Double-stranded nef RNA interferes with human immunodeficiency virus type 1 replication

An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review

The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.

The Role of Innate Immunity in Natural Elite Controllers of HIV-1 Infection

The natural process of human immunodeficiency virus type 1(HIV-1) infection is characterized by high viral load, immune cell exhaustion, and immunodeficiency, which eventually leads to the stage of acquired immunodeficiency syndrome (AIDS) and opportunistic infections. Rapidly progressing HIV-1 individuals often die of AIDS several years after infection without treatment. The promotion of ART greatly prolongs the survival time of HIV-infected persons. However, some patients have incomplete immune function reconstruction after ART due to latent storage of HIV-infected cells. Therefore, how to achieve a functional cure has always been the focus and hot spot of global AIDS research. Fortunately, the emergence of ECs/LTNPs who can control virus replication naturally has ignited new hope for realizing a functional cure for AIDS. Recently, a special category of infected individuals has attracted attention that can delay the progression of the disease more rigorously than the natural progression of HIV-1 infection described above. These patients are characterized by years of HIV-1 infection, long-term asymptomatic status, and normal CD4+T cell count without ART, classified as HIV-infected long-term nonprogressors (LTNPs) and elite controllers (ECs). Numerous studies have shown that the host and virus jointly determine the progression of HIV-1 infection, in which the level of innate immunity activation plays an important role. As the first line of defense against pathogen invasion, innate immunity is also a bridge to induce adaptive immunity. Compared with natural progressors, innate immunity plays an antiviral role in HIV-1 infection by inducing or activating many innate immune-related factors in the natural ECs. Learning the regulation of ECs immunity, especially the innate immunity in different characteristics, and thus studying the mechanism of the control of disease progression naturally, will contribute to the realization of the functional cure of AIDS. Therefore, this review will explore the relationship between innate immunity and disease progression in ECs of HIV-1 infection from the aspects of innate immune cells, signaling pathways, cytokines, which is helpful to provide new targets and theoretical references for the functional cure, prevention and control of AIDS, and development of a vaccine.

HIV-1-derived exosomal microRNAs miR88 and miR99 promote the release of cytokines from human alveolar macrophages by binding to TLR8

The human monocytic cell line U937 and human alveolar macrophages were used as in vitro models to explore the role of miR88 and miR99 in the chronic abnormal activation of the body caused by human immunodeficiency virus (HIV). The functions and underlying mechanisms of miR88 and miR99 were studied by real-time quantitative polymerase chain reaction, transwell, and chromatin immunoprecipitation (ChIP) assays. HIV-1-infected cells released miR88 and miR99 into the extracellular space through exosomes, and miR88 and miR99 promoted the release of tumor necrosis factor alpha (TNFα), interleukin (IL)-6, and IL-12 by activating inflammatory factors, such as TLR8, on the surface of macrophages. HIV-derived microRNAs miR88 and miR99 performed these functions by binding to TLR8 and stimulating the release of pro-inflammatory factors from macrophages, such as TNFα, IL-6, and IL-12; these factors may be involved in chronic abnormal immune activation induced by HIV infection.

Six Highly Conserved Targets of RNAi Revealed in HIV-1-Infected Patients from Russia Are Also Present in Many HIV-1 Strains Worldwide

RNAi has been suggested for use in gene therapy of HIV/AIDS, but the main problem is that HIV-1 is highly variable and could escape attack from the small interfering RNAs (siRNAs) due to even single nucleotide substitutions in the potential targets. To exhaustively check the variability in selected RNA targets of HIV-1, we used ultra-deep sequencing of six regions of HIV-1 from the plasma of two independent cohorts of patients from Russia. Six RNAi targets were found that are invariable in 82%-97% of viruses in both cohorts and are located inside the domains specifying reverse transcriptase (RT), integrase, vpu, gp120, and p17. The analysis of mutation frequencies and their characteristics inside the targets suggests a likely role for APOBEC3G (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G, A3G) in G-to-A mutations and a predominant effect of RT biases in the detected variability of the virus. The lowest frequency of mutations was detected in the central part of all six targets. We also discovered that the identical RNAi targets are present in many HIV-1 strains from many countries and from all continents. The data are important for both the understanding of the patterns of HIV-1 mutability and properties of RT and for the development of gene therapy approaches using RNAi for the treatment of HIV/AIDS.

Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic

Because of a high mutation rate, HIV exists as a viral swarm of many sequence variants evolving under various selective pressures from the human immune system. Although the Nef gene codes for the most immunogenic of HIV accessory proteins, which alone makes it of great interest to HIV research, it also encodes an RNA structure, whose contribution to HIV virulence has been largely unexplored. Nef RNA helps HIV escape RNA interference (RNAi) through nucleotide changes and alternative folding. This study examines Historic and Modern Datasets of patient HIV-1 Nef sequences during the evolution of the North American epidemic for local changes in RNA plasticity. By definition, RNA plasticity refers to an RNA molecule’s ability to take alternative folds (i.e., alternative conformations). Our most important finding is that an evolutionarily conserved region of the HIV-1 Nef gene, which we denote by R2, recently underwent a statistically significant increase in its RNA plasticity. Thus, our results indicate that Modern Nef R2 typically accommodates an alternative fold more readily than Historic Nef R2. Moreover, the increase in RNA plasticity resides mostly in synonymous nucleotide changes, which cannot be a response to selective pressures on the Nef protein. R2 may therefore be of interest in the development of antiviral RNAi therapies.

Gene Silencing of HIV-1 by RNA Interference

Short interfering RNAs (siRNAs) are as effective at targeting and silencing genes by RNA interference (RNAi) as long double-stranded RNAs (dsRNAs). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. siRNAs are also promising reagents for developing gene-specific therapeutics. Specifically, the inhibition of HIV-1 replication is particularly well-suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on recent advances in siRNA-based silencing technologies.

MicroRNAs and HIV-1 infection: antiviral activities and beyond

Cellular microRNAs (miRNAs) are an important class of small, non-coding RNAs that bind to host mRNAs based on sequence complementarity and regulate protein expression. They play important roles in controlling key cellular processes including cellular inception, differentiation and death. While several viruses have been shown to encode for viral miRNAs, controversy persists over the expression of a functional miRNA encoded in the human immunodeficiency virus type 1 (HIV-1) genome. However, it has been reported that HIV-1 infectivity is influenced by cellular miRNAs. Either through directly targeting the viral genome or by targeting host cellular proteins required for successful virus replication, multiple cellular miRNAs seem to modulate HIV-1 infection and replication. Perhaps as a survival strategy, HIV-1 may modulate proteins in the miRNA biogenesis pathway to subvert miRNA-induced antiviral effects. Global expression profiles of cellular miRNAs have also identified alterations of specific miRNAs post-HIV-1 infection both in vitro and in vivo (in various infected patient cohorts), suggesting potential roles for miRNAs in pathogenesis and disease progression. However, little attention has been devoted in understanding the roles played by these miRNAs at a cellular level. In this manuscript, we review past and current findings pertaining to the field of miRNA and HIV-1 interplay. In addition, we suggest strategies to exploit miRNAs therapeutically for curbing HIV-1 infectivity, replication and latency since they hold an untapped potential that deserves further investigation.

Inhibition of HIV-1 replication by RNA with a microRNA-like function

Human immunodeficiency virus type 1 (HIV-1) replication is suppressed by a small guide RNA (sgRNA) that targets the packaging signal of HIV-1 RNA. We unintentionally produced a plasmid with the reverse sequence of the sgRNA and its terminator (pR-Ψ-sgRNA-ter). Both sgRNA and R-Ψ-sgRNA suppress HIV-1, but the mechanism by which R-Ψ-sgRNA suppresses HIV is not clear. To evaluate whether the suppressive effect is caused by an RNA interference or microRNA (miRNA)-like mechanism, R-Ψ-sgRNA was synthesized in vitro and treated with the Dicer enzyme, an important enzyme for RNA interference and miRNA. The RNA was cleaved into fragments of approximately 24 nucleotides (nt). We analyzed the sequence of the RNA fragments and predicted the RNA secondary structure of R-Ψ-sgRNA to determine the region recognized by the Dicer enzyme. The lengths of the R-Ψ-sgRNA fragments ranged from 48 to 140 nt, and were predicted to form double strands, including mismatches, in this region. An HIV-1 p24 assay indicated that the R-Ψ-sgRNA fragments suppressed HIV-1 replication. These findings suggest that R-Ψ-sgRNA acts as a miRNA to inhibit HIV-1.

MicroRNA: implications in HIV, a brief overview

MicroRNAs (miRNAs) are 20-22 nucleotide length noncoding RNA molecules that represent key regulators of many normal cellular functions. miRNAs undergo two processing steps which transform a long primary transcript into the mature miRNA. Available literatures demonstrate the association between alterations in the expression of miRNAs and the progression of numerous human disorders. Even though significant advances have been made, many fundamental questions about their expression and function still remain unanswered. Identifying factors that block the negative action of drugs of abuse on the miRNAs could help in identifying new therapeutic strategies. In this review, we briefly discuss the importance of miRNAs on HIV, strategies used by virus to avoid the cells' antiviral miRNA defenses, and how HIV might control and regulate host cell genes by encoding viral miRNAs.

