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Properties of Parallel Tetramolecular G-Quadruplex Carrying N-Acetylgalactosamine as Potential Enhancer for Oligonucleotide Delivery to Hepatocytes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123944. [PMID: 35745067 PMCID: PMC9228010 DOI: 10.3390/molecules27123944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/09/2023]
Abstract
The development of oligonucleotide conjugates for in vivo targeting is one of the most exciting areas for oligonucleotide therapeutics. A major breakthrough in this field was the development of multifunctional GalNAc-oligonucleotides with high affinity to asialoglycoprotein receptors (ASGPR) that directed therapeutic oligonucleotides to hepatocytes. In the present study, we explore the use of G-rich sequences functionalized with one unit of GalNAc at the 3'-end for the formation of tetrameric GalNAc nanostructures upon formation of a parallel G-quadruplex. These compounds are expected to facilitate the synthetic protocols by providing the multifunctionality needed for the binding to ASGPR. To this end, several G-rich oligonucleotides carrying a TGGGGGGT sequence at the 3'-end functionalized with one molecule of N-acetylgalactosamine (GalNAc) were synthesized together with appropriate control sequences. The formation of a self-assembled parallel G-quadruplex was confirmed through various biophysical techniques such as circular dichroism, nuclear magnetic resonance, polyacrylamide electrophoresis and denaturation curves. Binding experiments to ASGPR show that the size and the relative position of the therapeutic cargo are critical for the binding of these nanostructures. The biological properties of the resulting parallel G-quadruplex were evaluated demonstrating the absence of the toxicity in cell lines. The internalization preferences of GalNAc-quadruplexes to hepatic cells were also demonstrated as well as the enhancement of the luciferase inhibition using the luciferase assay in HepG2 cell lines versus HeLa cells. All together, we demonstrate that tetramerization of G-rich oligonucleotide is a novel and simple route to obtain the beneficial effects of multivalent N-acetylgalactosamine functionalization.
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2
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Tuning G-Quadruplex Nanostructures with Lipids. Towards Designing Hybrid Scaffolds for Oligonucleotide Delivery. Int J Mol Sci 2020; 22:ijms22010121. [PMID: 33374392 PMCID: PMC7796380 DOI: 10.3390/ijms22010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Two G-quadruplex forming oligonucleotides [d(TG4T)4 and d(TG6T)4] were selected as two tetramolecular quadruplex nanostructures because of their demonstrated ability to be modified with hydrophobic molecules. This allowed us to synthesize two series of G-quadruplex conjugates that differed in the number of G-tetrads, as well as in the terminal position of the lipid modification. Both solution and solid-phase syntheses were carried out to yield the corresponding lipid oligonucleotide conjugates modified at their 3′- and 5′-termini, respectively. Biophysical studies confirmed that the presence of saturated alkyl chains with different lengths did not affect the G-quadruplex integrity, but increased the stability. Next, the G-quadruplex domain was added to an 18-mer antisense oligonucleotide. Gene silencing studies confirmed the ability of such G-rich oligonucleotides to facilitate the inhibition of target Renilla luciferase without showing signs of toxicity in tumor cell lines.
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3
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Yau EH, Taggart RT, Zuber M, Trujillo AJ, Fayazi ZS, Butler MC, Sheflin LG, Breen JB, Yu D, Sullivan JM. Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics. Transl Vis Sci Technol 2019; 8:28. [PMID: 31853424 PMCID: PMC6908138 DOI: 10.1167/tvst.8.6.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose To systematically evaluate human rod opsin (hRHO) mRNA for potential target sites sensitive to posttranscriptional gene silencing (PTGS) by hammerhead ribozyme (hhRz) or RNA interference (RNAi) in human cells. To develop a comprehensive strategy to identify and optimize lead candidate agents for PTGS gene therapeutics. Methods In multidisciplinary RNA drug discovery, computational mRNA accessibility and in vitro experimental methods using reverse transcription–polymerase chain reaction (RT-PCR) were used to map accessibility in full-length hRHO transcripts. HhRzs targeted predicted accessible and inaccessible sites and were screened for cellular knockdown using a bicistronic reporter construct. Lead hhRz and RNAi PTGS agents were rationally optimized for target knockdown in human cells. Results Systematic screening of hRHO mRNA targeting agents resulted in lead candidate identification of a novel hhRz embedded in an RNA scaffold. Rational optimization strategies identified a minimal 725 hhRz as the most active agent. Recently identified tertiary accessory elements did not enhance activity. A 725-short-hairpin RNA (shRNA) agent exerts log-order knockdown. Silent modulation of the 725-hhRz target site in hRHO mRNA resulted in resistance to knockdown. Conclusions Combining rational RNA drug design with cell-based screening allowed rapid identification of lead agents targeting hRHO. Optimization strategies identified the agent with highest intracellular activity. These agents have therapeutic potential in a mutation-independent strategy for adRP, or other degenerations where hRHO is a target. This approach can be broadly applied to any validated target mRNA, regardless of the disease. Translational Relevance This work establishes a platform approach to develop RNA biologicals for the treatment of human disease.
