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Dönmüş B, Ünal S, Kirmizitaş FC, Türkoğlu Laçin N. Virus-associated ribozymes and nano carriers against COVID-19. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:204-218. [PMID: 33645342 DOI: 10.1080/21691401.2021.1890103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoo tonic, highly pathogenic virus. The new type of coronavirus with contagious nature spread from Wuhan (China) to the whole world in a very short time and caused the new coronavirus disease (COVID-19). COVID-19 has turned into a global public health crisis due to spreading by close person-to-person contact with high transmission capacity. Thus, research about the treatment of the damages caused by the virus or prevention from infection increases everyday. Besides, there is still no approved and definitive, standardized treatment for COVID-19. However, this disaster experienced by human beings has made us realize the significance of having a system ready for use to prevent humanity from viral attacks without wasting time. As is known, nanocarriers can be targeted to the desired cells in vitro and in vivo. The nano-carrier system targeting a specific protein, containing the enzyme inhibiting the action of the virus can be developed. The system can be used by simple modifications when we encounter another virus epidemic in the future. In this review, we present a potential treatment method consisting of a nanoparticle-ribozyme conjugate, targeting ACE-2 receptors by reviewing the virus-associated ribozymes, their structures, types and working mechanisms.
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Affiliation(s)
- Beyza Dönmüş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Sinan Ünal
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Fatma Ceren Kirmizitaş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Nelisa Türkoğlu Laçin
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
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Kharma N, Varin L, Abu-Baker A, Ouellet J, Najeh S, Ehdaeivand MR, Belmonte G, Ambri A, Rouleau G, Perreault J. Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript. Nucleic Acids Res 2015; 44:e39. [PMID: 26527730 PMCID: PMC4770207 DOI: 10.1093/nar/gkv1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/12/2015] [Indexed: 12/23/2022] Open
Abstract
We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website http://ribosoft.fungalgenomics.ca/ribosoft/.
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Affiliation(s)
- Nawwaf Kharma
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Luc Varin
- Biology Department, Concordia University, 7141 rue Sherbrooke O., Montreal, QC, H4B 1R6, Canada
| | - Aida Abu-Baker
- Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Jonathan Ouellet
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Sabrine Najeh
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | | | - Gabriel Belmonte
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Anas Ambri
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Guy Rouleau
- Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Jonathan Perreault
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
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Scarborough RJ, Lévesque MV, Boudrias-Dalle E, Chute IC, Daniels SM, Ouellette RJ, Perreault JP, Gatignol A. A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e178. [PMID: 25072692 PMCID: PMC4121520 DOI: 10.1038/mtna.2014.31] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 06/03/2014] [Indexed: 12/18/2022]
Abstract
Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.
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Affiliation(s)
- Robert J Scarborough
- 1] Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, Québec, Canada [2] Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
| | - Michel V Lévesque
- Département de Biochimie, RNA Group/Groupe ARN, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Etienne Boudrias-Dalle
- 1] Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, Québec, Canada [2] Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
| | - Ian C Chute
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Sylvanne M Daniels
- 1] Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, Québec, Canada [2] Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
| | | | - Jean-Pierre Perreault
- Département de Biochimie, RNA Group/Groupe ARN, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Anne Gatignol
- 1] Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, Québec, Canada [2] Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada [3] Department of Medicine, McGill University, Montréal, Québec, Canada
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Scarborough RJ, Lévesque MV, Perreault JP, Gatignol A. Design and evaluation of clinically relevant SOFA-HDV ribozymes targeting HIV RNA. Methods Mol Biol 2014; 1103:31-43. [PMID: 24318884 DOI: 10.1007/978-1-62703-730-3_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nucleic acid therapies targeting HIV replication have the potential to be used in conjunction with or in place of the standard small-molecule therapies. Among the different classes of nucleic acid therapies, several ribozymes (Rzs, RNA enzymes) have been developed to target HIV RNA. The design of Rzs targeting HIV RNA is complicated by the sequence diversity of viral strains and the structural diversity of their target sites. Using the SOFA-HDV Rz as an example, this chapter describes methods that can be used to design Rzs for controlling HIV replication. We describe how to (1) identify highly conserved Rz target sites in HIV RNA; (2) generate a set of Rzs with the potential to be used as therapeutics; and (3) screen these Rzs for activity against HIV production.
