Vector design for liver-specific expression of multiple interfering RNAs that target hepatitis B virus transcripts. Antiviral Res. 2008;80:36-44. [PMID: 18499277 DOI: 10.1016/j.antiviral.2008.04.001]

Evaluation of the In Vitro and In Vivo Effects of Biglycan in Innate Immunity

Biglycan, a small leucine-rich proteoglycan (SLRP), is a crucial component of the extracellular matrix (ECM) associated with the maintenance of tissue homeostasis. In response to tissue damage, the ECM-derived soluble form of biglycan acts as a danger signal by triggering an inflammatory response via the toll-like receptor (TLR)2/TLR4 in macrophages and dendritic cells. The impact and signaling mechanism of biglycan in innate immunity is better understood with the use of specific and reliable research tools and investigation techniques. Accordingly, our lab has established explicit and detailed experimental protocols to examine the in vitro and in vivo effects of biglycan in cellular immune responses. To evaluate the in vitro effects of biglycan on macrophage activation, a comprehensive protocol that makes use of murine peritoneal macrophages has been described. Further, to study the in vivo effects of biglycan, a method that uses a pLIVE vector to generate transgenic mice transiently overexpressing human biglycan is detailed. A step-by-step protocol for analyzing the effects of soluble biglycan overexpression in transgenic mice is explained under the following sections: (1) construction of pLIVE-hBGN plasmid, (2) intravenous delivery of transgenic vector, (3) identification of hBGN transgene in hepatocytes (4) detection of transgenic biglycan protein in the plasma of transgenic mice, and (5) evaluation of the presence and pro-inflammatory effects of transgenic biglycan in extrahepatic mouse tissues.

MiR-664-2 impacts pubertal development in a precocious-puberty rat model through targeting the NMDA receptor-1†

Precocious puberty (PP) commonly results from premature activation of the hypothalamic-pituitary-gonadal axis (HPGA). Gonadotropin-releasing hormone (GnRH) is the initial trigger for HPGA activation and plays an important role in puberty onset. N-methyl-D-aspartate (NMDA) can promote pulsatile GnRH secretion and accelerates puberty onset. However, the mechanism of N-methyl-D-aspartate receptors (NMDARs) in PP pathogenesis remains obscure. We found that serum GnRH, luteinizing hormone (LH), follicle-stimulating hormone (FSH), estrogen (E2) levels, hypothalamic NMDAR1, and GnRH mRNA expression peaked at the vaginal opening (VO) day. Next, the hypothalamic NMDAR1 mRNA and protein levels in rats treated with danazol, a chemical commonly effecting on the reproductive system, were significantly increased at the VO day (postnatal day 24) compared to controls, accompanied by enhanced serum GnRH, LH, FSH, and E2 levels. Further, microRNA-664-2 (miR-664-2) was selected after bioinformatics analysis and approved in primary hypothalamic neurons, which binds to the 3'-untranslated regions of NMDAR1. Consistently, the miR-664-2 expression in hypothalamus of the Danazol group was decreased compared to Vehicle. Our results suggested that attenuated miR-664-2 might participate in PP pathogenesis through enhancing the NMDAR1 signaling.

Multi‑target inhibition by four tandem shRNAs embedded in homo‑ or hetero‑miRNA backbones

The functional influence of microRNA (miRNA)backbone selection remains unclear with respect to multiplexing miRNA‑based short hairpin RNAs (shRNAmiRs), due to a lack of comparative studies. To this end, a pair of shRNAmiR tetramers were designed in the present study that targeted four genes with a shared miR30a backbone (homo‑BB) or four miRNA backbones (hetero‑BB). A PBLT+ 293A cell line overexpressing four targets was established, which permitted simultaneous dissection of individual gene knockdown. Multi‑target inhibition was confirmed by a decrease in positive cell populations of the relative gene and mean fluorescence intensities, with almost comparable activities of homo‑ and hetero‑BB tetramers. Of note, this multi‑inhibition was sustained over a 1‑month period, with no notable difference, particularly in the late‑phased inhibitory effects between homo‑ and hetero‑BB tetra‑shRNA miRs. These preliminary data may indicate little influence of scaffold substitution in the functionalities of multiplexed shRNAmiRs and little recombination‑depleted risk of repetitively adopting the same miRNA backbone in this artificial in vitro system. More comparative studies are further required to explore extended repertoires of scaffold‑paralleled multi‑shRNAmiRs in more physiologically relevant models.

