1
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Sun X, Zhao X, Xu Y, Yan Y, Han L, Wei M, He M. Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes. Cancer Lett 2024; 588:216794. [PMID: 38453043 DOI: 10.1016/j.canlet.2024.216794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.
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Affiliation(s)
- Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Xinyi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China; Liaoning Medical Diagnosis and Treatment Center, Liaoning Province, China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
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2
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Li D, Guo F, Yue H, Huang Y, Lu C, Guo Y, Liu Q, Li Y. An Artificial Small RNA Editor by Chimeric dsRNase with RNA Binding Protein. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA plays a vital role in cell functions, but tools to manipulate it is limited. RNA interference (RNAi) is an important approach for biological and clinical applications, but the prone of non-target knockdown effects limited the usage. CRISPR-Cas13 systems recently have been identified
for RNA-guided RNA-interfering activity, and can be used in therapeutics, but the large size of Cas13 proteins and the off-targets effect also limit their further usage. Here we report that the chimeric protein containing a double strand nuclease/domain and a structure RNA binding domain (dsRNase-stRBD)
with structure guided RNA (sgRNA) can be engineered for mammalian RNA silencing effectively. The RNA knockdown mediated by this method was durable, efficient and stringent without off-target interfering by the sense strand of shRNA base method. Moreover, at size of only 307 aa, allowing dsRNase-stRBD
fitting for the versatile scAAV, while the most recent report displays that the smallest Cas13 protein is 775 aa. These results establish sgRNA-dsRBD-RNase as an excellent method for studying RNA function of cells and further clinical application.
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Affiliation(s)
- Danhua Li
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Fangfang Guo
- Department of Plastic and Reconstruction Surgery, Zhongda Hospital, Southeast University, Nanjing, 221001, Jiangsu, China
| | - Hongfang Yue
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yaqi Huang
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Chenchen Lu
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yubai Guo
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Qinghua Liu
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yanqiang Li
- School of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs,
Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
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3
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Fu XQ, Peng J, Wang AH, Luo ZG. Tumor necrosis factor alpha mediates neuromuscular synapse elimination. Cell Discov 2020; 6:9. [PMID: 32140252 PMCID: PMC7051980 DOI: 10.1038/s41421-020-0143-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022] Open
Abstract
During the development of mammalian neuromuscular junction (NMJ), the original supernumerary axon inputs are gradually eliminated, finally leaving each muscle fiber innervated by a single axon terminal. However, the molecular cues that mediate the elimination of redundant axon inputs remain unclear. Here we show that tumor necrosis factor-α (TNFα) expressed in postsynaptic muscle cells plays an important role in presynaptic axonal elimination at the NMJ. We found that intramuscular injection of TNFα into the levator auris longus (LAL) muscles caused disassociation of presynaptic nerve terminals from the postsynaptic acetylcholine receptor (AChR) clusters. By contrast, genetic ablation of TNFα globally or specifically in skeletal muscle cells, but not in motoneurons or Schwann cells, delayed the synaptic elimination. Moreover, ablation of TNFα in muscle cells attenuated the tendency of activity-dependent competition in a motoneuron-muscle coculture system. These results suggest a role of postsynaptic TNFα in the elimination of redundant synaptic inputs.
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Affiliation(s)
- Xiu-Qing Fu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Jian Peng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
- State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ai-Hua Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
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4
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Bradley JR, Wang J, Pacey S, Warren AY, Pober JS, Al‐Lamki RS. Tumor necrosis factor receptor-2 signaling pathways promote survival of cancer stem-like CD133 + cells in clear cell renal carcinoma. FASEB Bioadv 2020; 2:126-144. [PMID: 32123862 PMCID: PMC7003657 DOI: 10.1096/fba.2019-00071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 08/25/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) contains cancer stem-like cells (CSCs) that express CD133 (ccRCC-CD133+). CSCs are rarely in cell cycle and, as nonproliferating cells, resist most chemotherapeutic agents. Previously, we reported that tumor necrosis factor receptor-2 (TNFR2) signaling promotes the cell cycle entry of ccRCC-CD133+CSCs, rendering them susceptible to cell-cycle-dependent chemotherapeutics. Here, we describe a TNFR2-activated signaling pathway in ccRCC-CD133+CSCs that is required for cell survival. Wild-type (wt)TNF or R2TNF but not R1TNF (TNF muteins that selectively bind to TNFR2 and TNFR1) induces phosphorylation of signal transducer and activator of transcription 3 (STAT3) on serine727 but not tyrosine705, resulting in pSTAT3Ser727 translocation to and colocalization with TNFR2 in mitochondria. R2TNF signaling activates a kinase cascade involving the phosphorylation of VEGFR2, PI-3K, Akt, and mTORC. Inhibition of any of the kinases or siRNA knockdown of TNFR2 or STAT3 promotes cell death associated with mitochondrial morphological changes, cytochrome c release, generation of reactive oxygen species, and TUNEL+cells expressing phosphorylated mixed lineage kinase-like (MLKL). Pretreatment with necrostatin-1 is more protective than z-VAD.fmk, suggesting that most death is necroptotic and TNFR2 signaling promotes cell survival by preventing mitochondrial-mediated necroptosis. These data suggest that a TNFR2 selective agonist may offer a potential therapeutic strategy for ccRCC.
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Affiliation(s)
- John R. Bradley
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Jun Wang
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Simon Pacey
- Department of OncologyNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Anne Y. Warren
- Department of HistopathologyAddenbrooke's Hospital and University of CambridgeCambridgeUK
| | | | - Rafia S. Al‐Lamki
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
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5
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Cytoplasmic expression of EGFR shRNA using a modified T7 autogene-based hybrid mRNA/DNA system induces long-term EGFR silencing and prolongs antitumor effects. Biochem Pharmacol 2020; 171:113735. [DOI: 10.1016/j.bcp.2019.113735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022]
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6
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Mobergslien A, Sioud M. Exploring 5'-Biotinylation of the Sense Strand to Improve siRNA Specificity and Potency. Methods Mol Biol 2020; 2115:163-170. [PMID: 32006400 DOI: 10.1007/978-1-0716-0290-4_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Although RNA interference is widely used for gene silencing, unintended gene modulation generated by off-target effects represents a major barrier to its applications in biology and medicine. Off-targeting can be induced by both the sense and antisense siRNA strands. An approach to minimizing off-target gene silencing by the sense strand would be the blockade of the 5'-end phosphorylation, thereby impeding its entry into the RNA-induced silencing complex (RISC). In this chapter, a biotin group at the 5'-end of the sense strand was used to inhibit its incorporation into RISC, thereby facilitating the antisense strand selection and enhancing siRNA cleavage potency. Biotin is a naturally occurring compound, and its presence in siRNA sequences will not induce additional side effects.
