Identification of an NF-κB-dependent gene network in cells infected by mammalian reovirus

Reovirus infection activates NF-kappa B, which leads to programmed cell death in cultured cells and in the murine central nervous system. However, little is known about how NF-kappa B elicits this cellular response. To identify host genes activated by NF-kappa B following reovirus infection, we used HeLa cells engineered to express a degradation-resistant mutant Of I kappa B alpha (MI kappa B alpha) under the control of an inducible promoter. Induction of MI kappa B alpha inhibited the activation of NF-kappa B and blocked the expression of NF-kappa B-responsive genes. RNA extracted from infected and uninfected cells was used in high-density oligonucleotide microarrays to examine the expression of constitutively activated genes and reovirus-stimulated genes in the presence and absence of an intact NF-kappa B signaling axis. Comparison of the microarray profiles revealed that the expression of 176 genes was significantly altered in the presence Of mI kappa B alpha. Of these genes, 64 were constitutive and not regulated by reovirus, and 112 were induced in response to reovirus infection. NF-kappa B-regulated genes could be grouped into four distinct gene clusters that were temporally regulated. Gene ontology analysis identified biological processes that were significantly overrepresented in the reovirus-induced genes under NF-kappa B control. These processes include the antiviral innate immune response, cell proliferation, response to DNA damage, and taxis. Comparison with previously identified NF-kappa B-dependent gene networks induced by other stimuli, including respiratory syncytial virus, Epstein-Barr virus, tumor necrosis factor alpha, and heart disease, revealed a number of common components, including CCL5/RANTES, CXCL1/GRO-alpha, TNFAIP3/A20, and interleukin-6. Together, these results suggest a genetic program for reovirus-incluced apoptosis involving NF-kappa B-directed expression of cellular genes that activate death signaling pathways in infected cells.