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Chen MJ, Gatignol A, Scarborough RJ. The discovery and development of RNA-based therapies for treatment of HIV-1 infection. Expert Opin Drug Discov 2023; 18:163-179. [PMID: 36004505 DOI: 10.1080/17460441.2022.2117296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Long-term control of HIV-1 infection can potentially be achieved using autologous stem cell transplants with gene-modified cells. Non-coding RNAs represent a diverse class of therapeutic agents including ribozymes, RNA aptamers and decoys, small interfering RNAs, short hairpin RNAs, and U1 interference RNAs that can be designed to inhibit HIV-1 replication. They have been engineered for delivery as drugs to complement current HIV-1 therapies and as gene therapies for a potential HIV-1 functional cure. AREAS COVERED This review surveys the past three decades of development of these RNA technologies with a focus on their efficacy and safety for treating HIV-1 infections. We describe the mechanisms of each RNA-based agent, targets they have been developed against, efforts to enhance their stability and efficacy, and we evaluate their performance in past and ongoing preclinical and clinical trials. EXPERT OPINION RNA-based technologies are among the top candidates for gene therapies where they can be stably expressed for long-term suppression of HIV-1. Advances in both gene and drug delivery strategies and improvements to non-coding RNA stability and antiviral properties will cooperatively drive forward progress in improving drug therapy and engineering HIV-1 resistant cells.
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Affiliation(s)
- Michelle J Chen
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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Abstract
Ribozymes are structured RNA molecules that act as catalysts in different biological reactions. From simple genome cleaving activities in satellite RNAs to more complex functions in cellular protein synthesis and gene regulation, ribozymes play important roles in all forms of life. Several naturally existing ribozymes have been modified for use as therapeutics in different conditions, with HIV-1 infection being one of the most studied. This chapter summarizes data from different preclinical and clinical studies conducted to evaluate the potential of ribozymes to be used in HIV-1 therapies. The different ribozyme motifs that have been modified, as well as their target sites and expression strategies, are described. RNA conjugations used to enhance the antiviral effect of ribozymes are also presented and the results from clinical trials conducted to date are summarized. Studies on anti-HIV-1 ribozymes have provided valuable information on the optimal expression strategies and clinical protocols for RNA gene therapy and remain competitive candidates for future therapy.
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Mitsuyasu RT, Zack JA, Macpherson JL, Symonds GP. Phase I/II Clinical Trials Using Gene-Modified Adult Hematopoietic Stem Cells for HIV: Lessons Learnt. Stem Cells Int 2011; 2011:393698. [PMID: 21716651 PMCID: PMC3116533 DOI: 10.4061/2011/393698] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 03/15/2011] [Indexed: 12/20/2022] Open
Abstract
Gene therapy for individuals infected with HIV has the potential to provide a once-only treatment that will act to reduce viral load, preserve the immune system, and mitigate cumulative toxicities associated with highly active antiretroviral therapy (HAART). The authors have been involved in two clinical trials (phase I and phase II) using gene-modified adult hematopoietic stem cells (HSCs), and these are discussed as prototypic trials within the general field of HSC gene therapy trials for HIV. Taken as a group these trials have shown (i) the safety of both the procedure and the anti-HIV agents themselves and (ii) the feasibility of the approach. They point to the requirement for (i) the ability to transduce and infuse as many as possible gene-containing HSC and/or (ii) high engraftment and in vivo expansion of these cells, (iii) potentially increased efficacy of the anti-HIV agent(s) and (iv) automation of the cell processing procedure.
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Affiliation(s)
- Ronald T Mitsuyasu
- Center for Clinical AIDS Research and Education (CARE Center), University of California-Los Angeles, Los Angeles, CA 90035, USA
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Murray JM, Fanning GC, Macpherson JL, Evans LA, Pond SM, Symonds GP. Mathematical modelling of the impact of haematopoietic stem cell-delivered gene therapy for HIV. J Gene Med 2010; 11:1077-86. [PMID: 19777528 DOI: 10.1002/jgm.1401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gene therapy represents a new treatment paradigm for HIV that is potentially delivered by a safe, once-only therapeutic intervention. METHODS Using mathematical modelling, we assessed the possible impact of autologous haematopoietic stem cell (HSC) delivered, anti-HIV gene therapy. The therapy comprises a ribozyme construct (OZ1) directed to a conserved region of HIV-1 delivered by transduced HSC (OZ1+HSC). OZ1+HSC contributes to the CD4+ T lymphocyte and monocyte/macrophage cell pools that preferentially expand under the selective pressure of HIV infection. The model was used to predict the efficacy of OZ1 in a highly active antiretroviral therapy (HAART) naïve individual and a HAART-experienced individual undergoing two structured treatment operations. In the standard scenario, OZ1+HSC was taken as 20% of total body HSC. RESULTS For a HAART-naïve individual, modelling predicts a reduction of HIV RNA at 1 and 2 years post-OZ1 therapy of 0.5 log(10) and 1 log(10), respectively. Eight years after OZ1 therapy, the CD4+ T-lymphocyte count was 271 cells/mm(3) compared to 96 cells/mm(3) for an untreated individual. In a HAART-experienced individual HIV RNA was reduced by 0.34 log(10) and 0.86 log(10) at 1 and 2 years. The OZ1 effect was maximal when both CD4+ T lymphocytes and monocytes/macrophages were protected from successful, productive infection by OZ1. CONCLUSIONS The modelling indicates a single infusion of HSC cell-delivered gene therapy can impact on HIV viral load and CD4 T-lymphocyte count. Given that gene therapy avoids the complications associated with HAART, there is significant potential for this approach in the treatment of HIV.