Analysis of the roles of HIV-derived microRNAs

IMPORTANCE OF THE FIELD

HIV-1 is a retrovirus that has infected millions in recent decades. The level of life cycle complexity and host control exerted by this small virus with only nine proteins is astonishing. An interesting direction that has emerged in recent years is the role of small non-coding RNAs in viral gene expression.

AREAS COVERED IN THIS REVIEW

We focus on HIV-1 produced microRNAs (miRNAs), namely, TAR, Nef and miR-H1, and their roles in HIV-1 biogenesis. The article provides insights into TAR miRNA-mediated downregulation of viral and host gene expression by recruitment of chromatin remodeling components (HDAC1).

WHAT THE READER WILL GAIN

We address the influence of TAR miRNA on host cell cycle progression and apoptosis, and the role of Nef miRNA in the regulation of viral and host gene expression. The review also highlights an intriguing connection between miR-H1 and HIV-1-associated neurological pathogenesis, and the influence of the miRNA machinery in the establishment of latency. In the Expert Opinion section, we analyze the issue of host-based therapeutics against HIV-1 and how transcription inhibitors are influenced by viral miRNA production.

TAKE HOME MESSAGE

HIV-derived miRNAs are of significance not only to understand host-virus interactions, but also for the design of effective therapeutics.

HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses

DNAzymes are easier to prepare and less sensitive to chemical and enzymatic degradation than ribozymes; however, a DNA enzyme expression system has not yet been developed. In this study, we exploited the mechanism of HIV-1 reverse transcription (RT) in a DNA enzyme expression system. We constructed HIV-1 RT-dependent lentiviral DNAzyme expression vectors including the HIV-1 primer binding site, the DNA enzyme, and either a native tRNA (Lys-3), tR(M)DtR(L), or one of two truncated tRNAs (Lys-3), tR(M)DΔARMtR(L) or tR(M)D3'-endtR(L). Lentiviral vector-mediated DNAzyme expression showed high levels of inhibition of HIV-1 replication in SupT1 cells. We also demonstrated the usefulness of this approach in a long-term assay, in which we found that the DNAzymes prevented escape from inhibition of HIV. These results suggest that HIV-1 RT-dependent lentiviral vector-derived DNAzymes prevent the emergence of escape mutations.

Toward a durable anti-HIV gene therapy based on RNA interference

Basic research in the field of molecular biology led to the discovery of the mechanism of RNA interference (RNAi) in Caenorhabditis elegans in 1998. RNAi is now widely appreciated as an important gene control mechanism in mammals, and several RNAi-based gene-silencing applications have already been used in clinical trials. In this review I will discuss RNAi approaches to inhibit the pathogenic human immunodeficiency virus type 1 (HIV-1), which establishes a chronic infection that would most likely require a durable gene therapy approach. Viruses, such as HIV-1, are particularly difficult targets for RNAi attack because they mutate frequently, which allows viral escape by mutation of the RNAi target sequence. Combinatorial RNAi strategies are required to prevent viral escape.

Towards a durable RNAi gene therapy for HIV-AIDS

BACKGROUND

RNA interference (RNAi) can be employed as a potent antiviral mechanism.

OBJECTIVE

To discuss RNAi approaches to target pathogenic human viruses causing acute or chronic infections, in particular RNAi gene therapy against HIV-1.

METHODS

A review of relevant literature.

RESULTS/CONCLUSIONS

The future of antiviral RNAi therapeutics is very promising. RNAi was discovered only a decade ago, and although we are still in the early days, the first clinical trials are already ongoing.

Oncoviruses and Pathogenic MicroRNAs in Humans

For disease prognosis, the functional significance of the oncoviral integration locus in oncogenesis has remained enigmatic. The locus encodes several transcripts without protein products, but microRNAs (miRNAs) have recently been identified from a common oncoviral integration locus. miRNA is an endogenous, non-coding small RNA by which gene expression is suppressed. Although miRNA genes, such as let-7 in the nematode, have orthologs among animals, the relationship between miRNAs and tumorigenesis or tumor suppression has been mainly discovered in several human cancers. On the contrary, this review clearly demonstrates the potential for human tumorigenesis of both miRNA genes from oncoviral integration sites and other cellular onco-microRNA genes, and we conclude that alteration of the miRNA profile of cells can be defined as tumorigenic or tumor suppressive. Thus, we explain here that virally-pathogenic miRNAs could also be partly responsible for oncogenesis or oncogene suppression to confirm' the RNA wave', with the miRNAs hypothesized as a mobile and functional genetic element.