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Affiliation(s)
- Edwin H Yau
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Department of Medicine, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Robert T Taggart
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Mohammed Zuber
- Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Current affiliation: Biologist, Office of Pesticide Programs, Environmental Protection Agency, Arlington, VA, USA
| | - Alexandria J Trujillo
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Zahra S Fayazi
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Mark C Butler
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Current affiliation: Custom ColLABorators, Buffalo, NY, USA
| | - Lowell G Sheflin
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA
| | - Jennifer B Breen
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Research Analyst II, Athenex, Buffalo, NY, USA
| | - Dian Yu
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Washington National Eye Center, Medstar Georgetown University Hospital/Medstar Washington Hospital, Washington, DC, USA
| | - Jack M Sullivan
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Department of Physiology/Biophysics, University at Buffalo-SUNY, Buffalo, NY, USA.,Neuroscience Program, University at Buffalo-SUNY, Buffalo, NY, USA.,SUNY Eye Institute, Albany, NY, USA.,RNA Institute at University at Albany-SUNY, Albany, NY, USA
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4
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Grijalvo S, Puras G, Zárate J, Sainz-Ramos M, Qtaish NAL, López T, Mashal M, Attia N, Díaz D, Pons R, Fernández E, Pedraz JL, Eritja R. Cationic Niosomes as Non-Viral Vehicles for Nucleic Acids: Challenges and Opportunities in Gene Delivery. Pharmaceutics 2019; 11:E50. [PMID: 30678296 PMCID: PMC6409589 DOI: 10.3390/pharmaceutics11020050] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
Cationic niosomes have become important non-viral vehicles for transporting a good number of small drug molecules and macromolecules. Growing interest shown by these colloidal nanoparticles in therapy is determined by their structural similarities to liposomes. Cationic niosomes are usually obtained from the self-assembly of non-ionic surfactant molecules. This process can be governed not only by the nature of such surfactants but also by others factors like the presence of additives, formulation preparation and properties of the encapsulated hydrophobic or hydrophilic molecules. This review is aimed at providing recent information for using cationic niosomes for gene delivery purposes with particular emphasis on improving the transportation of antisense oligonucleotides (ASOs), small interference RNAs (siRNAs), aptamers and plasmids (pDNA).
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Affiliation(s)
- Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
| | - Gustavo Puras
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Jon Zárate
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Myriam Sainz-Ramos
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Nuseibah A L Qtaish
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Tania López
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Mohamed Mashal
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Noha Attia
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - David Díaz
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain.
- Institut für Organische Chemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany.
| | - Ramon Pons
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Eduardo Fernández
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, E-03202 Elche, Spain.
| | - José Luis Pedraz
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, E-01006 Vitoria-Gasteiz and E-03202 Elche, Spain.
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Grijalvo S, Alagia A, Puras G, Zárate J, Mayr J, Pedraz JL, Eritja R, Díaz DD. Cationic nioplexes-in-polysaccharide-based hydrogels as versatile biodegradable hybrid materials to deliver nucleic acids. J Mater Chem B 2017; 5:7756-7767. [DOI: 10.1039/c7tb01691c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two polysaccharide-based hydrogels made of only κ-carrageenan (4%; w/v) or of a mixture of methylcellulose:κ-carrageenan (2%; w/v) were used to encapsulate cationic nioplexes.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Organic Chemistry
- University of Rgensburg
- 93040 Regensburg
- Germany
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
| | - Adele Alagia
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- 08034 Barcelona
- Spain
| | - Gustavo Puras
- Biomedical Research Networking Centre in Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
- 08034 Barcelona
- Spain
- NanoBioCel Group
| | - Jon Zárate
- Biomedical Research Networking Centre in Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
- 08034 Barcelona
- Spain
- NanoBioCel Group
| | - Judith Mayr
- Institute of Organic Chemistry
- University of Rgensburg
- 93040 Regensburg
- Germany
| | - José Luis Pedraz
- Biomedical Research Networking Centre in Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
- 08034 Barcelona
- Spain
- NanoBioCel Group
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- 08034 Barcelona
- Spain
- Biomedical Research Networking Centre in Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
| | - David Díaz Díaz
- Institute of Organic Chemistry
- University of Rgensburg
- 93040 Regensburg
- Germany
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
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6
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Lipid-modified oligonucleotide conjugates: Insights into gene silencing, interaction with model membranes and cellular uptake mechanisms. Bioorg Med Chem 2016; 25:175-186. [PMID: 27810441 DOI: 10.1016/j.bmc.2016.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 12/13/2022]
Abstract
The ability of oligonucleotides to silence specific genes or inhibit the biological activity of specific proteins has generated great interest in their use as research tools and therapeutic agents. Unfortunately, their biological applications meet the limitation of their poor cellular accessibility. Developing an appropriate delivery system for oligonucleotides is essential to achieve their efficient cellular uptake. In the present work a series of phosphorothioate lipid-oligonucleotide hybrids were synthesized introducing covalently single or double lipid tails at both 3'- and 5'-termini of an antisense oligonucleotide. Gene transfections in cultured cells showed antisense luciferase inhibition without the use of a transfecting agent for conjugates modified with the double-lipid tail at 5'-termini. The effect of the double lipid-tailed modification was further studied in detail in several model membrane systems as well as in cellular uptake experiments. During these studies the spontaneous formation of self-assembled microstructures is clearly observed. Lipidation allowed the efficient incorporation of the oligonucleotide in HeLa cells by a macropinocytosis mechanism without causing cytotoxicity in cells or altering the binding properties of the oligonucleotide conjugates. In addition, both single- and double-tailed compounds showed a similar behavior in lipid model membranes, making them useful in nucleotide-based technologies.