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Affiliation(s)
- John M Murray
- School of Mathematics and Statistics, University of New South Wales, Sydney, Australia.
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Müller-Kuller T, Capalbo G, Klebba C, Engels JW, Klein SA. Identification and Characterization of a Highly Efficient Anti-HIV Pol Hammerhead Ribozyme. Oligonucleotides 2009; 19:265-72. [DOI: 10.1089/oli.2008.0150] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Thea Müller-Kuller
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Gianni Capalbo
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Christian Klebba
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Joachim W. Engels
- Institut für Organische Chemie, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Stefan A. Klein
- Klinikum Bayreuth, Medizinische Klinik IV, Bayreuth, Germany
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7
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Mitsuyasu RT, Merigan TC, Carr A, Zack JA, Winters MA, Workman C, Bloch M, Lalezari J, Becker S, Thornton L, Akil B, Khanlou H, Finlayson R, McFarlane R, Smith DE, Garsia R, Ma D, Law M, Murray JM, von Kalle C, Ely JA, Patino SM, Knop AE, Wong P, Todd AV, Haughton M, Fuery C, Macpherson JL, Symonds GP, Evans LA, Pond SM, Cooper DA. Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34+ cells. Nat Med 2009; 15:285-92. [PMID: 19219022 PMCID: PMC2768566 DOI: 10.1038/nm.1932] [Citation(s) in RCA: 200] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 01/16/2009] [Indexed: 11/22/2022]
Abstract
Gene transfer has potential as a once-only treatment that reduces viral load, preserves the immune system, and avoids lifetime highly active antiretroviral therapy. This study, the first randomized, double-blind, placebo-controlled, phase II cell-delivered gene transfer clinical trial, was conducted in 74 HIV-1 infected adults who received a tat/vpr specific anti-HIV ribozyme (OZ1) or placebo delivered in autologous CD34+ hematopoietic progenitor cells. There were no OZ1-related adverse events. There was no statistical difference in viral load between the OZ1 and placebo group at the primary end-point (average at weeks 47 and 48) but time weighted areas under the curve from weeks 40-48 and 40-100 were significantly lower in the OZ1 group. Throughout the 100 weeks, CD4+ lymphocyte counts were higher in the OZ1 group. This study provides the first indication that cell-delivered gene transfer is safe and biologically active in HIV patients and can be developed as a conventional therapeutic product.
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Affiliation(s)
- Ronald T Mitsuyasu
- Center for Clinical AIDS Research and Education, University of California-Los Angeles, 9911 West Pico Boulevard, Suite 980, Los Angeles, California 90035, USA.
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Kim K, Liu F. Inhibition of gene expression in human cells using RNase P-derived ribozymes and external guide sequences. ACTA ACUST UNITED AC 2007; 1769:603-12. [PMID: 17976837 DOI: 10.1016/j.bbaexp.2007.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 09/13/2007] [Accepted: 09/14/2007] [Indexed: 11/19/2022]
Abstract
Ribonuclease P (RNase P) complexed with an external guide sequence (EGS) represents a novel nucleic acid-based gene interference approach to modulate gene expression. This enzyme is a ribonucleoprotein complex for tRNA processing. In Escherichia coli, RNase P contains a catalytic RNA subunit (M1 ribozyme) and a protein subunit (C5 cofactor). EGSs, which are RNAs derived from natural tRNAs, bind to a target mRNA and render the mRNA susceptible to hydrolysis by RNase P and M1 ribozyme. When covalently linked with a guide sequence, M1 can be engineered into a sequence-specific endonuclease, M1GS ribozyme, which cleaves any target RNAs that base pair with the guide sequence. Studies have demonstrated efficient cleavage of mRNAs by M1GS and RNase P complexed with EGSs in vitro. Moreover, highly active M1GS and EGSs were successfully engineered using in vitro selection procedures. EGSs and M1GS ribozymes are effective in blocking gene expression in both bacteria and human cells, and exhibit promising activity for antimicrobial, antiviral, and anticancer applications. In this review, we highlight some recent results using the RNase P-based technology, and offer new insights into the future of using EGS and M1GS RNA as tools for basic research and as gene-targeting agents for clinical applications.