SgRNA Expression of CRIPSR-Cas9 System Based on MiRNA Polycistrons as a Versatile Tool to Manipulate Multiple and Tissue-Specific Genome Editing

CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications. Typically, sgRNA is constitutively expressed relying on RNA polymerase III promoters. Polymerase II promoters initiate transcription in a flexible manner, but sgRNAs generated by RNA polymerase II promoter lost their nuclease activity. To express sgRNAs in a tissue-specific fashion and endow CRISPR with more versatile function, a novel system was established in a polycistron, where miRNAs (or shRNAs) and sgRNAs alternately emerged and co-expressed under the control of a single polymerase II promoter. Effective expression and further processing of functional miRNAs and sgRNAs were achieved. The redundant nucleotides adjacent to sgRNA were degraded, and 5'- cap structure was responsible for the compromised nuclease capacity of sgRNA: Cas9 complex. Furthermore, this strategy fulfilled conducting multiplex genome editing, as well as executing neural- specific genome editing and enhancing the proportion of homologous recombination via inhibiting NHEJ pathway by shRNA. In summary, we designed a new construction for efficient expression of sgRNAs with miRNAs (shRNAs) by virtue of RNA polymerase II promoters, which will spur the development of safer, more controllable/regulable and powerful CRISPR/Cas9 system-mediated genome editing in a wide variety of further biomedical applications.

Inhibition of HIV-1 by a Lentiviral Vector with a Novel Tat-Inducible Expression System and a Specific Tropism to the Target Cells

Today, lentiviral vectors are favorable vectors for RNA interference delivery in anti-HIV therapeutic approaches. Nevertheless, problems such as the specific recognition of target cells and uncontrolled expression of the transgene can restrict their use in vivo. Herein we present a new HIV-inducible promoter to express anti-HIV short hairpin RNA (shRNA) by RNA Pol II in mammalian cells. We likewise showed a novel third-generation lentiviral vector system with more safety and a specific tropism to the target cells. The new promoter, CkRhsp, was constructed from the chicken β-actin core promoter with the R region of HIV-1 long terminal repeat fused upstream of minimal hsp70 promoter. This system was induced by HIV-1 Tat, and activates transcription of two shRNAs against two conserved regions of HIV-1 transcripts produced in two steps of the virus life cycle. We also mimicked HIV-1 cell tropism by using the HIV-1 envelope in structure of third-generation lentiviral vector. The new fusion promoter efficiently expressed shRNA in a Tat-inducible manner. HIV-1 replication was inhibited in transient transfection and stable transduction assays. The new viral vector infected only CD4+cells. CkRhsp promoter may be safer than other inducible promoters for shRNA-mediated gene therapies against HIV. The use of the wild envelope in the vector packaging system may provide the specific targeting T lymphocytes and hematopoietic stem cells for anti-HIV-1 therapeutic approaches in vivo.

Artificial MiRNA Knockdown of Platelet Glycoprotein lbα: A Tool for Platelet Gene Silencing

In recent years, candidate genes and proteins implicated in platelet function have been identified by various genomic approaches. To elucidate their exact role, we aimed to develop a method to apply miRNA interference in platelet progenitor cells by using GPIbα as a proof-of-concept target protein. After in silico and in vitro screening of siRNAs targeting GPIbα (siGPIBAs), we developed artificial miRNAs (miGPIBAs), which were tested in CHO cells stably expressing GPIb-IX complex and megakaryoblastic DAMI cells. Introduction of siGPIBAs in CHO GPIb-IX cells resulted in 44 to 75% and up to 80% knockdown of GPIbα expression using single or combined siRNAs, respectively. Conversion of siGPIBAs to miGPIBAs resulted in reduced silencing efficiency, which could however be circumvented by tandem integration of two hairpins targeting different regions of GPIBA mRNA where 72% GPIbα knockdown was achieved. CHO GPIb-IX cells transfected with the miGPIBA construct displayed a significant decrease in their ability to aggregate characterized by lower aggregate numbers and size compared to control CHO GPIb-IX cells. More importantly, we successfully silenced GPIbα in differentiating megakaryoblastic DAMI cells that exhibited morphological changes associated with actin organization. In conclusion, we here report the successful use of miRNA technology to silence a platelet protein in megakaryoblastic cells and demonstrate its usefulness in functional assays. Hence, we believe that artificial miRNAs are suitable tools to unravel the role of a protein of interest in stem cells, megakaryocytes and platelets, thereby expanding their application to novel fields of basic and translational research.

