Microarray analysis reveals that Type I interferon strongly increases the expression of immune-response related genes in Ubp43 (Usp18) deficient macrophages - PubMed (original) (raw)

Weiguo Zou et al. Biochem Biophys Res Commun. 2007.

Abstract

Type I interferon (IFN) contributes significantly to innate immune responses to pathogen infections in macrophages. Our previous studies demonstrate that Ubp43, an ISG15-specific isopeptidase, is highly expressed in macrophages and noncatalytically inhibits Type I IFN signaling. To understand the effect of Type I IFN and Ubp43 in macrophage activation, we analyzed the expression of IFN-beta stimulated genes in wild-type and Ubp43(-/-) bone marrow derived macrophages (BMMs). Here, we show that Ubp43 regulates IFN-beta stimulated genes at genome level. IFN hypersensitivity of Ubp43(-/-) BMMs resulted in the identification of 749 unique genes that are upregulated by IFN-beta, including a large group of previously unidentified IFN-stimulated genes. Functional analyses of these genes showed that Type I IFN strongly induced the expression of a group of immune response related genes, including genes for antigen presentation, antiviral responses, and chemokine and cytokine production. These results provide excellent biochemical support for the high resistance of viral and bacterial infection of Ubp43 knockout mice, suggesting that Ubp43 is a potential therapeutic target for the enhancement of immune responses against infections.

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Figures

Figure 1

Figure 1. Hierarchical clustering analyses

Seventy-seven unique known genes were found to be up-regulated by IFN-β in wild-type BMMs at 6 hours after 100 U/ml IFN treatment. The genes are ordered by clustering tightness. Each row represents a single Affymetrix probe set. Each column represents a sample treated with 100 U/ml IFN for indicated time.

Figure 2

Figure 2. IFN inducible gene expression in Ubp43−/− macrophages

(A) A summary of the subsequent analysis for the identified 1,270 probe sets, which were found to be up-regulated in Ubp43_−/_− BMMs after 100 U/ml IFN-β treatment for 6, 24, or 48 hours. (B) Hierarchical clustering of 749 unique genes from 1,270 probes, which are found to be up-regulated by IFN-β in Ubp43_−/_− BMMs at 6, 24, or 48 hours after 100 U/ml IFN treatment. The genes are ordered by clustering tightness. Each row represents a single Affymetrix probe set. Each column represents a sample treated with 100 U/ml IFN-β for indicated time.

Figure 3

Figure 3. Verification of the IFN hypersensitivity of gene expression in Ubp43_−/_− BMMs by Northern blotting analysis

Wild-type and Ubp43_−/_− BMMs were either untreated or treated with 100 U/ml IFN-β for 6, 24 and 48 hours. Total RNA was isolated and subjected to Northern blot analysis using cDNA probes for IRF7, OAS2, GBP1, IRF1, Mx1, HDAC1, Ly86, Gadd45γ, Lipg, P8, 5-Mar, Gnb4 and Serpina3γ. Relative RNA loading was evaluated by the amount of 28S rRNA.

Figure 4

Figure 4. Functional classification and analyses of immune responses related genes induced by IFN-β in Ubp43_−/_− macrophages

Each row represents a single Affymetrix probe set. Each column represents a sample treated with 100 U/ml IFN-β for indicated time.

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