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Affiliation(s)
- Kihoon Kim
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
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9
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Khan AU. Ribozyme: A clinical tool. Clin Chim Acta 2006; 367:20-7. [PMID: 16426595 DOI: 10.1016/j.cca.2005.11.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 11/18/2005] [Accepted: 11/22/2005] [Indexed: 01/15/2023]
Abstract
Catalytic RNAs (ribozymes) are capable of specifically cleaving RNA molecules, a property that enables them to act as potential antiviral and anti-cancer agents, as well as powerful tools for functional genomic studies. Recently, ribozymes have been used successfully to inhibit gene expression in a variety of biological systems in vitro and in vivo. Phase I clinical trials using ribozyme gene therapy to treat AIDS patients have been conducted. Despite initial success, there are many areas that require further investigation. These include stability of ribozymes in cells and designing highly active ribozymes in vivo, identification of target sequence sites and co-localization of ribozymes and substrates, and their delivery to specific tissues and maintenance of its stable long-term expression. This review gives a brief introduction to ribozyme structure, catalysis and its potential applications in biological systems as therapeutic agents.
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Affiliation(s)
- Asad U Khan
- Interdisciplinary Biotechnology unit, Aligarh Muslim University, Aligarh 202002, India.
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10
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Habu Y, Nagawa T, Matsumoto N, Takeuchi H, Miyano-Kurosaki N, Takaku H. Suppression of human immunodeficiency virus type 1 (HIV-1) replication by an HIV-1-dependent double locked vector with the Cre/loxP system. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:1907-17. [PMID: 16438057 DOI: 10.1080/15257770500269168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We previously demonstrated the function of an HIV-1-dependent ribozyme expression vector, with which the site-specific excision of loxP sequences can be achieved by using the Cre-loxP system (ON/OFF) as a molecular switch in an acute HIV-1 infection. However, this expression system also revealed the lower, non-specific expression of the anti-H1V-1 ribozyme in the absence of tat. To circumvent this problem, we used the more efficient HIV-1-dependent Cre recombinase gene expression vector, encoding the LTR-gag-p17 (extending from the 5'-LTR to the middle of the gag gene (pLTR-gag-p17-Cre)). Comparatively, the pLTR-gag-p17-Cre induces a higher Cre-protein expression level in an HIV-1 infection-dependent manner than the minimal pLTR-Cre. Furthermore, we constructed the ploxP-Rz-U5 and pLTR-gag-p17-Cre plasmids and also combined them into a single vector, pLTR-gag-p17-Cre/loxP-Rz-U5, for a comparison of their anti-HIV-1 activities. The resultant simultaneous expression of the Cre protein and the homologous recombination of the two loxP sequences induced a high level of HIV-1 replication inhibition (95%). Significantly, a high steady-state of ribozyme expression was observed in the RT-PCR analysis. These data imply that targeting the HIV-1 genes with the pLTR-gag-p17-Cre/loxP-Rz-U5 vector, which mediates HIV-1-dependent ribozyme expression, would be a useful tool for HIV-1 gene therapy applications.