The inhibitory efficacy of RNA POL III-expressed long hairpin RNAs targeted to untranslated regions of the HIV-1 5' long terminal repeat

Human immunodeficiency virus type 1 (HIV-1) is a lentivirus that causes persistent infection resulting in the demise of immune regulatory cells, and ensuing diseases associated with acquired immune deficiency syndrome (AIDS). Although current therapeutic modalities have had a significant impact on mortality rates, novel therapies are constantly needed to prevent the emergence of resistant viral variants that escape the effects of antivirals. RNA Interference (RNAi) is a promising therapeutic modality for the inhibition of HIV-1 RNAs. Traditionally, RNAi effector sequences include expressed short hairpin RNAs (shRNAs) or short interfering RNAs (siRNAs). Recently, expressed long hairpin RNAs (lhRNAs) have been used with the aim of generating multiple independent siRNAs, which simultaneously target different susceptible sites on HIV-1. Here, modified lhRNAs expressed from U6 RNA Pol III promoters were targeted to sites within the first transcribed sequences of the HIV-1 5' long terminal repeat (LTR) region. Both Tat-dependent and independent suppressive efficacy was demonstrated against subtype B and C reporter sequences; however, lhRNAs complementary to the TAR stem-loop were refractory to silencing. None of the lhRNAs induced an unwanted interferon response as measured by interferon beta levels. Silencing by the lhRNAs was not equal across the extent of its cognate sequence, with the greatest efficacy observed for sequences located at the base of the stem. Nevertheless, direct antireplicative activity was seen when targeting lhRNAs to a subtype B HIV clone pNL4-3 Luc and a subtype C wild-type HIV-1 strain, FV5. These data highlight distinct target loci within the 5' LTR of HIV-1 that are susceptible to lhRNA targeting, and may prove to have an important advantage over other RNAi target sites within HIV-1. Although lhRNAs themselves require further manipulation to improve their overall efficacy in generating multiple functioning siRNAs, they may prove useful in any combinatorial-based approach to treating HIV-1 infection.

RNA interference and HIV-1 infection

Life-prolonging antiretroviral therapy remarkably reduces viral load, but it does not eradicate the virus. An important obstacle preventing virus clearance is the presence of latent virion reservoirs in the host. However, new promising antiviral approaches are emerging, and a number of host cell factors involved in the disease progression and control of HIV-1 replication have been recently discovered. For instance, the RNA interference (RNAi) mechanism, besides many functions conserved throughout evolution, works as a defence mechanism against noxious transcripts which may provide a new tool to block viral replication. The recent definition of basic RNAi mechanisms, as well as the discovery of micro RNAs (microRNAs) encoded by the host cell genome and by HIV-1, also suggest that RNAi may be involved in the control of HIV replication.

RNA interference and antiviral therapy

RNA interference (RNAi) is an evolutionally conserved gene silencing mechanism present in a variety of eukaryotic species. RNAi uses short double-stranded RNA (dsRNA) to trigger degradation or translation repression of homologous RNA targets in a sequence-specific manner. This system can be induced effectively in vitro and in vivo by direct application of small interfering RNAs (siRNAs), or by expression of short hairpin RNA (shRNA) with non-viral and viral vectors. To date, RNAi has been extensively used as a novel and effective tool for functional genomic studies, and has displayed great potential in treating human diseases, including human genetic and acquired disorders such as cancer and viral infections. In the present review, we focus on the recent development in the use of RNAi in the prevention and treatment of viral infections. The mechanisms, strategies, hurdles and prospects of employing RNAi in the pharmaceutical industry are also discussed.

Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome

Background

Human immunodeficiency virus type 1 (HIV-1) can be inhibited by means of RNA silencing or interference (RNAi) using synthetic short interfering RNAs (siRNAs) or gene constructs encoding short hairpin RNAs (shRNAs) or long hairpin RNAs (lhRNAs). The use of siRNA and shRNA as antiviral therapeutic is limited because of the emergence of viral escape mutants. This problem is theoretically prevented by intracellular expression of lhRNAs generating multiple siRNAs that target the virus simultaneously, thus reducing the chance of viral escape. However, gene constructs encoding lhRNA molecules face problems with delivery to the right cells in an infected individual. In order to solve this problem, we constructed an HIV-1 variant with a 300 bp long hairpin structure in the 3' part of the genome corresponding to the Nef gene (HIV-lhNef).