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Affiliation(s)
- Anne Mobergslien
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Mouldy Sioud
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.
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7
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Circular siRNAs for Reducing Off-Target Effects and Enhancing Long-Term Gene Silencing in Cells and Mice. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 10:237-244. [PMID: 29499936 PMCID: PMC5768153 DOI: 10.1016/j.omtn.2017.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 11/17/2022]
Abstract
Circular non-coding RNAs are found to play important roles in biology but are still relatively unexplored as a structural motif for chemically regulating gene function. Here, we investigated whether small interfering RNA (siRNA) with a circular structure can circumvent off-target gene silencing, a problem often observed with standard linear duplex siRNA. In the present work, we, for the first time, synthesized a series of circular siRNAs by cyclizing two ends of a single-stranded RNA (sense or antisense strand) to construct circular siRNAs that were more resistant to enzymatic degradation. Gene silencing of GFP and luciferase was successfully achieved using these circular siRNAs with circular sense strand RNAs and their complementary linear antisense strand RNAs. The off-target effect of sense strand RNAs was evaluated and no cross off-target effects were observed. In addition, we successfully achieved longer gene-silencing efficiency in mice with circular siRNAs than with linear siRNAs. These results indicate the promise of circular siRNAs for overcoming off-target effects of siRNAs and enhancing the possible long-term effect of siRNA gene silencing in basic research and drug development.
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8
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Song X, Wang X, Ma Y, Liang Z, Yang Z, Cao H. Site-Specific Modification Using the 2'-Methoxyethyl Group Improves the Specificity and Activity of siRNAs. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:242-250. [PMID: 29246303 PMCID: PMC5675723 DOI: 10.1016/j.omtn.2017.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 11/29/2022]
Abstract
Rapid progress has been made toward small interfering RNA (siRNA)-based therapy for human disorders, but rationally optimizing siRNAs for high specificity and potent silencing remains a challenge. In this study, we explored the effect of chemical modification at the cleavage site of siRNAs. We found that modifications at positions 9 and 10 markedly reduced the silencing potency of the unmodified strand of siRNAs but were well tolerated by the modified strand. Intriguingly, addition of the 2′-methoxyethyl (MOE) group at the cleavage site improved both the specificity and silencing activity of siRNAs by facilitating the oriented RNA-induced silencing complex (RISC) loading of the modified strand. Furthermore, we combined MOE modifications at positions 9 and 10 of one strand together with 2′-O-methylation (OMe) at position 14 of the other strand and found a synergistic effect that improved the specificity of siRNAs. The surprisingly beneficial effect of the combined modification was validated using siRNA-targeting endogenous gene intercellular adhesion molecule 1 (ICAM1). We found that the combined modifications eliminated its off-target effects. In conclusion, we established effective strategies to optimize siRNAs using site-specific MOE modifications. The findings may allow the creation of superior siRNAs for therapy in terms of activity and specificity.
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Affiliation(s)
- Xinyun Song
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaoxia Wang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zicai Liang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Huiqing Cao
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
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9
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Michler T, Große S, Mockenhaupt S, Röder N, Stückler F, Knapp B, Ko C, Heikenwalder M, Protzer U, Grimm D. Blocking sense-strand activity improves potency, safety and specificity of anti-hepatitis B virus short hairpin RNA. EMBO Mol Med 2016; 8:1082-98. [PMID: 27473329 PMCID: PMC5009812 DOI: 10.15252/emmm.201506172] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is a promising target for therapies based on RNA interference (RNAi) since it replicates via RNA transcripts that are vulnerable to RNAi silencing. Clinical translation of RNAi technology, however, requires improvements in potency, specificity and safety. To this end, we systematically compared different strategies to express anti-HBV short hairpin RNA (shRNA) in a pre-clinical immunocompetent hepatitis B mouse model. Using recombinant Adeno-associated virus (AAV) 8 vectors for delivery, we either (i) embedded the shRNA in an artificial mi(cro)RNA under a liver-specific promoter; (ii) co-expressed Argonaute-2, a rate-limiting cellular factor whose saturation with excess RNAi triggers can be toxic; or (iii) co-delivered a decoy ("TuD") directed against the shRNA sense strand to curb off-target gene regulation. Remarkably, all three strategies minimised adverse side effects as compared to a conventional shRNA vector that caused weight loss, liver damage and dysregulation of > 100 hepatic genes. Importantly, the novel AAV8 vector co-expressing anti-HBV shRNA and TuD outperformed all other strategies regarding efficiency and persistence of HBV knock-down, thus showing substantial promise for clinical translation.
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Affiliation(s)
- Thomas Michler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany German Center for Infection Research (DZIF), partner site München, München, Germany
| | - Stefanie Große
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Stefan Mockenhaupt
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Natalie Röder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Ferdinand Stückler
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bettina Knapp
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Chunkyu Ko
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany German Center for Infection Research (DZIF), partner site München, München, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
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10
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Zagalak JA, Menzi M, Schmich F, Jahns H, Dogar AM, Wullschleger F, Towbin H, Hall J. Properties of short double-stranded RNAs carrying randomized base pairs: toward better controls for RNAi experiments. RNA (NEW YORK, N.Y.) 2015; 21:2132-2142. [PMID: 26516083 PMCID: PMC4647466 DOI: 10.1261/rna.053637.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 09/11/2015] [Indexed: 06/05/2023]
Abstract
Short interfering RNAs (siRNAs) are mediators of RNA interference (RNAi), a commonly used technique for selective down-regulation of target gene expression. Using an equimolar mixture of A, G, C, and U phosphoramidites during solid-phase synthesis, we introduced degenerate positions into RNA guide and passenger strands so that, when annealed, a large pool of distinct siRNA duplexes with randomized base pairs at defined sites was created. We assessed the randomization efficiency by deep sequencing one of the RNAs. All possible individual sequences were present in the pool with generally an excellent distribution of bases. Melting temperature analyses suggested that pools of randomized guide and passenger strands RNAs with up to eight degenerate positions annealed so that mismatched base-pairing was minimized. Transfections of randomized siRNAs (rnd-siRNAs) into cells led to inhibition of luciferase reporters by a miRNA-like mechanism when the seed regions of rnd-siRNA guide strands were devoid of degenerate positions. Furthermore, the mRNA levels of a select set of genes associated with siRNA off-target effects were measured and indicated that rnd-siRNAs with degenerate positions in the seed likely show typical non-sequence-specific effects, but not miRNA-like off-target effects. In the wake of recent reports showing the preponderance of miRNA-like off-target effects of siRNAs, our findings are of value for the design of a novel class of easily prepared and universally applicable negative siRNA controls.