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Affiliation(s)
- Yuichiro Habu
- Department of Life and Environmental Sciences, Chiba Institute of Technoloy, Narashino, Chiba, Japan
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11
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Macpherson JL, Boyd MP, Arndt AJ, Todd AV, Fanning GC, Ely JA, Elliott F, Knop A, Raponi M, Murray J, Gerlach W, Sun LQ, Penny R, Symonds GP, Carr A, Cooper DA. Long-term survival and concomitant gene expression of ribozyme-transduced CD4+ T-lymphocytes in HIV-infected patients. J Gene Med 2005; 7:552-64. [PMID: 15655805 DOI: 10.1002/jgm.705] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND An anti-HIV-1 tat ribozyme, termed Rz2, has been shown to inhibit HIV-1 infection/replication and to decrease HIV-1-induced pathogenicity in T-lymphocyte cell lines and normal peripheral blood T-lymphocytes. We report here the results of a phase I gene transfer clinical trial using Rz2. METHODS Apheresis was used to obtain a peripheral blood cell population from each of four HIV-negative donors. After enrichment for CD4+ T-lymphocytes, ex vivo expansion and genetic manipulation (approximately equal aliquots of the cells were transduced with the ribozyme-containing (RRz2) and the control (LNL6) retroviral vector), these cells were infused into the corresponding HIV-1-positive twin recipient. Marking was assessed over an initial 24-week period and in total over an approximate 4-year period. RESULTS The gene transfer procedure was shown to be safe, and technically feasible. Both RRz2- and LNL6-gene-containing peripheral blood mononuclear cells (PBMC) were detected at all time points examined to 4 years. There was concomitant gene construct expression in the absence of the need for ex vivo peripheral blood cell stimulation and there was no evidence of immune elimination of the neoR T-lymphocytes nor of silencing of the Moloney murine leukemia virus long terminal repeat. CONCLUSIONS The proof of principle results reported here demonstrate safety and feasibility of this type of gene transfer approach. While not specifically tested, T-lymphocytes containing an anti-HIV gene construct may impact on HIV-1 viral load and CD4+ T-lymphocyte count, potentially representing a new therapeutic modality for HIV-1 infection.
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Affiliation(s)
- Janet L Macpherson
- Johnson and Johnson Research Pty Limited, Locked Bag 4555, Strawberry Hills, Sydney, NSW Australia 2012.
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12
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Amado RG, Mitsuyasu RT, Rosenblatt JD, Ngok FK, Bakker A, Cole S, Chorn N, Lin LS, Bristol G, Boyd MP, MacPherson JL, Fanning GC, Todd AV, Ely JA, Zack JA, Symonds GP. Anti-Human Immunodeficiency Virus Hematopoietic Progenitor Cell-Delivered Ribozyme in a Phase I Study: Myeloid and Lymphoid Reconstitution in Human Immunodeficiency Virus Type-1–Infected Patients. Hum Gene Ther 2004; 15:251-62. [PMID: 15018734 DOI: 10.1089/104303404322886101] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A phase I gene transfer clinical study was undertaken to examine the ability to introduce a potential anti-human immunodeficiency virus (HIV) gene therapeutic into hematopoietic progenitor cells (HPC), thereby contributing to multilineage engraftment. The potential therapeutic effect of genetically modifying HPC with protective genes in HIV-infected adults depends in part on the presence of adult thymic activity and myeloid capacity in the setting of HIV replication. Herein we report the presence and expression of a retroviral vector encoding an anti-HIV-1 ribozyme in mature hematopoietic cells of different lineages, and de novo T-lymphocyte development ensuing from genetically engineered CD34(+) HPC. Sustained output of vector-containing mature myeloid and T-lymphoid cells was detected even in patients with multidrug-resistant infection. In addition, the study showed that the degree of persistence of gene-containing cells was dependent on transduced HPC dose. These novel findings support the concept of gene therapy as a modality to effect immune reconstitution with cells engineered to inhibit HIV replication and this report represents the first demonstration of long-term maintenance of a potential therapeutic transgene in HIV disease.
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Affiliation(s)
- Rafael G Amado
- Department of Medicine and UCLA AIDS Institute, University of California, Los Angeles, CA 90095, USA
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13
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Khan AU, Lal SK. Ribozymes: a modern tool in medicine. J Biomed Sci 2003; 10:457-67. [PMID: 12928586 DOI: 10.1007/bf02256107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Accepted: 05/07/2003] [Indexed: 01/20/2023] Open
Abstract
Since the discovery of ribozymes and self-splicing introns, it has been estimated that this biological property of RNA combined with other recombinant DNA technologies would become a tool to combat viral diseases and control oncogenes. These goals seem like a distinct possibility now. However, there is still a lot to be learned about the mobility of RNA inside the cells and the cellular factors that can impede ribozyme action in order to capitalize fully on the targeted RNA inactivation property of ribozymes. The most effective approach to maximize ribozyme function in a complex intracellular environment is to understand as much as possible about the intracellular fate of the RNA that is being targeted. As new techniques in cell biology become available, such understanding will be less problematic. Fundamental studies of ribozyme structure and mechanism of catalysis are flourishing both at the academic and industrial level and it can be expected that many new developments will continue to take place in these areas in the near future. Here, we review the design, stability and therapeutic application of these technologies illustrating relevant gene targets and applications in molecular medicine. Relevant problems in implementation of the technology, group I and II introns and the differences in applications, ribozyme structure and the application of this technology to virus attack and oncogene downregulation are discussed. Also some of the latest RNA-based technologies such as siRNA, RNA/DNA duplexes and RNA decoys have been introduced.
