1
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CNS Delivery of Nucleic Acid Therapeutics: Beyond the Blood-Brain Barrier and Towards Specific Cellular Targeting. Pharm Res 2023; 40:77-105. [PMID: 36380168 DOI: 10.1007/s11095-022-03433-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acid-based therapeutic molecules including small interfering RNA (siRNA), microRNA(miRNA), antisense oligonucleotides (ASOs), messenger RNA (mRNA), and DNA-based gene therapy have tremendous potential for treating diseases in the central nervous system (CNS). However, achieving clinically meaningful delivery to the brain and particularly to target cells and sub-cellular compartments is typically very challenging. Mediating cell-specific delivery in the CNS would be a crucial advance that mitigates off-target effects and toxicities. In this review, we describe these challenges and provide contemporary evidence of advances in cellular and sub-cellular delivery using a variety of delivery mechanisms and alternative routes of administration, including the nose-to-brain approach. Strategies to achieve subcellular localization, endosomal escape, cytosolic bioavailability, and nuclear transfer are also discussed. Ultimately, there are still many challenges to translating these experimental strategies into effective and clinically viable approaches for treating patients.
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2
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Andersson P. Preclinical Safety Assessment of Therapeutic Oligonucleotides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2434:355-370. [PMID: 35213031 DOI: 10.1007/978-1-0716-2010-6_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
During the last decade, therapeutic oligonucleotide drugs (OND) have witnessed a tremendous development in chemistry and mechanistic understanding that have translated into successful clinical applications. Depending on the specific OND mechanism, chemistry, and design, the DMPK and toxicity properties can vary significantly between different OND classes and delivery approaches, the latter including lipid formulations or conjugation approaches to enhance productive OND uptake. At the same time, with the only difference between compounds being the nucleobase sequence, ONDs with same mechanism of action, chemistry, and design show relatively consistent behavior, allowing certain extrapolations between compounds within an OND class. This chapter provides a summary of the most common toxicities, the improved mechanistic understanding and the safety assessment activities performed for therapeutic oligonucleotides during the drug discovery and development process. Several of the considerations described for therapeutic applications should also be of value for the scientists mainly using oligonucleotides as research tools to explore various biological processes.
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Affiliation(s)
- Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
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3
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Titze-de-Almeida SS, Soto-Sánchez C, Fernandez E, Koprich JB, Brotchie JM, Titze-de-Almeida R. The Promise and Challenges of Developing miRNA-Based Therapeutics for Parkinson's Disease. Cells 2020; 9:cells9040841. [PMID: 32244357 PMCID: PMC7226753 DOI: 10.3390/cells9040841] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small double-stranded RNAs that exert a fine-tuning sequence-specific regulation of cell transcriptome. While one unique miRNA regulates hundreds of mRNAs, each mRNA molecule is commonly regulated by various miRNAs that bind to complementary sequences at 3’-untranslated regions for triggering the mechanism of RNA interference. Unfortunately, dysregulated miRNAs play critical roles in many disorders, including Parkinson’s disease (PD), the second most prevalent neurodegenerative disease in the world. Treatment of this slowly, progressive, and yet incurable pathology challenges neurologists. In addition to L-DOPA that restores dopaminergic transmission and ameliorate motor signs (i.e., bradykinesia, rigidity, tremors), patients commonly receive medication for mood disorders and autonomic dysfunctions. However, the effectiveness of L-DOPA declines over time, and the L-DOPA-induced dyskinesias commonly appear and become highly disabling. The discovery of more effective therapies capable of slowing disease progression –a neuroprotective agent–remains a critical need in PD. The present review focus on miRNAs as promising drug targets for PD, examining their role in underlying mechanisms of the disease, the strategies for controlling aberrant expressions, and, finally, the current technologies for translating these small molecules from bench to clinics.