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Affiliation(s)
- Julian A Zagalak
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Mirjam Menzi
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Fabian Schmich
- Computational Biology Group (CBG), Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Hartmut Jahns
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Afzal M Dogar
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Florian Wullschleger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Harry Towbin
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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11
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Lu T, Yang W, Wang Z, Hu Z, Zeng X, Yang C, Wang Y, Zhang Y, Li F, Liu Z, Wang D, Ye Z. Knockdown of glucose-regulated protein 78/binding immunoglobulin heavy chain protein expression by asymmetric small interfering RNA induces apoptosis in prostate cancer cells and attenuates migratory capability. Mol Med Rep 2014; 11:249-56. [PMID: 25338653 DOI: 10.3892/mmr.2014.2737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 04/07/2014] [Indexed: 11/05/2022] Open
Abstract
Glucose-regulated protein 78 [GRP78, also termed binding immunoglobulin heavy chain protein (Bip)] may be involved in cancer progression and metastasis. However, to date there has been minimal investigation into its potential role in human prostate cancer cells. Recent studies have demonstrated that asymmetric small interfering RNA (asiRNA)-mediated gene silencing is more effective and longer-lasting than conventional symmetric siRNA. Thus, the current study aimed to investigate the effects of GRP78-specific asiRNA on human prostate cancer cells. A series of asiRNAs was synthesized and their efficiency in silencing GRP78 expression in PC-3 human prostate cancer cells was evaluated. The effects of knockdown using asiRNAs were compared to those of knockdown using symmetric siRNAs. The effect of GRP78 silencing on PC-3 cell apoptosis and migration, and the possible mechanisms governing these biological processes were examined. Compared with the symmetric siRNA, transfection with the 15 base pair asiRNA (asiGRP78-3) resulted in greater downregulation of GRP78 expression. GRP78 depletion in PC-3 cells resulted in increased apoptosis and decreased migration of these cells. Experiments investigating the underlying mechanisms of these effects revealed that knockdown of GRP78 attenuated protein kinase B activation and decreased the expression of pro-caspase 9, pro-caspase 3 and vimentin. In conclusion, knockdown of GRP78/Bip expression with asymmetric siRNA led to increased prostate cancer cell apoptosis and reduced cellular migration.
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Affiliation(s)
- Tong Lu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Weimin Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xing Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Chunguang Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ye Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yong Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhuo Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Dongbiao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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12
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A facile method for interfering with off-target silencing mediated by the sense strand. Methods Mol Biol 2014. [PMID: 25319659 DOI: 10.1007/978-1-4939-1538-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Although siRNA duplexes are widely used for gene silencing, several unwanted effects such as activation of innate immunity and off-target gene silencing can limit their therapeutic use. Off-targeting can be identified for both the sense and antisense siRNA strands. Some avenues of obstructing the incorporation of the sense strand into the RNA-induced silencing complex (RISC) are currently being pursued. Herein, a biotin group at the 5'-end of the sense strand was used to inhibit its incorporation into the RISC complex. In contrast to chemical modifications, biotin is a naturally occurring compound and its presence in siRNA sequences will not induce side effects.
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13
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Ida H, Fukuda K, Tachibana A, Tanabe T. Long DNA passenger strand highly improves the activity of RNA/DNA hybrid siRNAs. J Biosci Bioeng 2014; 117:401-6. [DOI: 10.1016/j.jbiosc.2013.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/06/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
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14
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Wang XF, Yang XT, Chen Y, Liu Y, Zou L, Yang ZJ, Zhang LH. Solid phase synthesis of peptide–siRNA conjugates containing disulfide bond unit. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2013.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Wang X, Huang Y, Liu Y, Chen Y, Jin H, Zheng Y, Du Q, Yang Z, Zhang L. Synthesis and biological evaluation of peptide-siRNA conjugates with phosphodiester unit as linker. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4912-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Zheng J, Zhang L, Zhang J, Wang X, Ye K, Xi Z, Du Q, Liang Z. Single modification at position 14 of siRNA strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. FASEB J 2013; 27:4017-26. [PMID: 23771927 DOI: 10.1096/fj.13-228668] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Normally siRNA has to be chemically stabilized in therapeutic applications. It is a challenge to obtain optimal stabilizing effects while maintaining full silencing activity due to a lack of understanding of how different chemical modifications would influence the efficacy of siRNA. In the current study, the effect of single 2'-sugar modifications was profiled across the length of the siRNA guide strand. This led to the surprising finding that a single 2'-OMe modification at position 14 of the siRNA guide strand substantially compromised its gene-silencing activity in a manner that was independent of the nucleotide identity at this site or the sequence context around it. We found that modification at position 14 of the siRNA guide strand reduced its RNA-induced silencing complex (RISC) loading tremendously, whereas the loading of the siRNA sense strand was only marginally affected. When comparing the silencing potency of 14th position-modified siRNA (transfected at 16.7 nM) and native control (transfected at 1 nM) at equivalent Ago2 loading levels, the silencing potency of modified siRNA was much lower, even lower than the level of native siRNA transfected at 0.1 nM. These data indicated that modification at position 14 of the siRNA guide strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. Using a computational modeling approach, we demonstrated an intimate interaction between the 14th nucleotide of guide strand and the amino acid Q675 in the AGO protein, which is located in a highly conserved loop of PIWI domain. In addition to gaining insights into siRNA-AGO interactions, this study of structure-activity relationship further established a general principle for siRNA modification in siRNA drug development.