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Affiliation(s)
- Asad U Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.
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Steele D, Kertsburg A, Soukup GA. Engineered catalytic RNA and DNA : new biochemical tools for drug discovery and design. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2003; 3:131-44. [PMID: 12749730 DOI: 10.2165/00129785-200303020-00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Since the fundamental discovery that RNA catalyzes critical biological reactions, the conceptual and practical utility of nucleic acid catalysts as molecular therapeutic and diagnostic agents continually develops. RNA and DNA catalysts are particularly attractive tools for drug discovery and design due to their relative ease of synthesis and tractable rational design features. Such catalysts can intervene in cellular or viral gene expression by effectively destroying virtually any target RNA, repairing messenger RNAs derived from mutant genes, or directly disrupting target genes. Consequently, catalytic nucleic acids are apt tools for dissecting gene function and for effecting gene pharmacogenomic strategies. It is in this capacity that RNA and DNA catalysts have been most widely utilized to affect gene expression of medically relevant targets associated with various disease states, where a number of such catalysts are presently being evaluated in clinical trials. Additionally, biotechnological prospects for catalytic nucleic acids are seemingly unlimited. Controllable nucleic acid catalysts, termed allosteric ribozymes or deoxyribozymes, form the basis of effector or ligand-dependent molecular switches and sensors. Allosteric nucleic acid catalysts promise to be useful tools for detecting and scrutinizing the function of specified components of the metabolome, proteome, transcriptome, and genome. The remarkable versatility of nucleic acid catalysis is thus the fountainhead for wide-ranging applications of ribozymes and deoxyribozymes in biomedical and biotechnological research.
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Affiliation(s)
- David Steele
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, USA
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15
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Fanning G, Amado R, Symonds G. Gene therapy for HIV/AIDS: the potential for a new therapeutic regimen. J Gene Med 2003; 5:645-53. [PMID: 12898634 DOI: 10.1002/jgm.436] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) is the etiologic agent of Acquired Immunodeficiency Syndrome (AIDS). HIV/AIDS is a disease that, compared with the not so distant past, is now better held in check by current antiretroviral drugs. However, it remains a disease not solved. Highly active antiretroviral therapy (HAART) generally uses two non-nucleoside and one nucleoside reverse transcriptase (RT) inhibitor or two non-nucleoside RT and one protease inhibitor. HAART is far more effective than the mono- or duo-therapy of the past, which used compounds like the nucleoside reverse transcriptase inhibitor AZT or two nucleoside reverse transcriptase inhibitors. However, even with the relatively potent drug cocktails that comprise HAART, there are the issues of (i). HIV escape mutants, (ii). an apparent need to take the drugs in an ongoing manner, and (iii). the drugs' side effects that are often severe. This review speaks to the potential addition to these potent regimens of another regimen, namely the genetic modification of target hematopoietic cells. Such a new treatment paradigm is conceptually attractive as it may yield the constant intracellular expression of an anti-HIV gene that acts to inhibit HIV replication and pathogenicity. A body of preclinical work exists showing the inhibition of HIV replication and decreased HIV pathogenicity by anti-HIV genetic agents. This preclinical work used hematopoietic cell lines and primary cells as the target tissue. More recently, several clinical trials have sought to test this concept in vivo.
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Affiliation(s)
- Greg Fanning
- Johnson & Johnson Research Pty Limited, Level 4, 1 Central Avenue, Eveleigh, Sydney, NSW 1430, Australia
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Lori F, Guallini P, Galluzzi L, Lisziewicz J. Gene therapy approaches to HIV infection. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2003; 2:245-52. [PMID: 12421095 DOI: 10.2165/00129785-200202040-00004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The HIV pandemic represents a new challenge to biomedical research. What began as a handful of recognized cases among homosexual men in the US has become a global pandemic of such proportions that it clearly ranks as one of the most destructive viral scourges in history. In the past few years new treatments and drugs have been developed and tested, but the development of a new generation of therapies remains a major priority, because of the lack of chemotherapeutic drugs or vaccines that show long-term efficacy in vivo. Recently, gene therapeutic strategies for the treatment of patients with HIV infection have received increased attention because they are able to offer the possibility of simultaneously targeting multiple sites in the HIV genome, thereby minimizing the production of resistant virus. Recombinant genes for gene therapy can be classified as expressing interfering proteins (intracellular antibodies, dominant negative proteins) or interfering RNAs (antisense RNAs, ribozymes, RNA decoys). The latter group offers the advantage of avoiding the stimulation of host immune response which might progressively decrease the efficacy of proteins. The stumbling block to achieving lasting antiviral effects is still represented by the lack of efficient gene transfer techniques capable of generating persistent transgene expression and a high number of transduced cells relative to untransduced cells. Novel delivery vectors, such as lentiviruses, might overcome some of these shortcomings. The use of recombinant genes to generate immunity is a very promising concept that is rapidly expanding. Since the immune system can significantly amplify the response to tiny amounts of antigen, DNA vaccines can indeed be delivered by exploiting traditional gene therapy approaches without the need of high transduction efficiency.