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Affiliation(s)
- Simoneide S. Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, FAV, University of Brasilia, Brasília 70910-900, Brazil;
| | - Cristina Soto-Sánchez
- Neuroprosthetics and Visual Rehabilitation Research Unit, Bioengineering Institute, Miguel Hernández University, 03202 Alicante, Spain; (C.S.-S.); (E.F.)
| | - Eduardo Fernandez
- Neuroprosthetics and Visual Rehabilitation Research Unit, Bioengineering Institute, Miguel Hernández University, 03202 Alicante, Spain; (C.S.-S.); (E.F.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine—CIBER-BBN, 28029 Madrid, Spain
| | - James B. Koprich
- Krembil Neuroscience Centre, Toronto Western Hospital, University Health Network, Toronto, Ontario M5T 2S8, Canada; (J.B.K.); (J.M.B.)
| | - Jonathan M. Brotchie
- Krembil Neuroscience Centre, Toronto Western Hospital, University Health Network, Toronto, Ontario M5T 2S8, Canada; (J.B.K.); (J.M.B.)
| | - Ricardo Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, FAV, University of Brasilia, Brasília 70910-900, Brazil;
- Correspondence: ; Tel.: +55-61-3107-7222
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4
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The Race of 10 Synthetic RNAi-Based Drugs to the Pharmaceutical Market. Pharm Res 2017; 34:1339-1363. [PMID: 28389707 DOI: 10.1007/s11095-017-2134-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/27/2017] [Indexed: 02/08/2023]
Abstract
Ten years after Fire and Melo's Nobel Prize for discovery of gene silencing by double-stranded RNA, a remarkable progress was achieved in RNA interference (RNAi). Changes in the chemical structure of synthetic oligonucleotides make them more stable and specific, and new delivery strategies became progressively available. The attention of pharmaceutical industry rapidly turned to RNAi, as an opportunity to explore new drug targets. This review addresses nine small-interfering RNAs (siRNAs) and one unique microRNA (miRNA) inhibitor, which entered the phase 2-3 clinical trials. The siRNAs in focus are PF-04523655, TKM-080301, Atu027, SYL040012, SYL1001, siG12D-LODER (phase 2), QPI-1002, QPI-1007, and patisiran (phase 3). Regarding miRNAs, their content can be down- or up-regulated, by using miRNA inhibitors (AntimiRs) or miRNA mimics. Miravirsen is an AntimiR-122 for hepatitis C virus infection. The flexibility of RNAi technology is easily understood taking into account: (i) the different drug targets (i.e. p53, caspase 2, PKN3, β2-adrenergic receptor, mutated KRAS, microRNAs); (ii) therapeutic conditions, including ophthalmic diseases, kidney injury, amyloidosis, pancreatic cancer, viral hepatitis; and (iii) routes of administration (ocular, intravenous, subcutaneous, intratumoral). Although some issues are still matters of concern (delivery, toxicity, cost, and biological barriers), RNAi definitively opens a wide avenue for drug development.
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5
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Madhusudanan P, Reade S, Shankarappa SA. Neuroglia as targets for drug delivery systems: A review. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:667-679. [DOI: 10.1016/j.nano.2016.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 12/13/2022]
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6
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Tan JKY, Sellers DL, Pham B, Pun SH, Horner PJ. Non-Viral Nucleic Acid Delivery Strategies to the Central Nervous System. Front Mol Neurosci 2016; 9:108. [PMID: 27847462 PMCID: PMC5088201 DOI: 10.3389/fnmol.2016.00108] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022] Open
Abstract
With an increased prevalence and understanding of central nervous system (CNS) injuries and neurological disorders, nucleic acid therapies are gaining promise as a way to regenerate lost neurons or halt disease progression. While more viral vectors have been used clinically as tools for gene delivery, non-viral vectors are gaining interest due to lower safety concerns and the ability to deliver all types of nucleic acids. Nevertheless, there are still a number of barriers to nucleic acid delivery. In this focused review, we explore the in vivo challenges hindering non-viral nucleic acid delivery to the CNS and the strategies and vehicles used to overcome them. Advantages and disadvantages of different routes of administration including: systemic injection, cerebrospinal fluid injection, intraparenchymal injection and peripheral administration are discussed. Non-viral vehicles and treatment strategies that have overcome delivery barriers and demonstrated in vivo gene transfer to the CNS are presented. These approaches can be used as guidelines in developing synthetic gene delivery vectors for CNS applications and will ultimately bring non-viral vectors closer to clinical application.
