RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities.

With rising rates of drug-resistant infections, there is a need for diagnostic methods that rapidly can detect the presence of pathogens and reveal their susceptibility to antibiotics. Here we propose an approach to diagnosing the presence and drug-susceptibility of infectious diseases based on direct detection of RNA from clinical samples. We demonstrate that species-specific RNA signatures can be used to identify a broad spectrum of infectious agents, including bacteria, viruses, yeast, and parasites. Moreover, we show that the behavior of a small set of bacterial transcripts after a brief antibiotic pulse can rapidly differentiate drug-susceptible and -resistant organisms and that these measurements can be made directly from clinical materials. Thus, transcriptional signatures could form the basis of a uniform diagnostic platform applicable across a broad range of infectious agents.

Viperin is highly induced in neutrophils and macrophages during acute and chronic lymphocytic choriomeningitis virus infection.

Although most cells are thought to respond to IFNs, there is limited information regarding specific cells that respond in vivo. Viperin is an IFN-induced antiviral protein and, therefore, is an excellent marker for IFN-responsive cells. In this study, we analyzed viperin expression in vivo during acute lymphocytic choriomeningitis virus Armstrong infection, which induces high levels of type I IFNs, and in persistently infected lymphocytic choriomeningitis virus carrier mice, which contain low levels of type I IFNs. Viperin was induced in lymphoid cells and dendritic cells (DCs) during acute infection and highly induced in neutrophils and macrophages. The expression kinetics in neutrophils, macrophages, and T and B cells paralleled IFN-alpha levels, but DCs expressed viperin with delayed kinetics. In carrier mice, viperin was expressed in neutrophils and macrophages but not in T and B cells or DCs. For acutely infected and carrier mice, viperin expression was IFN dependent, because treating type I IFNR knockout mice with IFN-gamma-neutralizing Abs inhibited viperin expression. Viperin localized to the endoplasmic reticulum and lipid droplet-like vesicles in neutrophils. These findings delineate the kinetics and cells responding to IFNs in vivo and suggest that the profile of IFN-responsive cells changes in chronic infections. Furthermore, these data suggest that viperin may contribute to the antimicrobial activity of neutrophils.

Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease.

RNase MRP is a conserved endoribonuclease, in humans consisting of a 267-nucleotide RNA associated with 7-10 proteins. Mutations in its RNA component lead to several autosomal recessive skeletal dysplasias, including cartilage-hair hypoplasia (CHH). Because the known substrates of mammalian RNase MRP, pre-ribosomal RNA, and RNA involved in mitochondrial DNA replication are not likely involved in CHH, we analyzed the effects of RNase MRP (and the structurally related RNase P) depletion on mRNAs using DNA microarrays. We confirmed the upregulation of the interferon-inducible viperin mRNA by RNAi experiments and this appeared to be independent of the interferon response. We detected two cleavage sites for RNase MRP/RNase P in the coding sequence of viperin mRNA. This is the first study providing direct evidence for the cleavage of a mRNA by RNase MRP/RNase P in human cells. Implications for the involvement in the pathophysiology of CHH are discussed.

The antiviral protein, viperin, localizes to lipid droplets via its N-terminal amphipathic alpha-helix.

Lipid droplets are intracellular lipid-storage organelles that are thought to be derived from the endoplasmic reticulum (ER). Several pathogens, notably hepatitis C virus, use lipid droplets for replication. Numerous questions remain about how lipid droplets are generated and used by viruses. Here we show that the IFN-induced antiviral protein viperin, which localizes to the cytosolic face of the ER and inhibits HCV, localizes to lipid droplets. We show that the N-terminal amphipathic alpha-helix of viperin that is responsible for ER localization is also necessary and sufficient to localize both viperin and the fluorescent protein dsRed to lipid droplets. Point mutations in the alpha-helix that prevent ER association also disrupt lipid droplet association, and sequential deletion mutants indicate that the same number of helical turns are necessary for ER and lipid droplet association. Finally, we show that the N-terminal amphipathic alpha-helix of the hepatitis C viral protein NS5A can localize dsRed and viperin to lipid droplets. These findings indicate that the amphipathic alpha-helices of viperin and NS5A are lipid droplet-targeting domains and suggest that viperin inhibits HCV by localizing to lipid droplets using a domain and mechanism similar to that used by HCV itself.

