JGV Papers in Press. Published May 14, 2014 as doi:10.1099/vir.0.066084-0

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Delivery of anti-viral siRNA with gold-nanoparticles inhibits dengue virus infection in vitro

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Running title: AuNPs deliver anti-dengue siRNA

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Amber M. Paul1, Yongliang Shi2, Dhiraj Acharya1, Jessica R. Douglas1, Amanda Cooley1, John

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F. Anderson3, Faqing Huang2 and Fengwei Bai1*

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Department of Biological Sciences, 2Department of Chemistry and Biochemistry, University of

Southern Mississippi, Hattiesburg, MS 39406, USA.

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06504, USA

Department of Entomology, Connecticut Agricultural Experiment Station, New Haven, CT

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Word count (Summary): 162 words

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Word count (Main Text): 4330 words

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Journal’s Content’s Category: Human and Animal virus- Positive-stranded RNA

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Number of figure: 5 and number of table: 0.

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Corresponding Author: Fengwei Bai, Ph.D., Department of Biological Sciences, The University of Southern Mississippi, 118 College Drive # 5018, Hattiesburg, MS 39406, USA. Email: [email protected]; Telephone 601-266-4748; Fax: 601-266-5797

AuNPs deliver anti-Dengue siRNA

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Summary

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Dengue virus (DENV) infection in humans can cause flu-like illness, life threatening

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hemorrhagic fever, or even death. There is no specific anti-DENV therapeutic or approved

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vaccine currently available, partially due to the possibility of antibody-dependent enhancement

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reaction. Small interfering RNAs (siRNAs) that target specific viral genes are considered a

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promising therapeutic alternative against DENV infection. However, in vivo, siRNAs are

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vulnerable to degradation by serum-nucleases and rapid renal excretion due to their small size

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and anionic character. To enhance siRNA delivery and stability, we complexed anti-DENV

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siRNAs with biocompatible gold nanoparticles (AuNPs) and tested them in vitro. We found that

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cationic AuNP-siRNA complexes can enter Vero cells and significantly reduce DENV-serotype

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2 replication and infectious virion release at both pre- and post-infection conditions. In addition,

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RNase-treated AuNP-siRNA complexes can still inhibit DENV replication, suggesting that

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AuNPs maintain siRNA stability. Collectively, these results demonstrate that AuNPs are able to

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efficiently deliver siRNAs and control infection in vitro, indicating a novel anti-DENV strategy.

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Keywords: dengue virus, siRNA delivery, gold nanoparticle

AuNPs deliver anti-Dengue siRNA

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Introduction

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Dengue virus (DENV) is a single-stranded, positive-sense RNA virus belonging to the

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family Flaviviridae. DENV is transmitted to humans primarily by the mosquito vectors, Aedes

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aegypti and Aedes albopictus (Xi et al., 2008). After DENV binds to host cellular receptors, it is

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endocytosed and uncoated within the endosome to release its RNA genome into the cytoplasm,

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where replication of the viral genome and assembly of virions occur (van der Schaar et al.,

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2008). The common symptoms of DENV infection in humans are characterized by fever,

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headache, joint and muscle pain and measle-like rashes (Halstead, 2007; Wilder-Smith et al.,

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2010). Although asymptomatic in most cases, DENV infection can lead to serious disease, such

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as hemorrhagic fever and systemic shock syndrome that can potentially be fatal. There are four

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serotypes of DENV (DENV-1, DENV-2, DENV-3 and DENV-4) and illness can be produced by

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any serotype (Tomashek & Margolis, 2011). Although recovery from infection to one serotype

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provides lifelong immunity against that particular serotype, subsequent infection by other co-

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circulating serotypes may cause an antibody-dependent enhancement reaction, which increases

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the risk of developing severe dengue hemorrhagic fever, shock and even death (Halstead, 1982;

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Kliks et al., 1989). DENV infection has been reported in more than 100 countries, including the

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United States (Gubler, 2002; Ramos et al., 2008; Tomashek & Margolis, 2011). A recent report

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has estimated that 390 million people are infected with DENV worldwide, with 96 million

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people manifesting clinical symptoms of disease (Bhatt et al., 2013).

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Since antibody-dependent enhancement hinders the development of an antibody-based

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vaccine, the development of therapeutics that target replication or expression of the viral genome

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may serve as promising alternatives to control DENV infection. Anti-host receptor (Alhoot et al.,

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2011) and anti-DENV (Stein et al., 2011; Subramanya et al., 2010) small interfering RNAs

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AuNPs deliver anti-Dengue siRNA

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(siRNAs) have considerably advanced both clinical- and laboratory-based applications as

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potential DENV therapeutic alternatives (Idrees et al., 2013). However, efficient delivery of

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siRNAs remains a great challenge for clinical applications. The most common siRNA delivery

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approach is with a lipid-based transfection reagent, whereby the negatively charged siRNA

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duplex binds to the cationic liposome transfection reagent, which allows for cell membrane

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endocytosis, micelle formation and intracellular release of the siRNA into the cytosol (Zuhorn et

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al., 2002). Although this method is successful for siRNA delivery in vitro, it is not an ideal

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candidate to use in vivo, as these chemically-based transfection reagents are physiologically toxic

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and could induce cellular stress or aberrant transcriptional profiles (Torchilin, 2005; Zhong et al.,

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2008).