Results

Intriguingly, HIV-lhNef potently inhibited wild-type HIV-1 production in trans. However, HIV-lhNef demonstrated a severe production and replication defect, which we were able to solve by selecting spontaneous virus variants with truncated hairpin structures. Although these escape variants lost the ability to trans-inhibit HIV-1, they effectively outgrew the wild-type virus in competition experiments in SupT1 cells.

Conclusion

Expression of the lhNef hairpin within the HIV-1 genome results in potent trans-inhibition of wild-type HIV-1. Although the mechanism of trans-inhibition is currently unknown, it remains of interest to study the molecular details because the observed effect is extremely potent. This may have implications for the development of virus strains to be used as live-attenuated virus vaccines.

Suppression of HIV-1 replication by a combination of endonucleolytic ribozymes (RNase P and tRNnase ZL)

We examined the combinatorial action of RNase P and tRNase ZL-mediated specific inhibition of HIV-1 in cultured cells. We designed two short extra guide sequences (sEGS) that specifically recognize the tat and vifregions of HIV-1 mRNA and mediate the subsequent cleavage of hybridized mRNA by the RNase P and tRNase ZL components. We constructed an RNase P and tRNase ZL-associated vif and tat sEGS expression vector; which used the RNA-polymerase III dependent U6 promoter, as an expression cassette for EGS. Together, the RNase P and tRNase ZL-associated sEGS molecules allow more efficient suppression of HIV-1 mRNA production when separately applied. The possibilities offered by the vector to encode sEGS will provide a powerful tool for gene therapy.

Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA

Inhibition of virus replication by means of RNA interference has been reported for several important human pathogens, including human immunodeficiency virus type 1 (HIV-1). RNA interference against these pathogens has been accomplished by introduction of virus-specific synthetic small interfering RNAs (siRNAs) or DNA constructs encoding short-hairpin RNAs (shRNAs). Their use as therapeutic antiviral against HIV-1 is limited, because of the emergence of viral escape mutants. In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. Expression of lhRNAs in mammalian cells may result in the synthesis of many siRNAs targeting different viral sequences, thus providing more potent inhibition and reducing the chance of viral escape. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes.

RNA interference: its use as antiviral therapy

RNA interference (RNAi) is a sequence-specific gene-silencing mechanism that has been proposed to function as a defence mechanism of eukaryotic cells against viruses and transposons. RNAi was first observed in plants in the form of a mysterious immune response to viral pathogens. But RNAi is more than just a response to exogenous genetic material. Small RNAs termed microRNA (miRNA) regulate cellular gene expression programs to control diverse steps in cell development and physiology. The discovery that exogenously delivered short interfering RNA (siRNA) can trigger RNAi in mammalian cells has made it into a powerful technique for generating genetic knock-outs. It also raises the possibility to use RNAi technology as a therapeutic tool against pathogenic viruses. Indeed, inhibition of virus replication has been reported for several human pathogens including human immunodeficiency virus, the hepatitis B and C viruses and influenza virus. We reviewed the field of antiviral RNAi research in 2003 (Haasnoot et al. 2003), but many new studies have recently been published. In this review, we present a complete listing of all antiviral strategies published up to and including December 2004. The latest developments in the RNAi field and their antiviral application are described.

Gene silencing of virus replication by RNA interference

Small interfering RNAs (siRNAs) are as effective as long double-stranded RNAs (dsRNAs) at targeting and silencing genes by RNA interference (RNAi). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. They are also promising reagents for developing gene-specific therapeutics. The specific inhibition of viral replication is particularly well suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on the recent advances in siRNA-based clinical trials.

Specific inhibition of HIV-1 replication by short hairpin RNAs targeting human cyclin T1 without inducing apoptosis

RNA interference (RNAi), a sequence-specific RNA degradation mechanism mediated by small interfering RNA (siRNA), can be used not only as a research tool but also as a therapeutic strategy for viral infection. We demonstrated that intracellular expression of short hairpin RNA (shRNA) targeting human cyclin T1 (hCycT1), a cellular factor essential for transcription of messenger and genomic RNAs from the long terminal repeat promoter of provirus of human immunodeficiency virus type 1 (HIV-1), could effectively suppress the replication of HIV-1. We also showed that downregulation of hCycT1 did not cause apoptotic cell death, therefore, targeting cellular factor hCycT1 by shRNAs may provide an attractive approach for genetic therapy of HIV-1 infection in the future.