Herceptin-geldanamycin immunoconjugates: pharmacokinetics, biodistribution, and enhanced antitumor activity.

The efficacy of monoclonal antibodies (mAbs) as single agents in targeted cancer therapy has proven to be limited. Arming mAbs with a potent toxic drug could enhance their activity. Here we report that conjugating geldanamycin (GA) to the anti-HER2 mAb Herceptin improved the activity of Herceptin. The IC(50)s of the immunoconjugate H-GA were 10-200-fold lower than that of Herceptin in antiproliferative assays, depending on the cell line. The H-GA mode of action involved HER2 degradation, which was partially lactacystin sensitive and thus proteasome dependent. The linkage between GA and Herceptin remained stable in the circulation, as suggested by the pharmacokinetics of Herceptin and conjugated GA, which were almost identical and significantly different from that of free GA. Tumor uptake of Herceptin and H-GA were similar (52 +/- 7 and 43 +/- 7% of the initial injected dose per gram tissue, respectively; P = 0.077), indicating no apparent damage attributable to conjugation. Therapy experiments in xenograft-bearing mice consisted of weekly i.p. doses, 4 mg/kg for 4 months. H-GA showed a greater antitumor effect than Herceptin because it induced tumor regression in 69% of the recipients compared with 7% by Herceptin alone. Median survival time was 145 days as opposed to 78 days, and 31% of the recipients remained tumor free 2 months after therapy was terminated versus 0% in the Herceptin group. Enhancement of Herceptin activity could be of significant clinical value. In addition, the chemical linkage and the considerations in therapeutic regimen described here could be applied to other immunoconjugates for targeted therapy of a broad spectrum of cancers.

Wounding: the primary mode of Seoul virus transmission among male Norway rats.

In rodent populations, males are more likely to be infected with hantaviruses and to engage in aggression than are females. To assess the relationship between aggression and Seoul virus infection, Norway rats were trapped in Baltimore, Maryland and wounding, infection status, and steroid hormone concentrations were examined. Older males and males with high-grade wounds were more likely to have IgG antibody to Seoul, to shed virus in saliva, urine, and feces, and to have viral RNA in organs than either juveniles or adult males with less severe wounds. In contrast, neither age nor wounding predicted virus shedding among females. Although viral antigen was not identified in the brain, viral protein was detected in the gonads and adrenal glands of adult males. Males with more severe wounds had higher testosterone concentrations than males with no or low-grade wounds. Because wounding, testosterone, and virus shedding are associated among males, aggression may be the primary mode of Seoul virus transmission among male, but not female, Norway rats.

Human cytomegalovirus directly induces the antiviral protein viperin to enhance infectivity.

Viperin is an interferon-inducible protein that is directly induced in cells by human cytomegalovirus (HCMV) infection. Why HCMV would induce viperin, which has antiviral activity, is unknown. We show that HCMV-induced viperin disrupts cellular metabolism to enhance the infectious process. Viperin interaction with the viral protein vMIA resulted in viperin relocalization from the endoplasmic reticulum to the mitochondria. There, viperin interacted with the mitochondrial trifunctional protein that mediates ß-oxidation of fatty acids to generate adenosine triphosphate (ATP). This interaction with viperin, but not with a mutant lacking the viperin iron-sulfur cluster-binding motif, reduced cellular ATP generation, which resulted in actin cytoskeleton disruption and enhancement of infection. This function of viperin, which was previously attributed to vMIA, suggests that HCMV has coopted viperin to facilitate the infectious process.

The N-terminal amphipathic alpha-helix of viperin mediates localization to the cytosolic face of the endoplasmic reticulum and inhibits protein secretion.

Viperin is an evolutionarily conserved interferon-inducible protein that localizes to the endoplasmic reticulum (ER) and inhibits a number of DNA and RNA viruses. In this study, we report that viperin specifically localizes to the cytoplasmic face of the ER and that an amphipathic alpha-helix at its N terminus is necessary for the ER localization of viperin and sufficient to promote ER localization of a reporter protein, dsRed. Overexpression of intact viperin but not the amphipathic alpha-helix fused to dsRed induced crystalloid ER. Consistent with other proteins that induce crystalloid ER, viperin self-associates, and it does so independently of the amphipathic alpha-helix. Viperin expression also affected the transport of soluble but not membrane-associated proteins. Expression of intact viperin or an N-terminal alpha-helix-dsRed fusion protein significantly reduced secretion of soluble alkaline phosphatase and reduced its rate of ER-to-Golgi trafficking. Similarly, viperin expression inhibited bulk protein secretion and secretion of endogenous alpha(1)-antitrypsin and serum albumin from HepG2 cells. Converting hydrophobic residues in the N-terminal alpha-helix to acidic residues partially or completely restored normal transport of soluble alkaline phosphatase, suggesting that the extended amphipathic nature of the N-terminal alpha-helical domain is essential for inhibiting protein secretion.

