miRNAs Targeting ICP4 and Delivered to Susceptible Cells in Exosomes Block HSV-1 Replication in a Dose-Dependent Manner

Abstract

miRNAs are potent tools that in principle can be used to control the replication of infectious agents. The objectives of the studies reported here were to design miRNAs that can block the replication of herpes simplex virus 1 and which could be delivered to infected cells via exosomes. We report the following: (1) We designed three miRNAs targeting the mRNA encoding ICP4, an essential viral regulatory protein. Of the three miRNAs, one miRNA401 effectively blocked ICP4 accumulation and viral replication on transfection into susceptible cells. (2) To facilitate packaging of the miRNA into exosomes, we incorporated into the sequence of miRNA401 an exosome-packaging motif. miRNA401 was shown to be packaged into exosomes and successfully delivered by exosomes to susceptible cells, where it remained stable for at least 72 hr. Finally, the results show that miRNA401 delivered to cells via exosomes effectively reduced virus yields in a miRNA401 dose-dependent fashion. The protocol described in this report can be applied to study viral gene functions without actually deleting or mutagenizing the gene.

Keywords: HSV-1; exosome; target miRNA; viral replication.

Figure 1

Derivation of Stable Cell Lines Expressing miRNAs Targeting ICP4 (A) Schematic diagram of the plasmid-encoding miRNAs targeting ICP4. The figure shows the nucleotide sequences of miR401, miR402, and miR403. The nucleotides highlighted in red indicate exosome-packaging-associated motifs (EXO-motifs). (B) Downregulation of ICP4 by designed miRNA. 12-well plates of HEp-2 were co-transfected with 0.5 μg of plasmids expressing miR401, miR402, miR403, or non-target miRNA (NT) and 0.2 μg of plasmid encoding a his-tagged ICP4 (pICP4-his). The cells were harvested after 48 hr. Accumulations of ICP4, GFP, and GAPDH were measured as described in the Materials and Methods. (C) Accumulation of GFP in stably transformed miR401 cells. The fluorescence associated with accumulation of GFP in HEp-2 cells stably transformed with miR401 (HEp-miR401) were captured with the aid of a Leica-inverted fluorescence microscope by a computer-based imaging system as described in the Materials and Methods. (D) Accumulation of miR401 in HEp-miR401 and parental HEp-2 cells. miR401 were quantified and normalized with respect to 18 s rRNA. The data are presented as mean ± SD of duplicate samples.

Figure 2

Accumulation of Viral Proteins in Stably Transformed HEp-miR401 Cells Infected with HSV-1(F) 12-well-plates of HEp-miR401 or HEp-2 cells were mock-infected or exposed to 0.1, 1, or 10 PFU of HSV-1(F) per cell. The cells were harvested at indicated hours post-infection. The proteins were electrophoretically separated in 10% denaturing gels and reacted with antibodies against ICP27, ICP8, VP16, GFP, or GAPDH. The protein bands were scanned with the aid of ImageJ scanner. The optical densities of the bands were normalized with respect to the optical density of corresponding bands generated from HEp-2 cells at 24 hr (1.0, 10 PFU/cell) or 48 hr (0.1 PFU/cell) after infection.

Figure 3

Virus Yields Recovered from Infected HEp-miR401 Cells HEp-miR401 or parental HEp-2 cells were exposed to 0.01 or 0.1 PFU of HSV-1(F) per cell. After 2 hr, the inoculum was replaced with fresh medium. The virus progeny was harvested at times shown and titered in Vero cells. The data are presented as mean ± SD of duplicate samples.

Figure 4

Characterization of Exosomes Purified from Extracellular Medium Harvested from HEp-2 or HEp-miR401 Cell Cultures (A) Exosomes purified from HEp-miR401 or parental HEp-2 cells conform with known size of exosomal particles. Cultured HEp-2 or HEp-miR401 cells each containing 1 × 10⁷ cells were rinsed with PBS and incubated in serum-free medium. After 18 hr, exosomes were isolated from collected cells by using Total Exosome Isolation Reagent (Thermo Fisher, cat. no. 4478359). Particle size distribution and number of isolated exosomes were determined by Izon’s qNano technology as described in the Materials and Methods. (B) Characterization of purified exosomes with respect to the presence of exosome-associated proteins. Purified exosomes were lysed with RIPA lysis buffer, and 45 μg of exosome proteins were subjected to electrophoresis in denaturing gels and reacted with antibodies to exosome marker proteins CD9, Annexin V, or Flotillin-1, respectively.

Figure 5

Analysis of miR401 from Purified Exosomes (A and B) Quantification of full-length CD9 protein (28 kDa) from band intensities of a CD9 protein fragment (11 kDa). (A) Immunoblot of standard dilution of CD9 protein fragment purchased from Sino Biological. Band intensities were quantified using ImageJ. (B) Standard curve relating band intensities of the 11-kDa CD9 fragment in (A) to full-size 28-kDa CD9 protein. (C and D) Quantitative analysis of purified exosomes with respect to CD9 content. Exosomes in 50 μL amounts purified from either extracellular medium of HEp-miR401 or HEp-2 cell cultures were lysed with RIPA lysis buffer and loaded in triplicate onto a 12% denaturing gel. The electrophoretically separated bands were reacted with CD9 antibody, and band intensities were quantified using ImageJ (C). (D) Calculated amounts of CD9 protein in 50 μL of purified exosomes on the basis of data presented in (B). The amounts of recovered CD9 were 283 ng from HEp-miR401 versus 251 ng from HEp-2 cells. (E) Quantitative analysis of miR401 from purified exosomes. miR401 were extracted from exosomes containing 1 ng of equivalent of CD9. The data are presented as mean ± SD of triplicate samples.

Figure 6

Penetration of miR401 Contained in Exosomes into HEp-2 Recipient Cells Replicate HEp-2 cultures containing 2.5 × 10⁵ cells were exposed to 10 μg of exosomes purified from HEp-miR401 cells for 2, 8, 12, 24, 48, or 72 hr. The cells were harvested and extensively rinsed with PBS, miR401 was extracted, quantified, and normalized with respect to 18 s rRNA. The data are presented as mean ± SD of duplicate samples.

Figure 7

Inhibition of Viral Gene Expression and Replication by Exosome-Mediated miR401 (A) Accumulation of selected viral proteins in cells exposed to exosomes containing miR401. Cultures containing 2.5 × 10⁵ HEp-2 cells were incubated with purified exosomes from HEp-miR401 cells. The miR401 copy numbers were determined as described in the legend of Figure 5. Exosomes purified from HEp-2 parental cells served as controls. After 12 hr of incubation, the cells were exposed to 0.1 PFU of HSV-1(F) per cell. After 24 hr, the cells were harvested and the cells lysates were electrophoretically separated in a 10% denaturing gel and reacted with indicated antibodies. The band density was normalized with respect to GAPDH and the yields obtained in mock-infected cells. (B) Virus yield from cells treated with exosomes containing miR401. 2.5 × 10⁵ HEp-2 cells were exposed to purified exosomes as described in (A) and then infected with 0.01 PFU per cell. After 2 hr, the inoculum was replaced with fresh culture medium. The infected cells were harvested at 48 hr post-infection (p.i.), and the virus yields were titered in Vero cells. The data are presented as mean ± SD of duplicate samples.