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7
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Grijalvo S, Alagia A, Gargallo R, Eritja R. Cellular uptake studies of antisense oligonucleotides using G-quadruplex-nanostructures. The effect of cationic residue on the biophysical and biological properties. RSC Adv 2016. [DOI: 10.1039/c6ra15336d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cellular uptake studies of G-quadruplex constructs having the Tetrahymena telomeric repeat sequence d(TGGGGT) modified with amino and guanidinium residues at the 3′-termini and an antisense oligonucleotide at 5′-termini were studied.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
| | - Adele Alagia
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
| | - Raimundo Gargallo
- University of Barcelona
- Department of Chemical Engineering and Analytical Chemistry
- E-08028 Barcelona
- Spain
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
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8
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Grijalvo S, Puras G, Zárate J, Pons R, Pedraz JL, Eritja R, Díaz DD. Nioplexes encapsulated in supramolecular hybrid biohydrogels as versatile delivery platforms for nucleic acids. RSC Adv 2016. [DOI: 10.1039/c6ra01005a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Supramolecular hydrogels based on N-protected phenylalanine (Fmoc–Phe–OH) were used to encapsulate non-ionic surfactant vesicles (niosomes).
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Affiliation(s)
- Santiago Grijalvo
- Institute of Organic Chemistry
- University of Regensburg
- D-93040 Regensburg
- Germany
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
| | - Gustavo Puras
- Biomedical Research Networking Center in Bioengineering
- Biomaterials and Nanomedicine (CIBER BBN)
- Spain
- NanoBioCel group
- University of the Basque Country (EHU-UPV)
| | - Jon Zárate
- Biomedical Research Networking Center in Bioengineering
- Biomaterials and Nanomedicine (CIBER BBN)
- Spain
- NanoBioCel group
- University of the Basque Country (EHU-UPV)
| | - Ramon Pons
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- Spain
| | - Jose Luis Pedraz
- Biomedical Research Networking Center in Bioengineering
- Biomaterials and Nanomedicine (CIBER BBN)
- Spain
- NanoBioCel group
- University of the Basque Country (EHU-UPV)
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- Spain
- Biomedical Research Networking Center in Bioengineering
- Biomaterials and Nanomedicine (CIBER BBN)
- Spain
| | - David Díaz Díaz
- Institute of Organic Chemistry
- University of Regensburg
- D-93040 Regensburg
- Germany
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
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9
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Grijalvo S, Eritja R. Synthesis and in vitro inhibition properties of oligonucleotide conjugates carrying amphipathic proline-rich peptide derivatives of the sweet arrow peptide (SAP). Mol Divers 2012; 16:307-17. [PMID: 22392648 DOI: 10.1007/s11030-012-9365-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/13/2012] [Indexed: 11/25/2022]
Abstract
In this study, a series of derivatives of the amphipathic proline-rich sweet arrow peptide (SAP) were covalently linked to antisense oligonucleotides designed to inhibit Renilla luciferase gene. Oligonucleotide-peptide conjugates carrying lysine (Lys) and ornithine (Orn) residues were prepared using the stepwise approach by assembling first the peptide sequence followed by the assembly of the DNA molecule. The resulting Lys, Orn-conjugates were transformed to the corresponding arginine and homoarginine oligonucleotide-peptide conjugates by reaction with O-methylisourea. The introduction of the SAP at 3'-termini of a phosphorothioate oligonucleotide did not affect the ability to inhibit gene expression when transfected with lipofectamine. However, these conjugates were not able to enter cells without transfecting agent. Further studies using SAP as a transfection agent showed promising results for the conjugates carrying the Orn-SAP. All conjugates showed high duplex stabilities.