Rnai as an experimental and therapeutic tool to study and regulate physiological and disease processes

Over the past four years RNA interference (RNAi) has exploded onto the research scene as a new approach to manipulate gene expression in mammalian systems. More recently, RNAi has garnered much interest as a potential therapeutic strategy. In this review, we briefly summarize the current understanding of RNAi biology and examine how RNAi has been used to study the genetic basis of physiological and disease processes in mammalian systems. We also explore some of the new developments in the use of RNAi for disease therapy and highlight the key challenges that currently limit its application in the laboratory, as well as in the clinical setting.

Regulation of human immunodeficiency virus 1 transcription by nef microRNA

MicroRNAs (miRNAs) are approximately 21-25 nt long and interact with mRNAs to lead to either translational repression or RNA cleavage through RNA interference. A previous study showed that human immunodeficiency virus 1 (HIV-1) nef dsRNA from AIDS patients who are long-term non-progressors inhibited HIV-1 transcription. In the study reported here, nef-derived miRNAs in HIV-1-infected and nef transduced cells were identified, and showed that HIV-1 transcription was suppressed by nef-expressing miRNA, miR-N367, in human T cells. The miR-N367 could reduce HIV-1 LTR promoter activity through the negative responsive element of the U3 region in the 5'-LTR. Therefore, nef miRNA produced in HIV-1-infected cells may downregulate HIV-1 transcription through both a post-transcriptional pathway and a transcriptional neo-pathway.

HIV-1 nef suppression by virally encoded microRNA

BACKGROUND

MicroRNAs (miRNAs) are 21 to approximately 25-nucleotides (nt) long and interact with mRNAs to trigger either translational repression or RNA cleavage through RNA interference (RNAi), depending on the degree of complementarity with the target mRNAs. Our recent study has shown that HIV-1 nef dsRNA from AIDS patients who are long-term non-progressors (LTNPs) inhibited the transcription of HIV-1.

RESULTS

Here, we show the possibility that nef-derived miRNAs are produced in HIV-1 persistently infected cells. Furthermore, nef short hairpin RNA (shRNA) that corresponded to a predicted nef miRNA (approximately 25 nt, miR-N367) can block HIV-1 Nef expression in vitro and the suppression by shRNA/miR-N367 would be related with low viremia in an LTNP (15-2-2). In the 15-2-2 model mice, the weight loss, which may be rendered by nef was also inhibited by shRNA/miR-N367 corresponding to suppression of nef expression in vivo.

CONCLUSIONS

These data suggest that nef/U3 miRNAs produced in HIV-1-infected cells may suppress both Nef function and HIV-1 virulence through the RNAi pathway.

Efficient gene transfer of HIV-1-specific short hairpin RNA into human lymphocytic cells using recombinant adeno-associated virus vectors

The cellular introduction of short, interfering RNA leads to sequence-specific degradation of homologous mRNA, a process termed RNA interference (RNAi). Here, we report that recombinant adeno-associated virus 2 (rAAV-2) can be used to transfer short hairpin (sh) RNA expression cassettes genetically into human cells. HIV-1 replication was suppressed by >95% in H9 cells and primary human lymphocytes that expressed shRNA targeting the first exon of the viral transactivator protein tat compared to control cells. rAAV-2 integrated stably into the host genome, leading to long-term expression of tat shRNA. Our findings demonstrate the utility of rAAV-2 for the genetic transfer of shRNA expression cassettes into human cells, providing an alternative to using retroviral vectors as RNAi delivery systems.

Feline foamy virus Tas protein is a DNA-binding transactivator

Foamy viruses (FVs) harbour a transcriptional transactivator (Tas) and two Tas-responsive promoter regions, one in the 5′ long terminal repeat (LTR) and the other an internal promoter (IP) in the envelope gene. To analyse the mechanism of transactivation of the FVs, the specificity of feline FV (FFV) Tas protein, which is more distantly related to the respective proteins of non-human primate origin, were investigated. FFV Tas has been shown specifically to activate gene expression from the cognate promoters. No cross-transactivation was noted of the prototype foamy virus and human immunodeficiency virus type 1 LTR. The putative transactivation response element of FFV Tas was mapped to the 5′ LTR U3 region (approximately nt −228 to −195). FFV Tas binds to this element in addition to a previously described sequence (position −66 to −51). It is therefore concluded that FFV Tas is a DNA-binding transactivator that interacts with at least two regions in the virus LTR.

