Haitang Li

Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells

RNA interference (RNAi) is the process of sequence-specific, posttranscriptional gene silencing in animals and plants initiated by double-stranded (ds) RNA that is homologous to the silenced gene. This technology has usually involved injection or transfection of dsRNA in model nonvertebrate organisms. The longer dsRNAs are processed into short (19–25 nucleotides) small interfering RNAs (siRNAs) by a ribonucleotide–protein complex that includes an RNAse III–related nuclease (Dicer), a helicase family member, and possibly a kinase and an RNA-dependent RNA polymerase (RdRP). In mammalian cells it is known that dsRNA 30 base pairs or longer can trigger interferon responses that are intrinsically sequence-nonspecific, thus limiting the application of RNAi as an experimental and therapeutic agent. Duplexes of 21-nucleotide siRNAs with short 3′ overhangs, however, can mediate RNAi in a sequence-specific manner in cultured mammalian cells. One limitation in the use of siRNA as a therapeutic reagent in vertebrate cells is that short, highly defined RNAs need to be delivered to target cells—a feat thus far only accomplished by the use of synthetic, duplex RNAs delivered exogenously to cells. In this report, we describe a mammalian Pol III promoter system capable of expressing functional double-stranded siRNAs following transfection into human cells. In the case of the 293 cells cotransfected with the HIV-1 pNL4-3 proviral DNA and the siRNA-producing constructs, we were able to achieve up to 4 logs of inhibition of expression from the HIV-1 DNA.

RNA-Based Gene Therapy for HIV with Lentiviral Vector–Modified CD34+ Cells in Patients Undergoing Transplantation for AIDS-Related Lymphoma

Transfected stem cells transplanted into patients with HIV infection resulted in sustained RNA expression of introduced genes in blood cells for up to 2 years. Steps Toward a Stable Source of Therapeutic RNA Gene therapy in humans has not been easy to implement. Genes inserted into complex human cells have triggered serious unintended consequences and have often proven to be short-lived. Yet perseverance may be paying off. DiGiusto et al. report a step toward workable gene therapy in the form of stable expression of a lentiviral vector encoding anti-HIV RNAs in blood stem cells transplanted into AIDS patients. None of these patients is cured, but the vector seems to stably express the potentially therapeutic RNAs. Putting exogenous gene sequences into humans is risky, and review boards are appropriately conservative. But DiGiusto et al. took advantage of a clinical situation to design a trial that minimized extra risk to the subjects. Blood cancer (lymphoma) is common in AIDS patients, and they are often treated by ablation of their diseased bone marrow with chemotherapy followed by a transplant with their own previously saved blood stem cells. Because these patients were being transplanted with their own blood cells anyway, the authors were able to get permission to transfect a few of the blood cells of four patients with a vector carrying anti-HIV entities and reinfuse them along with the normally transplanted cells. The vector made RNAs that could counteract viral replication in several ways: inhibition of viral entry (with a CCR5 ribozyme), inhibition of RNA transport [by a small interfering RNA (siRNA) to tat/rev], and inhibition of viral transcription initiation with a decoy RNA. The good news was that the patients showed no signs of toxicity besides problems usually associated with transplantation and that blood cells from all four patients contained signs of the transplanted genes, with the amounts increasing in two of the patients after 18 months. Although the fraction of cells containing the genes was <0.2%, this was not too different from the fraction of transfected cells that was infused into the patients. The three anti-HIV RNAs could also be detected as long as 1 year after the initial infusion, and examination of T cells, monocytes, and B cells from one patient confirmed the presence of vector in these three cell types. These cells that survived for long periods of time in patients, although too scarce to cure or even improve their HIV infections, nevertheless offer lessons for future applications of gene therapy. We know that this procedure is seemingly safe and that cells given new genetic material via a lentiviral vector outside the patient can survive once reimplanted. Continued perseverance can only bring us closer to realizing the potential of this promising therapy. AIDS patients who develop lymphoma are often treated with transplanted hematopoietic progenitor cells. As a first step in developing a hematopoietic cell–based gene therapy treatment, four patients undergoing treatment with these transplanted cells were also given gene-modified peripheral blood–derived (CD34+) hematopoietic progenitor cells expressing three RNA-based anti-HIV moieties (tat/rev short hairpin RNA, TAR decoy, and CCR5 ribozyme). In vitro analysis of these gene-modified cells showed no differences in their hematopoietic potential compared with nontransduced cells. In vitro estimates of successful expression of the anti-HIV moieties were initially as high as 22% but declined to ~1% over 4 weeks of culture. Ethical study design required that patients be transplanted with both gene-modified and unmanipulated hematopoietic progenitor cells obtained from the patient by apheresis. Transfected cells were successfully engrafted in all four infused patients by day 11, and there were no unexpected infusion-related toxicities. Persistent vector expression in multiple cell lineages was observed at low levels for up to 24 months, as was expression of the introduced small interfering RNA and ribozyme. Therefore, we have demonstrated stable vector expression in human blood cells after transplantation of autologous gene-modified hematopoietic progenitor cells. These results support the development of an RNA-based cell therapy platform for HIV.