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10
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Sullivan JM, Yau EH, Kolniak TA, Sheflin LG, Taggart RT, Abdelmaksoud HE. Variables and strategies in development of therapeutic post-transcriptional gene silencing agents. J Ophthalmol 2011; 2011:531380. [PMID: 21785698 PMCID: PMC3138052 DOI: 10.1155/2011/531380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 02/17/2011] [Accepted: 02/28/2011] [Indexed: 11/24/2022] Open
Abstract
Post-transcriptional gene silencing (PTGS) agents such as ribozymes, RNAi and antisense have substantial potential for gene therapy of human retinal degenerations. These technologies are used to knockdown a specific target RNA and its cognate protein. The disease target mRNA may be a mutant mRNA causing an autosomal dominant retinal degeneration or a normal mRNA that is overexpressed in certain diseases. All PTGS technologies depend upon the initial critical annealing event of the PTGS ligand to the target RNA. This event requires that the PTGS agent is in a conformational state able to support hybridization and that the target have a large and accessible single-stranded platform to allow rapid annealing, although such platforms are rare. We address the biocomplexity that currently limits PTGS therapeutic development with particular emphasis on biophysical variables that influence cellular performance. We address the different strategies that can be used for development of PTGS agents intended for therapeutic translation. These issues apply generally to the development of PTGS agents for retinal, ocular, or systemic diseases. This review should assist the interested reader to rapidly appreciate critical variables in PTGS development and facilitate initial design and testing of such agents against new targets of clinical interest.
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Affiliation(s)
- Jack M. Sullivan
- Department of Ophthalmology, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Department of Pharmacology and Toxicology, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Department of Physiology and Biophysics, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Neuroscience Program, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Ross Eye Institute, University at Buffalo SUNY, Buffalo, NY 14209, USA
- Veterans Administration Western New York Healthcare System, Medical Research, Buffalo, NY 14215, USA
| | - Edwin H. Yau
- Department of Ophthalmology, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Department of Pharmacology and Toxicology, University at Buffalo SUNY, Buffalo, NY 14214, USA
| | - Tiffany A. Kolniak
- Department of Ophthalmology, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Neuroscience Program, University at Buffalo SUNY, Buffalo, NY 14214, USA
| | - Lowell G. Sheflin
- Department of Ophthalmology, University at Buffalo SUNY, Buffalo, NY 14214, USA
- Veterans Administration Western New York Healthcare System, Medical Research, Buffalo, NY 14215, USA
| | - R. Thomas Taggart
- Department of Ophthalmology, University at Buffalo SUNY, Buffalo, NY 14214, USA
| | - Heba E. Abdelmaksoud
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY 13215, USA
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11
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Fang H, Shen Y, Taylor JS. Native mRNA antisense-accessible sites library for the selection of antisense oligonucleotides, PNAs, and siRNAs. RNA (NEW YORK, N.Y.) 2010; 16:1429-1435. [PMID: 20498459 PMCID: PMC2885691 DOI: 10.1261/rna.1940610] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 04/01/2010] [Indexed: 05/29/2023]
Abstract
A procedure for rapidly generating a library of antisense-accessible sites on native mRNAs (mRNA antisense-accessible sites library [MASL]) is described that involves reverse transcription of whole cell mRNA extracts with a random oligodeoxynucleotide primer followed by mRNA-specific polymerase chain reaction (PCR). Antisense phosphorothioate oligodeoxynucleotides (ODNs), peptide nucleic acids (PNAs), and small interfering RNAs (siRNAs) can then be identified by screening against the antisense-accessible sites. The utility of this methodology is demonstrated for the identification of more effective inhibitors of inducible nitric oxide synthase (iNOS) induction than have previously been reported. This method may also be useful for constraining folding calculations of native mRNAs and for designing mRNA imaging probes.
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Affiliation(s)
- Huafeng Fang
- Department of Chemistry, Washington University, St Louis, Missouri 63130, USA
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12
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Stepwise synthesis of oligonucleotide-peptide conjugates containing guanidinium and lipophilic groups in their 3'-termini. Bioorg Med Chem Lett 2010; 20:2144-7. [PMID: 20206515 DOI: 10.1016/j.bmcl.2010.02.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 02/04/2023]
Abstract
Two different series of oligonucleotide-peptide conjugates have been efficiently synthesized by stepwise solid-phase synthesis. First, oligonucleotides and oligonucleotide phosphorothioates containing polar groups at the 3'-termini, such as amine and guanidinium groups were prepared. ODNs conjugates carrying several lysine residues were obtained directly from Fmoc deprotection whereas ODN conjugates with guanidinium groups were obtained by post-synthetic guanidinylation. The second family contains different urea moieties that were achieved by standard protocols. All products were fully characterized by reversed phase HPLC and MALDI-TOF mass spectrometry yielding satisfactory results. Oligonucleotide-phosphorothioate conjugates were evaluated as potential antisense oligonucleotides in the inhibition of the luciferase gene.
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13
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Chen M, Du Q, Zhang HY, Wang X, Liang Z. High-throughput screening using siRNA (RNAi) libraries. Expert Rev Mol Diagn 2009; 7:281-91. [PMID: 17489735 DOI: 10.1586/14737159.7.3.281] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA interference (RNAi) has become one of the most important research tools in functional genomics analysis ever since the discovery of the phenomenon. The robustness of the method has enabled construction of RNAi libraries in the forms of long double-stranded RNA or short-interfering RNA that can cover the whole or significant parts of the genomes of different organisms. Over the last few years, such libraries have been used in different high-throughput formats to establish functional links between genes and phenotypes. In this review, available RNAi library resources and application of these strategic tools will be discussed.