Effects of length and location on the cellular response to double-stranded RNA

Since double-stranded RNA (dsRNA) has not until recently generally been thought to be deliberately expressed in cells, it has commonly been assumed that the major source of cellular dsRNA is viral infections. In this view, the cellular responses to dsRNA would be natural and perhaps ancient antiviral responses. While the cell may certainly react to some dsRNAs as an antiviral response, this does not represent the only response or even, perhaps, the major one. A number of recent observations have pointed to the possibility that dsRNA molecules are not seen only as evidence of viral infection or recognized for degradation because they cannot be translated. In some instances they may also play important roles in normal cell growth and function. The purpose of this review is to outline our current understanding of the fate of dsRNA in cells, with a focus on the apparent fact that their fates and functions appear to depend critically not only on where in the cell dsRNA molecules are found, but also on how long they are and perhaps on how abundant they are.

RNA interference as a new strategy against viral hepatitis

Hepatitis viruses are the leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. Since currently available treatment options against these viruses are limited, there is a need for development of alternative therapies. In this minireview, we concentrate on three hepatitis viruses--hepatitis C virus, hepatitis B virus, and hepatitis delta virus and discuss how RNA interference (RNAi) has been utilized against them. RNAi is a process by which small double-stranded RNA can effectively target a homologous RNA sequence for degradation by cellular ribonucleases. Though RNAi was exploited in the beginning for down-regulating cellular genes, it has recently been demonstrated that this process is equally effective against many types of human and animal viruses including the hepatitis viruses. Both synthetic small-interfering RNAs (siRNAs) and plasmid-based siRNA expression systems have been useful in suppressing the hepatitis viruses. Though this new approach looks promising, problems of nonspecific effects and delivery may need to be addressed before the full therapeutic potential of RNAi against viral infections in patients is realized.

HIV-1 Nef protein in the nucleus influences adipogenesis as well as viral transcription through the peroxisome proliferator-activated receptors

BACKGROUND

Although the HIV-1 Nef protein (27 kDa) localizes primarily in cytoplasm, there is considerable evidence suggesting its occasional localization in the nucleus. Nef is known to play an important role in transcriptional events and viral replication, but the actual target of Nef in the nucleus remains to be identified.

OBJECTIVE

To examine the functional roles of Nef in the nucleus and its possible interactions with other unknown factors in the nucleus.

METHODS

High-density microarray analysis was used to screen directly the unique functions of Nef on host gene transcription. The nuclear localization of Nef and its effects on the expression of peroxisome proliferator-activated receptors (PPAR) was examined using PPAR promoter/reporter assay and immunoblotting. A long terminal repeat/reporter assay was used to investigated the effects of Nef and PPAR on viral transcription.

RESULTS

Nef in the nucleus suppressed PPAR gamma expression and reduced fatty acid levels in human T and macrophage cell lines. Expression of Nef or PPAR suppressed viral replication; the effect of PPAR gamma or retinoid X receptor-alpha on viral replication were reduced by coexpression of Nef in MT(-)4 T cells.

CONCLUSION

Nef may be involved in both viral replication and the wasting syndrome associated with AIDS.

Human immunodeficiency virus type 1 escape from RNA interference

Sequence-specific degradation of mRNA by short interfering RNA (siRNA) allows the selective inhibition of viral proteins that are critical for human immunodeficiency virus type 1 (HIV-1) replication. The aim of this study was to characterize the potency and durability of virus-specific RNA interference (RNAi) in cell lines that stably express short hairpin RNA (shRNA) targeting the HIV-1 transactivator protein gene tat. We found that the antiviral activity of tat shRNA was abolished due to the emergence of viral quasispecies harboring a point mutation in the shRNA target region. Our results suggest that, in order for RNAi to durably suppress HIV-1 replication, it may be necessary to target highly conserved regions of the viral genome. Alternatively, similar to present antiviral drug therapy paradigms, DNA constructs expressing multiple siRNAs need to be developed that target different regions of the viral genome, thereby reducing the probability of generating escape mutants.

RNA interference: Antiviral weapon and beyond

RNA interference (RNAi) is a remarkable type of gene regulation based on sequence-specific targeting and degradation of RNA. The term encompasses related pathways found in a broad range of eukaryotic organisms, including fungi, plants, and animals. RNA interference is part of a sophisticated network of interconnected pathways for cellular defense, RNA surveillance, and development and it may become a powerful tool to manipulate gene expression experimentally. RNAi technology is currently being evaluated not only as an extremely powerful instrument for functional genomic analyses, but also as a potentially useful method to develop specific dsRNA based gene-silencing therapeutics. Several laboratories have been interested in using RNAi to control viral infection and many reports in Nature and in Cell show that short interfering (si) RNAs can inhibit infection by HIV-1, polio and hepatitis C viruses in a sequence-specific manner. RNA-based strategies for gene inhibition in mammalian cells have recently been described, which offer the promise of antiviral therapy.