The interferon-inducible protein viperin inhibits influenza virus release by perturbing lipid rafts.

Interferons initiate the host antiviral response by inducing a number of genes, most with no defined antiviral function. Here we show that the interferon-induced protein viperin inhibits influenza A virus release from the plasma membrane of infected cells. Viperin expression altered plasma membrane fluidity by affecting the formation of lipid rafts, which are detergent-resistant membrane microdomains known to be the sites of influenza virus budding. Intracellular interaction of viperin with farnesyl diphosphate synthase (FPPS), an enzyme essential for isoprenoid biosynthesis, decreased the activity of the enzyme. Overexpression of FPPS reversed viperin-mediated inhibition of virus production and restored normal membrane fluidity, and reduction of FPPS levels by siRNA inhibited virus release and replication, indicating that the FPPS interaction underlies viperin's effects. These findings suggest that targeting the release stage of the life cycle may affect the replication of many enveloped viruses. Furthermore, FPPS may be an attractive target for antiviral therapy.

Social status does not predict responses to Seoul virus infection or reproductive success among male Norway rats.

Trade-offs exist among life history strategies that are used to increase survival and reproduction; such that, males that engage in more competitive behaviors may be more susceptible to infection. Hantaviruses are transmitted horizontally between rodents through the passage of virus in saliva during wounding and male rodents are more likely to be infected with hantaviruses than females. To determine whether a trade-off exists between dominance and susceptibility to Seoul virus infection, male Long Evans rats were group housed (3/cage) with a female rat and aggressive and subordinate behaviors were monitored during a 10 day group housing condition. After behavioral testing, males were individually housed, inoculated with Seoul virus, and blood, saliva, and fecal samples were collected. Dominant males initiated more aggressive encounters than subordinate males. Dominant and subordinate males, however, had similar steroid hormone concentrations, anti-Seoul virus IgG responses, and weight gain over the course of infection. A similar proportion of dominant and subordinate males shed virus in saliva and feces during infection. Using microsatellite DNA markers paternity was assigned to pups derived during the group housing period. In contrast to our initial hypothesis, dominant and subordinate males sired a similar percentage of pups. Taken together, host social status may not predict reproductive success or susceptibility to hantaviruses in rodent reservoir populations.

Enhanced and prolonged cross-presentation following endosomal escape of exogenous antigens encapsulated in biodegradable nanoparticles.

CD8(+) T-cell responses are critical in the immunological control of tumours and infectious diseases. To prime CD8(+) T cells against these cell-associated antigens, exogenous antigens must be cross-presented by professional antigen-presenting cells (APCs). While cross-presentation of soluble antigens by dendritic cells is detectable in vivo, the efficiency is low, limiting the clinical utility of protein-based vaccinations. To enhance the efficiency of presentation, we generated nanoparticles from a biodegradable polymer, poly(D,L-lactide-co-glycolide) (PLGA), to deliver antigen into the major histocompatibility complex (MHC) class I antigen presentation pathway. In primary mouse bone marrow-derived dendritic cells (BMDCs), the MHC class I presentation of PLGA-encapsulated ovalbumin (OVA) stimulated T cell interleukin-2 secretion at 1000-fold lower concentration than soluble antigen and 10-fold lower than antigen-coated latex beads. The microparticles also served as an intracellular antigen reservoir, leading to sustained MHC class I presentation of OVA for 72 hr, decreasing by only 20% after 96 hr, a time at which the presentation of soluble and latex bead-associated antigens was undetectable. Cytosol extraction demonstrated that antigen delivery via PLGA particles increased the amount of protein that escaped from endosomes into the cytoplasm, thereby increasing the access of exogenous antigen to the classic MHC class I loading pathway. These data indicate that the unique properties of PLGA particle-mediated antigen delivery dramatically enhance and sustain exogenous antigen presentation by MHC class I, potentially facilitating the clinical use of these particles in vaccination.