Hepatitis B virus and microRNAs: Complex interactions affecting hepatitis B virus replication and hepatitis B virus-associated diseases

Chronic infection with the hepatitis B virus (HBV) is the leading risk factor for the development of hepatocellular carcinoma (HCC). With nearly 750000 deaths yearly, hepatocellular carcinoma is the second highest cause of cancer-related death in the world. Unfortunately, the molecular mechanisms that contribute to the development of HBV-associated HCC remain incompletely understood. Recently, microRNAs (miRNAs), a family of small non-coding RNAs that play a role primarily in post-transcriptional gene regulation, have been recognized as important regulators of cellular homeostasis, and altered regulation of miRNA expression has been suggested to play a significant role in virus-associated diseases and the development of many cancers. With this in mind, many groups have begun to investigate the relationship between miRNAs and HBV replication and HBV-associated disease. Multiple findings suggest that some miRNAs, such as miR-122, and miR-125 and miR-199 family members, are playing a role in HBV replication and HBV-associated disease, including the development of HBV-associated HCC. In this review, we discuss the current state of our understanding of the relationship between HBV and miRNAs, including how HBV affects cellular miRNAs, how these miRNAs impact HBV replication, and the relationship between HBV-mediated miRNA regulation and HCC development. We also address the impact of challenges in studying HBV, such as the lack of an effective model system for infectivity and a reliance on transformed cell lines, on our understanding of the relationship between HBV and miRNAs, and propose potential applications of miRNA-related techniques that could enhance our understanding of the role miRNAs play in HBV replication and HBV-associated disease, ultimately leading to new therapeutic options and improved patient outcomes.

Lentiviral vector-mediated doxycycline-inducible USP39 shRNA or cDNA expression in triple-negative breast cancer cells

Triple-negative breast cancer (TNBC), characterized by distinct biological and clinicopathological features, has a poor prognosis due to lack of effective therapeutic targets. Our previous data revealed that high levels of USP39 were selectively present in TNBC samples compared with their normal breast tissue samples and USP39 was also expressed at different levels in cultured TNBC cells and normal breast cells. Yet, the underlying cellular and molecular mechanisms of USP39 remain unclear. In the present study, we describe a doxycycline (DOX)-regulated lentiviral vector system expressing shRNA or cDNA of the USP39 gene in the TNBC cell line MDA-MB-231. USP39 expression was knocked down by the miR-30-based inducible lentiviral short hairpin RNA (shRNA) delivery system or overexpressed by the inducible cDNA system. The inducible shRNA-mediated downregulation of USP39 expression markedly reduced the proliferation and colony-forming ability of MDA-MB-231 cells, while overexpression of USP39 by the inducible system did not promote cancer cell proliferation. The lentiviral vector-mediated Tet-on system demonstrated efficient and inducible knockdown of USP39 or overexpression of USP39 in TNBC cells, facilitating a wide variety of applications for gene knockdown and overexpression experiments in gene functional studies in vitro and in vivo.

Construction and application of a novel hepatocyte-directed vector to simultaneous knockdown and overexpression of multiple genes

BACKGROUND & AIMS

Liver disease, such as malignancy and hepatitis, often correlates with several genetic disorders. We aimed to construct a hepatocyte-specific vector that could manipulate multiple genes simultaneously.

METHODS

We selected a highly efficient hepatocyte-specific α-foetoprotein (AFP) enhancer/albumin promoter (an RNA polymerase II promoter) to express our gene of interest and transcribe microRNA-based shRNAs (shRNAmir). Multiple shRNAmirs were assembled together in tandem to enhance the gene-silencing effect. By employing the AFP enhancer/albumin promoter and inserting an internal ribosome entry site (IRES), a hepatocyte-specific, multi-reporter vector that overexpressed both β-galactosidase (LacZ) and DsRed2 while simultaneously knocking down both EGFP and luciferase expression was successfully constructed and functionally tested in vitro.