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Affiliation(s)
- Franco Lori
- Research Institute for Genetic and Human Therapy at IRCCS Policlinico S. Matteo, Pavia, Italy.
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Puerta-Fernández E, Romero-López C, Barroso-delJesus A, Berzal-Herranz A. Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 2003; 27:75-97. [PMID: 12697343 DOI: 10.1016/s0168-6445(03)00020-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The discovery 20 years ago that some RNA molecules, called ribozymes, are able to catalyze chemical reactions was a breakthrough in biology. Over the last two decades numerous natural RNA motifs endowed with catalytic activity have been described. They all fit within a few well-defined types that respond to a specific RNA structure. The prototype catalytic domain of each one has been engineered to generate trans-acting ribozymes that catalyze the site-specific cleavage of other RNA molecules. On the 20th anniversary of ribozyme discovery we briefly summarize the main features of the different natural catalytic RNAs. We also describe progress towards developing strategies to ensure an efficient ribozyme-based technology, dedicating special attention to the ones aimed to achieve a new generation of therapeutic agents.
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Affiliation(s)
- Elena Puerta-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Ventanilla 11, 18001 Granada, Spain
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18
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Gennari F, Biasolo MA, Cancellotti E, Radaelli A, De Giuli Morghen C, Bozzoni I, Cereda PM, Mengoli C, Palù G, Parolin C. Additive and antagonist effects of therapeutic gene combinations for suppression of HIV-1 infection. Antiviral Res 2002; 55:77-90. [PMID: 12076753 DOI: 10.1016/s0166-3542(02)00009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A previously described Moloney-based vector expressing a double copy anti-tat antisense tRNA (DC-tRNA-AT) (Biasolo et al., 1996. J. Virol. 70, 2154-2161) was modified to increase the copy number of the antisense molecule and to target the intra-cytoplasmic localization of the HIV genome. To this end, an anti-U5 hammerhead ribozyme, engineered as a hybrid small adenoviral VAI RNA (VAIalpha), was inserted into the vector as a single molecule or in combination with the double copy anti-tat sequence. The retroviral vector expressing only VAIalpha (DC-VAIalpha) inhibited HIV-1 replication to an extent comparable to that of DC-tRNA-AT. A more effective inhibition was produced by the vector expressing multiple copies of the anti-tat antisense (DC-6tRNA-AT). This higher effectiveness correlated with anti-tat stochiometry, i.e. with the absolute number of therapeutic molecules being produced on a per cell basis at the steady state. Surprisingly, when the tRNA-AT and VAIalpha genes were combined in the same vector (DC-AT-VAIalpha), an enhancement of viral replication was noticed. This study indicates that it is possible to potentiate the antiviral activity of a retroviral vector by increasing the steady-state level of the therapeutic molecule. Results also show that the combined expression of two singularly active therapeutic RNAs can have antagonistic rather than synergistic effects.
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Affiliation(s)
- Francesca Gennari
- Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, via A. Gabelli 63, 35121, Padova, Italy
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19
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Abstract
RNA enzymes--ribozymes--are being developed as treatments for a variety of diseases ranging from inborn metabolic disorders to viral infections and acquired diseases such as cancer. Ribozymes can be used both to downregulate and to repair pathogenic genes. In some instances, short-term exogenous delivery of stabilized RNA is desirable, but many treatments will require viral-mediated delivery to provide long-term expression of the therapeutic catalyst. Current gene therapy applications employ variations on naturally occurring ribozymes, but in vitro selection has provided new RNA and DNA catalysts, and research on trans-splicing and RNase P has suggested ways to harness the endogenous ribozymes of the cell for therapeutic purposes.
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Affiliation(s)
- A S Lewin
- Dept of Molecular Genetics and Microbiology and the Powell Gene Therapy Center, University of Florida, Gainesville 32610-0266, USA.
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20
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Affiliation(s)
- N Dorman
- University of Cambridge Department of Medicine, Addenbrooke's Hospital, Cambridge, UK
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21
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Affiliation(s)
- A M Lever
- University of Cambridge Department of Medicine, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK.