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Affiliation(s)
- James-Kevin Y Tan
- Department of Bioengineering and Molecular Engineering & Sciences Institute, University of Washington Seattle, WA, USA
| | - Drew L Sellers
- Department of Bioengineering and Molecular Engineering & Sciences Institute, University of Washington Seattle, WA, USA
| | - Binhan Pham
- Department of Bioengineering and Molecular Engineering & Sciences Institute, University of Washington Seattle, WA, USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering & Sciences Institute, University of Washington Seattle, WA, USA
| | - Philip J Horner
- Center for Neuroregenerative Medicine, Houston Methodist Research Institute Houston, TX, USA
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7
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Enhancing the pharmacokinetic/pharmacodynamic properties of therapeutic nucleotides using lipid nanoparticle systems. Future Med Chem 2015; 7:1751-69. [PMID: 26399560 DOI: 10.4155/fmc.15.108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although activity has been reported in vivo, free nucleic acid-based drugs are rapidly degraded and cleared following systemic administration. To address these challenges and improve the potency and bioavailability of genetic drugs, significant efforts have been made to develop effective delivery systems of which lipid nanoparticles (LNP) represent the most advanced technology currently available. In this review, we will describe and discuss the improvements to the pharmacokinetic and pharmacodynamic properties of nucleic acid-based drugs mediated by LNP delivery. It is envisioned that the significant improvements in potency and safety, largely driven by the development of LNP encapsulated siRNA drugs, will be translatable to other types of genetic drugs and enable the rapid development of potent molecular tools and drugs.
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8
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Gupta K, Mattingly SJ, Knipp RJ, Afonin KA, Viard M, Bergman JT, Stepler M, Nantz MH, Puri A, Shapiro BA. Oxime ether lipids containing hydroxylated head groups are more superior siRNA delivery agents than their nonhydroxylated counterparts. Nanomedicine (Lond) 2015; 10:2805-18. [PMID: 26107486 DOI: 10.2217/nnm.15.105] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AIM To evaluate the structure-activity relationship of oxime ether lipids (OELs) containing modifications in the hydrophobic domains (chain length, degree of unsaturation) and hydrophilic head groups (polar domain hydroxyl groups) toward complex formation with siRNA molecules and siRNA delivery efficiency of resulting complexes to a human breast cancer cell line (MDA-MB-231). MATERIALS & METHODS Ability of lipoplex formation between oxime ether lipids with nucleic acids were examined using biophysical techniques. The potential of OELs to deliver nucleic acids and silence green fluorescent protein (GFP) gene was analyzed using MDA-MB-231 and MDA-MB-231/GFP cells, respectively. RESULTS & CONCLUSION Introduction of hydroxyl groups to the polar domain of the OELs and unsaturation into the hydrophobic domain favor higher transfection and gene silencing in a cell culture system.
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Affiliation(s)
- Kshitij Gupta
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | | | - Ralph J Knipp
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
| | - Kirill A Afonin
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.,Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Mathias Viard
- Basic Research Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.,Basic Science Program, Leidos Biomedical Research, Inc., National Cancer Institute, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Joseph T Bergman
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Marissa Stepler
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Michael H Nantz
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
| | - Anu Puri
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Bruce A Shapiro
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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9
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Akhtar J, Wang Z, Yu C, Zhang ZP. Effectiveness of local injection of lentivirus-delivered stathmin1 and stathmin1 shRNA in human gastric cancer xenograft mouse. J Gastroenterol Hepatol 2014; 29:1685-91. [PMID: 24720379 DOI: 10.1111/jgh.12594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM We have reported previously that RNA interference targeting stathmin1 (STMN1) gene in human gastric cancer cells inhibits proliferation in vitro and tumor growth in vivo. Based on these observations, in the present study, the possibility that local injection of lentivirus-delivered stathmin shRNA would induce regression of the established human gastric cancer xenograft in animal model was investigated. METHODS BALB/c nude mice were inoculated subcutaneously into the right armpit with human gastric cancer cells SGC-7901(2 × 10(6) cells in 200 μL phosphate-buffered saline) to develop a xenograft model of human gastric cancer. When tumor reached suitable size, mice were randomly divided into two groups. STMN1 shRNA group (n = 6) were given local injection of lentivirus-delivered STMN1 shRNA, and the non-silencing shRNA group (n = 6) were administered with local injection of lentivirus-delivered non-silencing shRNA. Quantitative reverse transcription-polymerase chain reaction and Western blot were used to verify the knockdown of the gene expression in dissected tumor at mRNA and protein level, respectively. RESULTS Experimental therapy on the nude mice model bearing subcutaneous tumor of SGC-7901 cells showed that local administration of STMN1 shRNA effectively regressed the pre-established tumors. Stathmin shRNA-treated tumors were significantly regressed as compared with that of the tumor injected with non-silencing shRNA (P < 0.05). Tumor weight was significantly decreased in STMN1-treated group as compared with non-silencing shRNA group (P < 0.05). Quantitative reverse transcription-polymerase chain reaction and Western blot showed downregulation of STMN1 gene expression in STMN1 shRNA group as compared with non-silencing shRNA group (P < 0.05). CONCLUSION These findings highlight the potential use of local injection of lentivirus-delivered shRNA for the treatment of early localized human gastric carcinoma.