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Affiliation(s)
- Jie Zheng
- 1Z.L., Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
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17
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Zhang J, Chen Y, Huang Y, Jin HW, Qiao RP, Xing L, Zhang LR, Yang ZJ, Zhang LH. Synthesis and properties of novel L-isonucleoside modified oligonucleotides and siRNAs. Org Biomol Chem 2013; 10:7566-77. [PMID: 22895883 DOI: 10.1039/c2ob26219c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides and siRNAs are potential therapeutic agents and their chemical modifications play an important role to improve the properties and activities of oligonucleotides. Isonucleoside is a type of nucleoside analogue, in which the nucleobase is moved from C-1 to other positions of ribose. In this report, a novel isonucleoside 5 containing a 5'-CH(2)-extended chain at the sugar moiety was synthesized, thus isoadenosine 5a and isothymidine 5b were incorporated into a DNA single strand and siRNA. It was found that isonucleoside 5 modified oligonucleotides can form stable double helical structures with their complementary DNA and RNA and the stability towards nuclease and ability to activate RNase H are more promising compared with the unmodified, natural analogues. In siRNA, passenger strand modified with isonucleoside (5a/b) at 3' or 5' terminal can retain the silencing activity and minimize the passenger strand specific off-target effect.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Kraus P, Sivakamasundari V, Lim SL, Xing X, Lipovich L, Lufkin T. Making sense of Dlx1 antisense RNA. Dev Biol 2013; 376:224-35. [PMID: 23415800 DOI: 10.1016/j.ydbio.2013.01.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 01/27/2013] [Accepted: 01/29/2013] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been recently recognized as a major class of regulators in mammalian systems. LncRNAs function by diverse and heterogeneous mechanisms in gene regulation, and are key contributors to development, neurological disorders, and cancer. This emerging importance of lncRNAs, along with recent reports of a functional lncRNA encoded by the mouse Dlx5-Dlx6 locus, led us to interrogate the biological significance of another distal-less antisense lncRNA, the previously uncharacterized Dlx1 antisense (Dlx1as) transcript. We have functionally ablated this antisense RNA via a highly customized gene targeting approach in vivo. Mice devoid of Dlx1as RNA are viable and fertile, and display a mild skeletal and neurological phenotype reminiscent of a Dlx1 gain-of function phenotype, suggesting a role for this non-coding antisense RNA in modulating Dlx1 transcript levels and stability. The reciprocal relationship between Dlx1as and Dlx1 places this sense-antisense pair into a growing class of mammalian lncRNA-mRNA pairs characterized by inverse regulation.
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Affiliation(s)
- Petra Kraus
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore
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Chang C, Hong SW, Dua P, Kim S, Lee DK. The design, preparation, and evaluation of asymmetric small interfering RNA for specific gene silencing in mammalian cells. Methods Mol Biol 2013; 942:135-52. [PMID: 23027049 DOI: 10.1007/978-1-62703-119-6_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
RNA interference (RNAi) is a highly efficient endogenous gene silencing mechanism mediated by short double-stranded RNAs termed small interfering RNAs (siRNAs). The current standard siRNA structure, which is used by most researchers to trigger sequence-specific target gene silencing, consists of a double strand region of 19 bp with 2 nt 3'-overhangs at both ends. However, in addition to the desired target gene silencing, this conventional siRNA structure also exhibits several unintended effects that constitute obstacles to the use of siRNA in gene function studies and therapeutics development. Here, we provide protocols for designing and preparing an alternative structure for RNAi trigger, termed asymmetric shorter-duplex RNA (asiRNA). The asiRNA structure has a duplex region shorter than 19 bp and has an asymmetric 3'-overhang structure. Importantly, the asiRNA structure not only triggers efficient target gene silencing comparable to that of the 19 bp standard siRNA structure but also significantly reduces nonspecific effects triggered by 19 bp siRNAs such as sense-strand-mediated off-target silencing and the saturation of RNAi machinery. Procedures are described for verifying that asiRNA activates gene silencing through an Ago2-dependent pathway and for assessing the miRNA pathway competition potency and specific and nonspecific silencing abilities of asiRNAs. We propose that asiRNA, an improved RNAi trigger that can overcome the nonspecific effects evoked by standard siRNA structures, can be developed as a precise and effective tool for both functional genomics and therapeutic applications.
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Affiliation(s)
- Chanil Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, BK21 School of Chemical Materials Science, Sungkyunkwan University, Suwon, South Korea
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20
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Abstract
Synthetic small interfering RNAs (siRNAs) have revolutionized functional genomics in mammalian cell cultures due to their reliability, efficiency, and ease of use. This success, however, has not fully translated into siRNA applications in vivo and in siRNA therapeutics where initial optimism has been dampened by a lack of efficient delivery strategies and reports of siRNA off-target effects and immunogenicity. Encouragingly, most aspects of siRNA behavior can be addressed by careful engineering of siRNAs incorporating beneficial chemical modifications into discrete nucleotide positions during siRNA synthesis. Here, we review the literature (Subheadings 1 -3) and provide a quick guide (Subheading 4) to how the performance of siRNA can be improved by chemical modification to suit specific applications in vitro and in vivo.
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Affiliation(s)
- Jesper B Bramsen
- Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus, Denmark.