RESULTS

The reporter genes in the multireporter vector were easily replaced by immune-related genes to construct the Multi-Vector, which overexpressed human interleukin 10 and silenced both CCL5 and CX3CL1 (FKN) simultaneously in vivo; visualization of DsRed2 coexpressed to monitor vector function in vivo confirmed that the Multi-Vector was successfully introduced into the host. Simultaneous manipulation of these multiple genes by the Multi-Vector synergistically inhibited acute liver injury induced by Poly I:C/D-GalN injection in mice. The multifunctional cassette was also packaged in and successfully delivered by an adenoviral vector.

CONCLUSIONS

We successfully engineered a vector that can simultaneously regulate multiple genes from a single multigene-containing vector in a hepatocyte-specific manner, suggesting the possibility that this method could be extensively and practically utilized in liver gene therapy.

Significant inhibition of two different genotypes of grass carp reovirus in vitro using multiple shRNAs expression vectors

The hemorrhagic disease of grass carp (Ctenopharyngodon idellus), caused by grass carp reovirus (GCRV), is the most severe disease of the fish that leads to huge economic losses. GCRV, belonging to the genus Aquareovirus of the family Reoviridae, has been classified into three genotypes based on their phylogenetic relationship. It is essential to develop an effective method to inhibit the replication of different genotypes of GCRV simultaneously. In this report, two multiple-shRNAs expression vectors, named pMultishVP2/2 and pMultishVP6/7, were generated and investigated. pMultishVP2/2 targeted the VP2 gene of GCRV-JX0901 (genotype I) and the VP2 gene of HGDRV (Hubei grass carp disease reovirus; genotype III). pMultishVP6/7 targeted the VP7 gene of GCRV-JX0901 and the VP6 gene of HGDRV. These two multiple-shRNAs expression vectors can simultaneously, significantly inhibit the replication of GCRV-JX0901 and HGDRV in vitro. Compared to the positive control, CPE induced by GCRV-JX0901 or HGDRV in cell transfected with shRNA transcribing vector was significantly delayed. The quantitative PCR analysis of the GCRV genomic RNA revealed that the pMultishVP2/2 could simultaneously inhibit the GCRV-JX0901 and HGDRV VP2 coding genes by 89.02% and 89.84%, respectively. The pMultishVP6/7 could simultaneously inhibit the GCRV-JX0901 VP7 coding gene and HGDRV VP6 coding gene by 80.63% and 86.78%, respectively. Furthermore, compared to the positive control, the indirect immunofluorescence assay and western blot demonstrated that the protein expression of the two genotypes of GCRV decreased significantly. The results in this study indicated that this multiple-shRNAs expression system could be used as a cross-reactive antiviral agent for treating the hemorrhagic disease of grass carp caused by multiple genotypes of GCRV.

Lentiviral miR30-based RNA interference against heparanase suppresses melanoma metastasis with lower liver and lung toxicity

Aim: To construct short hairpin RNAs (shRNAs) and miR30-based shRNAs against heparanase (HPSE) to compare their safety and their effects on HPSE down-modulation in vitro and in vivo to develop a more ideal therapeutic RNA interference (RNAi) vector targeting HPSE.

Methods: First, we constructed shRNAs and miR30-based shRNAs against HPSE (HPSE-shRNAs and HPSE-miRNAs) and packed them into lentiviral vectors. Next, we observed the effects of the shRNAs on knockdown for HPSE expression, adhesion, migration and invasion abilities in human malignant melanoma A375 cells in vitro. Furthermore, we compared the effects of the shRNAs on melanoma growth, metastasis and safety in xenograft models.

Results: Our data showed that these artificial miRNAs targeting HPSE could be effective RNAi agents mediated by Pol II promoters in vitro and in vivo, although these miRNAs were not more potent than the HPSE-shRNAs. It was noted that obvious lung injuries, rarely revealed previously, as well as hepatotoxicity could be caused by lentivirus-mediated shRNAs (LV shRNAs) rather than lentivirus-mediated miRNAs (LV miRNAs) in vivo. Furthermore, enhanced expression of pro-inflammatory cytokines IL-6 and TGF-β1 and endogenous mmu-miR-21a-5p were detected in lung tissues of shRNAs groups, whereas the expression of mmu-let-7a-5p, mmu-let-7b-5p and mmu-let-7c-5p were down-regulated.