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Affiliation(s)
- Javed Akhtar
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
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10
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Lin PJC, Tam Y, Cullis P. Development and clinical applications of siRNA-encapsulated lipid nanoparticles in cancer. ACTA ACUST UNITED AC 2014. [DOI: 10.2217/clp.14.27] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Oligonucleotide-based therapy for neurodegenerative diseases. Brain Res 2014; 1584:116-28. [PMID: 24727531 DOI: 10.1016/j.brainres.2014.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 12/12/2022]
Abstract
Molecular genetics insight into the pathogenesis of several neurodegenerative diseases, such as Alzheimer׳s disease, Parkinson׳s disease, Huntington׳s disease and amyotrophic lateral sclerosis, encourages direct interference with the activity of neurotoxic genes or the molecular activation of neuroprotective pathways. Oligonucleotide-based therapies are recently emerging as an efficient strategy for drug development and these can be employed as new treatments of neurodegenerative states. Here we review advances in this field in recent years which suggest an encouraging assessment that oligonucleotide technologies for targeting of RNAs will enable the development of new therapies and will contribute to preservation of brain integrity.
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12
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Sehgal A, Chen Q, Gibbings D, Sah DW, Bumcrot D. Tissue-specific gene silencing monitored in circulating RNA. RNA (NEW YORK, N.Y.) 2014; 20:143-149. [PMID: 24355758 PMCID: PMC3895267 DOI: 10.1261/rna.042507.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/12/2013] [Indexed: 06/03/2023]
Abstract
Pharmacologic target gene modulation is the primary objective for RNA antagonist strategies and gene therapy. Here we show that mRNAs encoding tissue-specific gene transcripts can be detected in biological fluids and that RNAi-mediated target gene silencing in the liver and brain results in quantitative reductions in serum and cerebrospinal fluid mRNA levels, respectively. Further, administration of an anti-miRNA oligonucleotide resulted in decreased levels of the miRNA in circulation. Moreover, ectopic expression of an adenoviral transgene in the liver was quantified based on measurement of serum mRNA levels. This noninvasive method for monitoring tissue-specific RNA modulation could greatly advance the clinical development of RNA-based therapeutics.
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Affiliation(s)
- Alfica Sehgal
- Alnylam Pharmaceuticals, Incorporated, Cambridge, Massachusetts 02142, USA
| | - Qingmin Chen
- Alnylam Pharmaceuticals, Incorporated, Cambridge, Massachusetts 02142, USA
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H8M5, Canada
| | - Dinah W.Y. Sah
- Alnylam Pharmaceuticals, Incorporated, Cambridge, Massachusetts 02142, USA
| | - David Bumcrot
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts 02139, USA
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13
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Silber J, Hashizume R, Felix T, Hariono S, Yu M, Berger MS, Huse JT, VandenBerg SR, James CD, Hodgson JG, Gupta N. Expression of miR-124 inhibits growth of medulloblastoma cells. Neuro Oncol 2012; 15:83-90. [PMID: 23172372 DOI: 10.1093/neuonc/nos281] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumor in children, and a substantial number of patients die as a result of tumor progression. Overexpression of CDK6 is present in approximately one-third of medulloblastomas and is an independent poor prognostic marker for this disease. MicroRNA (miR)-124 inhibits expression of CDK6 and prevents proliferation of glioblastoma and medulloblastoma cells in vitro. We examined the effects of miR-124 overexpression on medulloblastoma cells both in vitro and in vivo and compared cell lines that have low and high CDK6 expression. MiR-124 overexpression inhibits the proliferation of medulloblastoma cells, and this effect is mediated mostly through the action of miR-124 upon CDK6. We further show that induced expression of miR-124 potently inhibits growth of medulloblastoma xenograft tumors in rodents. Further testing of miR-124 will help define the ultimate therapeutic potential of preclinical models of medulloblastoma in conjunction with various delivery strategies for treatment.