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YIN YAN, CHEN XU, ZHANG CHANGDONG, LIU PEIFENG, DUAN YOURONG, FAN YANRONG, WU ZHIWEI, FU GENGFENG, WANG JIANJUN, XU GENXING. Asymmetric siRNA targeting the bcl-2 gene inhibits the proliferation of cancer cells in vitro and in vivo. Int J Oncol 2012; 42:253-60. [DOI: 10.3892/ijo.2012.1691] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 10/11/2012] [Indexed: 11/06/2022] Open
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Nolte A, Ott K, Rohayem J, Walker T, Schlensak C, Wendel HP. Modification of small interfering RNAs to prevent off-target effects by the sense strand. N Biotechnol 2012; 30:159-65. [PMID: 23124048 DOI: 10.1016/j.nbt.2012.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022]
Abstract
OBJECTIVE There is a broad therapeutic potential for the application of small interfering RNAs (siRNAs). However, one has to ensure that siRNAs act specifically, only targeting the expression of one gene. Off-target effects raised by the sense strand have to be eliminated. METHODS AND RESULTS We examined a particular bidirectional siRNA molecule, able to knockdown intercellular adhesion molecule-1 (ICAM-1) and tumor necrosis factor receptor-1 (TNFR-1) by the sense or antisense strand, respectively. Transfection of human venous endothelial cells with an unmodified siRNA molecule led to equal silencing of ICAM-1 and TNFR-1. In contrast, modified siRNA was able to knockdown ICAM-1 and TNFR-1 separately, with only the antisense strand. DISCUSSION We found the modified siRNAs to inhibit off-target effects originated by the sense strand. Our approach demonstrates one possibility to modify siRNAs before starting a clinical approach to eliminate off-target effects.
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Affiliation(s)
- Andrea Nolte
- Department of Thoracic, Cardiac, and Vascular Surgery, University of Tuebingen, Germany
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Liu Y, Wang XF, Chen Y, Zhang LH, Yang ZJ. A solid-phase method for peptide–siRNA covalent conjugates based on click chemistry. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00198e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Ito H, Urushihara M, Liang X, Asanuma H. Improvement of RNAi Activity and Strand Selectivity of RISC Formation by Modified siRNA Involving Intercalators near 5′ Termini. Chembiochem 2011; 13:311-5. [DOI: 10.1002/cbic.201100570] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Indexed: 01/04/2023]
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26
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Wang F, Chen Y, Huang Y, Jin HW, Zhang LR, Yang ZJ, Zhang LH. Synthesis, physicochemical and biological properties of oligonucleotides incorporated with amino-isonucleosides. Sci China Chem 2011; 55:70-79. [PMID: 32214999 PMCID: PMC7089117 DOI: 10.1007/s11426-011-4465-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/10/2011] [Indexed: 12/23/2022]
Abstract
Antisense oligonucleotides (ASONs) and siRNAs have been applied extensively for the regulation of cellular and viral gene expression, and RNAi is currently one of the most promising new approaches for anti-tumor and anti-viral therapy. In order to improve bioactivity properties and physicochemical properties of siRNA, we synthesized a novel class of ASONs II–VII incorporated with amino-isonucleoside (isoA1 and isoA2) for investigation on basic physicochemical properties. Then we designed amino-isonucleoside (isoA1, isoA2 and isoT1) incorporated siRNA 2–7. Some meaningful results have been obtained from the physicochemical property experiments in ASONs. In RNAi potency experiments, we investigated RNAi potency of each strand of the siRNA. These amino-isonucleosides incorporated siRNAs showed promising bioactivity properties and had position specificity. Reduced off target effect from sense strand loading in siRNA application was observed.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Yue Chen
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Ye Huang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Hong-Wei Jin
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Liang-Ren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Zhen-Jun Yang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Li-He Zhang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
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Jo SG, Hong SW, Yoo JW, Lee CH, Kim S, Kim S, Lee DK. Selection and optimization of asymmetric siRNA targeting the human c-MET gene. Mol Cells 2011; 32:543-8. [PMID: 22058018 PMCID: PMC3887682 DOI: 10.1007/s10059-011-0160-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022] Open
Abstract
The silencing of specific oncogenes via RNA interference (RNAi) holds great promise for the future of cancer therapy. RNAi is commonly carried out using small interfering RNA (siRNA) composed of a 19 bp duplex region with a 2-nucleotide overhang at each 3' end. This classical siRNA structure, however, can trigger non-specific effects, which has hampered the development of specific and safe RNAi therapeutics. Previously, we developed a novel siRNA structure, called asymmetric shorter-duplex siRNA (asiRNA), which did not cause the non-specific effects triggered by conventional siRNA, such as off-target gene silencing mediated by the sense strand. In this study, we first screened potent asiRNA molecules targeting the human c-MET gene, a promising anticancer target. Next, the activity of a selected asiRNA was further optimized by introducing a locked nucleic acid (LNA) to maximize the gene silencing potency. The optimized asiRNA targeted to c-MET may have potential as a specific and safe anticancer RNAi therapeutic.
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Affiliation(s)
- Seul-gi Jo
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
- These authors contributed equally to this work
| | - Sun Woo Hong
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
- Department of Biomedical Engineering, Dongguk University, Seoul 100-715, Korea
- These authors contributed equally to this work
| | - Jae Wook Yoo
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Chang Han Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sera Kim
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Soyoun Kim
- Department of Biomedical Engineering, Dongguk University, Seoul 100-715, Korea
| | - Dong-ki Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
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28
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Chang CI, Kim HA, Dua P, Kim S, Li CJ, Lee DK. Structural diversity repertoire of gene silencing small interfering RNAs. Nucleic Acid Ther 2011; 21:125-31. [PMID: 21749289 DOI: 10.1089/nat.2011.0286] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Since the discovery of double-stranded (ds) RNA-mediated RNA interference (RNAi) phenomenon in Caenorhabditis elegans, specific gene silencing based upon RNAi mechanism has become a novel biomedical tool that has extended our understanding of cell biology and opened the door to an innovative class of therapeutic agents. To silence genes in mammalian cells, short dsRNA referred to as small interfering RNA (siRNA) is used as an RNAi trigger to avoid nonspecific interferon responses induced by long dsRNAs. An early structure-activity relationship study performed in Drosophila melanogaster embryonic extract suggested the existence of strict siRNA structural design rules to achieve optimal gene silencing. These rules include the presence of a 3' overhang, a fixed duplex length, and structural symmetry, which defined the structure of a classical siRNA. However, several recent studies performed in mammalian cells have hinted that the gene silencing siRNA structure could be much more flexible than that originally proposed. Moreover, many of the nonclassical siRNA structural variants reported improved features over the classical siRNAs, including increased potency, reduced nonspecific responses, and enhanced cellular delivery. In this review, we summarize the recent progress in the development of gene silencing siRNA structural variants and discuss these in light of the flexibility of the RNAi machinery in mammalian cells.