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Recently, gold nanoparticles (AuNPs) have been suggested as promising vehicles to

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deliver siRNA both in vitro and in vivo (Conde et al., 2012; Conde et al., 2013; Mitra et al.,

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2013; Yang et al., 2013). Several advantages make them well suited for safe and efficient

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protection and transport of siRNA: a) biocompatibility (Chithrani & Chan, 2007; Lewinski et

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al., 2008); b) ease of preparation and facile surface modification (Elbakry et al., 2009; Lee et al.,

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2011; Song et al., 2010); and c) high siRNA loading capacity. In this study, we constructed novel

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anti-DENV AuNP-siRNA nanoplexes and found that AuNPs are able to promote siRNA stability

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and efficiently deliver anti-DENV siRNAs in vitro.

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AuNPs deliver anti-Dengue siRNA

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Results

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Antiviral siRNAs efficiently inhibit DENV replication

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Two antiviral siRNAs (si-1 and si-3) were designed to target the most prevalent dengue

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serotype, DENV-2. Vero cells were transfected with siRNA (20 nM) using a lipofectamine-based

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transfection reagent (TR) and subsequently infected with DENV-2 (multiplicity of infection,

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MOI = 0.1). Sequence scrambled siRNA (siSCRM) was used as a negative control and a

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previously described anti-DENV siRNA (DC-3) was used as a positive control (Stein et al.,

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2011). At 48 hr post-infection, the cells were harvested for total RNA extraction, cDNA

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synthesis and subjected to real-time quantitative polymerase chain reaction (Q-PCR) for the

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measurement of DENV capsid gene and cellular β-actin gene expression. The Q-PCR results

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showed that si-1, si-3 and DC-3 significantly reduced DENV-2 capsid gene expression compared

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to the control, in which cells were treated with TR only (p < 0.001, Fig. 1a). In contrast, siSCRM

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did not show any inhibitory effect (p = ns, Fig. 1a), suggesting that siRNA inhibition is

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sequence-specific. To test if infectious viral particles released from the infected cells were

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reduced with siRNA transfection, the media were quantified by a plaque forming assay (plaque

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forming unit, PFU) and an immunostaining assay (focus forming unit, FFU), with the latter

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detecting viral envelope (E) protein expression. Since the DENV-2 genome shares some

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homology with other DENV-serotypes, the antiviral effect of si-1 and si-3 (20 nM) was also

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evaluated against the replication of DENV-1, DENV-3 and DENV-4 (MOI = 0.1). Q-PCR

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analysis showed that si-1 and si-3 were able to inhibit DENV-3 and DENV-4 replication, but

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showed no inhibitory activity for DENV-1, compared to the control in which cells were treated

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with TR, without siRNA (p < 0.001 and p = ns, Fig. 1d-f). RNA sequence alignment analysis

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suggested that the lack of inhibition of si-1 and si-3 against DENV-1 replication might be due to

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AuNPs deliver anti-Dengue siRNA

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lower homology between their targeting sequences (approximately 50% and 70% respectively,

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data not shown). In summary, these results demonstrated that both si-1 and si-3 were able to

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significantly inhibit replication of DENV serotypes 2, 3 and 4.

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Design and optimization of AuNP complexes for anti-DENV siRNA delivery in vitro

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Recently, AuNPs have been designed and optimized as delivery vehicles for siRNA both

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in vitro and in vivo (Conde et al., 2013; Gilleron et al., 2013; Mitra et al., 2013; Yang et al.,

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2013; Zheng et al., 2012). Optimization of AuNPs has been focused on certain properties that

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enhance siRNA delivery and reduce possible cytotoxicity. Such properties include surface

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charge, surface complexity and size of the AuNPs (De Jong & Borm, 2008). In this study, three

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AuNP-siRNA complexes (anionic, neutral and cationic) were prepared by a novel layer-by-layer

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(LbL) approach to deliver anti-DENV siRNA into Vero cells. To confirm each layer was

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successfully coated on the AuNPs, the AuNP complexes were characterized by UV-Vis spectra,

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DLS and Zeta potential. AuNPs and AuNP-PEI-siRNAs (PEI: polyethylenimine) were measured

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by UV-Vis, which disclosed a shift in the Surface Plasmon Resonance (SPR) peaks with the

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addition of siRNA (Fig. 2a). DLS measured the hydrodynamic diameters of the different

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complexes: AuNPs (12.92 nm), AuNP-PEI (24.97 nm), AuNP-PEI-siRNA (41.79 nm), and

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AuNP-PEI-siRNA-PEI (43.25 nm), which indicated that the diameters increased with the

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addition of each layer (Fig. 2b). AuNPs were first coated with an inner layer of HS-PEI (thiol-