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Affiliation(s)
- Joachim Silber
- Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California 94143, USA
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14
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Matsui M, Corey DR. Allele-selective inhibition of trinucleotide repeat genes. Drug Discov Today 2012; 17:443-50. [PMID: 22285529 PMCID: PMC3468950 DOI: 10.1016/j.drudis.2012.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/06/2011] [Accepted: 01/11/2012] [Indexed: 01/09/2023]
Abstract
Expanded trinucleotide repeats cause Huntington's disease (HD) and many other neurodegenerative disorders. There are no cures for these devastating illnesses and treatments are urgently needed. Each trinucleotide repeat disorder is the result of the mutation of just one gene, and agents that block expression of the mutant gene offer a promising option for treatment. Therapies that block expression of both mutant and wild-type alleles can have adverse effects, challenging researchers to develop strategies to lower levels of mutant protein while leaving adequate wild-type protein levels. Here, we review approaches that use synthetic nucleic acids to inhibit expression of trinucleotide repeat genes.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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15
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Abstract
RNA interference (RNAi) has been extensively employed for in vivo research since its use was first demonstrated in mammalian cells 10 years ago. Design rules have improved, and it is now routinely possible to obtain reagents that suppress expression of any gene desired. At the same time, increased understanding of the molecular basis of unwanted side effects has led to the development of chemical modification strategies that mitigate these concerns. Delivery remains the single greatest hurdle to widespread adoption of in vivo RNAi methods. However, exciting advances have been made and new delivery systems under development may help to overcome these barriers. This review discusses advances in RNAi biochemistry and biology that impact in vivo use and provides an overview of select publications that demonstrate interesting applications of these principles. Emphasis is placed on work with synthetic, small interfering RNAs (siRNAs) published since the first installment of this review which appeared in 2006.
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16
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Subcellular fate and off-target effects of siRNA, shRNA, and miRNA. Pharm Res 2011; 28:2996-3015. [PMID: 22033880 DOI: 10.1007/s11095-011-0608-1] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/12/2011] [Indexed: 12/13/2022]
Abstract
RNA interference (RNAi) strategies include double-stranded RNA (dsRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), and microRNA (miRNA). As this is a highly specific technique, efforts have been made to utilize RNAi towards potential knock down of disease-causing genes in a targeted fashion. RNAi has the potential to selectively inhibit gene expression by degrading or blocking the translation of the target mRNA. However, delivering these RNAs to specific cells presents a significant challenge. Some of these challenges result from the necessity of traversing the circulatory system while avoiding kidney filtration, degradation by endonucleases, aggregation with serum proteins, and uptake by phagocytes. Further, non-specific delivery may result in side-effects, including the activation of immune response. We discuss the challenges in the systemic delivery to target cells, cellular uptake, endosomal release and intracellular transport of RNAi drugs and recent progress in overcoming these barriers. We also discuss approaches that increase the specificity and metabolic stability and reduce the off-target effects of RNAi strategy.
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17
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Abstract
A brief historical introduction describes early attempts to silence specific genes using the antisense oligonucleotides that flourished in the 1980s. Early aspirations for therapeutic applications were almost extinguished by the unexpected complexity of oligonucleotide pharmacology. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. The biochemistry of small nucleic acids is outlined in Section 2. Various approaches employing oligonucleotides to control cellular functions are reviewed in Section 3. These include antisense oligonucleotides and siRNA that bind to RNA, antigene oligonucleotides that bind to DNA, and aptamers, decoys, and CpG oligonucleotides that bind to proteins.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Communicable Diseases/drug therapy
- Communicable Diseases/pathology
- CpG Islands
- DNA/chemistry
- DNA/metabolism
- DNA, Catalytic/chemistry
- DNA, Catalytic/pharmacology
- DNA, Catalytic/therapeutic use
- Diabetes Mellitus/drug therapy
- Diabetes Mellitus/pathology
- Humans
- MicroRNAs/chemistry
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Molecular Targeted Therapy/methods
- Neoplasms/drug therapy
- Neoplasms/pathology
- Neurodegenerative Diseases/drug therapy
- Neurodegenerative Diseases/pathology
- Nucleic Acid Hybridization
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- RNA, Catalytic/chemistry
- RNA, Catalytic/pharmacology
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
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Affiliation(s)
- John Goodchild
- Department of Chemistry, Worcester State University, Worcester, MA 01602-2597, USA.