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Affiliation(s)
- Chan Il Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon, Korea
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29
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Bosquesi PL, Melo TRF, Vizioli EO, Santos JLD, Chung MC. Anti-Inflammatory Drug Design Using a Molecular Hybridization Approach. Pharmaceuticals (Basel) 2011; 4:1450-1474. [PMID: 27721332 PMCID: PMC4060134 DOI: 10.3390/ph4111450] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/20/2011] [Accepted: 10/20/2011] [Indexed: 12/21/2022] Open
Abstract
The design of new drugs with better physiochemical properties, adequate absorption, distribution, metabolism, and excretion, effective pharmacologic potency and lacking toxicity remains is a challenge. Inflammation is the initial trigger of several different diseases, such as Alzheimer's disease, asthma, atherosclerosis, colitis, rheumatoid arthritis, depression, cancer; and disorders such as obesity and sexual dysfunction. Although inflammation is not the direct cause of these disorders, inflammatory processes often increase related pain and suffering. New anti-inflammatory drugs developed using molecular hybridization techniques to obtain multiple-ligand drugs can act at one or multiple targets, allowing for synergic action and minimizing toxicity. This work is a review of new anti-inflammatory drugs developed using the molecular modification approach.
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Affiliation(s)
- Priscila Longhin Bosquesi
- Lapdesf, Laboratory of Drug Design, Department of Drugs and Medicines, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), Rodovia Araraquara-Jaú, km 1, Araraquara, SP, Cep. 14.802-901, Brazil.
| | - Thais Regina Ferreira Melo
- Lapdesf, Laboratory of Drug Design, Department of Drugs and Medicines, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), Rodovia Araraquara-Jaú, km 1, Araraquara, SP, Cep. 14.802-901, Brazil
| | - Ednir Oliveira Vizioli
- Lapdesf, Laboratory of Drug Design, Department of Drugs and Medicines, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), Rodovia Araraquara-Jaú, km 1, Araraquara, SP, Cep. 14.802-901, Brazil.
| | - Jean Leandro Dos Santos
- Lapdesf, Laboratory of Drug Design, Department of Drugs and Medicines, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), Rodovia Araraquara-Jaú, km 1, Araraquara, SP, Cep. 14.802-901, Brazil.
| | - Man Chin Chung
- Lapdesf, Laboratory of Drug Design, Department of Drugs and Medicines, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), Rodovia Araraquara-Jaú, km 1, Araraquara, SP, Cep. 14.802-901, Brazil.
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Wei PC, Lo WT, Su MI, Shew JY, Lee WH. Non-targeting siRNA induces NPGPx expression to cooperate with exoribonuclease XRN2 for releasing the stress. Nucleic Acids Res 2011; 40:323-32. [PMID: 21908404 PMCID: PMC3245931 DOI: 10.1093/nar/gkr714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Short interfering RNAs (siRNAs) target specific mRNAs for their degradation mediated by RNA-induced silencing complex (RISC). Persistent activation of siRNA-RISC frequently leads to non-targeting toxicity. However, how cells mediate this stress remains elusive. In this communication, we found that the presence of non-targeting siRNA selectively induced the expression of an endoplasmic reticulum (ER)-resident protein, non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx), but not other ER-stress proteins including GRP78, Calnexin and XBP1. Cells suffering from constant non-targeting siRNA stress grew slower and prolonged G1 phase, while NPGPx-depleted cells accumulated mature non-targeting siRNA and underwent apoptosis. Upon the stress, NPGPx covalently bound to exoribonuclease XRN2, facilitating XRN2 to remove accumulated non-targeting siRNA. These results suggest that NPGPx serves as a novel responder to non-targeting siRNA-induced stress in facilitating XRN2 to release the non-targeting siRNA accumulation.
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Affiliation(s)
- Pei-Chi Wei
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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31
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Modified siRNA structure with a single nucleotide bulge overcomes conventional siRNA-mediated off-target silencing. Mol Ther 2011; 19:1676-87. [PMID: 21673662 DOI: 10.1038/mt.2011.109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Off-target gene silencing is a major concern when using RNA interference. Imperfect pairing of the antisense strand with unintended mRNA targets is one of the main causes of small interfering RNA (siRNA) off-target silencing. To overcome this, we have developed "bulge-siRNA," a modified siRNA backbone structure with a single nucleotide (nt) bulge placed in the antisense strand. We found that siRNAs with a bulge at position 2 of the antisense strand were able to discriminate better between perfectly matched and mismatched targets, with no loss in silencing of the intended target. Genome-wide analysis also revealed that the bulge-siRNAs significantly reduced off-target silencing of transcripts with complementarity to the seed region of the siRNA antisense strand. When compared to 2'-methoxy ribosyl (2'-OMe) modified siRNAs previously developed to alleviate antisense off-target silencing; the bulge modification could better discriminate between on- versus off-targets. Our results suggest that the bulge-siRNA structure is a simple, yet superior alternative to chemical modifications for minimizing off-target silencing triggered by conventional siRNA structures.
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32
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Chang CI, Kim HA, Dua P, Kim S, Li CJ, Lee DK. Structural Diversity Repertoire of Gene Silencing Small Interfering RNAs. Oligonucleotides 2011. [DOI: 10.1089/oli.2011.0286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Tan Y, You H, Coffey FJ, Wiest DL, Testa JR. Appl1 is dispensable for Akt signaling in vivo and mouse T-cell development. Genesis 2011; 48:531-9. [PMID: 20665729 DOI: 10.1002/dvg.20657] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Appl1 (Adaptor protein containing pleckstrin homology [PH], phosphotyrosine binding [PTB], and Leucine zipper motifs) is an adaptor that participates in cell signaling by interacting with various signaling molecules including Akt, PI3-kinase (PI3K), Rab5, adiponectin receptor, and TrkA. By using RNA knockdown technology, Appl1 has been implicated in zebrafish development and murine glucose metabolism. To investigate the unambiguous role of Appl1 in vivo, we generated a knockout mouse in which exon1 of the Appl1 gene was disrupted using gene trap methodology. Homozygous Appl1 knockout mice with ubiquitous loss of Appl1 protein expression were viable, grossly normal, and born at expected Mendelian ratios. Moreover, activation of Akt and the downstream effecter Gsk3β was unaffected in vivo. We next performed glucose and insulin tolerance tests and found that glucose metabolism is normal in Appl1-null mice. We also tested the effect of Appl1 loss on Akt signaling in T cells, because we discovered that Appl1 strongly interacts with the p110β subunit of PI3K in T lymphocytes. However, such interaction was found to be dispensable for Akt signaling in thymic T cells and T-cell development. Moreover, Appl1 loss did not affect DNA synthesis in cultured thymocytes, although loss of Appl1 was associated with a slight increase in ConA-stimulated splenic T-cell viability/proliferation. Collectively, our findings indicate that Appl1 is dispensable for Akt signaling in vivo and T-cell differentiation.