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Affiliation(s)
- Meihong Chen
- Chinese Human Genome Center Beijing, Institute of Basic Medical Sciences, Beijing, China.
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14
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Ahmad S. Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA. Gene 2008; 428:25-30. [PMID: 18955120 DOI: 10.1016/j.gene.2008.09.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 09/06/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
Solvent accessibility of amino acid residues in proteins has been widely studied and many methods for its prediction from sequence and evolutionary information are available. Some of the advantages of studying amino acid solvent accessibility also apply to DNA. However, currently there are no methods to estimate the solvent accessibility of nucleotides, as most works on DNA structures have focused on elastic deformations and other structural attributes. In this work, an attempt has been made to analyze the distribution of different nucleotides in various accessibility ranges. Effect of neighboring nucleotides on the predictability of exposure has been evaluated by developing a linear perceptron model that takes sequence information as the input. Five different types of solvent accessibility (overall nucleotide, side chain, main chain, polar and non-polar) have been predicted. From the analysis, it is observed that Thymine stands out in terms of its higher exposed surface area, particularly its side chain and non-polar atoms. It is also concluded that the solvent accessibility of a nucleotide strongly depends on its sequence neighbors and can be predicted with fair success using this information.
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Affiliation(s)
- Shandar Ahmad
- National Institute of Biomedical Innovation, 7-6-8 Saito-asagi, Ibaraki-shi, Osaka, Japan.
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15
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Sullivan JM, Yau EH, Taggart RT, Butler MC, Kolniak TA. Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents. Vision Res 2007; 48:453-69. [PMID: 17976683 DOI: 10.1016/j.visres.2007.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 08/31/2007] [Accepted: 09/04/2007] [Indexed: 11/28/2022]
Abstract
Development of post-transcriptional gene silencing (PTGS) agents for therapeutic purposes is an immense challenge in modern biology. Established technologies used to knockdown a specific target RNA and its cognate protein: antisense, ribozyme, RNAi, all conditionally depend upon an initial, critical annealing event of the PTGS ligand to a target RNA. In this review we address the nature of the bottlenecks, emphasizing the biocomplexity of target RNA structure, that currently limit PTGS therapeutic development. We briefly review existing and emerging technologies designed to release these constraints to realize the potential of PTGS agents in gene based therapies.
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Affiliation(s)
- Jack M Sullivan
- Department of Ophthalmology, SUNY, University at Buffalo, Veterans Administration Western New York Healthcare System, Medical Research, Building 20, Room 245, 3495 Bailey Avenue, Buffalo, NY 14215, USA.
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16
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17
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Bo X, Lou S, Sun D, Shu W, Yang J, Wang S. Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. BMC Bioinformatics 2006; 7:122. [PMID: 16526963 PMCID: PMC1421440 DOI: 10.1186/1471-2105-7-122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 03/09/2006] [Indexed: 01/31/2023] Open
Abstract
Background Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed. Results Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly correlated with efficacy than indices of the proportion of bases in single-stranded or double-stranded regions. The local structures of the target site 5' and 3' termini were also shown to be important in target selection. Neural network efficacy predictors using these features, defined on integrated structures as inputs, performed well in "minus-one-gene" cross-validation experiments. Conclusion Topologically different target mRNA structures can be merged into integrated representations and then used in computer-aided ODN design. The results of this paper imply that some features characterizing multiple predicted target site structures can be used to predict ODN efficacy.
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Affiliation(s)
- Xiaochen Bo
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
| | - Shaoke Lou
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
| | - Daochun Sun
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
| | - Wenjie Shu
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
| | - Jing Yang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, P R China
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18
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Bo X, Lou S, Sun D, Yang J, Wang S. AOBase: a database for antisense oligonucleotides selection and design. Nucleic Acids Res 2006; 34:D664-7. [PMID: 16381954 PMCID: PMC1347428 DOI: 10.1093/nar/gkj065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antisense oligonucleotides (ODNs) technology is one of the important approaches for the sequence-specific knockdown of gene expression. ODNs have been used as research tools in the post-genome era, as well as new types of therapeutic agents. Since finding effective target sites within RNA is a hard work for antisense ODNs design, various experimental methods and computational approaches have been proposed. For better sharing of the experimented and published ODNs, valid and invalid ODNs reported in literatures are screened, collected and stored in AOBase. Till now, ∼700 ODNs against 46 target mRNAs are contained in AOBase. Entries can be explored via TargetSearch and AOSearch web retrieval interfaces. AOBase can not only be useful in ODNs selection for gene function exploration, but also contribute to mining rules and developing algorithms for rational ODNs design. AOBase is freely accessible via .