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18
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Patwa A, Gissot A, Bestel I, Barthélémy P. Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications. Chem Soc Rev 2011; 40:5844-54. [PMID: 21611637 DOI: 10.1039/c1cs15038c] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hybrid lipid oligonucleotide conjugates are finding more and more biotechnological applications. This short critical review highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology (111 references).
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Affiliation(s)
- Amit Patwa
- Université Bordeaux Segalen, Bordeaux, F-33076, France
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19
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Maraganore DM. Rationale for therapeutic silencing of alpha-synuclein in Parkinson's disease. J Mov Disord 2011; 4:1-7. [PMID: 24868385 PMCID: PMC4027709 DOI: 10.14802/jmd.11001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 12/28/2010] [Indexed: 02/05/2023] Open
Abstract
The purpose of this paper is to provide the rationale for therapeutic silencing of the alpha-synuclein gene (SNCA) in Parkinson’s disease (PD). The paper reviews the public health significance of PD; the causal links between rare SNCA variants and familial PD; the association of common SNCA variants and PD susceptibility; the association of SNCA variants also with age at onset and motor and cognitive outcomes in PD; therapeutic strategies targeting SNCA in PD; and preliminary findings and considerations on small interfering RNA-based therapies and PD.
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Affiliation(s)
- Demetrius M Maraganore
- Ruth Cain Ruggles Chairman, Department of Neurology, and Medical Director, Neurological Institute, NorthShore University Health System, Evanston, IL, USA. Clinical Professor of Neurology, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
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20
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Uno Y, Piao W, Miyata K, Nishina K, Mizusawa H, Yokota T. High-density lipoprotein facilitates in vivo delivery of α-tocopherol-conjugated short-interfering RNA to the brain. Hum Gene Ther 2011; 22:711-9. [PMID: 21166521 DOI: 10.1089/hum.2010.083] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We originally reported the use of vitamin E (α-tocopherol) as an in vivo vector of short-interfering RNA (siRNA) to the liver. Here, we apply our strategy to the brain. By combining high-density lipoprotein (HDL) as a second carrier with α-tocopherol-conjugated siRNA (Toc-siRNA) in the brain, we achieved dramatic improvement of siRNA delivery to neurons. After direct intracerebroventricular (ICV) infusion of Toc-siRNA/HDL for 7 days, extensive and specific knock-down of a target gene, β-site amyloid precursor protein cleaving enzyme 1 (BACE1), was observed in both mRNA and protein levels, especially in the cerebral cortex and hippocampus. This new delivery method achieved a much more prominent down-regulation effect than conventional silencing methods of the brain gene, i.e., ICV infusion of nonconjugated siRNA or oligonucleotides. With only 3 nmol Toc-siRNA with HDL, BACE1 mRNA in the parietal cortex could be reduced by ∼ 70%. We suppose that this dramatic improvement of siRNA delivery to the brain is due to the use of lipoprotein receptor-mediated endocytosis because the silencing efficiency was significantly increased by binding of Toc-siRNA to the lipoprotein, and in contrast, was clearly decreased in lipoprotein-receptor knockout mice. These results suggest exogenous siRNA could be used clinically for otherwise incurable neurological diseases.
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Affiliation(s)
- Yoshitaka Uno
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-0034, Japan
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21
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Abstract
RNA interference (RNAi) has been regarded as a revolutionary tool for manipulating target biological processes as well as an emerging and promising therapeutic strategy. In contrast to the tangible and obvious effectiveness of RNAi in vitro, silencing target gene expression in vivo using small interfering RNA (siRNA) has been a very challenging task due to multiscale barriers, including rapid excretion, low stability in blood serum, nonspecific accumulation in tissues, poor cellular uptake and inefficient intracellular release. This minireview introduces major challenges in achieving efficient siRNA delivery in vivo and discusses recent advances in overcoming them using chemically modified siRNA, viral siRNA vectors and nonviral siRNA carriers. Enhanced specificity and efficiency of RNAi in vivo via selective accumulations in desired tissues, specific binding to target cells and facilitated intracellular trafficking are also commonly attempted utilizing targeting moieties, cell-penetrating peptides, fusogenic peptides and stimuli-responsive polymers. Overall, the crucial roles of the interdisciplinary approaches to optimizing RNAi in vivo, by efficiently and specifically delivering siRNA to target tissues and cells, are highlighted.