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Affiliation(s)
- Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, McGill University, Montréal, QC, Canada
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Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis 2012; 2012:947147. [PMID: 22482079 PMCID: PMC3296272 DOI: 10.1155/2012/947147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 11/01/2011] [Indexed: 11/17/2022] Open
Abstract
Alzheimer's disease (AD) etiological studies suggest that an elevation in amyloid-β peptides (Aβ) level contributes to aggregations of the peptide and subsequent development of the disease. The major constituent of these amyloid peptides is the 1 to 40–42 residue peptide (Aβ40−42) derived from amyloid protein precursor (APP). Most likely, reducing Aβ levels in the brain may block both its aggregation and neurotoxicity and would be beneficial for patients with AD. Among the several possible ways to lower Aβ accumulation in the cells, we have selectively chosen to target the primary step in the Aβ cascade, namely, to reduce APP gene expression. Toward this end, we engineered specific SOFA-HDV ribozymes, a new generation of catalytic RNA tools, to decrease APP mRNA levels. Additionally, we demonstrated that APP-ribozymes are effective at decreasing APP mRNA and protein levels as well as Aβ levels in neuronal cells. Our results could lay the groundwork for a new protective treatment for AD.
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Abstract
Small cis-acting ribozymes have been converted into trans-acting ribozymes possessing the ability to cleave RNA substrates. The Hepatitis Delta Virus (HDV) ribozyme is one of the rare examples of these that is derived from an RNA species that is found in human cells. Consequently, it possesses the natural ability to function in the presence of human proteins in addition to an outstanding stability in human cells, two significant advantages in its use. The development of an additional specific on/off adaptor (SOFA) has led to the production of a new generation of HDV ribozymes with improved specificities that provide a tool with significant potential for future development in the fields of both functional genomics and gene -therapy. SOFA-HDV ribozyme-based gene inactivation systems have been reported in both prokaryotic and eukaryotic cells. Here, a step-by-step approach for the efficient design of highly specific SOFA-HDV ribozymes with a minimum investment of time and effort is described.
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Affiliation(s)
- Michel V Lévesque
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada
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Motard J, Rouxel R, Paun A, von Messling V, Bisaillon M, Perreault JP. A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One 2011; 6:e27327. [PMID: 22110627 PMCID: PMC3215696 DOI: 10.1371/journal.pone.0027327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/13/2011] [Indexed: 12/17/2022] Open
Abstract
Influenza A virus seasonal outbreaks and occasional pandemics represent a global health threat. The high genetic instability of this virus permits rapid escape from the host immune system and emergence of resistance to antivirals. There is thus an urgent need to develop novel approaches for efficient treatment of newly emerging strains. Based on a sequence alignment of representatives from every subtype known to infect humans, we identified nucleic acid regions that are conserved amongst these influenza A populations. We then engineered SOFA-HDV-Ribozymes as therapeutic tools recognizing these conserved regions to catalytically cleave the corresponding viral mRNA targets. The most promising ribozymes were chosen based on an initial in silico screening, and their efficacy was assessed using in vitro cleavage assays. Further characterization of their antiviral effect in cell culture and in mice led to the gradual identification of prophylactic SOFA-HDV-Ribozyme combinations, providing proof-of-principle for the potential of this novel strategy to develop antivirals against genetically highly variable viruses.
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MESH Headings
- Animals
- Antiviral Agents/metabolism
- Antiviral Agents/pharmacology
- Base Sequence
- Biocatalysis
- Female
- HEK293 Cells
- Hepatitis Delta Virus/enzymology
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Mice
- Nucleoproteins/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/pharmacology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombinant Proteins/pharmacology
- Virus Replication/drug effects
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Affiliation(s)
- Julie Motard
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Ronan Rouxel
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Canada
| | - Alexandra Paun
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Martin Bisaillon
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
| | - Jean-Pierre Perreault
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
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8
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Molecular Validation of PACE4 as a Target in Prostate Cancer. Transl Oncol 2011; 4:157-72. [PMID: 21633671 DOI: 10.1593/tlo.10295] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/02/2011] [Accepted: 02/14/2011] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer remains the single most prevalent cancer in men. Standard therapies are still limited and include androgen ablation that initially causes tumor regression. However, tumor cells eventually relapse and develop into a hormone-refractory prostate cancer. One of the current challenges in this disease is to define new therapeutic targets, which have been virtually unchanged in the past 30 years. Recent studies have suggested that the family of enzymes known as the proprotein convertases (PCs) is involved in various types of cancers and their progression. The present study examined PC expression in prostate cancer and validates one PC, namely PACE4, as a target. The evidence includes the observed high expression of PACE4 in all different clinical stages of human prostate tumor tissues. Gene silencing studies targeting PACE4 in the DU145 prostate cancer cell line produced cells (cell line 4-2) with slower proliferation rates, reduced clonogenic activity, and inability to grow as xenografts in nude mice. Gene expression and proteomic profiling of the 4-2 cell line reveals an increased expression of known cancer-related genes (e.g., GJA1, CD44, IGFBP6) that are downregulated in prostate cancer. Similarly, cancer genes whose expression is decreased in the 4-2 cell line were upregulated in prostate cancer (e.g., MUC1, IL6). The direct role of PACE4 in prostate cancer is most likely through the upregulated processing of growth factors or through the aberrant processing of growth factors leading to sustained cancer progression, suggesting that PACE4 holds a central role in prostate cancer.