Novel Dual Inhibitory Function Aptamer–siRNA Delivery System for HIV-1 Therapy

The successful use of small interfering RNAs (siRNAs) for therapeutic purposes requires safe and efficient delivery to specific cells and tissues. In this study, we demonstrate cell type-specific delivery of anti-human immunodeficiency virus (anti-HIV) siRNAs through fusion to an anti-gp120 aptamer. The envelope glycoprotein is expressed on the surface of HIV-1-infected cells, allowing binding and internalization of the aptamer-siRNA chimeric molecules. We demonstrate that the anti-gp120 aptamer-siRNA chimera is specifically taken up by cells expressing HIV-1 gp120, and that the appended siRNA is processed by Dicer; this releases an anti-tat/rev siRNA which, in turn, inhibits HIV replication. We show for the first time a dual functioning aptamer-siRNA chimera in which both the aptamer and the siRNA portions have potent anti-HIV activities. We also show that gp120 expressed on the surface of HIV-infected cells can be used for aptamer-mediated delivery of anti-HIV siRNAs.

SNPs in human miRNA genes affect biogenesis and function

MicroRNAs (miRNAs) are 21-25-nucleotide-long, noncoding RNAs that are involved in translational regulation. Most miRNAs derive from a two-step sequential processing: the generation of pre-miRNA from pri-miRNA by the Drosha/DGCR8 complex in the nucleus, and the generation of mature miRNAs from pre-miRNAs by the Dicer/TRBP complex in the cytoplasm. Sequence variation around the processing sites, and sequence variations in the mature miRNA, especially the seed sequence, may have profound affects on miRNA biogenesis and function. In the context of analyzing the roles of miRNAs in Schizophrenia and Autism, we defined at least 24 human X-linked miRNA variants. Functional assays were developed and performed on these variants. In this study we investigate the affects of single nucleotide polymorphisms (SNPs) on the generation of mature miRNAs and their function, and report that naturally occurring SNPs can impair or enhance miRNA processing as well as alter the sites of processing. Since miRNAs are small functional units, single base changes in both the precursor elements as well as the mature miRNA sequence may drive the evolution of new microRNAs by altering their biological function. Finally, the miRNAs examined in this study are X-linked, suggesting that the mutant alleles could be determinants in the etiology of diseases.

Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC

Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a combinatorial approach. We show that both synthetic siRNAs and expressed shRNAs compete against each other and with the endogenous microRNAs for transport and for incorporation into the RNA induced silencing complex (RISC). The same siRNA sequences do not display competition when expressed from a microRNA backbone. We also show that TAR RNA binding protein (TRBP) is one of the sensors for selection and incorporation of the guide sequence of interfering RNAs. These findings reveal that combinatorial siRNA approaches can be problematic and have important implications for the methodology of expression and use of therapeutic interfering RNAs.

Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells

The envelope glycoprotein of human immunodeficiency virus (HIV) consists of an exterior glycoprotein (gp120) and a trans-membrane domain (gp41) and has an important role in viral entry into cells. HIV-1 entry has been validated as a clinically relevant anti-viral strategy for drug discovery. In the present work, several 2′-F substituted RNA aptamers that bind to the HIV-1BaL gp120 protein with nanomole affinity were isolated from a RNA library by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure. From two of these aptamers we created a series of new dual inhibitory function anti-gp120 aptamer–siRNA chimeras. The aptamers and aptamer–siRNA chimeras specifically bind to and are internalized into cells expressing HIV gp160. The Dicer-substrate siRNA delivered by the aptamers is functionally processed by Dicer, resulting in specific inhibition of HIV-1 replication and infectivity in cultured CEM T-cells and primary blood mononuclear cells (PBMCs). Moreover, we have introduced a ‘sticky’ sequence onto a chemically synthesized aptamer which facilitates attachment of the Dicer substrate siRNAs for potential multiplexing. Our results provide a set of novel inhibitory agents for blocking HIV replication and further validate the use of aptamers for delivery of Dicer substrate siRNAs.

An Aptamer-siRNA Chimera Suppresses HIV-1 Viral Loads and Protects from Helper CD4+ T Cell Decline in Humanized Mice

A dual-function aptamer that targets both a HIV-1 surface protein and a critical messenger RNA can inhibit HIV infection in humanized mice. A Small but Deadly Therapy for HIV Simultaneously precise and fragile, small interfering RNAs (siRNAs) have not as yet shown much success as therapeutic agents, despite their high specificity for selected targets. When injected into an organism, siRNAs tend to be destroyed in the blood, sometimes provoking the body’s own innate immune defenses against this foreign object. But there are ways around these problems, and Neff et al. have developed one by harnessing an RNA aptamer in the pursuit of a successful approach to vanquishing the HIV. Their aptamer, artificially evolved to bind tightly to the gp120 molecule on the surface of HIV, interrupts cell infection by the virus by itself. But by attaching an inhibitory siRNA directed against the essential tat/rev gene to one end of the aptamer, the authors enhanced its deadliness. HIV-infected mice treated with this chimeric agent showed reduced viral loads and improved CD4+ T cell status, indicating that such an approach may be beneficial to HIV-infected patients. Mice do not generally become infected with HIV, and so they have not been as informative as nonhuman primates in the fight against AIDS. But the authors Neff et al. got around this problem using an improved version of the BALB/c mouse, in which the animals have been engrafted with human hematopoietic stem cells and so carry a human instead of a mouse immune system. When infected with HIV, these animals showed viremia and CD4+ T cell loss, mimicking key aspects of AIDS. Treatment with the chimeric aptamer-siRNA against gp120 and tat/rev decreased HIV concentrations in the blood, with many mice showing a sharp drop, and restored the CD4+ T cell level—a measure of immune function that decreases in HIV-infected patients. siRNA was detected in the immune cells of the mice, showing that the chimera delivered its cargo to the intended target, and the amounts of tat-rev RNA were markedly reduced in these same cells, showing that the siRNA was doing its job to thwart viral gene expression. The dual-function aptamer avoided another problem often found with therapeutic RNAs: No interferon responses were generated, indicating that the chimera was not causing an immune reaction. These results are good news for two reasons: They show that the inhibition of two key molecules crucial for the HIV life cycle can in turn inhibit viral spread, pointing to an alternative therapy for this still burdensome infection. They also lay out a general approach for delivering siRNAs to particular target cells, shown here to be useful for HIV but potentially applicable to other diseases that require exact delivery of a deadly agent to a tiny target. Therapeutic strategies designed to treat HIV infection with combinations of antiviral drugs have proven to be the best approach for slowing the progression to AIDS. Despite this progress, there are problems with viral drug resistance and toxicity, necessitating new approaches to combating HIV-1 infection. We have therefore developed a different combination approach for the treatment of HIV infection in which an RNA aptamer, with high binding affinity to the HIV-1 envelope (gp120) protein and virus neutralization properties, is attached to and delivers a small interfering RNA (siRNA) that triggers sequence-specific degradation of HIV RNAs. We have tested the antiviral activities of these chimeric RNAs in a humanized Rag2−/−γc−/− (RAG-hu) mouse model with multilineage human hematopoiesis. In this animal model, HIV-1 replication and CD4+ T cell depletion mimic the situation seen in human HIV-infected patients. Our results show that treatment with either the anti-gp120 aptamer or the aptamer-siRNA chimera suppressed HIV-1 replication by several orders of magnitude and prevented the viral-induced helper CD4+ T cell decline. In comparison to the aptamer alone, the aptamer-siRNA combination provided more extensive inhibition, resulting in a significantly longer antiviral effect that extended several weeks beyond the last injected dose. The aptamer thus acts as a broad-spectrum HIV-neutralizing agent and an siRNA delivery vehicle. The combined aptamer-siRNA agent provides an attractive, nontoxic therapeutic approach for treatment of HIV infection.