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Affiliation(s)
- Min Suk Shim
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697, USA
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22
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Abstract
Fire and Mello initiated the current explosion of interest in RNA interference (RNAi) biology with their seminal work in Caenorhabditis elegans. These observations were closely followed by the demonstration of RNAi in Drosophila melanogaster. However, the full potential of these new discoveries only became clear when Tuschl and colleagues showed that 21-22 bp RNA duplexes with 3" overhangs, termed small interfering (si)RNAs, could reliably execute RNAi in a range of mammalian cells. Soon afterwards, it became clear that many different human cell types had endogenous machinery, the RNA-induced silencing complex (RISC), which could be harnessed to silence any gene in the genome. Beyond the availability of a novel way to dissect biology, an important target validation tool was now available. More importantly, two key properties of the RNAi pathway - sequence-mediated specificity and potency - suggested that RNAi might be the most important pharmacological advance since the advent of protein therapeutics. The implications were profound. One could now envisage selecting disease-associated targets at will and expect to suppress proteins that had remained intractable to inhibition by conventional methods, such as small molecules. This review attempts to summarize the current understanding on siRNA lead discovery, the delivery of RNAi therapeutics, typical in vivo pharmacological profiles, preclinical safety evaluation and an overview of the 14 programs that have already entered clinical practice.
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Pasha S, Gupta K. Various drug delivery approaches to the central nervous system. Expert Opin Drug Deliv 2010; 7:113-35. [PMID: 20017662 DOI: 10.1517/17425240903405581] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
IMPORTANCE OF THE FIELD The presence of the blood-brain barrier (BBB), an insurmountable obstacle, in particular, and other barriers in brain and periphery contribute to hindrance of the successful diagnosis and treatment of a myriad of central nervous system pathologies. This review discusses several strategies adopted to define a rational drug delivery approach to the CNS along with a short description of the strategies implemented by the authors' group to enhance the analgesic activity, a CNS property, of chimeric peptide of Met-enkephalin and FMRFa (YGGFMKKKFMRFa-YFa). AREAS COVERED IN THIS REVIEW Various approaches for drug delivery to the CNS with their beneficial and non-beneficial aspects, supported by an extensive literature survey published recently, up to August 2009. WHAT THE READER WILL GAIN The reader will have the privilege of gaining an understanding of previous as well as recent approaches to breaching the CNS barriers. TAKE HOME MESSAGE Among the various strategies discussed, the potential for efficacious CNS drug targeting in future lies either with the non-invasively administered multifunctional nanosystems or these nanosystems without characterstics such as long systemic circulating capability and avoiding reticuloendothelial system scavenging system of the body, endogenous transporters and efflux inhibitors administered by convection-enhanced delivery.
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Affiliation(s)
- Santosh Pasha
- Institute of Genomics and Integrative Biology, Peptide Synthesis Laboratory, Mall Road, Delhi-110007, India.
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24
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Chen Q, Butler D, Querbes W, Pandey RK, Ge P, Maier MA, Zhang L, Rajeev KG, Nechev L, Kotelianski V, Manoharan M, Sah DWY. Lipophilic siRNAs mediate efficient gene silencing in oligodendrocytes with direct CNS delivery. J Control Release 2010; 144:227-32. [PMID: 20170694 DOI: 10.1016/j.jconrel.2010.02.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 10/19/2022]
Abstract
Conjugation of small interfering RNA (siRNA) with lipophilic molecules has been demonstrated to enhance cellular uptake in cell culture and to produce efficient endogenous gene silencing in the liver after systemic administration and in neurons after direct local injection. Here, we evaluated the in vivo delivery of siRNAs conjugated with different linkers to cholesterol by targeting CNPase (2'-3'-cyclic nucleotide 3'-phosphodiesterase) in oligodendrocytes. Cholesterol-conjugated siRNAs administered to the rat corpus callosum by intraparenchymal central nervous system (CNS) infusion show improved silencing ability compared with unconjugated siRNA. Furthermore, conjugation of siRNA to cholesterol with a cleavable disulfide linker appears to be beneficial for improving the potency of silencing of CNPase mRNA in oligodendrocytes in vivo. Taken together, these findings indicate that cholesterol-conjugated siRNAs are effective for direct CNS delivery to oligodendrocytes, and that the biocleavable disulfide linker appears to be beneficial for improving the potency of silencing of target mRNA in vivo.