Conclusion: These findings suggest that artificial miRNAs display an improved safety profile of lowered lung injury or hepatotoxicity relative to shRNAs in vivo. The mechanism of lung injuries caused by shRNAs may be correlated with changes of endogenous miRNAs in the lung. Our data here increase the flexibility of a miRNA-based RNAi system for functional genomic and gene therapy applications.

An artificial miRNA against HPSE suppresses melanoma invasion properties, correlating with a down-regulation of chemokines and MAPK phosphorylation

Ribonucleic acid interference (RNAi) based on microRNA (miRNA) context may provide an efficient and safe therapeutic knockdown effect and can be driven by ribonucleic acid polymerase II (RNAP II). In this study, we designed and synthesized miR155-based artificial miRNAs against heparanase (HPSE) constructed with BLOCK-iT™ Pol II miR RNAi Expression Vector Kit. The expression levels of HPSE declined significantly in both the mRNA and protein levels in HPSE-miRNA transfected melanoma cells that exhibited reduction of adhesion, migration, and invasion ability in vitro and in vivo. We also observed that HPSE miRNA could inhibit the expressions of chemokines of interleukin-8 (IL8) and chemokine (C-X-C motif) ligand 1 (CXCL1), at both the transcriptional and translational levels. Further study on its probable mechanism declared that down-regulation of IL8 and CXCL1 by HPSE-miRNA may be correlated with reduced growth-factor simulated mitogen-activated kinase (MAPK) phosphorylation including p38 MAPK, c-Jun N-terminal kinase (JNK) and extracellular-signal-regulated kinase (ERK) 1 and 2, which could be rescued by miRNA incompatible mutated HPSE cDNA. In conclusion, we demonstrated that artificial miRNAs against HPSE might serve as an alterative mean of therapy to low HPSE expression and to block the adhesion, invasion, and metastasis of melanoma cells. Furthermore, miRNA-based RNAi was also a powerful tool for gene function study.

Polycistronic expression of interfering RNAs from RNA polymerase III promoters

In many RNA silencing applications, there is a benefit to expressing multiple interfering RNAs simultaneously. This can be achieved by using a single RNA polymerase II promoter to express multiple micro(mi)RNA-formatted interfering RNAs that are arranged in a polycistronic cluster, mimicking the organization of naturally clustered, endogenous miRNAs. While RNA pol III promoters are often used to express individual short hairpin (sh) RNAs, we have recently shown that pol III promoters can also be used to drive polycistronic expression of miRNA-formatted interfering RNAs. Here, we present methods for the assembly of polycistronic miRNA expression vectors that use pol III promoters. In addition, we present methods for testing the potency and the level of expression of each of the individual miRNAs encoded in the construct.

Antiviral RNAi: translating science towards therapeutic success

Viruses continuously evolve to contend with an ever-changing environment that involves transmission between hosts and sometimes species, immune responses, and in some cases therapeutic interventions. Given the high mutation rate of viruses relative to the timescales of host evolution and drug development, novel drug classes that are readily screened and translated to the clinic are needed. RNA interference (RNAi)-a natural mechanism for specific degradation of target RNAs that is conserved from plants to invertebrates and vertebrates-can potentially be harnessed to yield therapies with extensive specificity, ease of design, and broad application. In this review, we discuss basic mechanisms of action and therapeutic applications of RNAi, including design considerations and areas for future development in the field.

Countering hepatitis B virus infection using RNAi: how far are we from the clinic?