Functional siRNA expression from transfected PCR products.

RNA interference (RNAi) is a process in which double-stranded RNA (dsRNA) induces the postranscriptional degradation of homologous transcripts. RNAi can be initiated by exposing cells to dsRNA either via transfection or endogenous expression. In mammalian systems, the sequence-specific RNAi effect has been observed by expression of 21-23 base transcripts capable of forming duplexes, or via expression of short hairpin RNAs. We describe here a facile PCR based strategy for rapid synthesis of siRNA expression units and their testing in mammalian cells. The siRNA expression constructs are constructed by PCR, and the PCR products are directly transfected into mammalian cells resulting in functional expression of siRNAs. This approach should prove useful for identification of optimal siRNA-target combinations and for multiplexing siRNA expression in mammalian cells.

Stable expression of shRNAs in human CD34 + progenitor cells can avoid induction of interferon responses to siRNAs in vitro

RNA interference occurs when cytoplasmic small interfering RNAs (siRNAs) enter the RNA-induced silencing complex and one strand guides cleavage of the target RNA by the Argonaute 2 protein. A significant concern when applying siRNAs or expressing small hairpin RNAs (shRNAs) in human cells is activation of the interferon (IFN) response. Synthetic siRNAs harboring certain motifs can induce an immune response when delivered to mouse and human immune cells such as peripheral blood mononuclear cells, monocytes, plasmacytoid dendritic cells (pDCs) and nonplasmacytoid dendritic cells (mDCs). In the present study we have tested the immunostimulatory effects of lipid-delivered siRNAs versus Pol III promoter–expressed shRNAs in primary CD34+ progenitor–derived hematopoietic cells. We show that in this system, lipid-delivered siRNAs are potent inducers of IFNα and type I IFN gene expression, whereas the same sequences when expressed endogenously are nonimmunostimulatory.

Systemic Administration of Combinatorial dsiRNAs via Nanoparticles Efficiently Suppresses HIV-1 Infection in Humanized Mice

We evaluated the in vivo efficacy of structurally flexible, cationic PAMAM dendrimers as a small interfering RNA (siRNA) delivery system in a Rag2(-)/-γc-/- (RAG-hu) humanized mouse model for HIV-1 infection. HIV-infected humanized Rag2-/-γc-/- mice (RAG-hu) were injected intravenously (i.v.) with dendrimer-siRNA nanoparticles consisting of a cocktail of dicer substrate siRNAs (dsiRNAs) targeting both viral and cellular transcripts. We report in this study that the dendrimer-dsiRNA treatment suppressed HIV-1 infection by several orders of magnitude and protected against viral induced CD4(+) T-cell depletion. We also demonstrated that follow-up injections of the dendrimer-cocktailed dsiRNAs following viral rebound resulted in complete inhibition of HIV-1 titers. Biodistribution studies demonstrate that the dendrimer-dsiRNAs preferentially accumulate in peripheral blood mononuclear cells (PBMCs) and liver and do not exhibit any discernable toxicity. These data demonstrate for the first time efficacious combinatorial delivery of anti-host and -viral siRNAs for HIV-1 treatment in vivo. The dendrimer delivery approach therefore represents a promising method for systemic delivery of combinations of siRNAs for treatment of HIV-1 infection.