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Affiliation(s)
- Qingmin Chen
- Alnylam Pharmaceuticals Inc., 300 Third Street, Cambridge, MA 02142, USA.
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25
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Huang V, Qin Y, Wang J, Wang X, Place RF, Lin G, Lue TF, Li LC. RNAa is conserved in mammalian cells. PLoS One 2010; 5:e8848. [PMID: 20107511 PMCID: PMC2809750 DOI: 10.1371/journal.pone.0008848] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Accepted: 01/06/2010] [Indexed: 11/18/2022] Open
Abstract
Background RNA activation (RNAa) is a newly discovered mechanism of gene activation triggered by small double-stranded RNAs termed ‘small activating RNAs’ (saRNAs). Thus far, RNAa has only been demonstrated in human cells and is unclear whether it is conserved in other mammals. Methodology/Principal Findings In the present study, we evaluated RNAa in cells derived from four mammalian species including nonhuman primates (African green monkey and chimpanzee), mouse, and rat. Previously, we identified saRNAs leading to the activation of E-cadherin, p21, and VEGF in human cells. As the targeted sequences are highly conserved in primates, transfection of each human saRNA into African green monkey (COS1) and chimpanzee (WES) cells also resulted in induction of the intended gene. Additional saRNAs targeting clinically relevant genes including p53, PAR4, WT1, RB1, p27, NKX3-1, VDR, IL2, and pS2 were also designed and transfected into COS1 and WES cells. Of the nine genes, p53, PAR4, WT1, and NKX3-1 were induced by their corresponding saRNAs. We further extended our analysis of RNAa into rodent cell types. We identified two saRNAs that induced the expression of mouse Cyclin B1 in NIH/3T3 and TRAMP C1 cells, which led to increased phosphorylation of histone H3, a downstream marker for chromosome condensation and entry into mitosis. We also identified two saRNAs that activated the expression of CXCR4 in primary rat adipose–derived stem cells. Conclusions/Significance This study demonstrates that RNAa exists in mammalian species other than human. Our findings also suggest that nonhuman primate disease models may have clinical applicability for validating RNAa-based drugs.
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Affiliation(s)
- Vera Huang
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Yi Qin
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Ji Wang
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Xiaoling Wang
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Robert F. Place
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Guiting Lin
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Tom F. Lue
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Long-Cheng Li
- Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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26
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Lasham A, Herbert M, Coppieters 't Wallant N, Patel R, Feng S, Eszes M, Cao H, Reid G. A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5' RACE and a molecular beacon probe. Nucleic Acids Res 2009; 38:e19. [PMID: 19942683 PMCID: PMC2817477 DOI: 10.1093/nar/gkp1076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Specific detection of mRNA cleavage by 5'RACE is the only method to confirm the knockdown of mRNA by RNA interference, but is rarely reported for in vivo studies. We have combined 5'-RNA-linker-mediated RACE (5'-RLM-RACE) with real-time PCR using a molecular beacon to develop a rapid and specific method termed MBRACE, which we have used to detect small-interfering RNA (siRNA)-induced cleavage of ApoB, RRM1 and YBX1 transcripts in vitro, and ApoB in vivo. When RNA from siRNA-transfected cells was used for 5'-RLM-RACE and a cleavage site-specific molecular beacon probe was included in subsequent real-time PCR analysis, the specific mRNA cleavage product was detected. Detection of siRNA-mediated cleavage was also observed when RNA from mouse liver following administration of ApoB-specific siRNA was analysed, even in cases where ApoB knockdown measured by real-time PCR was <10%. With its sensitivity and specificity, this variation on the 5'RACE method should prove a useful tool to detect mRNA cleavage and corroborate knockdown studies following siRNA use in vivo.
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Affiliation(s)
- Annette Lasham
- Genesis Research and Development Corporation Limited, Auckland, New Zealand
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