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22
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Miyake K, Iijima O, Suzuki N, Matsukura M, Shimada T. Selective killing of human immunodeficiency virus-infected cells by targeted gene transfer and inducible gene expression using a recombinant human immunodeficiency virus vector. Hum Gene Ther 2001; 12:227-33. [PMID: 11177560 DOI: 10.1089/10430340150218378] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A human immunodeficiency virus type 1 (HIV-1)-based retroviral vector pseudotyped with HIV envelope containing the herpes simplex virus-thymidine kinase (HSV-TK) gene under the control of the HIV LTR promoter (pHXTKN) was constructed and stably transferred into human CD4(+) H9, CEM, and U937 cells. RNase protection assays did not initially detect expression of the HSV-TK gene in HXTKN-transduced CD4(+) cells (HXTKN/CD4), but expression was then efficiently induced by infection with HIV-1. MTT assays showed that after HIV-1 infection, the susceptibility of HXTKN/CD4 cells to ganciclovir (GCV) was 1000-fold higher than prior to infection. This enabled HIV-1-infected cells to be selectively killed by transduction with HXTKN followed by exposure to GCV. Because the HSV-TK gene is specifically transferred into HIV-1-permissive cells and expressed only after HIV-1 infection, the frequency of unwanted cell death should be low. Elimination of the HIV-1-infected cells effectively inhibited further spread of infectious virus. In addition, the integrated HIV vector sequences were repackaged on infection with HIV-1 and transferred to surrounding untransduced cells. These results are indicative of the potential benefits of using HIV vectors in gene therapies for the treatment of HIV-1 infection.
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Affiliation(s)
- K Miyake
- Department of Biochemistry and Molecular Biology, Division of Gene Therapy Research, Center for Advanced Medical Technology, Nippon Medical School, Tokyo 113-8602, Japan.
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23
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Pandya S, Klimatcheva E, Planelles V. Lentivirus and foamy virus vectors: novel gene therapy tools. Expert Opin Biol Ther 2001; 1:17-40. [PMID: 11727544 DOI: 10.1517/14712598.1.1.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The aim of gene therapy is to modify the genetic material of living cells to achieve therapeutic benefit. Gene therapy involves the insertion of a functional gene into a cell, to replace an absent or defective gene, or to fight an infectious agent or a tumour. At present, a wide variety of somatic tissues are being explored for the introduction of foreign genes with a view towards treatment. A prime requirement for successful gene therapy is the sustained expression of the therapeutic gene without any adverse effect on the recipient. A highly desirable vector would be generated at high titres, integrate into target cells (including non-dividing cells) and have little or no associated immune reactions. Lentiviruses have the ability to infect dividing and non-dividing cells and, therefore, constitute ideal candidates for development of vectors for gene therapy. This review presents a description of available lentiviral vectors, including vector design, applications to disease treatment and safety considerations. In addition, general aspects of the biology of lentiviruses with relevance to vector development will be discussed. Recent investigations have revealed that foamy viruses, another group of retroviruses, are also capable of infecting non-dividing cells. Thus, foamy virus vectors are actively being developed in parallel to lentivirus vectors. This review will also include various aspects of the biology of foamy viruses with relevance to vector development.
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Affiliation(s)
- S Pandya
- Departments of Medicine and Microbiology and Immunology, University of Rochester Cancer Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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24
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Bramlage B, Luzi E, Eckstein F. HIV-1 LTR as a target for synthetic ribozyme-mediated inhibition of gene expression: site selection and inhibition in cell culture. Nucleic Acids Res 2000; 28:4059-67. [PMID: 11058100 PMCID: PMC113160 DOI: 10.1093/nar/28.21.4059] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed against these sites, either unmodified or with 2'-modifications and phosphorothioate groups, and their cleavage activities of the transcript were determined. Their biological activities were assessed in cell culture, using a HIV-1 model assay system where the LTR is a promoter for the expression of the reporter gene luciferase in a transient expression system. Intracellular efficiency of the ribozymes were determined by cotransfection of ribozyme and plasmid DNA, expressing the target RNA. Modified ribozymes, directed against positions 115 and 161, lowered the level of LTR mRNA in the cell resulting in inhibition of expression of the LTR-driven reporter gene luciferase of 87 and 61%, respectively. In the presence of Tat the inhibitions were 43 and 25%. The inactive variants of these ribozymes exhibited a similar inhibitory effect. RNase protection revealed a reduction of RNA which was somewhat stronger for the active than the inactive ribozymes, particularly for ribozyme 115. Unmodified ribozymes showed no inhibition in the cell. The third ribozyme, targeting a GUG-triplet at position 109, possessed only low cleavage activity in vitro and no inhibitory effect in cell culture.
