Small interfering RNAs (siRNA) are potent reagents for directed post-transcriptional gene silencing and a major new genetic tool for investigating mammalian cells. When synthetic siRNAs are used for gene silencing, the costs can be substantial because of variations in siRNA efficacies. An alternative to chemically synthesized siRNAs are siRNAs produced by bacteriophage T7 RNA polymerase. We found that siRNAs synthesized from the T7 RNA polymerase system can trigger a potent induction of interferon alpha and beta in a variety of cell lines. Surprisingly, we also found very potent induction of interferon alpha and beta by short single-stranded RNAs (ssRNAs) transcribed with T3, T7 and Sp6 RNA polymerases. Analyses of the potential mediators of this response revealed that the initiating 5' triphosphate is required for interferon induction. We describe here an improved method for T7 siRNA synthesis that alleviates the interferon response while maintaining full efficacy of the siRNAs.

Rationale Foxp3+ T regulatory cells (Tregs) are key players in maintaining immune homeostasis. Evidence suggests that Tregs respond to environmental cues to permit or suppress inflammation. In atherosclerosis, Th1-driven inflammation affects Treg homeostasis, but the mechanisms governing this phenomenon are unclear. Objective Here, we address whether atherosclerosis impacts Treg plasticity and functionality in Apoe−/− mice, and what effect Treg plasticity might have on the pathology of atherosclerosis. Methods and Results We demonstrate that atherosclerosis promotes Treg plasticity, resulting in the reduction of CXCR3+ Tregs, and the accumulation of an intermediate Th1-like IFNγ+CCR5+ Treg subset (Th1/Tregs) within the aorta. Importantly, Th1/Tregs arise in atherosclerosis from bona fide Tregs, rather than T effector cells. We show that Th1/Tregs recovered from atherosclerotic mice are dysfunctional in suppression assays. Using an adoptive transfer system and plasticity-prone Mir146a−/− Tregs, we demonstrate that elevated IFNγ+ Mir146a−/− Th1/Tregs are unable to adequately reduce atherosclerosis, arterial Th1, or macrophage content within Apoe−/− mice, in comparison to Mir146a+/+ Tregs. Lastly, via single cell RNA-sequencing and RT-PCR we show that Th1/Tregs possess a unique transcriptional phenotype characterized by co-expression of Treg and Th1 lineage genes, and a down-regulation of Treg-related genes, including Ikzf2, Ikzf4, Tigit, Lilrb4, and Il10. Additionally, an ingenuity pathway analysis further implicates IFNγ, IFNα, IL-2, IL-7, CTLA4, T cell receptor, and Csnk2b-related pathways in regulating Treg plasticity. Conclusions Atherosclerosis drives Treg plasticity, resulting in the accumulation of dysfunctional IFNγ+ Th1/Tregs that may permit further arterial inflammation and atherogenesis.

Herpes simplex virus type 1 (HSV-1) infections are widespread in developed countries, with estimates of seropositivity exceeding 50% (54). Primary infections in immunocompetent individuals are usually mild or even asymptomatic and result in lifelong latent infections in sensory ganglia and the central nervous system (CNS) (5). Reactivated HSV-1 can result in recurrent diseases of mucous membranes (e.g., gingivostomatitis and herpes labialis) and herpes keratitis, an immunopathological disease that is a leading cause of blindness (39). Also, HSV-1 is the most common cause of fatal, sporadic encephalitis in immunocompetent individuals (40, 56). Improvements in diagnosis and antiviral drug treatment have dramatically reduced the morbidity and mortality of HSV-1 encephalitis (HSE) (55), although some patients fail to respond or subsequently suffer neurological relapses after completing a standard treatment course (18,55).Clinical and animal model studies have clearly demonstrated the importance of genetic makeup in resistance to a broad range of infectious agents (15,41). In regard to HSV-1, C57BL/6 (B6) and related B10 mouse strains are resistant, while other strains, such A/J, BALB/c, 129S6 (129), and DBA/ 2J, are susceptible to fatal infections (21,23,25). In these animal models, mortality results from CNS infection. In prior studies, we defined the herpes resistance locus (Hrl) on mouse chromosome 6 as a major determinant of resistance (22, 25); however, ongoing studies indicate that resistance to HSE is genetically very complex, involving multiple interacting loci, with tumor necrosis factor playing a critical role (26) (unpublished results). The mechanism by which HSV-1 CNS infection causes death has not been defined. Counterintuitively, necropsy virus titers of nervous system tissues do not correlate with mouse resistance or susceptibility genotype (25,26). These and other observations have led to the suggestion that variation of the host inflammatory response may play a major role in determining HSV fatality. Intense inflammatory responses in CNS tissues in a mouse model of HSE have been reported, with tumor necrosis factor and macrophage chemoattractant protein 1 being expressed prominently (43). Also, in vitro and in vivo studies have shown that human and mouse microglia nonproductively infected with HSV-1 express a variety of proinflammatory cytokines and chemokines, consistent with their involvement in

RNA interference is a powerful tool for target-specific knockdown of gene expression. The triggers for this process are duplex small interfering RNAs (siRNAs) of 21-25 nt with 2-bp 3' overhangs produced in cells by the RNase III family member Dicer. We have observed that short RNAs that are long enough to serve as Dicer substrates (D-siRNA) can often evoke more potent RNA interference than the corresponding 21-nt siRNAs; this is probably a consequence of the physical handoff of the Dicer-produced siRNAs to the RNA-induced silencing complex. Here we describe the design parameters for D-siRNAs and a protocol for in vitro and in vivo intraperitoneal delivery of D-siRNAs and siRNAs to macrophages. siRNA delivery and transfection and analysis of macrophages in vivo can be accomplished within 36 h.

Gender influences the incidence and severity of some bacterial and viral infections and autoimmune diseases in animal models and humans. To determine a gender-based difference, comparisons were made between male and female mice inoculated with herpes simplex virus type 1 (HSV-1) by the corneal route. Mortality was higher in the male mice of the three strains tested: 129/Sv//Ev wild type, gamma interferon (IFN-␥) knockout (GKO), and IFN-␥ receptor knockout (RGKO). Similarly, in vivo HSV-1 reactivation occurred more commonly in male mice, but the male-female difference in reactivation was restricted to the two knockout strains and was not seen in the 129/Sv//Ev control. Comparison among male mice of the three strains showed a higher mortality of the RGKO mice and a higher reactivation rate of the GKO and RGKO mice than of the 129/Sv//Ev males. In contrast, female RGKO and GKO mice did not differ from female 129/Sv//Ev controls in either mortality or reactivation. HSV-1 periocular and eyelid disease was also more severe in male and dihydrotestosterone (DHT)-treated female mice than in control female mice. These results show a consistent gender difference in HSV-1 infection, with a worse outcome in male mice. In addition, the results comparing GKO and RGKO mice to controls show differences only in male mice, suggesting that some effects of IFN-␥, a key immunoregulatory molecule, are gender specific.