1
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Li Q, Dong M, Chen P. Advances in structural-guided modifications of siRNA. Bioorg Med Chem 2024; 110:117825. [PMID: 38954918 DOI: 10.1016/j.bmc.2024.117825] [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: 05/16/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.
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Affiliation(s)
- Qiang Li
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China; Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China.
| | - Pu Chen
- Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China; Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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2
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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3
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Bobadilla Ugarte P, Barendse P, Swarts DC. Argonaute proteins confer immunity in all domains of life. Curr Opin Microbiol 2023; 74:102313. [PMID: 37023508 DOI: 10.1016/j.mib.2023.102313] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
Both eukaryotes and prokaryotes (archaea and bacteria) encode an arsenal of immune systems that protect the host against mobile genetic elements (MGEs) including viruses, plasmids, and transposons. Whereas Argonaute proteins (Agos) are best known for post-transcriptional gene silencing in eukaryotes, in all domains of life, members from the highly diverse Argonaute protein family act as programmable immune systems. To this end, Agos are programmed with small single-stranded RNA or DNA guides to detect and silence complementary MGEs. Across and within the different domains of life, Agos function in distinct pathways and MGE detection can trigger various mechanisms that provide immunity. In this review, we delineate the diverse immune pathways and underlying mechanisms for both eukaryotic Argonautes (eAgos) and prokaryotic Argonautes (pAgos).
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Affiliation(s)
| | - Patrick Barendse
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands.
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4
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Hybrid extracellular vesicles for drug delivery. Cancer Lett 2023; 558:216107. [PMID: 36841417 DOI: 10.1016/j.canlet.2023.216107] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Extracellular vesicles (EVs) are expected to serve as interesting drug delivery vectors as they may offer unique and new properties for drug delivery. Their natural origin, protein and nucleic acid composition, and intrinsic pleiotropic therapeutic effects could enable new possibilities in the field of drug delivery. Here, we aimed to review the methods used to produce Hybrid EVs, a recently emerged type of EV-based vector made from both EVs and synthetic vectors to exploit their respective properties. Hybrid EV/synthetic objects can be obtained by incubation, electrostatic interactions, polyethylene glycol (PEG)-mediated fusion, co-extrusion, freeze-thawing, or simple EV surface modification, leading to different types of objects. We also opted to review the properties of these vectors, and specifically compared them with those of other drug delivery vectors. It has to be noticed that only a limited number of study report loading metrics that allow cross article comparison. Based on this critical analysis, we attempted to draw the pith and marrow from these relatively difficult-to-compare studies and integrate them into the more general context of opportunities in drug delivery and drug development, with a particular focus on oncology.
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5
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Stein RA, Thompson LM. Epigenetic changes induced by pathogenic Chlamydia spp. Pathog Dis 2023; 81:ftad034. [PMID: 38031337 DOI: 10.1093/femspd/ftad034] [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: 06/15/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Chlamydia trachomatis, C. pneumoniae, and C. psittaci, the three Chlamydia species known to cause human disease, have been collectively linked to several pathologies, including conjunctivitis, trachoma, respiratory disease, acute and chronic urogenital infections and their complications, and psittacosis. In vitro, animal, and human studies also established additional correlations, such as between C. pneumoniae and atherosclerosis and between C. trachomatis and ovarian cancer. As part of their survival and pathogenesis strategies as obligate intracellular bacteria, Chlamydia spp. modulate all three major types of epigenetic changes, which include deoxyribonucleic acid (DNA) methylation, histone post-translational modifications, and microRNA-mediated gene silencing. Some of these epigenetic changes may be implicated in key aspects of pathogenesis, such as the ability of the Chlamydia spp. to induce epithelial-to-mesenchymal transition, interfere with DNA damage repair, suppress cholesterol efflux from infected macrophages, act as a co-factor in human papillomavirus (HPV)-mediated cervical cancer, prevent apoptosis, and preserve the integrity of mitochondrial networks in infected host cells. A better understanding of the individual and collective contribution of epigenetic changes to pathogenesis will enhance our knowledge about the biology of Chlamydia spp. and facilitate the development of novel therapies and biomarkers. Pathogenic Chlamydia spp. contribute to epigenetically-mediated gene expression changes in host cells by multiple mechanisms.
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Affiliation(s)
- Richard A Stein
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Lily M Thompson
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
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Lu ZG, Shen J, Yang J, Wang JW, Zhao RC, Zhang TL, Guo J, Zhang X. Nucleic acid drug vectors for diagnosis and treatment of brain diseases. Signal Transduct Target Ther 2023; 8:39. [PMID: 36650130 PMCID: PMC9844208 DOI: 10.1038/s41392-022-01298-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Nucleic acid drugs have the advantages of rich target selection, simple in design, good and enduring effect. They have been demonstrated to have irreplaceable superiority in brain disease treatment, while vectors are a decisive factor in therapeutic efficacy. Strict physiological barriers, such as degradation and clearance in circulation, blood-brain barrier, cellular uptake, endosome/lysosome barriers, release, obstruct the delivery of nucleic acid drugs to the brain by the vectors. Nucleic acid drugs against a single target are inefficient in treating brain diseases of complex pathogenesis. Differences between individual patients lead to severe uncertainties in brain disease treatment with nucleic acid drugs. In this Review, we briefly summarize the classification of nucleic acid drugs. Next, we discuss physiological barriers during drug delivery and universal coping strategies and introduce the application methods of these universal strategies to nucleic acid drug vectors. Subsequently, we explore nucleic acid drug-based multidrug regimens for the combination treatment of brain diseases and the construction of the corresponding vectors. In the following, we address the feasibility of patient stratification and personalized therapy through diagnostic information from medical imaging and the manner of introducing contrast agents into vectors. Finally, we take a perspective on the future feasibility and remaining challenges of vector-based integrated diagnosis and gene therapy for brain diseases.
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Affiliation(s)
- Zhi-Guo Lu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
| | - Jie Shen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jun Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jing-Wen Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Rui-Chen Zhao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Tian-Lu Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Jing Guo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Xin Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
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7
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Jia Y, Zhao J, Yu T, Zhang X, Qi X, Hao T, Jin Z, Zhao X. PSMC3 promotes RNAi by maintaining AGO2 stability through USP14. Cell Mol Biol Lett 2022; 27:111. [PMID: 36528617 PMCID: PMC9759854 DOI: 10.1186/s11658-022-00411-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Argonaute 2 (AGO2), the only protein with catalytic activity in the human Argonaute family, is considered as a key component of RNA interference (RNAi) pathway. Here we performed a yeast two-hybrid screen using the human Argonaute 2 PIWI domain as bait to screen for new AGO2-interacting proteins and explored the specific mechanism through a series of molecular biology and biochemistry experiments. METHODS The yeast two-hybrid system was used to screen for AGO2-interacting proteins. Co-immunoprecipitation and immunofluorescence assays were used to further determine interactions and co-localization. Truncated plasmids were constructed to clarify the interaction domain. EGFP fluorescence assay was performed to determine the effect of PSMC3 on RNAi. Regulation of AGO2 protein expression and ubiquitination by PSMC3 and USP14 was examined by western blotting. RT-qPCR assays were applied to assess the level of AGO2 mRNA. Rescue assays were also performed. RESULTS We identified PSMC3 (proteasome 26S subunit, ATPase, 3) as a novel AGO2 binding partner. Biochemical and bioinformatic analysis demonstrates that this interaction is performed in an RNA-independent manner and the N-terminal coiled-coil motif of PSMC3 is required. Depletion of PSMC3 impairs the activity of the targeted cleavage mediated by small RNAs. Further studies showed that depletion of PSMC3 decreased AGO2 protein amount, whereas PSMC3 overexpression increased the expression of AGO2 at a post-translational level. Cycloheximide treatment indicated that PSMC3 depletion resulted in a decrease in cytoplasmic AGO2 amount due to an increase in AGO2 protein turnover. The absence of PSMC3 promoted ubiquitination of AGO2, resulting in its degradation by the 26S proteasome. Mechanistically, PSMC3 assists in the interaction of AGO2 with the deubiquitylase USP14(ubiquitin specific peptidase 14) and facilitates USP14-mediated deubiquitination of AGO2. As a result, AGO2 is stabilized, which then promotes RNAi. CONCLUSION Our findings demonstrate that PSMC3 plays an essential role in regulating the stability of AGO2 and thus in maintaining effective RNAi.
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Affiliation(s)
- Yan Jia
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Jianing Zhao
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Tao Yu
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Xue Zhang
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Xiaozhen Qi
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Tongxin Hao
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Zeyuan Jin
- grid.265021.20000 0000 9792 1228Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, No. 22 Qi-Xiang- Tai Road, Tianjin, 300070 China
| | - Xiaoqing Zhao
- grid.452704.00000 0004 7475 0672Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong China
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8
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Li W, Liu Y, He R, Wang L, Wang Y, Zeng W, Zhang Z, Wang F, Ma L. A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis. Nucleic Acids Res 2022; 50:5226-5238. [PMID: 35524569 PMCID: PMC9122594 DOI: 10.1093/nar/gkac315] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Argonaute (Ago) proteins are programmable nucleases found in eukaryotes and prokaryotes. Prokaryotic Agos (pAgos) share a high degree of structural homology with eukaryotic Agos (eAgos), and eAgos originate from pAgos. Although eAgos exclusively cleave RNA targets, most characterized pAgos cleave DNA targets. This study characterized a novel pAgo, MbpAgo, from the psychrotolerant bacterium Mucilaginibacter paludis which prefers to cleave RNA targets rather than DNA targets. Compared to previously studied Agos, MbpAgo can utilize both 5′phosphorylated(5′P) and 5′hydroxylated(5′OH) DNA guides (gDNAs) to efficiently cleave RNA targets at the canonical cleavage site if the guide is between 15 and 17 nt long. Furthermore, MbpAgo is active at a wide range of temperatures (4–65°C) and displays no obvious preference for the 5′-nucleotide of a guide. Single-nucleotide and most dinucleotide mismatches have no or little effects on cleavage efficiency, except for dinucleotide mismatches at positions 11–13 that dramatically reduce target cleavage. MbpAgo can efficiently cleave highly structured RNA targets using both 5′P and 5′OH gDNAs in the presence of Mg2+ or Mn2+. The biochemical characterization of MbpAgo paves the way for its use in RNA manipulations such as nucleic acid detection and clearance of RNA viruses.
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Affiliation(s)
- Wenqiang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ruyi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanting Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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9
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Fàbrega C, Aviñó A, Eritja R. Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications. CHEM REC 2021; 22:e202100270. [DOI: 10.1002/tcr.202100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Carme Fàbrega
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Anna Aviñó
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Ramon Eritja
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
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10
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Liu QL, Zhang Z, Wei X, Zhou ZG. Noncoding RNAs in tumor metastasis: molecular and clinical perspectives. Cell Mol Life Sci 2021; 78:6823-6850. [PMID: 34499209 PMCID: PMC11073083 DOI: 10.1007/s00018-021-03929-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Metastasis is the main culprit of cancer-associated mortality and involves a complex and multistage process termed the metastatic cascade, which requires tumor cells to detach from the primary site, intravasate, disseminate in the circulation, extravasate, adapt to the foreign microenvironment, and form organ-specific colonization. Each of these processes has been already studied extensively for molecular mechanisms focused mainly on protein-coding genes. Recently, increasing evidence is pointing towards RNAs without coding potential for proteins, referred to as non-coding RNAs, as regulators in shaping cellular activity. Since those first reports, the detection and characterization of non-coding RNA have explosively thrived and greatly enriched the understanding of the molecular regulatory networks in metastasis. Moreover, a comprehensive description of ncRNA dysregulation will provide new insights into novel tools for the early detection and treatment of metastatic cancer. In this review, we focus on discussion of the emerging role of ncRNAs in governing cancer metastasis and describe step by step how ncRNAs impinge on cancer metastasis. In particular, we highlight the diagnostic and therapeutic applications of ncRNAs in metastatic cancer.
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Affiliation(s)
- Qiu-Luo Liu
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Zhe Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Zong-Guang Zhou
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
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11
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Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
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Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
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12
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Liu Y, Li W, Jiang X, Wang Y, Zhang Z, Liu Q, He R, Chen Q, Yang J, Wang L, Wang F, Ma L. A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis. Nucleic Acids Res 2021; 49:1597-1608. [PMID: 33444443 PMCID: PMC7897485 DOI: 10.1093/nar/gkaa1278] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022] Open
Abstract
Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA interference pathways and function as RNA-guided RNA endonucleases at physiological temperatures. Although eAgos are considered to evolve from prokaryotic Argonaute proteins (pAgos), previously studied pAgos were unable to catalyze RNA-guided RNA cleavage at physiological temperatures. Here, we describe a distinctive pAgo from mesophilic bacteria Kurthia massiliensis (KmAgo). KmAgo utilizes DNA guides to cleave single-stranded DNA (ssDNA) and RNA targets with high activity. KmAgo also utilizes RNA guides to cleave ssDNA and RNA targets at moderate temperatures. We show that KmAgo can use 5′ phosphorylated DNA guides as small as 9-mers to cut ssDNA and RNA, like Clostridium butyricum Ago. Small DNA binding confers remarkable thermostability on KmAgo, and we can suppress the guide-independent plasmid processing activity of empty KmAgo by elevating the DNA guide loaded temperature. Moreover, KmAgo performs programmable cleavage of double-stranded DNA and highly structured RNA at 37°C. Therefore, KmAgo can be regarded as a DNA-guided programmable omnipotent nuclease for cleaving most types of nucleic acids efficiently. This study broadens our understanding of Ago proteins and could expand the pAgo-based DNA and RNA manipulation toolbox.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wenqiang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xiaoman Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ruyi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Quan Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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13
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Ashrafizadeh M, Hushmandi K, Rahmani Moghadam E, Zarrin V, Hosseinzadeh Kashani S, Bokaie S, Najafi M, Tavakol S, Mohammadinejad R, Nabavi N, Hsieh CL, Zarepour A, Zare EN, Zarrabi A, Makvandi P. Progress in Delivery of siRNA-Based Therapeutics Employing Nano-Vehicles for Treatment of Prostate Cancer. Bioengineering (Basel) 2020; 7:E91. [PMID: 32784981 PMCID: PMC7552721 DOI: 10.3390/bioengineering7030091] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) accounts for a high number of deaths in males with no available curative treatments. Patients with PCa are commonly diagnosed in advanced stages due to the lack of symptoms in the early stages. Recently, the research focus was directed toward gene editing in cancer therapy. Small interfering RNA (siRNA) intervention is considered as a powerful tool for gene silencing (knockdown), enabling the suppression of oncogene factors in cancer. This strategy is applied to the treatment of various cancers including PCa. The siRNA can inhibit proliferation and invasion of PCa cells and is able to promote the anti-tumor activity of chemotherapeutic agents. However, the off-target effects of siRNA therapy remarkably reduce its efficacy in PCa therapy. To date, various carriers were designed to improve the delivery of siRNA and, among them, nanoparticles are of importance. Nanoparticles enable the targeted delivery of siRNAs and enhance their potential in the downregulation of target genes of interest. Additionally, nanoparticles can provide a platform for the co-delivery of siRNAs and anti-tumor drugs, resulting in decreased growth and migration of PCa cells. The efficacy, specificity, and delivery of siRNAs are comprehensively discussed in this review to direct further studies toward using siRNAs and their nanoscale-delivery systems in PCa therapy and perhaps other cancer types.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran;
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963114, Iran; (K.H.); (S.B.)
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical Sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
| | - Vahideh Zarrin
- Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
| | | | - Saied Bokaie
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963114, Iran; (K.H.); (S.B.)
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran;
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614525, Iran;
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kermaan 55425147, Iran;
| | - Noushin Nabavi
- Research Services, University of Victoria, Victoria, BC V8W 2Y2, Canada;
| | - Chia-Ling Hsieh
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei City 110, Taiwan;
| | - Atefeh Zarepour
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran;
| | | | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul 34956, Turkey
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 61537-53843, Iran
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14
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Zhuo Z, Wan Y, Guan D, Ni S, Wang L, Zhang Z, Liu J, Liang C, Yu Y, Lu A, Zhang G, Zhang B. A Loop-Based and AGO-Incorporated Virtual Screening Model Targeting AGO-Mediated miRNA-mRNA Interactions for Drug Discovery to Rescue Bone Phenotype in Genetically Modified Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903451. [PMID: 32670749 PMCID: PMC7341099 DOI: 10.1002/advs.201903451] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/18/2020] [Indexed: 05/05/2023]
Abstract
Several virtual screening models are proposed to screen small molecules only targeting primary miRNAs without selectivity. Few attempts have been made to develop virtual screening strategies for discovering small molecules targeting mature miRNAs. Mature miRNAs and their specific target mRNA can form unique functional loops during argonaute (AGO)-mediated miRNA-mRNA interactions, which may serve as potential targets for small-molecule drug discovery. Thus, a loop-based and AGO-incorporated virtual screening model is constructed for targeting the loops. The previously published studies have found that miR-214 can target ATF4 to inhibit osteoblastic bone formation, whereas miR-214 can target TRAF3 to promote osteoclast activity. By using the virtual model, the top ten candidate small molecules targeting miR-214-ATF4 mRNA interactions and top ten candidate small molecules targeting miR-214-TRAF3 mRNA interactions are selected, respectively. Based on both in vitro and in vivo data, one small molecule can target miR-214-ATF4 mRNA to promote ATF4 protein expression and enhance osteogenic potential, whereas one small molecule can target miR-214-TRAF3 mRNA to promote TRAF3 protein expression and inhibit osteoclast activity. These data indicate that the loop-based and AGO-incorporated virtual screening model can help to obtain small molecules specifically targeting miRNA-mRNA interactions to rescue bone phenotype in genetically modified mice.
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Affiliation(s)
- Zhenjian Zhuo
- School of Chinese MedicineFaculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
- Aptacure Therapeutics LimitedKowloonHong Kong SARChina
| | - Youyang Wan
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Daogang Guan
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangdong Provincial Key Laboratory of Single Cell Technology and ApplicationGuangzhou510515China
| | - Shuaijian Ni
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Guangdong‐Hong Kong‐Macao Greater BayArea International Research Platform for Aptamer‐based Translational Medicine and Drug DiscoveryHong Kong999077China
| | - Luyao Wang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Guangdong‐Hong Kong‐Macao Greater BayArea International Research Platform for Aptamer‐based Translational Medicine and Drug DiscoveryHong Kong999077China
| | - Zongkang Zhang
- School of Chinese MedicineFaculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Jin Liu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Chao Liang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Guangdong‐Hong Kong‐Macao Greater BayArea International Research Platform for Aptamer‐based Translational Medicine and Drug DiscoveryHong Kong999077China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Guangdong‐Hong Kong‐Macao Greater BayArea International Research Platform for Aptamer‐based Translational Medicine and Drug DiscoveryHong Kong999077China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint DiseasesSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
- Institute of Integrated Bioinformedicine and Translational ScienceSchool of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Bao‐Ting Zhang
- School of Chinese MedicineFaculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
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15
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Humphreys SC, Thayer MB, Campbell J, Chen WLK, Adams D, Lade JM, Rock BM. Emerging siRNA Design Principles and Consequences for Biotransformation and Disposition in Drug Development. J Med Chem 2020; 63:6407-6422. [PMID: 32352779 DOI: 10.1021/acs.jmedchem.9b01839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
After two decades teetering at the intersection of laboratory tool and therapeutic reality, with two siRNA drugs now clinically approved, this modality has finally come into fruition. Consistent with other emerging modalities, initial proof-of-concept efforts concentrated on coupling pharmacologic efficacy with desirable safety profiles. Consequently, thorough investigations of siRNA absorption, distribution, metabolism, and excretion (ADME) properties are lacking. Advancing ADME knowledge will aid establishment of in vitro-in vivo correlations and pharmacokinetic-pharmacodynamic relationships to optimize candidate selection through discovery and translation. Here, we outline the emerging siRNA design principles and discuss the consequences for siRNA disposition and biotransformation. We propose a conceptual framework for siRNA ADME evaluation, contextualizing the site of biotransformation product formation with PK-PD modulation, and end with a discussion around safety and regulatory considerations and future directions for this modality.
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Affiliation(s)
- Sara C Humphreys
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Mai B Thayer
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Jabbar Campbell
- Neuroscience Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Wen Li Kelly Chen
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Dan Adams
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Julie M Lade
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Brooke M Rock
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
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16
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Unal O, Akkoc Y, Kocak M, Nalbat E, Dogan-Ekici AI, Yagci Acar H, Gozuacik D. Treatment of breast cancer with autophagy inhibitory microRNAs carried by AGO2-conjugated nanoparticles. J Nanobiotechnology 2020; 18:65. [PMID: 32345308 PMCID: PMC7189576 DOI: 10.1186/s12951-020-00615-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Nanoparticle based gene delivery systems holds great promise. Superparamagnetic iron oxide nanoparticles (SPIONs) are being heavily investigated due to good biocompatibility and added diagnostic potential, rendering such nanoparticles theranostic. Yet, commonly used cationic coatings for efficient delivery of such anionic cargos, results in significant toxicity limiting translation of the technology to the clinic. Here, we describe a highly biocompatible, small and non-cationic SPION-based theranostic nanoparticles as novel gene therapy agents. We propose for the first-time, the usage of the microRNA machinery RISC complex component Argonaute 2 (AGO2) protein as a microRNA stabilizing agent and a delivery vehicle. In this study, AGO2 protein-conjugated, anti-HER2 antibody-linked and fluorophore-tagged SPION nanoparticles were developed (SP-AH nanoparticles) and used as a carrier for an autophagy inhibitory microRNA, MIR376B. These functionalized nanoparticles selectively delivered an effective amount of the microRNA into HER2-positive breast cancer cell lines in vitro and in a xenograft nude mice model of breast cancer in vivo, and successfully blocked autophagy. Furthermore, combination of the chemotherapy agent cisplatin with MIR376B-loaded SP-AH nanoparticles increased the efficacy of the anti-cancer treatment both in vitro in cells and in vivo in the nude mice. Therefore, we propose that AGO2 protein conjugated SPIONs are a new class of theranostic nanoparticles and can be efficiently used as innovative, non-cationic, non-toxic gene therapy tools for targeted therapy of cancer.
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Affiliation(s)
- Ozlem Unal
- Koc University, Graduate School of Material Science and Engineering, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey
| | - Yunus Akkoc
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Muhammed Kocak
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Esra Nalbat
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Asiye Isin Dogan-Ekici
- Acıbadem Mehmet Ali Aydınlar University, School of Medicine Department of Pathology, Ataşehir, 34755, Istanbul, Turkey
| | - Havva Yagci Acar
- Koc University, Graduate School of Material Science and Engineering, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey. .,Koc University, Department of Chemistry, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey. .,Koc University Surface Science and Technology Center (KUYTAM), Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey.
| | - Devrim Gozuacik
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey. .,Koç University, School of Medicine, Koç University Research Center for Translational Medicine (KUTTAM), Topkapı, 34010, Istanbul, Turkey.
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17
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Abstract
Small RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.
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Affiliation(s)
- Saife Niaz
- Department of Biotechnology, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
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18
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Coenen-Stass AML, Pauwels MJ, Hanson B, Martin Perez C, Conceição M, Wood MJA, Mäger I, Roberts TC. Extracellular microRNAs exhibit sequence-dependent stability and cellular release kinetics. RNA Biol 2019; 16:696-706. [PMID: 30836828 PMCID: PMC6546368 DOI: 10.1080/15476286.2019.1582956] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multiple studies have described extracellular microRNAs (ex-miRNAs) as being remarkably stable despite the hostile extracellular environment, when stored at 4ºC or lower. Here we show that many ex-miRNAs are rapidly degraded when incubated at 37ºC in the presence of serum (thereby simulating physiologically relevant conditions). Stability varied widely between miRNAs, with half-lives ranging from ~1.5 hours to more than 13 hours. Notably, ex-miRNA half-lives calculated in two different biofluids (murine serum and C2C12 mouse myotube conditioned medium) were highly similar, suggesting that intrinsic sequence properties are a determining factor in miRNA stability. By contrast, ex-miRNAs associated with extracellular vesicles (isolated by size exclusion chromatography) were highly stable. The release of ex-miRNAs from C2C12 myotubes was measured over time, and mathematical modelling revealed miRNA-specific release kinetics. While some ex-miRNAs reached the steady state in cell culture medium within 24 hours, the extracellular level of miR-16 did not reach equilibrium, even after 3 days in culture. These findings are indicative of miRNA-specific release and degradation kinetics with implications for the utility of ex-miRNAs as biomarkers, and for the potential of ex-miRNAs to transfer gene regulatory information between cells.
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Affiliation(s)
- Anna M L Coenen-Stass
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK
| | - Marie J Pauwels
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,b VIB-UGent Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University , Ghent , Belgium.,c Department of Biomedical Molecular Biology , Ghent University , Ghent , Belgium
| | - Britt Hanson
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK
| | - Carla Martin Perez
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK
| | - Mariana Conceição
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK
| | - Matthew J A Wood
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK
| | - Imre Mäger
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK.,e Institute of Technology , University of Tartu , Tartu , Estonia
| | - Thomas C Roberts
- a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.,d Department of Paediatrics , University of Oxford , Oxford , UK.,f Sanford Burnham Prebys Medical Discovery Institute , Development, Aging and Regeneration Program , La Jolla , CA , USA
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19
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Pottash AE, Kuffner C, Noonan-Shueh M, Jay SM. Protein-based vehicles for biomimetic RNAi delivery. J Biol Eng 2019; 13:19. [PMID: 30891095 PMCID: PMC6390323 DOI: 10.1186/s13036-018-0130-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022] Open
Abstract
Broad translational success of RNA interference (RNAi) technology depends on the development of effective delivery approaches. To that end, researchers have developed a variety of strategies, including chemical modification of RNA, viral and non-viral transfection approaches, and incorporation with delivery vehicles such as polymer- and lipid-based nanoparticles, engineered and native proteins, extracellular vesicles (EVs), and others. Among these, EVs and protein-based vehicles stand out as biomimetically-inspired approaches, as both proteins (e.g. Apolipoprotein A-1, Argonaute 2, and Arc) and EVs mediate intercellular RNA transfer physiologically. Proteins specifically offer significant therapeutic potential due to their biophysical and biochemical properties as well as their ability to facilitate and tolerate manipulation; these characteristics have made proteins highly successful translational therapeutic molecules in the last two decades. This review covers engineered protein vehicles for RNAi delivery along with what is currently known about naturally-occurring extracellular RNA carriers towards uncovering design rules that will inform future engineering of protein-based vehicles.
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Affiliation(s)
- Alex Eli Pottash
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Christopher Kuffner
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Madeleine Noonan-Shueh
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Steven M Jay
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA.,2Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 USA.,3Program in Molecular and Cellular Biology, University of Maryland, College Park, MD 20742 USA
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20
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Broecker F, Moelling K. Evolution of Immune Systems From Viruses and Transposable Elements. Front Microbiol 2019; 10:51. [PMID: 30761103 PMCID: PMC6361761 DOI: 10.3389/fmicb.2019.00051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Virus-derived sequences and transposable elements constitute a substantial portion of many cellular genomes. Recent insights reveal the intimate evolutionary relationship between these sequences and various cellular immune pathways. At the most basic level, superinfection exclusion may be considered a prototypical virus-mediated immune system that has been described in both prokaryotes and eukaryotes. More complex immune mechanisms fully or partially derived from mobile genetic elements include CRISPR-Cas of prokaryotes and the RAG1/2 system of vertebrates, which provide immunological memory of foreign genetic elements and generate antibody and T cell receptor diversity, respectively. In this review, we summarize the current knowledge on the contribution of mobile genetic elements to the evolution of cellular immune pathways. A picture is emerging in which the various cellular immune systems originate from and are spread by viruses and transposable elements. Immune systems likely evolved from simple superinfection exclusion to highly complex defense strategies.
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Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
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21
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Cultrara CN, Shah S, Kozuch SD, Patel MR, Sabatino D. Solid phase synthesis and self-assembly of higher-order siRNAs and their bioconjugates. Chem Biol Drug Des 2018; 93:999-1010. [PMID: 30480355 DOI: 10.1111/cbdd.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/10/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
New methods for the synthesis of higher-order siRNA motifs and their bioconjugates have recently gained widespread attention in the development of new and improved gene therapeutics. Our efforts aim to produce new chemical tools and protocols for the generation of modified siRNAs that screen for important oncogene targets as well as silence their activity for effective gene therapy in cancer models. More specifically, we have developed an efficient solution-phase synthesis for the production of a ribouridine branchpoint synthon that can be effectively incorporated by solid phase synthesis within higher-order RNA structures, including those adopting V-, and Y- and >-< shape RNA templates. Self-assembly of complementary RNA to the template strands produced higher-order siRNA nanostructures that were characterized by a combination of PAGE, DLS, and TEM techniques. In an effort to extend the repertoire of functionally diverse siRNAs, we have also developed solid phase bioconjugation strategies for incorporating bio-active probes such as fatty acid appendages and fluorescent reporters. Taken together, these methods highlight the ability to generate higher-order siRNAs and their bioconjugates for exploring the influence of modified siRNA structure on anti-cancer activity.
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Affiliation(s)
- Christopher N Cultrara
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | - Sunil Shah
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | - Stephen D Kozuch
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | | | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
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22
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Syntheses of prodrug-type 2'-O-methyldithiomethyl oligonucleotides modified at natural four nucleoside residues and their conversions into natural 2'-hydroxy oligonucleotides under reducing condition. Bioorg Med Chem 2018; 26:5838-5844. [PMID: 30420326 DOI: 10.1016/j.bmc.2018.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023]
Abstract
We previously reported that reducing-environment-responsive prodrug-type small interfering RNA (siRNA) bearing 2'-O-methyldithiomethyl (2'-O-MDTM) uridine exhibits efficient knockdown activity and nuclease resistance. In this report, we describe the preparation of 2'-O-MDTM oligonucleotides modified not only at uridine but also at adenosine, guanosine and cytidine residues by post-synthetic modification. Precursor oligonucleotides bearing 2'-O-(2,4,6-trimethoxybenzylthiomethyl) (2'-O-TMBTM) adenosine, guanosine, and cytidine were reacted with dimethyl(methylthio)sulfonium tetrafluoroborate to form 2'-O-MDTM oligonucleotides in the same manner as the oligonucleotide bearing 2'-O-TMBTM uridine. Furthermore, the oligonucleotides bearing 2'-O-MDTM adenosine, guanosine, and cytidine were efficiently converted into corresponding natural 2'-hydroxy oligonucleotides under the cytosol-mimetic reducing condition.
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23
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Glackin CA. Nanoparticle Delivery of TWIST Small Interfering RNA and Anticancer Drugs: A Therapeutic Approach for Combating Cancer. Enzymes 2018; 44:83-101. [PMID: 30360816 DOI: 10.1016/bs.enz.2018.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Breast and ovarian cancer are the leading cause of cancer-related deaths in women in the United States with over 232,000 new Breast Cancer (BC) diagnoses expected in 2018 and almost 40,000 deaths and an estimated 239,000 new ovarian cancer (OC) cases and 152,000 deaths worldwide annually. OC is the most lethal gynecologic malignancy. This high mortality rate is due to tumor recurrence and metastasis, primarily caused by chemoresistant cancer stem-like cells (CSCs). Triple Negative Breast Cancer (TNBC) patients also become resistant to chemotherapy due to recurrence of CSCs. Currently, no ovarian or breast cancer therapies target CSC specifically. TWIST is overexpressed in the majority of chemoresistant cancers resulting in a low survival rate. Our long-term goal is to develop novel treatments for women with ovarian and breast cancer, specifically treatments that sensitize chemoresistant tumors. Despite successful initial surgery and chemotherapy, over 70% of advanced EOC will recur, and only 15-30% of recurrent disease will respond to chemotherapy (Cortez et al., 2017; Berezhnaya, 2010; Jackson et al., 2015). Moreover, drug resistance causes treatment failure in over 90% of patients with metastatic disease (Solmaz et al., 2015). Thus, recurrent metastatic disease is a major clinical challenge without effective therapy. One of the major challenges in the treatment of breast cancer is the presence of a subpopulation of cancer cells that are chemoresistant (CRC) and metastatic. Given that metastasis is the driving force behind mortality for breast and ovarian cancer patients, it is essential to identify the characteristics of these aberrant cancer cells that allow them to spread to distant sites in the body and develop into metastatic tumors. Understanding the metastatic mechanisms driving cancer cell dispersal will open the door to developing novel therapies that prevent metastasis and improve long-term outcomes for patients. In this chapter we assess the feasibility of targeting the Twist and EMT signaling pathways in breast and ovarian cancer. Additional discussions of the pathways that mediate epithelial-mesenchymal transition (EMT), a process that can give rise to chemoresistance. We review potential treatment strategies for targeting EMT and drug resistance as well as the problems that may arise with these targeted delivery therapeutic approaches. Finally, we examine recent advances in the field, including cancer stem cell targeted nanoparticle delivery and small interference RNA (siRNA) technology, and discuss the impact that these approaches may have on translating much needed therapeutic approaches into the clinic, for the benefit of patients battling this devastating disease.
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Affiliation(s)
- Carlotta A Glackin
- Developmental and Stem Cell Biology, City of Hope Medical Center, Duarte, CA, United States.
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24
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Yan Y, Acevedo M, Mignacca L, Desjardins P, Scott N, Imane R, Quenneville J, Robitaille J, Feghaly A, Gagnon E, Ferbeyre G, Major F. The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides. Nucleic Acids Res 2018; 46:8181-8196. [PMID: 30239883 PMCID: PMC6144789 DOI: 10.1093/nar/gky546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/10/2018] [Accepted: 06/05/2018] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are ribonucleic acids (RNAs) of ∼21 nucleotides that interfere with the translation of messenger RNAs (mRNAs) and play significant roles in development and diseases. In bilaterian animals, the specificity of miRNA targeting is determined by sequence complementarity involving the seed. However, the role of the remaining nucleotides (non-seed) is only vaguely defined, impacting negatively on our ability to efficiently use miRNAs exogenously to control gene expression. Here, using reporter assays, we deciphered the role of the base pairs formed between the non-seed region and target mRNA. We used molecular modeling to reveal that this mechanism corresponds to the formation of base pairs mediated by ordered motions of the miRNA-induced silencing complex. Subsequently, we developed an algorithm based on this distinctive recognition to predict from sequence the levels of mRNA downregulation with high accuracy (r2 > 0.5, P-value < 10-12). Overall, our discovery improves the design of miRNA-guide sequences used to simultaneously downregulate the expression of multiple predetermined target genes.
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Affiliation(s)
- Yifei Yan
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mariana Acevedo
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Lian Mignacca
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Philippe Desjardins
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Nicolas Scott
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département d’informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Roqaya Imane
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Jordan Quenneville
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Julie Robitaille
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Albert Feghaly
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Etienne Gagnon
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - François Major
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département d’informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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25
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Hayashi J, Nishigaki M, Ochi Y, Wada SI, Wada F, Nakagawa O, Obika S, Harada-Shiba M, Urata H. Effective gene silencing activity of prodrug-type 2′-O-methyldithiomethyl siRNA compared with non-prodrug-type 2′-O-methyl siRNA. Bioorg Med Chem Lett 2018; 28:2171-2174. [DOI: 10.1016/j.bmcl.2018.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
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26
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Deshpande S, Singh N. Probing the nanoparticle-AGO2 interaction for enhanced gene knockdown. SOFT MATTER 2018; 14:4169-4177. [PMID: 29687822 DOI: 10.1039/c8sm00534f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
RNAi is emerging as a promising technology for treatment of various diseases due to its ability to silence specific target genes. To date, a number of nanoparticle based formulations have been reported for the delivery of small interfering RNA (siRNA), with continuous modifications in the nanoparticle design for enhancing their efficiency. While majority of the design aspects are focused on avoiding or overcoming endosomal entrapment, limited studies are available that address the role of interaction of nanoparticles with the RNA induced silencing complex (RISC) machinery, which is a crucial aspect deciding the outcome. Here, we systematically probed the effect of steric hindrance of nanoparticles on RISC interaction, by modulating two parameters, nanoparticle size and hardness. An assay was developed for quantifying the extent of RISC interaction of different nanoparticles in vitro, which was then correlated with their gene knockdown efficiency. The results suggest that the soft and small nanoparticles were most efficacious in knocking down polo-like-kinase 1 (PLK1) siRNA, a gene overexpressed in a variety of cancer types.
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Affiliation(s)
- Sonal Deshpande
- Centre for Biomedical Engineering, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi-110016, India. sneetu.iitd.ac.in
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Ghosh N, Katare R. Molecular mechanism of diabetic cardiomyopathy and modulation of microRNA function by synthetic oligonucleotides. Cardiovasc Diabetol 2018; 17:43. [PMID: 29566757 PMCID: PMC5863891 DOI: 10.1186/s12933-018-0684-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/10/2018] [Indexed: 02/06/2023] Open
Abstract
Diabetic cardiomyopathy (DCM) is a chronic complication in individuals with diabetes and is characterized by ventricular dilation and hypertrophy, diastolic dysfunction, decreased or preserved systolic function and reduced ejection fraction eventually resulting in heart failure. Despite being well characterized, the fundamental mechanisms leading to DCM are still elusive. Recent studies identified the involvement of small non-coding small RNA molecules such as microRNAs (miRs) playing a key role in the etiology of DCM. Therefore, miRs associated with DCM represents a new class of targets for the development of mechanistic therapeutics, which may yield marked benefits compared to other therapeutic approaches. Indeed, few miRs currently under active clinical investigation, with many expressing cautious optimism that miRs based therapies will succeed in the coming years. The major caution in using miRs based therapy is the need to improve the stability and specificity following systemic injection, which can be achieved through chemical and structural modification. In this review, we first discuss the established role of miRs in DCM and the advances in miRs based therapeutic strategies for the prevention/treatment of DCM. We next discuss the currently employed chemical modification of miR oligonucleotides and their utility in therapies specifically focusing on the DCM. Finally, we summarize the commonly used delivery system and approaches for assessment of miRNA modulation and potential off-target effects.
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Affiliation(s)
- Nilanjan Ghosh
- Department of Physiology-HeartOtago, University of Otago, 270, Great King Street, Dunedin, 9010 New Zealand
| | - Rajesh Katare
- Department of Physiology-HeartOtago, University of Otago, 270, Great King Street, Dunedin, 9010 New Zealand
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28
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Qu H, Zheng L, Song H, Jiao W, Li D, Fang E, Wang X, Mei H, Pu J, Huang K, Tong Q. microRNA-558 facilitates the expression of hypoxia-inducible factor 2 alpha through binding to 5'-untranslated region in neuroblastoma. Oncotarget 2018; 7:40657-40673. [PMID: 27276678 PMCID: PMC5130034 DOI: 10.18632/oncotarget.9813] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/20/2016] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. Our previous studies have shown that hypoxia-inducible factor 2 alpha (HIF-2α), one member of the bHLH-PAS transcription factor family, facilitates the progression of NB under non-hypoxic conditions. However, the mechanisms underlying HIF-2α expression in NB still remain largely unknown. Herein, through analyzing the computational algorithm programs, we identified microRNA-558 (miR-558) as a crucial regulator of HIF-2α expression in NB. We demonstrated that miR-558 promoted the expression of HIF-2α at translational levels in NB cells through recruiting Argonaute 2 (AGO2). Mechanistically, miR-558 directly bound with its complementary site within 5′-untranslated region (5′-UTR) to facilitate the binding of AGO2 to eukaryotic translation initiation factor 4E (eIF4E) binding protein 1, resulting in increased eIF4E enrichment and HIF-2α translation. In addition, miR-558 promoted the growth, invasion, metastasis, and angiogenesis of NB cells in vitro and in vivo, and these biological features were rescued by knockdown of AGO2, eIF4E, or HIF-2α. In clinical NB specimens, miR-558, AGO2, and eIF4E were highly expressed and positively correlated with HIF-2α expression. Patients with high miR-558, HIF-2α, AGO2, or eIF4E levels had lower survival probability. Taken together, these results demonstrate that miR-558 facilitates the expression of HIF-2α through bindingto its 5′-UTR, thus promoting the tumorigenesis and aggressiveness of NB.
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Affiliation(s)
- Hongxia Qu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Huajie Song
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Wanju Jiao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Hong Mei
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Jiarui Pu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
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29
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Setten RL, Lightfoot HL, Habib NA, Rossi JJ. Development of MTL-CEBPA: Small Activating RNA Drug for Hepatocellular Carcinoma. Curr Pharm Biotechnol 2018; 19:611-621. [PMID: 29886828 PMCID: PMC6204661 DOI: 10.2174/1389201019666180611093428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND Oligonucleotide drug development has revolutionised the drug discovery field. Within this field, 'small' or 'short' activating RNAs (saRNA) are a more recently discovered category of short double-stranded RNA with clinical potential. saRNAs promote transcription from target loci, a phenomenon widely observed in mammals known as RNA activation (RNAa). OBJECTIVE The ability to target a particular gene is dependent on the sequence of the saRNA. Hence, the potential clinical application of saRNAs is to increase target gene expression in a sequence-specific manner. saRNA-based therapeutics present opportunities for expanding the "druggable genome" with particular areas of interest including transcription factor activation and cases of haploinsufficiency. RESULTS AND CONCLUSION In this mini-review, we describe the pre-clinical development of the first saRNA drug to enter the clinic. This saRNA, referred to as MTL-CEBPA, induces increased expression of the transcription factor CCAAT/enhancer-binding protein alpha (CEBPα), a tumour suppressor and critical regulator of hepatocyte function. MTL-CEBPA is presently in Phase I clinical trials for hepatocellular carcinoma (HCC). The clinical development of MTL-CEBPA will demonstrate "proof of concept" that saRNAs can provide the basis for drugs which enhance target gene expression and consequently improve treatment outcome in patients.
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Affiliation(s)
| | | | | | - John J. Rossi
- Address correspondence to this author at the Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA; Tel: 626-218-7390; Fax: 626-301-8371; E-mail:
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30
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The CAG-polyglutamine repeat diseases: a clinical, molecular, genetic, and pathophysiologic nosology. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:143-170. [PMID: 29325609 DOI: 10.1016/b978-0-444-63233-3.00011-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Throughout the genome, unstable tandem nucleotide repeats can expand to cause a variety of neurologic disorders. Expansion of a CAG triplet repeat within a coding exon gives rise to an elongated polyglutamine (polyQ) tract in the resultant protein product, and accounts for a unique category of neurodegenerative disorders, known as the CAG-polyglutamine repeat diseases. The nine members of the CAG-polyglutamine disease family include spinal and bulbar muscular atrophy (SBMA), Huntington disease, dentatorubral pallidoluysian atrophy, and six spinocerebellar ataxias (SCA 1, 2, 3, 6, 7, and 17). All CAG-polyglutamine diseases are dominantly inherited, with the exception of SBMA, which is X-linked, and many CAG-polyglutamine diseases display anticipation, which is defined as increasing disease severity in successive generations of an affected kindred. Despite widespread expression of the different polyQ-expanded disease proteins throughout the body, each CAG-polyglutamine disease strikes a particular subset of neurons, although the mechanism for this cell-type selectivity remains poorly understood. While the different genes implicated in these disorders display amino acid homology only in the repeat tract domain, certain pathologic molecular processes have been implicated in almost all of the CAG-polyglutamine repeat diseases, including protein aggregation, proteolytic cleavage, transcription dysregulation, autophagy impairment, and mitochondrial dysfunction. Here we highlight the clinical and molecular genetic features of each distinct disorder, and then discuss common themes in CAG-polyglutamine disease pathogenesis, closing with emerging advances in therapy development.
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Zhang L, Liang D, Wang Y, Li D, Zhang J, Wu L, Feng M, Yi F, Xu L, Lei L, Du Q, Tang X. Caged circular siRNAs for photomodulation of gene expression in cells and mice. Chem Sci 2017; 9:44-51. [PMID: 29629072 PMCID: PMC5869302 DOI: 10.1039/c7sc03842a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Caged siRNAs with a circular structure were successfully used for photoregulation of target genes in both cells and mice.
By means of RNA interference (RNAi), small interfering RNAs (siRNAs) play important roles in gene function study and drug development. Recently, photolabile siRNAs were developed to elucidate the process of gene silencing in terms of space, time and degree through chemical modification of siRNAs. We report herein a novel type of photolabile siRNA that was synthesized through cyclizing two ends of a single stranded RNA with a photocleavable linker. These circular siRNAs became more resistant to serum degradation. Using reporter assays of firefly/Renilla luciferase and GFP/RFP, the gene silencing activities of caged circular siRNAs for both genes were evaluated in HEK293 cells. The results indicated that the target genes were successfully photomodulated using these caged circular siRNAs that were formed by caged circular antisense guide RNAs and their linear complementary sense RNAs. Using the caged circular siRNA targeting GFP, we also successfully achieved photomodulation of GFP expression in mice. Upon further optimization, this new type of caged circular siRNA is expected to be a promising tool for studying gene therapy.
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Affiliation(s)
- Liangliang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Duanwei Liang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Dong Li
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Jinhao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Li Wu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Fan Yi
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Luzheng Xu
- Medical and Health Analytical Center , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China
| | - Liandi Lei
- Medical and Health Analytical Center , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China
| | - Quan Du
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
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Voutila J, Reebye V, Roberts TC, Protopapa P, Andrikakou P, Blakey DC, Habib R, Huber H, Saetrom P, Rossi JJ, Habib NA. Development and Mechanism of Small Activating RNA Targeting CEBPA, a Novel Therapeutic in Clinical Trials for Liver Cancer. Mol Ther 2017; 25:2705-2714. [PMID: 28882451 PMCID: PMC5768526 DOI: 10.1016/j.ymthe.2017.07.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/31/2017] [Accepted: 07/31/2017] [Indexed: 01/05/2023] Open
Abstract
Small activating RNAs (saRNAs) are short double-stranded oligonucleotides that selectively increase gene transcription. Here, we describe the development of an saRNA that upregulates the transcription factor CCATT/enhancer binding protein alpha (CEBPA), investigate its mode of action, and describe its development into a clinical candidate. A bioinformatically directed nucleotide walk around the CEBPA gene identified an saRNA sequence that upregulates CEBPA mRNA 2.5-fold in human hepatocellular carcinoma cells. A nuclear run-on assay confirmed that this upregulation is a transcriptionally driven process. Mechanistic experiments demonstrate that Argonaute-2 (Ago2) is required for saRNA activity, with the guide strand of the saRNA shown to be associated with Ago2 and localized at the CEBPA genomic locus using RNA chromatin immunoprecipitation (ChIP) assays. The data support a sequence-specific on-target saRNA activity that leads to enhanced CEBPA mRNA transcription. Chemical modifications were introduced in the saRNA duplex to prevent activation of the innate immunity. This modified saRNA retains activation of CEBPA mRNA and downstream targets and inhibits growth of liver cancer cell lines in vitro. This novel drug has been encapsulated in a liposomal formulation for liver delivery, is currently in a phase I clinical trial for patients with liver cancer, and represents the first human study of an saRNA therapeutic.
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Affiliation(s)
| | - Vikash Reebye
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | | | | | | | - Hans Huber
- BioTD Strategies, LLC, Philadelphia, PA, USA
| | - Pal Saetrom
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Nagy A Habib
- Department of Surgery and Cancer, Imperial College London, London, UK.
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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34
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Elkayam E, Parmar R, Brown CR, Willoughby JL, Theile CS, Manoharan M, Joshua-Tor L. siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res 2017; 45:3528-3536. [PMID: 27903888 PMCID: PMC5389677 DOI: 10.1093/nar/gkw1171] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/20/2023] Open
Abstract
Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5΄- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5΄- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5΄-(E)-vinylphosphonate (5΄-E-VP) guide RNA at 2.5-Å resolution. The structure demonstrates how the 5΄ binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5΄-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5΄-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA.
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Affiliation(s)
- Elad Elkayam
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | | | | | | | - Leemor Joshua-Tor
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Crooke ST. Molecular Mechanisms of Antisense Oligonucleotides. Nucleic Acid Ther 2017; 27:70-77. [PMID: 28080221 PMCID: PMC5372764 DOI: 10.1089/nat.2016.0656] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022] Open
Abstract
In 1987, when I became interested in the notion of antisense technology, I returned to my roots in RNA biochemistry and began work to understand how oligonucleotides behave in biological systems. Since 1989, my research has focused primarily on this topic, although I have been involved in most areas of research in antisense technology. I believe that the art of excellent science is to frame large important questions that are perhaps not immediately answerable with existing knowledge and methods, and then conceive a long-term (multiyear) research strategy that begins by answering the most pressing answerable questions on the path to the long-term goals. Then, a step-by-step research pathway that will address the strategic questions posed must be implemented, adjusting the plan as new things are learned. This is the approach we have taken at Ionis. Obviously, to create antisense technology, we have had to address a wide array of strategic questions, for example, the medicinal chemistry of oligonucleotides, manufacturing and analytical methods, pharmacokinetics and toxicology, as well as questions about the molecular pharmacology of antisense oligonucleotides (ASOs). Each of these endeavors has consumed nearly three decades of scientific effort, is still very much a work-in-progress, and has resulted in hundreds of publications. As a recipient of the Lifetime Achievement Award 2016 granted by the Oligonucleotide Therapeutic Society, in this note, my goal is to summarize the contributions of my group to the efforts to understand the molecular mechanisms of ASOs.
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Affiliation(s)
- Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. , Carlsbad, California
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36
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Trubetskoy VS, Griffin JB, Nicholas AL, Nord EM, Xu Z, Peterson RM, Wooddell CI, Rozema DB, Wakefield DH, Lewis DL, Kanner SB. Phosphorylation-specific status of RNAi triggers in pharmacokinetic and biodistribution analyses. Nucleic Acids Res 2017; 45:1469-1478. [PMID: 28180327 PMCID: PMC5388421 DOI: 10.1093/nar/gkw828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 01/23/2023] Open
Abstract
The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5΄-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites. Compared to PCR- or ELISA-based methods, this assay enables separate quantitation of non-phosphorylated full-length guide strands from 5΄-phosphorylated forms that may associate with RNA-induced silencing complexes (RISC). Biodistribution studies in mice indicated that ARC-520 guide strands predominantly accumulated in liver. 5΄-phosphorylation of guide strands was observed within 5 min after ARC-520 injection, and was detected for at least 4 weeks corresponding to the duration of HBV mRNA silencing. Guide strands detected in RISC by AGO2 immuno-isolation represented 16% of total 5΄-phosphorylated guide strands in liver, correlating with a 2.7 log10 reduction of HBsAg. The PNA method enables pharmacokinetic analysis of RNAi triggers, elucidates potential metabolic processing events and defines pharmacokinetic-pharmacodynamic relationships.
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MESH Headings
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Female
- Gene Knockdown Techniques
- Hepatitis B Surface Antigens/blood
- Hepatitis B Surface Antigens/genetics
- Hepatitis B virus/genetics
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/metabolism
- Hepatitis B, Chronic/therapy
- Hepatitis B, Chronic/virology
- Humans
- Kinetics
- Liver/metabolism
- Liver/virology
- Mice
- Mice, Inbred ICR
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Peptide Nucleic Acids/genetics
- Peptide Nucleic Acids/metabolism
- Phosphorylation
- RNA Interference
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Induced Silencing Complex/genetics
- RNA-Induced Silencing Complex/metabolism
- Tissue Distribution
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Affiliation(s)
| | - Jacob B. Griffin
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Anthony L. Nicholas
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Eric M. Nord
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Zhao Xu
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Ryan M. Peterson
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | | | - David B. Rozema
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Darren H. Wakefield
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | | | - Steven B. Kanner
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
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Zealy RW, Wrenn SP, Davila S, Min KW, Yoon JH. microRNA-binding proteins: specificity and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1414] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Richard W. Zealy
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Samuel P. Wrenn
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
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38
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Willkomm S, Zander A, Grohmann D, Restle T. Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties. PLoS One 2016; 11:e0164695. [PMID: 27741323 PMCID: PMC5065165 DOI: 10.1371/journal.pone.0164695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022] Open
Abstract
Argonaute (Ago) proteins from all three domains of life are key players in processes that specifically regulate cellular nucleic acid levels. Some of these Ago proteins, among them human Argonaute2 (hAgo2) and Ago from the archaeal organism Methanocaldococcus jannaschii (MjAgo), are able to cleave nucleic acid target strands that are recognised via an Ago-associated complementary guide strand. Here we present an in-depth kinetic side-by-side analysis of hAgo2 and MjAgo guide and target substrate binding as well as target strand cleavage, which enabled us to disclose similarities and differences in the mechanistic pathways as a function of the chemical nature of the substrate. Testing all possible guide-target combinations (i.e. RNA/RNA, RNA/DNA, DNA/RNA and DNA/DNA) with both Ago variants we demonstrate that the molecular mechanism of substrate association is highly conserved among archaeal-eukaryotic Argonautes. Furthermore, we show that hAgo2 binds RNA and DNA guide strands in the same fashion. On the other hand, despite striking homology between the two Ago variants, MjAgo cannot orientate guide RNA substrates in a way that allows interaction with the target DNA in a cleavage-compatible orientation.
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Affiliation(s)
- Sarah Willkomm
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
| | - Adrian Zander
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Tobias Restle
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
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Mukherjee K, Ghoshal B, Ghosh S, Chakrabarty Y, Shwetha S, Das S, Bhattacharyya SN. Reversible HuR-microRNA binding controls extracellular export of miR-122 and augments stress response. EMBO Rep 2016; 17:1184-203. [PMID: 27402548 PMCID: PMC4967961 DOI: 10.15252/embr.201541930] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/09/2016] [Indexed: 01/10/2023] Open
Abstract
microRNAs (miRNAs), the tiny but stable regulatory RNAs in metazoan cells, can undergo selective turnover in presence of specific internal and external cues to control cellular response against the changing environment. We have observed reduction in cellular miR-122 content, due to their accelerated extracellular export in human hepatic cells starved for small metabolites including amino acids. In this context, a new role of human ELAV protein HuR has been identified. HuR, a negative regulator of miRNA function, accelerates extracellular vesicle (EV)-mediated export of miRNAs in human cells. In stressed cells, HuR replaces miRNPs from target messages and is both necessary and sufficient for the extracellular export of corresponding miRNAs. HuR could reversibly bind miRNAs to replace them from Ago2 and subsequently itself gets freed from bound miRNAs upon ubiquitination. The ubiquitinated form of HuR is predominantly associated with multivesicular bodies (MVB) where HuR-unbound miRNAs also reside. These MVB-associated pool of miRNAs get exported out via EVs thereby delimiting cellular miR-122 level during starvation. Therefore, by modulating extracellular export of miR-122, HuR could control stress response in starved human hepatic cells.
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Affiliation(s)
- Kamalika Mukherjee
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Bartika Ghoshal
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Souvik Ghosh
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Yogaditya Chakrabarty
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shivaprasad Shwetha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Suvendra N Bhattacharyya
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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40
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Alagia A, Eritja R. siRNA and RNAi optimization. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:316-29. [PMID: 26840434 DOI: 10.1002/wrna.1337] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
The discovery and examination of the posttranscriptional gene regulatory mechanism known as RNA interference (RNAi) contributed to the identification of small interfering RNA (siRNA) and the comprehension of its enormous potential for clinical purposes. Theoretically, the ability of specific target gene downregulation makes the RNAi pathway an appealing solution for several diseases. Despite numerous hurdles resulting from the inherent properties of siRNA molecule and proper delivery to the target tissue, more than 50 RNA-based drugs are currently under clinical testing. In this work, we analyze the recent literature in the optimization of siRNA molecules. In detail, we focused on describing the most recent advances of siRNA field aimed at optimize siRNA pharmacokinetic properties. Special attention has been given in describing the impact of RNA modifications in the potential off-target effects (OTEs) such as saturation of the RNAi machinery, passenger strand-mediated silencing, immunostimulation, and miRNA-like OTEs as well as to recent developments on the delivery issue. The novel delivery systems and modified siRNA provide significant steps toward the development of reliable siRNA molecules for therapeutic use. WIREs RNA 2016, 7:316-329. doi: 10.1002/wrna.1337 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Adele Alagia
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
| | - Ramon Eritja
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
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41
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siRNA Versus miRNA as Therapeutics for Gene Silencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e252. [PMID: 26372022 PMCID: PMC4877448 DOI: 10.1038/mtna.2015.23] [Citation(s) in RCA: 653] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/18/2015] [Indexed: 02/06/2023]
Abstract
Discovered a little over two decades ago, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are noncoding RNAs with important roles in gene regulation. They have recently been investigated as novel classes of therapeutic agents for the treatment of a wide range of disorders including cancers and infections. Clinical trials of siRNA- and miRNA-based drugs have already been initiated. siRNAs and miRNAs share many similarities, both are short duplex RNA molecules that exert gene silencing effects at the post-transcriptional level by targeting messenger RNA (mRNA), yet their mechanisms of action and clinical applications are distinct. The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets. The therapeutic approaches of siRNAs and miRNAs are therefore very different. Hence, this review provides a comparison between therapeutic siRNAs and miRNAs in terms of their mechanisms of action, physicochemical properties, delivery, and clinical applications. Moreover, the challenges in developing both classes of RNA as therapeutics are also discussed.
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42
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Conformational Dynamics of Ago-Mediated Silencing Processes. Int J Mol Sci 2015; 16:14769-85. [PMID: 26140373 PMCID: PMC4519871 DOI: 10.3390/ijms160714769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/10/2015] [Accepted: 06/17/2015] [Indexed: 12/15/2022] Open
Abstract
Argonaute (Ago) proteins are key players of nucleic acid-based interference mechanisms. Their domains and structural organization are widely conserved in all three domains of life. However, different Ago proteins display various substrate preferences. While some Ago proteins are able to use several substrates, others are limited to a single one. Thereby, they were demonstrated to act specifically on their preferred substrates. Here, we discuss mechanisms of Ago-mediated silencing in relation to structural and biochemical insights. The combination of biochemical and structural information enables detailed analyses of the complex dynamic interplay between Ago proteins and their substrates. Especially, transient binding data allow precise investigations of structural transitions taking place upon Ago-mediated guide and target binding.
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43
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Gioia U, di Fagagna FD. Human nuclear ARGONAUTE 2 interacts in vivo only with small RNAs and not with DNA. Cell Cycle 2015; 14:2001-2. [PMID: 25970378 PMCID: PMC4615022 DOI: 10.1080/15384101.2015.1044171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Ubaldo Gioia
- IFOM – the FIRC Institute of Molecular Oncology; Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM – the FIRC Institute of Molecular Oncology; Milan, Italy
- Istituto di Genetica Molecolare; Consiglio Nazionale delle Ricerche; Pavia, Italy
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44
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Kokil GR, Veedu RN, Ramm GA, Prins JB, Parekh HS. Type 2 diabetes mellitus: limitations of conventional therapies and intervention with nucleic acid-based therapeutics. Chem Rev 2015; 115:4719-43. [PMID: 25918949 DOI: 10.1021/cr5002832] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ganesh R Kokil
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Rakesh N Veedu
- §Center for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.,∥Western Australian Neuroscience Research Institute, Perth, WA 6150, Australia.,‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Grant A Ramm
- ⊥The Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,#Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Johannes B Prins
- ∇Mater Research Institute, The University of Queensland, Brisbane, QLD 4101, Australia
| | - Harendra S Parekh
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
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45
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Bernard MA, Wang L, Tachado SD. DICER-ARGONAUTE2 complex in continuous fluorogenic assays of RNA interference enzymes. PLoS One 2015; 10:e0120614. [PMID: 25793518 PMCID: PMC4368098 DOI: 10.1371/journal.pone.0120614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 02/05/2015] [Indexed: 12/30/2022] Open
Abstract
Mechanistic studies of RNA processing in the RNA-Induced Silencing Complex (RISC) have been hindered by lack of methods for continuous monitoring of enzymatic activity. “Quencherless” fluorogenic substrates of RNAi enzymes enable continuous monitoring of enzymatic reactions for detailed kinetics studies. Recombinant RISC enzymes cleave the fluorogenic substrates targeting human thymidylate synthase (TYMS) and hypoxia-inducible factor 1-α subunit (HIF1A). Using fluorogenic dsRNA DICER substrates and fluorogenic siRNA, DICER+ARGONAUTE2 mixtures exhibit synergistic enzymatic activity relative to either enzyme alone, and addition of TRBP does not enhance the apparent activity. Titration of AGO2 and DICER in enzyme assays suggests that AGO2 and DICER form a functional high-affinity complex in equimolar ratio. DICER and DICER+AGO2 exhibit Michaelis-Menten kinetics with DICER substrates. However, AGO2 cannot process the fluorogenic siRNA without DICER enzyme, suggesting that AGO2 cannot self-load siRNA into its active site. The DICER+AGO2 combination processes the fluorogenic siRNA substrate (Km=74 nM) with substrate inhibition kinetics (Ki=105 nM), demonstrating experimentally that siRNA binds two different sites that affect Dicing and AGO2-loading reactions in RISC. This result suggests that siRNA (product of DICER) bound in the active site of DICER may undergo direct transfer (as AGO2 substrate) to the active site of AGO2 in the DICER+AGO2 complex. Competitive substrate assays indicate that DICER+AGO2 cleavage of fluorogenic siRNA is specific, since unlabeled siRNA and DICER substrates serve as competing substrates that cause a concentration-dependent decrease in fluorescent rates. Competitive substrate assays of a series of DICER substrates in vitro were correlated with cell-based assays of HIF1A mRNA knockdown (log-log slope=0.29), suggesting that improved DICER substrate designs with 10-fold greater processing by the DICER+AGO2 complex can provide a strong (~2800-fold) improvement in potency for mRNA knockdown. This study lays the foundation of a systematic biochemical approach to optimize nucleic acid-based therapeutics for Dicing and ARGONAUTE2-loading for improving efficacy.
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Affiliation(s)
- Mark A. Bernard
- Department of Target Biology, Pfizer Oligonucleotide Therapeutics Unit, Cambridge South Campus, Cambridge, Massachusetts, United States of America
- Department of Protein Biology, Pfizer Global Biotherapeutics Technology Unit, Cambridge North Campus, Cambridge, Massachusetts, United States of America
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Leyu Wang
- Department of Target Biology, Pfizer Oligonucleotide Therapeutics Unit, Cambridge South Campus, Cambridge, Massachusetts, United States of America
| | - Souvenir D. Tachado
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
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Jahns H, Roos M, Imig J, Baumann F, Wang Y, Gilmour R, Hall J. Stereochemical bias introduced during RNA synthesis modulates the activity of phosphorothioate siRNAs. Nat Commun 2015; 6:6317. [PMID: 25744034 PMCID: PMC4366519 DOI: 10.1038/ncomms7317] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/19/2015] [Indexed: 12/18/2022] Open
Abstract
An established means of improving the pharmacokinetics properties of oligoribonucleotides (ORNs) is to exchange their phosphodiester linkages for phosphorothioates (PSs). However, this strategy has not been pursued for small interfering RNAs (siRNAs), possibly because of sporadic reports that PS siRNAs show reduced inhibitory activity. The PS group is chiral at phosphorous (Rp/Sp centres), and conventional solid-phase synthesis of PS ORNs produces a population of diastereoisomers. Here we show that the choice of the activating agent for the synthesis of a PS ORN influences the Rp/Sp ratio of PS linkages throughout the strand. Furthermore, PS siRNAs composed of ORNs with a higher fraction of Rp centres show greater resistance to nucleases in serum and are more effective inhibitors in cells than their Sp counterparts. The finding that a stereochemically biased population of ORN diastereoisomers can be synthesized and exploited pharmacologically is important because uniform PS modification of siRNAs may provide a useful compromise of their pharmacokinetics and pharmacodynamics properties in RNAi therapeutics. Therapeutic oligonucleotides can be made more stable by substituting their achiral phosphodiester groups for chiral phosphorothioate linkages. Here, the authors present a synthesis of phosphorothioated RNAs, where the activator controls strand stereochemistry, and also the activity of assembled siRNAs.
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Affiliation(s)
- Hartmut Jahns
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Martina Roos
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Jochen Imig
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Fabienne Baumann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Yuluan Wang
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Ryan Gilmour
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
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Abstract
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.
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48
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Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that have been found highly conserved among species. MiRNAs are able to negatively regulate gene expression through base pairing of 3' UTRs of their target genes. Therefore, miRNAs have been shown to play an important role in regulating various cellular activities. Over the past decade, substantial evidences have been obtained to show that miRNAs are aberrantly expressed in human malignancies and could act as "OncomiRs" or "Tumor suppressor miRs". In recent years, increasing number of studies have demonstrated the involvement of miRNAs in cancer metastasis. Many studies have shown that microRNAs could directly target genes playing a central role in epithelia-mesenchymal-transition (EMT), a cellular transformation process that allows cancer cells to acquire motility and invasiveness. EMT is considered an essential step driving the early phase of cancer metastasis. This review will summarize the recent findings and characterization of miRNAs that are involved in the regulation of EMT, migration, invasion and metastasis of cancer cells. Lastly, we will discuss potential use of miRNAs as diagnostic and prognostic biomarkers as well as therapeutic targets for cancer.
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Affiliation(s)
- Shih-Hsuan Chan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan.
| | - Lu-Hai Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan.
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RNA/aTNA chimeras: RNAi effects and nucleases resistance of single and double stranded RNAs. Molecules 2014; 19:17872-96. [PMID: 25375332 PMCID: PMC6271724 DOI: 10.3390/molecules191117872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/13/2022] Open
Abstract
The RNA interference pathway (RNAi) is a specific and powerful biological process, triggered by small non-coding RNA molecules and involved in gene expression regulation. In this work, we explored the possibility of increasing the biological stability of these RNA molecules by replacing their natural ribose ring with an acyclic L-threoninol backbone. In particular, this modification has been incorporated at certain positions of the oligonucleotide strands and its effects on the biological properties of the siRNA have been evaluated. In vitro cellular RNAi assays have demonstrated that the L-threoninol backbone is well tolerated by the RNAi machinery in both double and single-stranded fashion, with activities significantly higher than those evinced by the unmodified RNAs and comparable to the well-known phosphorothioate modification. Additionally, this modification conferred extremely strong resistance to serum and 3'/5'-exonucleases. In view of these results, we applied this modification to the knockdown of a therapeutically relevant human gene such as apolipoprotein B (ApoB). Further studies on the activation of the innate immune system showed that L-threoninol-modified RNAs are slightly less stimulatory than unmodified RNAs.
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50
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Huang Y, Ma Y, Guo Y, Zou L, Jin H, Zhong L, Wu Y, Zhang L, Yang Z. Exploring Directional Invasion of Serum Nuclease into siRNA Duplexes by Asymmetrical Terminal Modifications. ChemMedChem 2014; 9:2111-9. [DOI: 10.1002/cmdc.201402115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 02/02/2023]
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