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MESH Headings
- Base Sequence
- Binding Sites
- Codon/genetics
- Down-Regulation
- Gene Expression Regulation, Viral
- Gene Library
- Genes, Reporter/genetics
- Genetic Engineering
- HIV Long Terminal Repeat/genetics
- HIV-1/genetics
- HeLa Cells
- Humans
- Kinetics
- Nuclease Protection Assays
- Nucleic Acid Conformation
- Oligoribonucleotides/chemical synthesis
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- RNA Stability
- RNA, Catalytic/chemical synthesis
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Substrate Specificity
- Transcription, Genetic/genetics
- Transfection
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Affiliation(s)
- B Bramlage
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Strabetae 3, D-37075 Göttingen, Germany
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25
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Abstract
Within the past few years encouraging progress has been made in the treatment of HIV-1 infection, largely due to the combined use of HIV-1 protease inhibitors with nucleoside and non-nucleoside reverse transcriptase inhibitors. Despite this, HIV-1 infection is still a major global problem and the emergence of a drug resistant virus is ever present. There is a continuing need to develop new therapeutic strategies as well as improve upon all forms of existing therapies for the treatment of this viral infection. It has now been almost a decade since the first demonstration that ribozymes can effectively inhibit HIV-1 infectious spread in cell culture. Since then, ribozymes have progressed into human clinical trials primarily through gene therapy approaches. This progression brings ribozymes into the forefront as an important addition to the growing arsenal of anti-HIV-1 weapons. The following review covers the developments in anti-HIV-1 ribozyme usage over the past decade and summarizes the current state of ribozyme development for the purpose of inhibiting HIV-1 infection.
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Affiliation(s)
- J J Rossi
- Department of Molecular Biology, Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
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26
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Abstract
Ribozymes are RNA molecules that possess the ability to cleave and thus destroy other RNA molecules. As a result of this ability, they are ideal specific agents to use against the messenger RNAs of important genes found to be linked with disease (of cellular and viral origin). This review will briefly describe the different types of ribozyme and the potential they have as therapeutic compounds against viruses, oncogenes and drug resistance in haematological settings. The latest news from the various Phase I and II ribozyme clinical trials is discussed, as is the potential for the ribozymes' future as therapeutic agents.
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Affiliation(s)
- H A James
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
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27
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Klebba C, Ottmann OG, Scherr M, Pape M, Engels JW, Grez M, Hoelzer D, Klein SA. Retrovirally expressed anti-HIV ribozymes confer a selective survival advantage on CD4+ T cells in vitro. Gene Ther 2000; 7:408-16. [PMID: 10694823 DOI: 10.1038/sj.gt.3301094] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To date, a selective advantage of cells expressing anti-HIV ribozymes has not been shown. This study was undertaken to determine whether such a selective advantage can be demonstrated in vitro. A retroviral vector coding for a hairpin ribozyme targeting the HIV 5'LTR and for the low affinity nerve growth factor receptor (LNGF-RDelta) was designed. Since we demonstrated by RT-PCR that the amount of ribozyme transcripts was highly correlated with the level of surface LNGF-RDelta expression, the vector was utilized to assess ribozyme expression by flow cytometry. Transduced Hut78 and primary CD4+ T cells were purified and subsequently mixed with unmodified cells. After HIV challenge the percentage of ribozyme expressing cells in the cell mixture was monitored by flow cytometry. Twenty-one days after HIV infection the proportion of ribozyme expressing CD4+ T cells was 2.6 times higher in comparison to cells with the control vector. CD4+ T cells with a strong ribozyme expression conferred a 7.4-fold selective advantage at day 21 and a 11.7-fold at day 28. For Hut78 cells a selective advantage was detected exclusively for strongly ribozyme expressing cells. As a mechanism underlying the selective advantage an inhibition of HIV induced apoptosis was shown. These results demonstrate that anti-HIV ribozymes are able to confer a selective survival advantage and indicate that the protective effect is dependent on the amount of ribozyme expression. Gene Therapy (2000) 7, 408-416.
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Affiliation(s)
- C Klebba
- Medizinische Klinik III der Johann Wolfgang Goethe Universität, Frankfurt, Germany
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28
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Cooper D, Penny R, Symonds G, Carr A, Gerlach W, Sun LQ, Ely J. A marker study of therapeutically transduced CD4+ peripheral blood lymphocytes in HIV discordant identical twins. Hum Gene Ther 1999; 10:1401-21. [PMID: 10365669 DOI: 10.1089/10430349950018067] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D Cooper
- National Centre in HIV Epidemiology and Clinical Research, Sydney, Australia
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