Globally, persistent HBV infection is a significant cause of public health problems. Currently available HBV therapies have variable efficacy and there is a need to develop improved treatment to prevent cirrhosis and hepatocellular carcinoma. Although RNA interference (RNAi)-based approaches have shown promise, accomplishing safe and sustained silencing by RNAi activators, as well as their efficient delivery to hepatocytes have hampered clinical translation of this very promising technology. Expressed silencers may be produced in a sustained manner from stable DNA templates, which makes them suited to treatment of chronic HBV infection. DNA expression cassettes can be incorporated into both viral and non-viral vectors, but in vivo delivery of these cassettes with non-viral vectors is currently inefficient. Synthetic short interfering RNAs (siRNAs), which may be chemically modified to improve stability, specificity and efficacy, are more conveniently delivered to their cytoplasmic sites of action with synthetic non-viral vectors. However, the short duration of action of this class of RNAi activator is a drawback for treatment of chronic HBV infection. Despite the impressive progress that has been made in developing highly effective HBV gene silencers, challenges continue to face implementation of RNAi-based HBV therapy. This review will discuss the current status of the topic and consider the developments that are required to advance RNAi-based HBV therapy to clinical application.

A re-examination of global suppression of RNA interference by HIV-1

The nature of the interaction between replicating HIV-1 and the cellular RNAi pathway has been controversial, but it is clear that it can be complex and multifaceted. It has been proposed that the interaction is bi-directional, whereby cellular silencing pathways can restrict HIV-1 replication, and in turn, HIV-1 can suppress silencing pathways. Overall suppression of RNAi has been suggested to occur via direct binding and inhibition of Dicer by the HIV-1 Tat protein or through sequestration of TRBP, a Dicer co-factor, by the structured TAR element of HIV-1 transcripts. The role of Tat as an inhibitor of Dicer has been questioned and our results support and extend the conclusion that Tat does not inhibit RNAi that is mediated by either exogenous or endogenous miRNAs. Similarly, we find no suppression of silencing pathways in cells with replicating virus, suggesting that viral products such as the TAR RNA elements also do not reduce the efficacy of cellular RNA silencing. However, knockdown of Dicer does allow increased viral replication and this occurs at a post-transcriptional level. These results support the idea that although individual miRNAs can act to restrict HIV-1 replication, the virus does not counter these effects through a global suppression of RNAi synthesis or processing.

Toward a durable treatment of HIV-1 infection using RNA interference

RNA interference (RNAi) is a cellular mechanism that mediates sequence-specific gene silencing at the posttranscriptional level. RNAi can be used as an antiviral approach against human pathogens. An attractive target for RNAi therapeutics is the human immunodeficiency virus type 1 (HIV-1), and the first clinical trial using a lentiviral gene therapy was initiated in early 2008. In this chapter, we focus on some basic principles of such an RNAi-based gene therapy against HIV-1. This includes the subjects of target site selection within the viral RNA genome, the phenomenon of viral escape, and therapeutic strategies to prevent viral escape. The latter antiescape strategies include diverse combinatorial RNAi approaches that are all directed against the HIV-1 RNA genome. As an alternative strategy, we also discuss the possibilities and restrictions of targeting cellular cofactors that are essential for virus replication, but less important for cell physiology.

Expression of interfering RNAs from an HIV-1 Tat-inducible chimeric promoter

The therapeutic value of antiviral interfering RNAs could be improved by technologies that limit their expression to the infected cell population. The HIV-1 Tat-inducible viral LTR and LTR-containing chimeric promoters have previously been used to drive expression of antiviral RNAs and proteins directed against HIV-1. Here, we characterize an alternative promoter, consisting of a chicken β-actin core promoter fused to the viral TAR element, for the conditional expression of interfering RNAs. This promoter, that we refer to as the CK-TAR promoter, can induce levels of silencing comparable to the viral LTR in response to Tat produced from co-transfected plasmids or during viral replication. While the CK-TAR promoter shows a modest level of basal activity, similar to the viral LTR, it is less responsive to the extracellular stimuli tested including LPS, TNFα, and PMA. The CK-TAR promoter is an alternative Tat-inducible promoter with the potential to minimize the risk of vector mobilization and to drive polycistronic expression of interfering RNAs.

