Author Affiliations

1 Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK

2 Centre for Systems Biology at Edinburgh, The University of Edinburgh, Darwin Building, King's Buildings Campus, Mayfield Road, Edinburgh, UK

3 Affymetrix Laboratory, Affymetrix, Inc. 3380 Central Expressway, Santa Clara, USA

4 The Roslin Institute, University of Edinburgh, Midlothian, UK

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BMC Genomics 2009, 10:372  doi:10.1186/1471-2164-10-372

Published: 10 August 2009

Abstract

Background

Interferons (IFNs) are potent antiviral cytokines capable of reprogramming the macrophage phenotype through the induction of interferon-stimulated genes (ISGs). Here we have used targeted RNA interference to suppress the expression of a number of key genes associated with IFN signalling in murine macrophages prior to stimulation with interferon-gamma. Genome-wide changes in transcript abundance caused by siRNA activity were measured using exon-level microarrays in the presence or absence of IFNγ.

Results

Transfection of murine bone-marrow derived macrophages (BMDMs) with a non-targeting (control) siRNA and 11 sequence-specific siRNAs was performed using a cationic lipid transfection reagent (Lipofectamine2000) prior to stimulation with IFNγ. Total RNA was harvested from cells and gene expression measured on Affymetrix GeneChip Mouse Exon 1.0 ST Arrays. Network-based analysis of these data revealed six siRNAs to cause a marked shift in the macrophage transcriptome in the presence or absence IFNγ. These six siRNAs targeted the Ifnb1, Irf3, Irf5, Stat1, Stat2 and Nfkb2 transcripts. The perturbation of the transcriptome by the six siRNAs was highly similar in each case and affected the expression of over 600 downstream transcripts. Regulated transcripts were clustered based on co-expression into five major groups corresponding to transcriptional networks associated with the type I and II IFN response, cell cycle regulation, and NF-KB signalling. In addition we have observed a significant non-specific immune stimulation of cells transfected with siRNA using Lipofectamine2000, suggesting use of this reagent in BMDMs, even at low concentrations, is enough to induce a type I IFN response.

Conclusion

Our results provide evidence that the type I IFN response in murine BMDMs is dependent on Ifnb1, Irf3, Irf5, Stat1, Stat2 and Nfkb2, and that siRNAs targeted to these genes results in perturbation of key transcriptional networks associated with type I and type II IFN signalling and a suppression of macrophage M1 polarization.