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Affiliation(s)
| | | | | | | | - Shengqi Wang
- To whom correspondence should be addressed. Tel/Fax: +86 10 68210077 932211;
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19
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Abstract
Antisense agents are powerful tools to inhibit gene expression in a sequence-specific manner. They are used for functional genomics, as diagnostic tools and for therapeutic purposes. Three classes of antisense agents can be distinguished by their mode of action: single-stranded antisense oligodeoxynucleotides; catalytic active RNA/DNA such as ribozymes, DNA- or locked nucleic acid (LNA)zymes; and small interfering RNA molecules known as siRNA. The selection of target sites in highly structured RNA molecules is crucial for their successful application. This is a difficult task, since RNA is assembled into nucleoprotein complexes and forms stable secondary structures in vivo, rendering most of the molecule inaccessible to intermolecular base pairing with complementary nucleic acids. In this review, we discuss several selection strategies to identify potential target sites in RNA molecules. In particular, we focus on combinatorial library approaches that allow high throughput screening of sequences for the design of antisense agents.
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Affiliation(s)
- M Lützelberger
- Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé 130, 8000 Aarhus C, Denmark
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20
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Fang H, Yue X, Li X, Taylor JS. Identification and characterization of high affinity antisense PNAs for the human unr (upstream of N-ras) mRNA which is uniquely overexpressed in MCF-7 breast cancer cells. Nucleic Acids Res 2005; 33:6700-11. [PMID: 16314303 PMCID: PMC1297704 DOI: 10.1093/nar/gki968] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have recently shown that an MCF-7 tumor can be imaged in a mouse by PET with 64Cu-labeled Peptide nucleic acids (PNAs) tethered to the permeation peptide Lys4 that recognize the uniquely overexpressed and very abundant upstream of N-ras or N-ras related gene (unr mRNA) expressed in these cells. Herein we describe how the high affinity antisense PNAs to the unr mRNA were identified and characterized. First, antisense binding sites on the unr mRNA were mapped by an reverse transcriptase random oligonucleotide library (RT-ROL) method that we have improved, and by a serial analysis of antisense binding sites (SAABS) method that we have developed which is similar to another recently described method. The relative binding affinities of oligodeoxynucleotides (ODNs) complementary to the antisense binding sites were then qualitatively ranked by a new Dynabead-based dot blot assay. Dissociation constants for a subset of the ODNs were determined by a new Dynabead-based solution assay and were found to be 300 pM for the best binders in 1 M salt. PNAs corresponding to the ODNs with the highest affinities were synthesized with an N-terminal CysTyr and C-terminal Lys4 sequence. Dissociation constants of these hybrid PNAs were determined by the Dynabead-based solution assay to be about 10 pM for the highest affinity binders.
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Affiliation(s)
| | | | | | - John-Stephen Taylor
- To whom correspondence should be addressed. Tel: +1 314 935 6721; Fax: +1 314 935 4481;
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21
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Far RKK, Leppert J, Frank K, Sczakiel G. Technical improvements in the computational target search for antisense oligonucleotides. Oligonucleotides 2005; 15:223-33. [PMID: 16201910 DOI: 10.1089/oli.2005.15.223] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A number of theoretical and experimental approaches to design biologically active antisense oligonucleotides (AS-ON) have proven their usefulness. This includes systematic computational strategies that are based on the understanding of antisense mechanisms. Here, we investigate in detail the relationship between computational parameters of the local target search for the theoretical design of AS-ON and the hit rate, that is, the biologic efficacy of AS-ON in cell culture. The computational design of AS-ON studied in this work is based on an established algorithm to predict structurally favorable local target sites along a given target RNA against which AS-ON are directed. Briefly, a sequence segment of a certain length (window) is used to predict a group of lowest-energy RNA secondary structures. Subsequently, this window is shifted along the target sequence by a certain step width. To date, those technical parameters of the systematic structural target analysis have been chosen arbitrarily. Here, we investigate their role for the successful design of AS-ON and suggest an optimized computer-based protocol for the selection of favorable local target sequences and, hence, an improved design of active AS-ON. Further, this study provides systematic insights into the structure- function relationship of AS-ON.
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22
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Thonberg H, Dahlgren C, Wahlestedt C. Antisense-induced Fas mRNA degradation produces site-specific stable 3'-mRNA fragment by exonuclease cleavage at the complementary sequence. Oligonucleotides 2005; 14:221-6. [PMID: 15625917 DOI: 10.1089/oli.2004.14.221] [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: 11/13/2022]
Abstract
Antisense-mediated degradation of target mRNA is achieved by the enzymatic action of nuclease RNase H. The enzyme recognizes hybrid RNA-DNA duplexes and hydrolyzes the RNA strand. Here, we compared six different phosphorothioate oligonucleotides for their ability to induce target-specific mRNA degradation in cultured mouse AML12 cells. We targeted transcripts of the cell surface receptor Fas and analyzed the levels of mRNA by Northern blotting and ribonuclease protection assay (RPA). Four of the tested antisense oligonucleotides reduced the mRNA levels significantly. Cultures treated with one of the antisense molecules resulted in a shifted band on Northern blots. This band of lower molecular weight was not detected after 6 hours of transfection but appeared at 24 hours. By RPA, the product was shown to be a 3'-cleavage fragment of the full-length Fas mRNA. The RPA also mapped the stable fragment to start within the antisense complementary sequence.