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Inhibition of HIV-1 infection by lentiviral vectors expressing Pol III-promoted anti-HIV RNAs

A primary advantage of lentiviral vectors is their ability to pass through the nuclear envelope into the cell nucleus thereby allowing transduction of nondividing cells. Using HIV-based lentiviral vectors, we delivered an anti-CCR5 ribozyme (CCR5RZ), a nucleolar localizing TAR RNA decoy, or Pol III-expressed siRNA genes into cultured and primary cells. The CCR5RZ is driven by the adenoviral VA1 Pol III promoter, while the human U6 snRNA Pol III-transcribed TAR decoy is embedded in a U16 snoRNA (designated U16TAR), and the siRNAs were expressed from the human U6 Pol III promoter. The transduction efficiencies of these vectors ranged from 96-98% in 293 cells to 15-20% in primary PBMCs. A combination of the CCR5RZ and U16TAR decoy in a single vector backbone gave enhanced protection against HIV-1 challenge in a selective survival assay in both primary T cells and CD34(+)-derived monocytes. The lentiviral vector backbone-expressed siRNAs also showed potent inhibition of p24 expression in PBMCs challenged with HIV-1. Overall our results demonstrate that the lentiviral-based vectors can efficiently deliver single constructs as well as combinations of Pol III therapeutic expression units into primary hematopoietic cells for anti-HIV gene therapy and hold promise for stem or T-cell-based gene therapy for HIV-1 infection.

RNA interference: potentials for the prevention of HIV infections and the challenges ahead

Presently, Phase III efficacy trials with subunit immune antigens against the human immunodeficiency virus (HIV) infection are occurring in both the USA and some Southeast Asian countries. However, there is no feeling of dèja vu within the scientific community that these studies will demonstrate meaningful protection against HIV infection, perhaps because the immune responses crucial for containment of the virus might not be elicited by this approach. Under this prevailing gloomy setting for international acquired immune deficiency syndrome (AIDS) therapy, RNA interference has been identified as a likely strategy in the understanding that inhibition of HIV replication can be mediated by post-transcriptional gene silencing through the production of double-stranded RNA (dsRNA) nucleotide intermediates. This review briefly explores the role of the nef gene during HIV-1 infection and highlights the expectation that RNA interference might serve as a new sequence-specific therapeutic arsenal in AIDS prevention, and possibly treatment, in the years ahead.

Repression of allo-cell transplant rejection through CIITA ribonuclease P+ hepatocyte

AIM: Allo-cell transplant rejection and autoimmune responses were associated with the presence of class II major histocompatibility complex (MHC II) molecules on cells. This paper studied the effect of Ribonuclease P (RNase P) against CIITA, which was a major regulator of MHCII molecules, on repressing the expression of MHCII molecules on hepatocyte.

METHODS: M1-RNA is the catalytic RNA subunit of RNase P from Escherichia coli. It were constructed that M1-RNA with guide sequences (GS) recognizing the 452, 3408 site of CIITA by PCR from pTK117 plasmid, then were cloned into the EcoR I/Bgl II or EcoR I/Sal I site of vector psNAV (psNAV-M1-452-GS, psNAV-M1-3408-GS) respectively. The target mould plate (3176-3560) of CIITA was obtained from Raji cell by RT-PCR, and then inserted into the Xho I/EcoR I of pGEM-7zf(+) plasmid (pGEM-3176). These recombinant plasmids were screened out by sequence analysis. psNAV-M1-452-GS, psNAV-M1-3408-GS and its target RNA pGEM-3176 were transcribed and then mixed up and incubated in vitro. It showed that M1-3408-GS could exclusively cleave target RNA that formed a base pair with the GS. Stable transfectants of hepatocyte cell line with psNAV-M1-3408-GS were tested for expression of class II MHC through FCM, for mRNA abundance of MHCII, Ii and CIITA by RT-PCR, for the level of IL-2 mRNA on T cell by mixed lymphocyte reaction.

RESULTS: When induced with recombinant human interferon-gamma (IFN-γ), the expression of HLA-DR, -DP, -DQ on psNAV-M1-3408-GS⁺ hepatocyte was reduced 83.27%, 88.93%, 58.82% respectively, the mRNA contents of CIITA, HLA-DR, -DP, -DQ and Ii decreased significantly. While T cell expressed less IL-2 mRNA in the case of psNAV-M1-3408-GS⁺ hepatocyte.

CONCLUSION: The Ribonuclease P against CIITA-M1-3408-GS could effectively induce antigen-specific tolerance through cleaving CIITA. These results provided insight into the future application of M1-3408-GS as a new nucleic acid drug against allo-transplantation rejection and autoimmune diseases.