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Tedeschi L, Lande C, Cecchettini A, Citti L. Hammerhead ribozymes in therapeutic target discovery and validation. Drug Discov Today 2009; 14:776-83. [PMID: 19477286 DOI: 10.1016/j.drudis.2009.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
Gene function assessment is a main task in biological networking investigations and system biology. High throughput technologies provide an impressive body of data that enables the design of hypotheses linking genes to phenotypes. When a putative scenario is depicted, gene knockdown technologies and RNA-dependent gene silencing are the most frequent approaches to assess the role of key effectors. In this paper, we discuss the relevance of hammerhead ribozymes in target discovery and validation, describing their properties and applications and highlighting their selectivity. In particular, similarities with siRNAs are presented and advantages and drawbacks are discussed. A description of the perspectives of ribozyme application in wide range studies is also provided, strengthening the value of these inhibitors for target validation purposes.
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Affiliation(s)
- Lorena Tedeschi
- Institute of Clinical Physiology, National Research Council, CNR, via Moruzzi, 1, 56124 Pisa, Italy.
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Robichaud GA, Perreault JP, Ouellette RJ. Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element. Nucleic Acids Res 2008; 36:4609-20. [PMID: 18617575 PMCID: PMC2504290 DOI: 10.1093/nar/gkn432] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Pax-5, is vital during B lymphocyte differentiation and is known to contribute to the oncogenesis of certain cancers. The Pax-5 locus generates multiple yet structurally related mRNA transcripts through the specific activation of alternative promoter regions and/or alternative splicing events which poses challenges in the study of specific isoform function. In this study, we investigated the function of a major Pax-5 transcript, Pax-5B using an enhanced version of the Hepatitis Delta Virus ribozyme (HDV Rz) suppression system that is specifically designed to recognize and cleave the human Pax-5B mRNA. The activity of these ribozymes resulted in the specific suppression of the Pax-5B transcripts without altering the transcript levels of other closely related Pax-5 isoforms mRNAs both in vitro and in an intracellular setting. Following stable transfection of the ribozymes into a model B cell line (REH), we showed that Pax-5B suppression led to an increase of CD19 mRNA and cell surface protein expression. In response to this Pax-5B specific deregulation, a marked increase in apoptotic activity compared to control cell lines was observed. These results suggest that Pax-5B has distinct roles in physiological processes in cell fate events during lymphocyte development.
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Affiliation(s)
- Gilles A Robichaud
- Département de biochimie, RNA Group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
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Tinsley RA, Walter NG. Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme. Biol Chem 2007; 388:705-15. [PMID: 17570823 DOI: 10.1515/bc.2007.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The HDV ribozyme is an RNA enzyme from the human pathogenic hepatitis delta virus (HDV) that has recently also been identified in the human genome. It folds into a compact, nested double-pseudoknot. We examined here the functional relevance of the capping loop L4 and the helical crossover J1/2, which tightly interlace the two helical stacks of the ribozyme. Peripheral structural elements such as these are present in cis-acting, but not trans-acting ribozymes, which may explain the order-of-magnitude decrease in cleavage activity observed in trans-acting ribozymes with promise in gene therapy applications. Comparison of a systematic set of cis- and trans-acting HDV ribozymes shows that the absence of either L4 or J1/2 significantly and independently impacts catalytic activity. Using terbium(III) footprinting and affinity studies, as well as distance measurements based on time-resolved fluorescence resonance energy transfer, we find that J1/2 is most important for conferring structural properties similar to those of the cis-acting ribozyme. Our results are consistent with a model in which removal of either a helical crossover or surprisingly a capping loop induces greater dynamics and expansion of the catalytic core at long range, impacting local and global folding, as well as catalytic function.
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Affiliation(s)
- Rebecca A Tinsley
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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