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Affiliation(s)
- Håkan Thonberg
- Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, Sweden.
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23
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Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 2005; 6:31. [PMID: 15755320 PMCID: PMC555549 DOI: 10.1186/1471-2164-6-31] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Accepted: 03/08/2005] [Indexed: 12/23/2022] Open
Abstract
Background Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybridization by stable secondary structures in the probe binding site. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment. Results Despite the relatively high hybridization temperatures and 1M monovalent salt imposed in the modeling process to approximate hybridization conditions used in the laboratory, we find that parts of the target molecules are likely to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. For example, at 65°C, 28 ± 7% of the average cDNA target sequence is predicted to be inaccessible to hybridization. We also analyzed the specific binding sites of a set of 70mer probes previously designed for Brucella using a freely available oligo design software package. 21 ± 13% of the nucleotides in each probe binding site are within a double-stranded structure in over half of the folds predicted for the cDNA target at 65°C. The intramolecular structures formed are more stable and extensive when an RNA target is modeled rather than cDNA. When random shearing of the target is modeled for fragments of 200, 100 and 50 nt, an overall destabilization of secondary structure is predicted, but shearing does not eliminate secondary structure. Conclusion Secondary structure in the target is pervasive, and a significant fraction of the target is found in double stranded conformations even at high temperature. Stable structure in the target has the potential to interfere with hybridization and should be a factor in interpretation of microarray results, as well as an explicit criterion in array design. Inclusion of this property in an oligonucleotide design procedure would change the definition of an optimal oligonucleotide significantly.
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24
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Bo X, Wang S. TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatics 2004; 21:1401-2. [PMID: 15598838 DOI: 10.1093/bioinformatics/bti211] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotide (AO) selection based on mRNA accessible site tagging (MAST) and secondary structures of target mRNA. To make MAST result intuitive, both the alignment result and tag frequency profile is illustrated. As theoretical reference, secondary structure and single strand probability profile of target mRNA is also represented. All of these sequences and profiles are displayed in aligned mode, which facilitates identification of the accessible sites in target mRNA. Graphical, user-friendly interface makes TargetFinder a useful tool in AO target site selection. AVAILABILITY The software is freely available at http://www.bioit.org.cn/ao/targetfinder.htm CONTACT sqwang@nic.bmi.ac.cn.
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Affiliation(s)
- Xiaochen Bo
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China
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25
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Camps-Valls G, Chalk AM, Serrano-López AJ, Martín-Guerrero JD, Sonnhammer ELL. Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinformatics 2004; 5:135. [PMID: 15383156 PMCID: PMC526382 DOI: 10.1186/1471-2105-5-135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 09/22/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules including 68 features each, inducing a problem well-suited to SVMs. The task of feature selection is crucial given the presence of noisy or redundant features, and the well-known problem of the curse of dimensionality. We propose a two-stage strategy to develop an optimal model: (1) feature selection using correlation analysis, mutual information, and SVM-based recursive feature elimination (SVM-RFE), and (2) AO prediction using standard and profiled SVM formulations. A profiled SVM gives different weights to different parts of the training data to focus the training on the most important regions. RESULTS In the first stage, the SVM-RFE technique was most efficient and robust in the presence of low number of samples and high input space dimension. This method yielded an optimal subset of 14 representative features, which were all related to energy and sequence motifs. The second stage evaluated the performance of the predictors (overall correlation coefficient between observed and predicted efficacy, r; mean error, ME; and root-mean-square-error, RMSE) using 8-fold and minus-one-RNA cross-validation methods. The profiled SVM produced the best results (r = 0.44, ME = 0.022, and RMSE= 0.278) and predicted high (>75% inhibition of gene expression) and low efficacy (<25%) AOs with a success rate of 83.3% and 82.9%, respectively, which is better than by previous approaches. A web server for AO prediction is available online at http://aosvm.cgb.ki.se/. CONCLUSIONS The SVM approach is well suited to the AO prediction problem, and yields a prediction accuracy superior to previous methods. The profiled SVM was found to perform better than the standard SVM, suggesting that it could lead to improvements in other prediction problems as well.