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labeled PEI) via Au-S bonds, rendering the particles cationic. The negatively charged siRNAs

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were then coated on the AuNP-PEIs through electrostatic interactions, rendering the complexes

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anionic. Adjusting the concentration of the outer layer PEI with the AuNP-PEI-siRNA

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complexes (Fig. 2c) altered the overall charge from negative to positive. Zeta potential

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AuNPs deliver anti-Dengue siRNA

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determined the surface charges of the complexes: AuNPs (-34.9 mV), AuNP-PEI (46.9 mV),

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AuNP-PEI-siRNA (-38.8 mV) and AuNP-PEI-siRNA-PEI (53.3 mV) (Fig. 2d, neutral charge

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data not shown). These results demonstrated the optimization of AuNPs and successful synthesis

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of AuNP-siRNA complexes.

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To test the effect of surface charge on siRNA delivery efficiency, we treated Vero cells

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with anionic (-40 mV), neutral (0 mV) and cationic (+40 mV) AuNP-siRNA complexes (20 nM)

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for 48 hrs and subsequently infected them with DENV-2 (MOI = 0.1) for an additional 48 hrs. Q-

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PCR analysis showed that cationic AuNP-si-1 and AuNP-si-3 complexes significantly reduced

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DENV-2 replication (p < 0.005, Fig. 2e). While anionic AuNP-si-3, but not AuNP-si-1

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complexes, also inhibited DENV-2 replication compared to the control, in which cells were

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infected with DENV-2 only (p < 0.05, Fig. 2e). In contrast, neither the neutrally charged AuNP-

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si-1 nor the AuNP-si-3 complex inhibited viral replication, suggesting inefficient delivery of

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siRNAs by neutral AuNP-siRNA complexes (Fig. 2e). In summary, these results showed that

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cationic AuNP-siRNA complexes could effectively deliver anti-DENV siRNAs into cells.

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To confirm cationic AuNP-siRNAs are able to enter cells, Vero cells were cultured with

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cationic AuNP-si-1 (80nM) for 48 hrs and subsequently infected with DENV-2 (MOI = 0.1) for

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an additional 72 hrs. Ultra-thin sections embedded in epoxy resin were imaged using a

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transmission electron microscope (TEM). The TEM images showed that AuNPs localized within

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the cytoplasm of Vero cells (Fig. 2f, g and inserts), which implied AuNP complexes were able to

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deliver siRNAs into the cells.

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Cationic AuNP-siRNA complexes are non-toxic to Vero cells

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AuNPs deliver anti-Dengue siRNA

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AuNPs have been noted as biocompatible vehicles for drug delivery (Connor et al., 2005;

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Shukla et al., 2005). However, they also have been suggested to have some cytotoxicity due to

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their cationic polarity and surface modifications (Gerber et al., 2013; Goodman et al., 2004). To

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exclude the possibility that inhibition of DENV-2 replication was due to the AuNP-siRNA

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complexes causing Vero cell death, we assessed the cytotoxicity of the AuNP-siRNA complexes

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when exposed to Vero cells. We incubated AuNP-siRNA complexes (+40 mV) with Vero cells

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at the same experimental conditions and concentrations that were used for the pre-treatment

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transfection assays, without DENV-2 infection. Cellular morphology was imaged and cell

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number was quantified by using DAPI-nuclear staining and examined under a confocal

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microscope. No morphological changes (Fig. 3a, i and ii) or cell number reduction (Fig. 3b) were

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observed with any AuNP-siRNA treated samples compared to the untreated control. To further

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confirm this, cellular lactate dehydrogenase (LDH) released from broken cell membrane was

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also measured. The LDH cytotoxicity assay results showed no significant toxicity (≤ 6.5%

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cytotoxicity), which was similar with the untreated cell control (2% cytotoxicity, Fig. 3c). These

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data suggested that Vero cells exposed to AuNP-siRNA complexes have negligible cytotoxicity,

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which indicated that inhibition of DENV-2 replication was due to siRNA mediated RNA

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interference.

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Cationic AuNP-siRNA complexes inhibit DENV-2 infection in both pre- and post-infection

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conditions

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To further confirm that cationic AuNP-siRNA complexes inhibit DENV-2 replication, we

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pre-treated Vero cells with cationic AuNP-siRNAs (+40 mV) at 20 nM and 80 nM for 48 hrs and

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subsequently infected them with DENV-2 (MOI = 0.1) for an additional 48 and 72 hrs, followed

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AuNPs deliver anti-Dengue siRNA

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by Q-PCR analysis. The results showed that compared to DENV-2 only infected controls,

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AuNP-si-1 (20 nM) reduced DENV replication approximately 2-fold at both 48 and 72 hrs (p

Delivery of antiviral small interfering RNA with gold nanoparticles inhibits dengue virus infection in vitro.

Dengue virus (DENV) infection in humans can cause flu-like illness, life-threatening haemorrhagic fever or even death. There is no specific anti-DENV ...
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