Ming-Jie 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.

Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34+ progenitor cell-derived macrophages

The phenomenon of RNA interference mediated by small interfering RNAs (siRNAs) is a potent gene-silencing mechanism. A number of recent studies demonstrated inhibition of HIV-1 replication in cultured cells using this approach. To make further progress and harness this technology for HIV-1 gene therapy in a stem cell setting, in vivo studies using primary hematopoietic cells are needed. Using an HIV-based lentiviral vector we introduced an anti-Rev siRNA construct into CD34(+) hematopoietic progenitor cells. The siRNA-transduced progenitor cells were allowed to mature into macrophages in vitro and T cells in vivo in SCID-hu mouse thy/liv grafts. Phenotypically normal T cells and macrophages displaying characteristic surface markers were obtained. In vitro HIV-1 challenge of the siRNA-expressing macrophages and T cells with macrophage-tropic and T-cell-tropic HIV-1, respectively, showed marked viral resistance. These experiments demonstrate the utility of siRNAs delivered into hematopoietic stem cells via lentiviral vectors for future in vivo applications.

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.

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.

Safety and Efficacy of a Lentiviral Vector Containing Three Anti-HIV Genes—CCR5 Ribozyme, Tat-rev siRNA, and TAR Decoy—in SCID-hu Mouse–Derived T Cells

Gene therapeutic strategies show promise in controlling human immunodeficiency virus (HIV) infection and in restoring immunological function. A number of efficacious anti-HIV gene constructs have been described so far, including small interfering RNAs (siRNAs), RNA decoys, transdominant proteins, and ribozymes, each with a different mode of action. However, as HIV is prone to generating escape mutants, the use of a single anti-HIV construct would not be adequate to afford long range-viral protection. On this basis, a combination of highly potent anti-HIV genes-namely, a short hairpin siRNA (shRNA) targeting rev and tat, a transactivation response (TAR) decoy, and a CCR5 ribozyme-have been inserted into a third-generation lentiviral vector. Our recent in vitro studies with this construct, Triple-R, established its efficacy in both T-cell lines and CD34 cell-derived macrophages. In this study, we have evaluated this combinatorial vector in vivo. Vector-transduced CD34 cells were injected into severe combined immunodeficiency (SCID)-hu mouse thy/liv grafts to determine their capacity to give rise to T cells. Our results show that phenotypically normal transgenic T cells are generated that are able to resist HIV-1 infection when challenged in vitro. These important attributes of this combinatorial vector show its promise as an excellent candidate for use in human clinical trials.

Negative feedback inhibition of HIV-1 by TAT-inducible expression of siRNA

Here we demonstrate that an inducible anti-HIV short hairpin RNA (shRNA) expressed from a Pol II promoter inhibits HIV-1 gene expression in mammalian cells. Our strategy is based on a promoter system in which the HIV-1 LTR is fused to the Drosophila hsp70 minimal heat shock promoter. This system is inducible by HIV-1 TAT, which functions in a negative feedback loop to activate transcription of an shRNA directed against HIV-1 rev. Upon induction the shRNA is processed to an siRNA that guides inhibition of HIV replication in cultured T-lymphocytes and hematopoietic stem cell–derived monocytes. The fusion promoter system may be safer than drug-inducible systems for shRNA-mediated gene therapy against HIV as the shRNAs are only expressed following HIV infection.

Localization and dynamic relocalization of mammalian Rad52 during the cell cycle and in response to DNA damage

The importance of RAD52 in establishment and maintenance of genomic structure has been established by genetic experiments in the yeast Saccharomyces cerevisiae, where mutation of RAD52 has been shown to diminish DNA repair and recombination of a variety of markers, including the rDNA [1] [2] [3]. Biochemical analysis has shown that yeast and mammalian Rad52 proteins have some identical functions in vitro [4] [5] [6], but targeted deletion of Rad52 in vertebrates has little effect on repair and recombination [7] [8]. These results raise the question of whether mammalian Rad52 does indeed function in recombination and/or repair. Here we show that Rad52 is distributed throughout the nucleoplasm in actively cycling mammalian cells and is localized specifically to the nucleoli in S phase. In response to ionizing radiation, Rad52 relocalizes to form distinctive foci which are distributed throughout the nucleus and which colocalize with Rad50 foci in the DNA damage response. These data suggest that rDNA recombination and DNA repair are functions shared by mammalian Rad52 and its S. cerevisiae homolog, and provide evidence for the coordinated action of Rad50 and Rad52 in DNA repair.

Novel Pol II Fusion Promoter Directs Human Immunodeficiency Virus Type 1-Inducible Coexpression of a Short Hairpin RNA and Protein

ABSTRACT We demonstrate a novel approach for coexpression of a short hairpin RNA (shRNA) with an open reading frame which exploits transcriptional read-through of a minimal polyadenylation signal from a Pol II promoter. We first observed efficient inducible expression of enhanced green fluorescent protein along with an anti-rev shRNA. We took advantage of this observation to test coexpression of the transdominant negative mutant (humanized) of human immunodeficiency type 1 (HIV-1) Rev (huRevM10) along with an anti-rev shRNA via an HIV-1-inducible fusion promoter. The coexpression of the shRNA and transdominant protein resulted in potent, long-term inhibition of HIV-1 gene expression and suppression of shRNA-resistant mutants. This dual expression system has broad-based potential for other shRNA applications, such as cases where simultaneous knockdown of mutant and wild-type transcripts must be accompanied by replacement of the wild-type protein.

Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells.

Abstract Lentiviral vectors are able to transduce non-dividing cells and maintain sustained long-term expression of the transgenes. Many cell types including brain, liver, muscle, and hematopoietic stem cells have been successfully transduced with lentiviral vectors carrying a variety of genes. These properties make lentiviral vectors attractive vehicles for delivering small interfering RNA (siRNA) genes into mammalian cells. RNA polymerase III (Pol III) promoters are most commonly used for expressing siRNAs from lentiviral vectors. Pol III promoters are relatively small, have high activity, and use simple termination signals of short stretches of U. It is possible to include several Pol III expression cassettes in a single lentiviral vector backbone to express different siRNAs or to combine siRNAs with other transgenes. This chapter describes the delivery of Pol III promoted siRNAs by HIV-based lentiviral vectors and covers vector design, production, and verification of siRNA expression and function. This chapter should be useful for establishing a lentiviral vector-based delivery of siRNAs in experiments that require long-term gene knockdown or developing siRNA-based approaches for gene therapy applications.