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Affiliation(s)
- Yinfei Tan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Abstract
Chemically synthesized siRNAs are widely used for gene silencing. For in vitro applications, stability, delivery, and immunological issues are rarely problematic, but for in vivo applications the situation is different. Limited stability, undesirable pharmacokinetic behaviour, and unanticipated side effects from the immune system call for more careful structural siRNA design and inclusion of chemical modifications at selected positions. Also the notion that siRNA induces significant off-target silencing of many non-related genes has promted new effective measures to enhance specificity. The scope of this review is to provide a simple guide to successful chemical and structural modification of siRNAs with improved activity, stability, specificity, and low toxicity.
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The sense strand pre-cleaved RNA duplex mediates an efficient RNA interference with less off-target and immune response effects. Appl Microbiol Biotechnol 2010; 90:583-9. [DOI: 10.1007/s00253-010-3065-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/03/2010] [Accepted: 12/03/2010] [Indexed: 01/31/2023]
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36
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Sakurai K, Amarzguioui M, Kim DH, Alluin J, Heale B, Song MS, Gatignol A, Behlke MA, Rossi JJ. A role for human Dicer in pre-RISC loading of siRNAs. Nucleic Acids Res 2010; 39:1510-25. [PMID: 20972213 PMCID: PMC3045585 DOI: 10.1093/nar/gkq846] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA interference is a powerful mechanism for sequence-specific inhibition of gene expression. It is widely known that small interfering RNAs (siRNAs) targeting the same region of a target-messenger RNA can have widely different efficacies. In efforts to better understand the siRNA features that influence knockdown efficiency, we analyzed siRNA interactions with a high-molecular weight complex in whole cell extracts prepared from two different cell lines. Using biochemical tools to study the nature of the complex, our results demonstrate that the primary siRNA-binding protein in the whole cell extracts is Dicer. We find that Dicer is capable of discriminating highly functional versus poorly functional siRNAs by recognizing the presence of 2-nt 3′ overhangs and the thermodynamic properties of 2–4 bp on both ends of effective siRNAs. Our results suggest a role for Dicer in pre-selection of effective siRNAs for handoff to Ago2. This initial selection is reflective of the overall silencing potential of an siRNA.
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Affiliation(s)
- Kumi Sakurai
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA
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Shukla S, Sumaria CS, Pradeepkumar PI. Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 2010; 5:328-49. [PMID: 20043313 DOI: 10.1002/cmdc.200900444] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data. The X-ray crystal structures of the Argonaute (Ago)-DNA-RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago-RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Bramsen JB, Pakula MM, Hansen TB, Bus C, Langkjær N, Odadzic D, Smicius R, Wengel SL, Chattopadhyaya J, Engels JW, Herdewijn P, Wengel J, Kjems J. A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Res 2010; 38:5761-73. [PMID: 20453030 PMCID: PMC2943616 DOI: 10.1093/nar/gkq341] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low.
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Affiliation(s)
- Jesper B Bramsen
- Department of Molecular Biology, University of Aarhus, Arhus, Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark.
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Naito Y, Yoshimura J, Morishita S, Ui-Tei K. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics 2009; 10:392. [PMID: 19948054 PMCID: PMC2791777 DOI: 10.1186/1471-2105-10-392] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 11/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value. RESULTS We present siDirect 2.0, an update of our web-based software siDirect, which provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. CONCLUSION siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in RefSeq. siDirect 2.0 is available at http://siDirect2.RNAi.jp/.
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Affiliation(s)
- Yuki Naito
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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Chen XS, Collins LJ, Biggs PJ, Penny D. High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol 2009; 1:165-75. [PMID: 20333187 PMCID: PMC2817412 DOI: 10.1093/gbe/evp017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2009] [Indexed: 12/26/2022] Open
Abstract
RNA interference (RNAi) is a set of mechanisms which regulate gene expression in eukaryotes. Key elements of RNAi are small sense and antisense RNAs from 19 to 26 nt generated from double-stranded RNAs. MicroRNAs (miRNAs) are a major type of RNAi-associated small RNAs and are found in most eukaryotes studied to date. To investigate whether small RNAs associated with RNAi appear to be present in all eukaryotic lineages, and therefore present in the ancestral eukaryote, we studied two deep-branching protozoan parasites, Giardia intestinalis and Trichomonas vaginalis. Little is known about endogenous small RNAs involved in RNAi of these organisms. Using Illumina Solexa sequencing and genome-wide analysis of small RNAs from these distantly related deep-branching eukaryotes, we identified 10 strong miRNA candidates from Giardia and 11 from Trichomonas. We also found evidence of Giardia short-interfering RNAs potentially involved in the expression of variant-specific surface proteins. In addition, eight new small nucleolar RNAs from Trichomonas are identified. Our results indicate that miRNAs are likely to be general in ancestral eukaryotes and therefore are likely to be a universal feature of eukaryotes.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.
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Chang CI, Kang HS, Ban C, Kim S, Lee DK. Dual-target gene silencing by using long, synthetic siRNA duplexes without triggering antiviral responses. Mol Cells 2009; 27:689-95. [PMID: 19533030 DOI: 10.1007/s10059-009-0093-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 05/20/2009] [Accepted: 05/20/2009] [Indexed: 12/18/2022] Open
Abstract
Chemically synthesized small interfering RNAs (siRNAs) can specifically knock-down expression of target genes via RNA interference (RNAi) pathway. To date, the length of synthetic siRNA duplex has been strictly maintained less than 30 bp, because an early study suggested that double-stranded RNAs (dsRNAs) longer than 30 bp could not trigger specific gene silencing due to the induction of nonspecific antiviral interferon responses. Contrary to the current belief, here we show that synthetic dsRNA as long as 38 bp can result in specific target gene silencing without nonspecific antiviral responses. Using this longer duplex structure, we have generated dsRNAs, which can simultaneously knock-down expression of two target genes (termed as dual-target siRNAs or dsiRNAs). Our results thus demonstrate the structural flexibility of gene silencing siRNAs, and provide a starting point to construct multifunctional RNA structures. The dsiRNAs could be utilized to develop a novel therapeutic gene silencing strategy against diseases with multiple gene alternations such as viral infection and cancer.
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Affiliation(s)
- Chan Il Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
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Wei JX, Yang J, Sun JF, Jia LT, Zhang Y, Zhang HZ, Li X, Meng YL, Yao LB, Yang AG. Both strands of siRNA have potential to guide posttranscriptional gene silencing in mammalian cells. PLoS One 2009; 4:e5382. [PMID: 19401777 PMCID: PMC2671169 DOI: 10.1371/journal.pone.0005382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/27/2009] [Indexed: 11/19/2022] Open
Abstract
Despite the widespread application of RNA interference (RNAi) as a research tool for diverse purposes, the key step of strand selection of siRNAs during the formation of RNA-induced silencing complex (RISC) remains poorly understood. Here, using siRNAs targeted to the complementary region of Survivin and the effector protease receptor 1 (EPR-1), we show that both strands of the siRNA duplex can find their target mRNA and are equally eligible for assembly into Argonaute 2 (Ago2) of RISC in HEK293 cells. Transfection of the synthetic siRNA duplexes with different thermodynamic profiles or short hairpin RNA (shRNA) vectors that generate double-stranded RNAs (dsRNAs), permitting processing specifically from either the 5' or 3' end of the incipient siRNA, results in the degradation of the respective target mRNAs of either strand of the siRNA duplex with comparable efficiencies. Thus, while most RNAi reactions may follow the thermodynamic asymmetry rule in strand selection, our study suggests an exceptional mode for certain siRNAs in which both strands of the duplex are competent in sponsoring RNAi, and implies additional factors that might dictate the RNAi targets.
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MESH Headings
- Argonaute Proteins
- Base Sequence
- Carboxypeptidases/metabolism
- Cell Line
- Cytidine/analogs & derivatives
- DNA Primers/genetics
- Eukaryotic Initiation Factor-2/metabolism
- Humans
- Inhibitor of Apoptosis Proteins
- Microtubule-Associated Proteins/antagonists & inhibitors
- Microtubule-Associated Proteins/genetics
- RNA Interference
- RNA Processing, Post-Transcriptional
- RNA, Complementary/chemistry
- RNA, Complementary/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Receptors, Cell Surface/antagonists & inhibitors
- Receptors, Cell Surface/genetics
- Ribonuclease III/metabolism
- Survivin
- Thermodynamics
- Uridine/analogs & derivatives
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Affiliation(s)
- Jun-Xia Wei
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Clinical Diagnosis, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jie Yang
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Nephrology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Ji-Feng Sun
- Department of Nephrology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Lin-Tao Jia
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yong Zhang
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Hui-Zhong Zhang
- Department of Clinical Diagnosis, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xia Li
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yan-Ling Meng
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Li-Bo Yao
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - An-Gang Yang
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Immunology, Fourth Military Medical University, Xi'an, China
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Abstract
Well over a hundred reports have been published describing use of synthetic small-interfering RNAs (siRNAs) in animals. The majority of these reports employed unmodified RNA duplexes. While unmodified RNA is the natural effector molecule of RNA interference, certain problems arise with experimental or therapeutic use of RNA duplexes in vivo, some of which can be improved or solved through use of chemical modifications. Judicious use of chemical modifications can improve the nuclease stability of an RNA duplex, decrease the likelihood of triggering an innate immune response, lower the incidence of off-target effects (OTEs), and improve pharmacodynamics. This review will examine studies that document the utility of various chemical modifications for use in siRNAs, both in vitro and in vivo, with close attention given to reports demonstrating actual performance in animal model systems.
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Affiliation(s)
- Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa 52241, USA.
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Chang CI, Yoo JW, Hong SW, Lee SE, Kang HS, Sun X, Rogoff HA, Ban C, Kim S, Li CJ, Lee DK. Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects. Mol Ther 2009; 17:725-32. [PMID: 19156133 DOI: 10.1038/mt.2008.298] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Small interfering RNAs (siRNAs) are short, double-stranded RNAs that mediate efficient gene silencing in a sequence-specific manner by utilizing the endogenous RNA interference (RNAi) pathway. The current standard synthetic siRNA structure harbors a 19-base-pair duplex region with 3' overhangs of 2 nucleotides (the so-called 19+2 form). However, the synthetic 19+2 siRNA structure exhibits several sequence-independent, nonspecific effects, which has posed challenges to the development of RNAi therapeutics and specific silencing of genes in research. In this study, we report on the identification of truncated siRNA backbone structures with duplex regions shorter than 19 bp (referred to as asymmetric shorter-duplex siRNAs or asiRNAs) that can efficiently trigger gene silencing in human cell lines. Importantly, this asiRNA structure significantly reduces nonspecific effects triggered by conventional 19+2 siRNA scaffold, such as sense-strand-mediated off-target gene silencing and saturation of the cellular RNAi machinery. Our results suggest that this asiRNA structure is an important alternative to conventional siRNAs for both functional genomics studies and therapeutic applications.
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Affiliation(s)
- Chan Il Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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45
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Sun X, Rogoff HA, Li CJ. Asymmetric RNA duplexes mediate RNA interference in mammalian cells. Nat Biotechnol 2008; 26:1379-82. [DOI: 10.1038/nbt.1512] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 11/03/2008] [Indexed: 02/06/2023]
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46
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Tancharoen S, Matsuyama T, Abeyama K, Matsushita K, Kawahara K, Sangalungkarn V, Tokuda M, Hashiguchi T, Maruyama I, Izumi Y. The role of water channel aquaporin 3 in the mechanism of TNF-α-mediated proinflammatory events: Implication in periodontal inflammation. J Cell Physiol 2008; 217:338-49. [DOI: 10.1002/jcp.21506] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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