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Affiliation(s)
- Gustavo Camps-Valls
- Grup de Processament Digital de Senyals, Universitat de València, Spain. C/ Dr. Moliner, 50. 46100 Burjassot, València, Spain
| | - Alistair M Chalk
- Center for Genomics and Bioinformatics (CGB), Karolinska Institutet, S-17177, Stockholm, Sweden
| | - Antonio J Serrano-López
- Grup de Processament Digital de Senyals, Universitat de València, Spain. C/ Dr. Moliner, 50. 46100 Burjassot, València, Spain
| | - José D Martín-Guerrero
- Grup de Processament Digital de Senyals, Universitat de València, Spain. C/ Dr. Moliner, 50. 46100 Burjassot, València, Spain
| | - Erik LL Sonnhammer
- Center for Genomics and Bioinformatics (CGB), Karolinska Institutet, S-17177, Stockholm, Sweden
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26
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Thonberg H, Schéele CC, Dahlgren C, Wahlestedt C. Characterization of RNA interference in rat PC12 cells: requirement of GERp95. Biochem Biophys Res Commun 2004; 318:927-34. [PMID: 15147961 DOI: 10.1016/j.bbrc.2004.04.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Indexed: 11/22/2022]
Abstract
Double-stranded RNA can initiate post transcriptional gene silencing in mammalian cell cultures via a mechanism known as RNA interference (RNAi). The sequence-specific degradation of homologous mRNA is triggered by 21-nucleotide RNA-duplexes termed short interfering RNA (siRNA). The homologous strand of the siRNA guides a multi-protein complex, RNA-induced silencing complex (RISC), to cleave target mRNA. Although the exact function and composition of RISC is still unclear, it has been shown to include several proteins of the Argonaute protein family. Here we report of a robust system to achieve RNAi in a cultured rat neuronal cell line, PC12. Targeting of neuropeptide Y mRNA by synthetic siRNA results in knock down of the mRNA levels with an IC50 of approximately 0.1 nM. The mRNA knockdown lasts for at least 96 h and is not dependent on protein synthesis. Further, PC12 cells were ablated of the rat Golgi-ER protein 95 kDa (GERp95), an Argonaute family protein, by siRNA methodology. After GERp95-ablation, sequential knockdown of NPY by siRNA was shown to be impaired. Thus, we report that the GERp95 protein is functionally required for RNAi targeting NPY in rat PC12 cells.
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Affiliation(s)
- Håkan Thonberg
- Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, S-171 77 Stockholm, Sweden.
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27
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Wu Y, Zhang X, Zehner ZE. c-Jun and the dominant-negative mutant, TAM67, induce vimentin gene expression by interacting with the activator Sp1. Oncogene 2004; 22:8891-901. [PMID: 14654785 DOI: 10.1038/sj.onc.1206898] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Vimentin exhibits a complex pattern of developmental- and tissue-specific expression. Since it is aberrantly expressed in metastatic tumors, which have progressed through the epithelial-mesenchymal transition, it has been cited as a marker for tumor progression. Previous studies have indicated that the transcription factor activator protein (AP1) is important in tumor progression. The stable transformation of the MCF7 cell line with the oncogene c-Jun resulted in a cell line (MCF7Jun), which displayed a change in morphology, enhanced migratory and invasive properties, and metastatic behavior. Of the 21 genes whose expression levels were altered in the MCF7Jun cell line, the greatest change in expression occurred for the vimentin gene. Previously, tandem AP1 sites in the promoter were reported to be important for the serum and TPA inducibility of the vimentin gene. However, we find that the AP1 elements only contribute in part to c-Jun activation. Moreover, this activation can be duplicated in COS-1 or S2 cells by expression of c-Jun or TAM67, and is dependent only on the leucine-zipper region of c-Jun. Transient transfection analyses, electrophoretic mobility shift assays, DNA precipitation assays, and coimmunoprecipitation studies suggest that c-Jun is able to synergize with the activator protein Sp1 in binding to GC-box1 to enhance vimentin gene expression.
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Affiliation(s)
- Yongzhong Wu
- Department of Biochemistry and the Massey Cancer Center, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298-0614, USA
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28
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Xu Y, Zhang HY, Thormeyer D, Larsson O, Du Q, Elmén J, Wahlestedt C, Liang Z. Effective small interfering RNAs and phosphorothioate antisense DNAs have different preferences for target sites in the luciferase mRNAs. Biochem Biophys Res Commun 2003; 306:712-7. [PMID: 12810077 DOI: 10.1016/s0006-291x(03)01024-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antisense DNA target sites can be selected by the accessibility of the mRNA target. It remains unknown whether a mRNA site that is accessible to an antisense DNA is also a good candidate target site for a siRNA. Here, we reported a parallel analysis of 12 pairs of antisense DNAs and siRNA duplexes for their potency to inhibit reporter luciferase activity in mammalian cells, both of the antisense DNA and siRNA agents in a pair being directed to same site in the mRNA. Five siRNAs and two antisense DNAs turned out to be effective, but the sites targeted by those effective siRNAs and antisense DNAs did not overlap. Our results indicated that effective antisense DNAs and siRNAs have different preferences for target sites in the mRNA.
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Affiliation(s)
- Yunhe Xu
- Center for Genomics and Bioinformatics, Karolinska Institute, 17177, Stockholm, Sweden
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