Progress in the use of RNA interference as a therapy for chronic hepatitis B virus infection

Chronic infection with hepatitis B virus (HBV) occurs in approximately 6% of the world's population and carriers of the virus are at risk for hepatocellular carcinoma and cirrhosis. Current treatment regimens, which include interferon-α and nucleoside/nucleotide analogs, are only partially effective and new treatment methods remain an important objective. Harnessing the RNA interference (RNAi) pathway to achieve post-transcriptional silencing of rogue genetic elements is an exciting avenue for development of novel therapeutic strategies. The specific and potent suppression of HBV gene expression and replication is an attractive option as a novel and effective approach for the treatment of chronic HBV infection. However, despite significant and rapid progress, existing RNAi technologies require further refinement before clinical applications can be realized. Here, we review current efforts aimed at improving the efficiency of anti-HBV RNAi-based delivery systems, at limiting the toxicities associated with RNAi modalities and at preventing reactivation of viral replication. We discuss the progress towards clinical implementation of anti-HBV RNAi therapies.

RNA polymerase III can drive polycistronic expression of functional interfering RNAs designed to resemble microRNAs

In both research and therapeutic applications of RNA interference, it is often advantageous to silence several targets simultaneously. Toward this end, several groups have developed vectors that utilize the model of endogenously encoded micro (mi) RNAs, where a single RNA polymerase II promoter can drive the expression of multiple interfering RNAs. Stronger pol III promoters have been used to drive individual short hairpin (sh) RNAs, but to date, it has been necessary to repeat the promoter in each silencing cassette to achieve multiplexed expression from a single vector. Here, we show that it is possible to drive polycistronic expression from a single pol III promoter when the interfering RNAs are formatted to resemble miRNAs rather than shRNAs. As many as four miRNAs designed to target hepatitis B virus (HBV) transcripts are shown to be processed and functional in reporter assays as well as in the context of replicating virus in cell culture systems. Although it has been observed that high levels of expression of shRNAs can lead to cytotoxicity, we find no significant evidence in transient transfection assays that the HBV-miRNAs produced by our vectors compete for the activity of endogenously produced miR-122 or for processing of an exogenously expressed miR-EGFP.

Regulated and multiple miRNA and siRNA delivery into primary cells by a lentiviral platform

RNA interference (RNAi) has tremendous potential for investigating gene function and developing new therapies. However, the design and validation of proficient vehicles for stable and safe microRNA (miR) and small interfering RNA (siRNA) delivery into relevant target cells remains an active area of investigation. Here, we developed a lentiviral platform to efficiently coexpress one or more natural/artificial miR together with a gene of interest from constitutive or regulated polymerase-II (Pol-II) promoters. By swapping the stem-loop (sl) sequence of a selected primary transcript (pri-miR) with that of other miR or replacing the stem with an siRNA of choice, we consistently obtained robust expression of the chimeric/artificial miR in several cell types. We validated our platform transducing a panel of engineered cells stably expressing sensitive reporters for miR activity and on a natural target. This approach allowed us to quantitatively assess at steady state the target suppression activity and expression level of each delivered miR and to compare it to those of endogenous miR. Exogenous/artificial miR reached the concentration and activity typical of highly expressed natural miR without perturbing endogenous miR maturation or regulation. Finally, we demonstrate the robust performance of the platform reversing the anergic/suppressive phenotype of human primary regulatory T cells (Treg) by knocking-down their master gene Forkhead Transcription Factor P3 (FOXP3).

RNA-interference-based Gene Therapy Approaches to HIV Type-1 Treatment: Tackling the Hurdles from Bench to Bedside

RNA interference (RNAi) is a cellular mechanism that can be induced by small interfering RNAs (siRNAs) to mediate sequence-specific gene silencing by cleavage of the targeted messenger RNA. RNAi can be used as an antiviral approach to silence HIV type-1 (HIV-1) through stable expression of precursors, such as short hairpin RNAs (shRNAs), which are processed into siRNAs that can elicit degradation of HIV-1 RNAs. At the beginning of 2008, the first clinical trial using a lentivirus with an RNA-based gene therapy against HIV-1 was initiated. The antiviral molecules in this gene therapy consist of three RNA effectors, one of which triggers the RNAi pathway. This review article focuses on the basic principles of an RNAi-based gene therapy against HIV-1, including delivery methods, target selection, viral escape possibilities, systems for multiplexing siRNAs to achieve a durable therapy and the in vitro and in vivo test systems to evaluate the efficacy and safety of such a therapy.

Silencing viral microRNA as a novel antiviral therapy?

Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases.