1
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Chen L, Bosmajian C, Woo S. A highly sensitive stem-loop RT-qPCR method to study siRNA intracellular pharmacokinetics and pharmacodynamics. Biol Methods Protoc 2024; 9:bpae029. [PMID: 38783988 PMCID: PMC11112049 DOI: 10.1093/biomethods/bpae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Small interfering RNA (siRNA) is a powerful tool for sequence-specific silencing of disease-related genes. In this study, we established and validated a stem-loop reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method applicable for both chemically unmodified and modified siRNA, aiming to elucidate mechanistic intracellular pharmacokinetic and pharmacodynamic (PK/PD) properties of siRNA. We conducted a comprehensive evaluation of factors affecting intracellular siRNA quantification. Our study revealed that immobilization-based siRNA extraction introduced high variation, making it unsuitable for absolute quantification. Conversely, direct cell lysis followed by stem-loop RT-qPCR demonstrated excellent reproducibility, with a quantification range from 0.0002 to 20 femtomole (fmole) for unmodified siRNA and 0.02 to 20 fmole for modified siRNA. The design of a 6-bp overlapping RT primer facilitated the distinction of full-length antisense from its 3'-metabolites, and pre-annealing of antisense to RT primer enhanced sensitivity and reproducibility. Differences in siRNA loss during storage and sample processing were noted among microcentrifuge tubes from various manufacturers. Endogenous miR-16 served as a reference for normalizing cytoplasmic siRNA, while protein concentration post-immunoprecipitation lysis was used to normalize RNA-induced silencing complex (RISC)-loaded siRNA levels. This method successfully enabled a detailed characterization of the time profiles of cytoplasmic and RISC-loaded siRNA, advancing the in vitro-in vivo translation of siRNA therapeutics.
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Affiliation(s)
- Lin Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Caroline Bosmajian
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Sukyung Woo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
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2
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Xu R, Njumbe Ediage E, Verhaeghe T, Snoeys J, Dillen L. Therapeutic siRNA Loaded to RISC as Single and Double Strands Requires an Appropriate Quantitative Assay for RISC PK Assessment. Nucleic Acid Ther 2024. [PMID: 38638105 DOI: 10.1089/nat.2023.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
In recent years, therapeutic siRNA projects are booming in the biotech and pharmaceutical industries. As these drugs act by silencing the target gene expression, a critical step is the binding of antisense strands of siRNA to RNA-induced silencing complex (RISC) and then degrading their target mRNA. However, data that we recently obtained suggest that double-stranded siRNA can also load to RISC. This brings a new understanding of the mechanism of RISC loading which may have a potential impact on how quantification of RISC loaded siRNA should be performed. By combining RNA immune precipitation and probe-based hybridization LC-fluorescence approach, we have developed a novel assay that can accurately quantify the RISC-bound antisense strand, irrespective of which form (double-stranded or single-stranded) is loaded on RISC. In addition, this novel assay can discriminate between the 5'-phosphorylated antisense (5'p-AS) and the nonphosphorylated forms, therefore specifically quantifying the RISC bound 5'p-AS. In comparison, stem-loop qPCR assay does not provide discrimination and accurate quantification when the oligonucleotide analyte exists as a mixture of double and single-stranded forms. Taking together, RISC loading assay with probe-hybridization LC-fluorescence technique would be a more accurate and specific quantitative approach for RISC-associated pharmacokinetic assessment.
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Affiliation(s)
- Rui Xu
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Emmanuel Njumbe Ediage
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Tom Verhaeghe
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Jan Snoeys
- Translational Pharmacokinetics/ Pharmacodynamics & Investigative Toxicology (TPPIT), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Lieve Dillen
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
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3
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López-Estévez AM, Lapuhs P, Pineiro-Alonso L, Alonso MJ. Personalized Cancer Nanomedicine: Overcoming Biological Barriers for Intracellular Delivery of Biopharmaceuticals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309355. [PMID: 38104275 DOI: 10.1002/adma.202309355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/09/2023] [Indexed: 12/19/2023]
Abstract
The success of personalized medicine in oncology relies on using highly effective and precise therapeutic modalities such as small interfering RNA (siRNA) and monoclonal antibodies (mAbs). Unfortunately, the clinical exploitation of these biological drugs has encountered obstacles in overcoming intricate biological barriers. Drug delivery technologies represent a plausible strategy to overcome such barriers, ultimately facilitating the access to intracellular domains. Here, an overview of the current landscape on how nanotechnology has dealt with protein corona phenomena as a first and determinant biological barrier is presented. This continues with the analysis of strategies facilitating access to the tumor, along with conceivable methods for enhanced tumor penetration. As a final step, the cellular barriers that nanocarriers must confront in order for their biological cargo to reach their target are deeply analyzed. This review concludes with a critical analysis and future perspectives of the translational advances in personalized oncological nanomedicine.
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Affiliation(s)
- Ana María López-Estévez
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Philipp Lapuhs
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Laura Pineiro-Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
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4
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Klipp A, Burger M, Leroux JC. Get out or die trying: Peptide- and protein-based endosomal escape of RNA therapeutics. Adv Drug Deliv Rev 2023; 200:115047. [PMID: 37536508 DOI: 10.1016/j.addr.2023.115047] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
RNA therapeutics offer great potential to transform the biomedical landscape, encompassing the treatment of hereditary conditions and the development of better vaccines. However, the delivery of RNAs into the cell is hampered, among others, by poor endosomal escape. This major hurdle is often tackled using special lipids, polymers, or protein-based delivery vectors. In this review, we will focus on the most prominent peptide- and protein-based endosomal escape strategies with focus on RNA drugs. We discuss cell penetrating peptides, which are still incorporated into novel transfection systems today to promote endosomal escape. However, direct evidence for enhanced endosomal escape by the action of such peptides is missing and their transfection efficiency, even in permissive cell culture conditions, is rather low. Endosomal escape by the help of pore forming proteins or phospholipases, on the other hand, allowed to generate more efficient transfection systems. These are, however, often hampered by considerable toxicity and immunogenicity. We conclude that the perfect enhancer of endosomal escape has yet to be devised. To increase the chances of success, any new transfection system should be tested under relevant conditions and guided by assays that allow direct quantification of endosomal escape.
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Affiliation(s)
- Alexander Klipp
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
| | - Michael Burger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
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5
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Chen L, Wang Y. Interdisciplinary advances reshape the delivery tools for effective NASH treatment. Mol Metab 2023; 73:101730. [PMID: 37142161 DOI: 10.1016/j.molmet.2023.101730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Nonalcoholic steatohepatitis (NASH), a severe systemic and inflammatory subtype of nonalcoholic fatty liver disease, eventually develops into cirrhosis and hepatocellular carcinoma with few options for effective treatment. Currently potent small molecules identified in preclinical studies are confronted with adverse effects and long-term ineffectiveness in clinical trials. Nevertheless, highly specific delivery tools designed from interdisciplinary concepts may address the significant challenges by either effectively increasing the concentrations of drugs in target cell types, or selectively manipulating the gene expression in liver to resolve NASH. SCOPE OF REVIEW We focus on dissecting the detailed principles of the latest interdisciplinary advances and concepts that direct the design of future delivery tools to enhance the efficacy. Recent advances have indicated that cell and organelle-specific vehicles, non-coding RNA research (e.g. saRNA, hybrid miRNA) improve the specificity, while small extracellular vesicles and coacervates increase the cellular uptake of therapeutics. Moreover, strategies based on interdisciplinary advances drastically elevate drug loading capacity and delivery efficiency and ameliorate NASH and other liver diseases. MAJOR CONCLUSIONS The latest concepts and advances in chemistry, biochemistry and machine learning technology provide the framework and strategies for the design of more effective tools to treat NASH, other pivotal liver diseases and metabolic disorders.
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Affiliation(s)
- Linshan Chen
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health.
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6
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Liu CH, Ho YJ, Wang CY, Hsu CC, Chu YH, Hsu MY, Chen SJ, Hsiao WC, Liao WC. Targeting Chondroitin Sulphate Synthase 1 (Chsy1) Promotes Axon Growth Following Neurorrhaphy by Suppressing Versican Accumulation. Molecules 2023; 28:molecules28093742. [PMID: 37175152 PMCID: PMC10180239 DOI: 10.3390/molecules28093742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Versican is a chondroitin sulfate proteoglycan (CSPG), which deposits in perineurium as a physical barrier and prevents the growth of axons out of the fascial boundary. Several studies have indicated that the chondroitin sulfate (CS) chains on versican have several possible functions beyond the physical barrier, including the ability to stabilize versican core protein in the extracellular matrix. As chondroitin sulfate synthase 1 (Chsy1) is a crucial enzyme for CS elongation, we hypothesized that in vivo knockdown of Chsy1 at peripheral nerve lesion site may decrease CS and versican accumulation, and result in accelerating neurite regeneration. In the present study, end-to-side neurorrhaphy (ESN) in Wistar rats was used as an in vivo model of peripheral nerve injury to evaluate nerve regeneration after surgical intervention. The distribution and expression of versican and Chsy1 in regenerating axons after ESN was studied using confocal microscopy and western blotting. Chsy1 was silenced at the nerve lesion (surgical) site using in vivo siRNA transfection. The results indicated that Chsy1 was successfully silenced in nerve tissue, and its downregulation was associated with functional recovery of compound muscle action potential. Silencing of Chsy1 also decreased the accumulation of versican core protein, suggesting that transient treating of Chsy1-siRNA may be an alternative and an effective strategy to promote injured peripheral nerve regeneration.
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Affiliation(s)
- Chiung-Hui Liu
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Ying-Jui Ho
- Department of Psychology, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 402306, Taiwan
| | - Che-Yu Wang
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan
| | - Chao-Chun Hsu
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan
| | - Yin-Hung Chu
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Min-Yen Hsu
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan
- Department of Ophthalmology, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Shiu-Jau Chen
- Department of Medicine, MacKay Medical College, New Taipei City 252005, Taiwan
- Department of Neurosurgery, MacKay Memorial Hospital, New Taipei City 251020, Taiwan
| | - Wen-Chuan Hsiao
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Wen-Chieh Liao
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
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7
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Hedlund H, Du Rietz H, Johansson JM, Eriksson HC, Zedan W, Huang L, Wallin J, Wittrup A. Single-cell quantification and dose-response of cytosolic siRNA delivery. Nat Commun 2023; 14:1075. [PMID: 36841822 PMCID: PMC9968291 DOI: 10.1038/s41467-023-36752-1] [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: 10/14/2021] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Endosomal escape and subsequent cytosolic delivery of small interfering RNA (siRNA) therapeutics is believed to be highly inefficient. Since it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determining delivery bottlenecks and total efficiency has been difficult. Here, we present a confocal microscopy-based method to quantify cytosolic delivery of fluorescently labeled siRNA during lipid-mediated delivery. This method enables detection and quantification of sub-nanomolar cytosolic siRNA release amounts from individual release events with measures of quantitation confidence for each event. Single-cell kinetics of siRNA-mediated knockdown in cells expressing destabilized eGFP unveiled a dose-response relationship with respect to knockdown induction, depth and duration in the range from several hundred to thousands of cytosolic siRNA molecules. Accurate quantification of cytosolic siRNA, and the establishment of the intracellular dose-response relationships, will aid the development and characterization of novel delivery strategies for nucleic acid therapeutics.
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Affiliation(s)
- Hampus Hedlund
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hampus Du Rietz
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johanna M Johansson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hanna C Eriksson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wahed Zedan
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Linfeng Huang
- Wang-Cai Biochemistry Lab, Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Jonas Wallin
- Department of Mathematical Statistics, Lund University, Lund, Sweden
| | - Anders Wittrup
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden. .,Skane University Hospital, Oncology, Lund, Sweden. .,Wallenberg Center for Molecular Medicine, Lund, Sweden.
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8
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Nanduri B, Shack LA, Santelices J, Edelmann MJ. Using Activity-Based Proteomics for the Quantification of Deubiquitinases in Animal Tissue. Methods Mol Biol 2023; 2591:45-57. [PMID: 36350542 DOI: 10.1007/978-1-0716-2803-4_4] [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] [Indexed: 06/16/2023]
Abstract
Ubiquitination is a post-translational modification, that regulates essential cellular functions, and the enzymes that control the removal of this modification, deubiquitinases (DUBs), have been well described for the model organisms. However, the information about DUBs is still largely lacking for the non-model organisms, such as agriculturally relevant animals. To understand the expression of these enzymes in animal tissues, we have used chemical proteomics which can be used to identify biologically active DUBs present in tissues based on their reactivity with the activity-based probes (ABPs). Here we describe a sample preparation protocol for ABP-based purification of DUBs from animal tissue using two approaches to homogenize and lyse the animal tissue compatible with ABP labeling of DUBs, including an ultrasonication-based tissue processing method and bead-beating method. Both of these methods retain the enzymatic activity of DUBs. In addition, we describe a protocol for ABP labeling of DUBs in tissue lysates and the immunoprecipitation of the probe-reactive DUBs that can be used along with mass spectrometric identification of proteins and the detection of these DUBs by Western blotting.
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Affiliation(s)
- Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Leslie A Shack
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - John Santelices
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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9
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McCann J, Sosa‐Miranda CD, Guo H, Reshke R, Savard A, Zardini Buzatto A, Taylor JA, Li L, Gibbings DJ. Contaminating transfection complexes can masquerade as small extracellular vesicles and impair their delivery of RNA. J Extracell Vesicles 2022; 11:e12220. [PMID: 36214496 PMCID: PMC9549735 DOI: 10.1002/jev2.12220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 02/02/2022] [Accepted: 03/29/2022] [Indexed: 11/06/2022] Open
Abstract
One of the functions of small extracellular vesicles (sEVs) which has received the most attention is their capacity to deliver RNA into the cytoplasm of target cells. These studies have often been performed by transfecting RNAs into sEV-producing cells, to later purify and study sEV delivery of RNA. Transfection complexes and other delivery vehicles accumulate in late endosomes where sEV are formed and over 50% of transfection complexes or delivery vehicles administered to cells are released again to the extracellular space by exocytosis. This raises the possibility that transfection complexes could alter sEVs and contaminate sEV preparations. We found that widely used transfection reagents including RNAiMax and INTERFERin accumulated in late endosomes. These transfection complexes had a size similar to sEV and were purified by ultracentrifugation like sEV. Focusing on the lipid-based transfection reagent RNAiMax, we found that preparations of sEV from transfected cells contained lipids from transfection complexes and transfected siRNA was predominantly in particles with the density of transfection complexes, rather than sEV. This suggests that transfection complexes, such as lipid-based RNAiMax, may frequently contaminate sEV preparations and could account for some reports of sEV-mediated delivery of nucleic acids. Transfection of cells also impaired the capacity of sEVs to deliver stably-expressed siRNAs, suggesting that transfection of cells may alter sEVs and prevent the study of their endogenous capacity to deliver RNA to target cells.
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Affiliation(s)
- Jenna McCann
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | | | - Huishan Guo
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Ryan Reshke
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Alexandre Savard
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | | | - James A. Taylor
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Liang Li
- The Metabolomics Innovation CentreUniversity of AlbertaEdmontonAlbertaCanada,Department of ChemistryUniversity of AlbertaEdmontonAlbertaCanada
| | - Derrick J. Gibbings
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada,Institute for Systems BiologyUniversity of OttawaOttawaOntarioCanada,Faculty of MedicineEric Poulin Centre for Neuromuscular DiseaseUniversity of OttawaOttawaOntarioCanada
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10
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Hammill ML, Tsubaki K, Wang Y, Islam G, Kitamura M, Okauchi T, Desaulniers JP. Synthesis, derivatization and photochemical control of an ortho-functionalized tetrafluorinated azoben---zene-modified siRNA. Chembiochem 2022; 23:e202200386. [PMID: 36001232 DOI: 10.1002/cbic.202200386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/24/2022] [Indexed: 11/06/2022]
Abstract
We report the synthesis of an ortho -functionalized tetrafluorinated azobenzene phosphoramidite for its site-specific incorporation into RNA. The tetrafluorinated azobenzene is embedded within the antisense strand of an siRNA duplex to form an ortho -functionalized tetrafluorinated azobenzene-containing siRNA (F-siRNAzo). The F-siRNAzo is inactivated via trans to cis conversion with green light (530 nm), and reactivated with blue light (470 nm) via cis to trans conversion in cell culture. The long half-life and stability of the tetrafluorinated azobenzene unit allows for reversible control of the F-siRNAzo in cell culture for up 72 hours.
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Affiliation(s)
| | - Kouta Tsubaki
- University of Ontario Institute of Technology, Chemistry, CANADA
| | - Yuwei Wang
- University of Ontario Institute of Technology, Chemistry, CANADA
| | - Golam Islam
- University of Ontario Institute of Technology, Chemistry, 6 Aster Cres, L1M 1J4, Whitby, CANADA
| | - Mitsuru Kitamura
- Kyushu Institute of Technology: Kyushu Kogyo Daigaku, Chemistry, CANADA
| | - Tatsuo Okauchi
- Kyushu Institute of Technology: Kyushu Kogyo Daigaku, Chemistry, CANADA
| | - Jean-Paul Desaulniers
- University of Ontario Institute of Technology, Chemistry, 2000 Simcoe Street North, L1G 0C5, Oshawa, CANADA
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11
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Schlegel MK, Janas MM, Jiang Y, Barry JD, Davis W, Agarwal S, Berman D, Brown CR, Castoreno A, LeBlanc S, Liebow A, Mayo T, Milstein S, Nguyen T, Shulga-Morskaya S, Hyde S, Schofield S, Szeto J, Woods L, Yilmaz V, Manoharan M, Egli M, Charissé K, Sepp-Lorenzino L, Haslett P, Fitzgerald K, Jadhav V, Maier M. From bench to bedside: Improving the clinical safety of GalNAc-siRNA conjugates using seed-pairing destabilization. Nucleic Acids Res 2022; 50:6656-6670. [PMID: 35736224 PMCID: PMC9262600 DOI: 10.1093/nar/gkac539] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
Preclinical mechanistic studies have pointed towards RNA interference-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here, we demonstrate that a single glycol nucleic acid or 2'-5'-RNA modification can substantially reduce small interfering RNA (siRNA) seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established hepatotoxicity driven by off-target effects, these novel designs with seed-pairing destabilization, termed enhanced stabilization chemistry plus (ESC+), demonstrated a substantially improved therapeutic window in rats. In contrast, siRNAs thermally destabilized to a similar extent by the incorporation of multiple DNA nucleotides in the seed region showed little to no improvement in rat safety suggesting that factors in addition to global thermodynamics play a role in off-target mitigation. We utilized the ESC+ strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient and asymptomatic alanine aminotransferase elevations in healthy volunteers. The redesigned ALN-HBV02 (VIR-2218) showed improved specificity with comparable on-target activity and the program was reintroduced into clinical development.
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Affiliation(s)
| | | | | | | | - Wendell Davis
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Saket Agarwal
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tara Mayo
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Sarah Hyde
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Martin A Maier
- To whom correspondence should be addressed: Tel: +1 617 551 8274; Fax: +1 617 682 4020;
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12
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Deprey K, Batistatou N, Debets MF, Godfrey J, VanderWall KB, Miles RR, Shehaj L, Guo J, Andreucci A, Kandasamy P, Lu G, Shimizu M, Vargeese C, Kritzer JA. Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics. ACS Chem Biol 2022; 17:348-360. [PMID: 35034446 PMCID: PMC9252293 DOI: 10.1021/acschembio.1c00830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide therapeutics. CAPA was used to quantitate cytosolic delivery of antisense oligonucleotides (ASOs) and siRNAs and to explore the effects of a wide variety of commonly used chemical modifications and their patterning. We evaluated potential artifacts by exploring the effects of serum, comparing activity data and CAPA data, and assessing the impact of the chloroalkane tag and its linker chemistry. We also used viral transduction to expand CAPA to the nuclear compartment in epithelial and neuronal cell lines. Using this enhanced method, we measured a 48-h time course of nuclear penetration for a panel of chemically diverse modified RNAs. Moving forward, CAPA will be a useful tool for deconvoluting the complex processes of endosomal uptake, escape into the cytosol, and subcellular trafficking of oligonucleotide therapeutics in therapeutically relevant cell types.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marjoke F. Debets
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jack Godfrey
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Kirstin B. VanderWall
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rebecca R. Miles
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Livia Shehaj
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiaxing Guo
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Amy Andreucci
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | | | - Genliang Lu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Mamoru Shimizu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Chandra Vargeese
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States,corresponding author:
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13
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Schlegel MK, Matsuda S, Brown CR, Harp JM, Barry JD, Berman D, Castoreno A, Schofield S, Szeto J, Manoharan M, Charissé K, Egli M, Maier MA. Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs. Nucleic Acids Res 2021; 49:10851-10867. [PMID: 34648028 PMCID: PMC8565336 DOI: 10.1093/nar/gkab916] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
We recently reported that RNAi-mediated off-target effects are important drivers of the hepatotoxicity observed for a subset of GalNAc–siRNA conjugates in rodents, and that these findings could be mitigated by seed-pairing destabilization using a single GNA nucleotide placed within the seed region of the guide strand. Here, we report further investigation of the unique and poorly understood GNA/RNA cross-pairing behavior to better inform GNA-containing siRNA design. A reexamination of published GNA homoduplex crystal structures, along with a novel structure containing a single (S)-GNA-A residue in duplex RNA, indicated that GNA nucleotides universally adopt a rotated nucleobase orientation within all duplex contexts. Such an orientation strongly affects GNA-C and GNA-G but not GNA-A or GNA-T pairing in GNA/RNA heteroduplexes. Transposition of the hydrogen-bond donor/acceptor pairs using the novel (S)-GNA-isocytidine and -isoguanosine nucleotides could rescue productive base-pairing with the complementary G or C ribonucleotides, respectively. GalNAc-siRNAs containing these GNA isonucleotides showed an improved in vitro activity, a similar improvement in off-target profile, and maintained in vivo activity and guide strand liver levels more consistent with the parent siRNAs than those modified with isomeric GNA-C or -G, thereby expanding our toolbox for the design of siRNAs with minimized off-target activity.
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Affiliation(s)
| | | | | | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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14
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Marschall ALJ. Targeting the Inside of Cells with Biologicals: Chemicals as a Delivery Strategy. BioDrugs 2021; 35:643-671. [PMID: 34705260 PMCID: PMC8548996 DOI: 10.1007/s40259-021-00500-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
Delivering macromolecules into the cytosol or nucleus is possible in vitro for DNA, RNA and proteins, but translation for clinical use has been limited. Therapeutic delivery of macromolecules into cells requires overcoming substantially higher barriers compared to the use of small molecule drugs or proteins in the extracellular space. Breakthroughs like DNA delivery for approved gene therapies and RNA delivery for silencing of genes (patisiran, ONPATTRO®, Alnylam Pharmaceuticals, Cambridge, MA, USA) or for vaccination such as the RNA-based coronavirus disease 2019 (COVID-19) vaccines demonstrated the feasibility of using macromolecules inside cells for therapy. Chemical carriers are part of the reason why these novel RNA-based therapeutics possess sufficient efficacy for their clinical application. A clear advantage of synthetic chemicals as carriers for macromolecule delivery is their favourable properties with respect to production and storage compared to more bioinspired vehicles like viral vectors or more complex drugs like cellular therapies. If biologicals can be applied to intracellular targets, the druggable space is substantially broadened by circumventing the limited utility of small molecules for blocking protein–protein interactions and the limitation of protein-based drugs to the extracellular space. An in depth understanding of the macromolecular cargo types, carrier types and the cell biology of delivery is crucial for optimal application and further development of biologicals inside cells. Basic mechanistic principles of the molecular and cell biological aspects of cytosolic/nuclear delivery of macromolecules, with particular consideration of protein delivery, are reviewed here. The efficiency of macromolecule delivery and applications in research and therapy are highlighted.
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Affiliation(s)
- Andrea L J Marschall
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Brunswick, Germany.
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15
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Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, Plavec J, Egli M, Manoharan M, Zlatev I. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Res 2021; 49:10250-10264. [PMID: 34508350 PMCID: PMC8501968 DOI: 10.1093/nar/gkab724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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16
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Jahns H, Taneja N, Willoughby JLS, Akabane-Nakata M, Brown CR, Nguyen T, Bisbe A, Matsuda S, Hettinger M, Manoharan RM, Rajeev KG, Maier MA, Zlatev I, Charisse K, Egli M, Manoharan M. Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo. Nucleic Acids Res 2021; 50:1221-1240. [PMID: 34268578 PMCID: PMC8860597 DOI: 10.1093/nar/gkab544] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/29/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022] Open
Abstract
A critical challenge for the successful development of RNA interference-based therapeutics therapeutics has been the enhancement of their in vivo metabolic stability. In therapeutically relevant, fully chemically modified small interfering RNAs (siRNAs), modification of the two terminal phosphodiester linkages in each strand of the siRNA duplex with phosphorothioate (PS) is generally sufficient to protect against exonuclease degradation in vivo. Since PS linkages are chiral, we systematically studied the properties of siRNAs containing single chiral PS linkages at each strand terminus. We report an efficient and simple method to introduce chiral PS linkages and demonstrate that Rp diastereomers at the 5′ end and Sp diastereomers at the 3′ end of the antisense siRNA strand improved pharmacokinetic and pharmacodynamic properties in a mouse model. In silico modeling studies provide mechanistic insights into how the Rp isomer at the 5′ end and Sp isomer at the 3′ end of the antisense siRNA enhance Argonaute 2 (Ago2) loading and metabolic stability of siRNAs in a concerted manner.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Nate Taneja
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | | | | | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Matt Hettinger
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | | | - Martin A Maier
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
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17
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Brown CR, Gupta S, Qin J, Racie T, He G, Lentini S, Malone R, Yu M, Matsuda S, Shulga-Morskaya S, Nair AV, Theile CS, Schmidt K, Shahraz A, Goel V, Parmar RG, Zlatev I, Schlegel MK, Nair JK, Jayaraman M, Manoharan M, Brown D, Maier MA, Jadhav V. Investigating the pharmacodynamic durability of GalNAc-siRNA conjugates. Nucleic Acids Res 2020; 48:11827-11844. [PMID: 32808038 PMCID: PMC7708070 DOI: 10.1093/nar/gkaa670] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
One hallmark of trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNAs is the remarkable durability of silencing that can persist for months in preclinical species and humans. Here, we investigated the underlying biology supporting this extended duration of pharmacological activity. We found that siRNA accumulation and stability in acidic intracellular compartments is critical for long-term activity. We show that functional siRNA can be liberated from these compartments and loaded into newly generated Argonaute 2 protein complexes weeks after dosing, enabling continuous RNAi activity over time. Identical siRNAs delivered in lipid nanoparticles or as GalNAc conjugates were dose-adjusted to achieve similar knockdown, but only GalNAc–siRNAs supported an extended duration of activity, illustrating the importance of receptor-mediated siRNA trafficking in the process. Taken together, we provide several lines of evidence that acidic intracellular compartments serve as a long-term depot for GalNAc–siRNA conjugates and are the major contributor to the extended duration of activity observed in vivo.
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Affiliation(s)
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Timothy Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Guo He
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Scott Lentini
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Ryan Malone
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Mikyung Yu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Anil V Nair
- MGH Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Karyn Schmidt
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Azar Shahraz
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Varun Goel
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | | | - Dennis Brown
- MGH Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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18
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Attarwala HZ, Suri K, Amiji MM. Pharmacokinetics and Biodistribution Analysis of Small Interference RNA for Silencing Tissue Transglutaminase-2 in Celiac Disease After Oral Administration in Mice Using Gelatin-Based Multicompartmental Delivery Systems. Bioelectricity 2020; 2:167-174. [PMID: 34471844 DOI: 10.1089/bioe.2020.0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background: RNA interference (RNAi) therapy has tremendous potential in treating diseases that are characterized by overexpression of genes. However, the biggest challenge to utilize the therapy is to engineer delivery systems that can efficiently transport small interfering RNA (siRNA) to appropriate target sites. Our objective in this study was to develop and evaluate multi-compartmental systems for the oral delivery of siRNA that targets the overexpressed TG2 gene (TG2-siRNA) in the small intestine for the treatment of celiac disease (CD). Materials and Methods: Two types of multicompartmental systems were developed and evaluated: (1) a solid-in-solid multicompartmental system featuring "nanoparticle in microsphere oral system (NiMOS)" where type B gelatin nanoparticles containing TG2-siRNA (TG2-NiMOS) were encapsulated within poly(ɛ-caprolactone) (PCL) based microspheres, and (2) a solid-in-liquid multicompartmental system, "Nanoparticle-in-Emulsion (NiE)" consisting of type-B gelatin nanoparticles containing TG2-siRNA encapsulated within safflower oil containing water-in-oil-in-water (W/O/W) multiple emulsion (TG2-NiE). Results: Evaluation of the biodistribution and pharmacokinetics (PK) after a single oral dose of siRNA containing multicompartmental systems to C57BL/6 mice showed that TG2-siRNA was delivered to the small intestine (duodenum, jejunum and ileum), and colon with minimal systemic exposure via both TG2-NiE and TG2-NiMOS systems. TG2-siRNA exposure (AUC0-t) in the duodenum, jejunum, ileum and colon was 56.4-, 34.3-, 85.5- and 35.5-fold greater for the TG2-NiMOS formulation, relative to the TG2-NiE formulation. Conclusion: The results of this study suggest that TG2-NiMOS formulation was more superior than TG2-NiE formulation in facilitating intestinal delivery of siRNA via the oral route of administration and can be potentially used in the treatment of CD.
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Affiliation(s)
- Husain Z Attarwala
- Department of Pharmaceutical Sciences, School of Pharmacy Northeastern University, Boston, Massachusetts, USA
| | - Kanika Suri
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy Northeastern University, Boston, Massachusetts, USA
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19
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Hammill ML, Islam G, Desaulniers JP. Synthesis, Derivatization and Photochemical Control of ortho-Functionalized Tetrachlorinated Azobenzene-Modified siRNAs. Chembiochem 2020; 21:2367-2372. [PMID: 32232952 DOI: 10.1002/cbic.202000188] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Indexed: 12/12/2022]
Abstract
We report the chemical synthesis and derivatization of an ortho-functionalized tetrachlorinated azobenzene diol. A 4',4-dimethoxytrityl (DMT) phosphoramidite was synthesized for its site-specific incorporation within the sense strand of an siRNA duplex to form ortho-functionalized tetrachlorinated azobenzene-containing siRNAs (Cl-siRNAzos). Compared to a non-halogenated azobenzene, ortho-functionalized tetrachlorinated azobenzenes are capable of red-shifting the π→π* transition from the ultraviolet (UV) portion of the electromagnetic spectrum into the visible range. Within this visible range, the azobenzene molecule can be reliably converted from trans to cis with red light (660 nm), and converted back to trans with violet wavelength light (410 nm) and/or thermal relaxation. We also report the gene-silencing ability of these Cl-siRNAzos in cell culture as well as their reversible control with visible light for up to 24 hours.
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Affiliation(s)
- Matthew L Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Golam Islam
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
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20
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Ickenstein LM, Garidel P. Lipid-based nanoparticle formulations for small molecules and RNA drugs. Expert Opin Drug Deliv 2020; 16:1205-1226. [PMID: 31530041 DOI: 10.1080/17425247.2019.1669558] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Liposomes and lipid-based nanoparticles (LNPs) effectively deliver cargo molecules to specific tissues, cells, and cellular compartments. Patients benefit from these nanoparticle formulations by altered pharmacokinetic properties, higher efficacy, or reduced side effects. While liposomes are an established delivery option for small molecules, Onpattro® (Sanofi Genzyme, Cambridge, MA) is the first commercially available LNP formulation of a small interfering ribonucleic acid (siRNA). Areas covered: This review article summarizes key features of liposomal formulations for small molecule drugs and LNP formulations for RNA therapeutics. We describe liposomal formulations that are commercially available or in late-stage clinical development and the most promising LNP formulations for ASOs, siRNAs, saRNA, and mRNA therapeutics. Expert opinion: Similar to liposomes, LNPs for RNA therapeutics have matured but still possess a niche application status. RNA therapeutics, however, bear an immense hope for difficult to treat diseases and fuel the imagination for further applications of RNA drugs. LNPs face similar challenges as liposomes including limitations in biodistribution, the risk to provoke immune responses, and other toxicities. However, since properties of RNA molecules within the same group are very similar, the entire class of therapeutic molecules would benefit from improvements in a few key parameters of the delivery technology.
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Affiliation(s)
- Ludger M Ickenstein
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, Pharmaceutical Development Biologicals , Biberach an der Riss , Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, Pharmaceutical Development Biologicals , Biberach an der Riss , Germany
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21
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Reduction of the therapeutic dose of silencing RNA by packaging it in extracellular vesicles via a pre-microRNA backbone. Nat Biomed Eng 2020; 4:52-68. [PMID: 31937944 DOI: 10.1038/s41551-019-0502-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 12/04/2019] [Indexed: 12/12/2022]
Abstract
A small percentage of the short interfering RNA (siRNA) delivered via passive lipid nanoparticles and other delivery vehicles reaches the cytoplasm of cells. The high doses of siRNA and delivery vehicle that are thus required to achieve therapeutic outcomes can lead to toxicity. Here, we show that the integration of siRNA sequences into a Dicer-independent RNA stem-loop based on pre-miR-451 microRNA-which is highly enriched in small extracellular vesicles secreted by many cell types-reduces the expression of the genes targeted by the siRNA in the liver, intestine and kidney glomeruli of mice at siRNA doses that are at least tenfold lower than the siRNA doses typically delivered via lipid nanoparticles. Small extracellular vesicles that efficiently package siRNA can significantly reduce its therapeutic dose.
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22
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Hammill ML, Islam G, Desaulniers JP. Reversible control of RNA interference by siRNAzos. Org Biomol Chem 2020; 18:41-46. [DOI: 10.1039/c9ob02509j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study, we report the reversible control of RNA interference using siRNAzos, a class of siRNAs that contain azobenzene.
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Affiliation(s)
- Matthew L. Hammill
- University of Ontario Institute of Technology
- Faculty of Science
- Oshawa
- Canada
| | - Golam Islam
- University of Ontario Institute of Technology
- Faculty of Science
- Oshawa
- Canada
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23
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Kim B, Park JH, Sailor MJ. Rekindling RNAi Therapy: Materials Design Requirements for In Vivo siRNA Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1903637. [PMID: 31566258 PMCID: PMC6891135 DOI: 10.1002/adma.201903637] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/12/2019] [Indexed: 05/07/2023]
Abstract
With the recent FDA approval of the first siRNA-derived therapeutic, RNA interference (RNAi)-mediated gene therapy is undergoing a transition from research to the clinical space. The primary obstacle to realization of RNAi therapy has been the delivery of oligonucleotide payloads. Therefore, the main aims is to identify and describe key design features needed for nanoscale vehicles to achieve effective delivery of siRNA-mediated gene silencing agents in vivo. The problem is broken into three elements: 1) protection of siRNA from degradation and clearance; 2) selective homing to target cell types; and 3) cytoplasmic release of the siRNA payload by escaping or bypassing endocytic uptake. The in vitro and in vivo gene silencing efficiency values that have been reported in publications over the past decade are quantitatively summarized by material type (lipid, polymer, metal, mesoporous silica, and porous silicon), and the overall trends in research publication and in clinical translation are discussed to reflect on the direction of the RNAi therapeutics field.
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Affiliation(s)
- Byungji Kim
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Ji-Ho Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Michael J Sailor
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
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24
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Mihaila R, Ruhela D, Galinski B, Card A, Cancilla M, Shadel T, Kang J, Tep S, Wei J, Haas RM, Caldwell J, Flanagan WM, Kuklin N, Cherkaev E, Ason B. Modeling the Kinetics of Lipid-Nanoparticle- Mediated Delivery of Multiple siRNAs to Evaluate the Effect on Competition for Ago2. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:367-377. [PMID: 30991218 PMCID: PMC6463220 DOI: 10.1016/j.omtn.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
Drug combinations can improve the control of diseases involving redundant and highly regulated pathways. Validating a multi-target therapy early in drug development remains difficult. Small interfering RNAs (siRNAs) are routinely used to selectively silence a target of interest. Owing to the ease of design and synthesis, siRNAs hold promise for combination therapies. Combining siRNAs against multiple targets remains an attractive approach to interrogating highly regulated pathways. Currently, questions remain regarding how broadly such an approach can be applied, since siRNAs have been shown to compete with one another for binding to Argonaute2 (Ago2), the protein responsible for initiating siRNA-mediated mRNA degradation. Mathematical modeling, coupled with in vitro and in vivo experiments, led us to conclude that endosomal escape kinetics had the highest impact on Ago2 depletion by competing lipid-nanoparticle (LNP)-formulated siRNAs. This, in turn, affected the level of competition observed between them. A future application of this model would be to optimize delivery of desired siRNA combinations in vitro to attenuate competition and maximize the combined therapeutic effect.
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Affiliation(s)
- Radu Mihaila
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Dipali Ruhela
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Beverly Galinski
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ananda Card
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Timothy Shadel
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Jing Kang
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Samnang Tep
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Jie Wei
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Jeremy Caldwell
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - W Michael Flanagan
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Nelly Kuklin
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Elena Cherkaev
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA
| | - Brandon Ason
- Sirna Therapeutics a former subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA.
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25
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Hochrein LM, Ge TJ, Schwarzkopf M, Pierce NA. Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. ACS Synth Biol 2018; 7:2796-2802. [PMID: 30525469 PMCID: PMC6305621 DOI: 10.1021/acssynbio.8b00424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Dynamic
RNA nanotechnology with small conditional RNAs (scRNAs)
offers a promising conceptual approach to introducing synthetic regulatory
links into endogenous biological circuits. Here, we use human cell
lysate containing functional Dicer and RNases as a testbed for engineering
scRNAs for conditional RNA interference (RNAi). scRNAs perform signal
transduction via conditional shape change: detection
of a subsequence of mRNA input X triggers formation of a Dicer substrate
that is processed to yield small interfering RNA (siRNA) output anti-Y
targeting independent mRNA Y for destruction. Automated sequence design
is performed using the reaction pathway designer within NUPACK to
encode this conditional hybridization cascade into the scRNA sequence
subject to the sequence constraints imposed by X and Y. Because it
is difficult for secondary structure models to predict which subsequences
of mRNA input X will be accessible for detection, here we develop
the RNAhyb method to experimentally determine accessible windows within
the mRNA that are provided to the designer as sequence constraints.
We demonstrate the programmability of scRNA regulators by engineering scRNAs for transducing
in both directions between two full-length mRNAs X and Y, corresponding
to either the forward molecular logic “if X then not Y”
(X Y) or
the reverse molecular logic “if Y then not X” (Y X). In human cell lysate, we
observe a strong OFF/ON conditional response with low crosstalk, corresponding
to a ≈20-fold increase in production of the siRNA output in
response to the cognate versus noncognate full-length mRNA input.
2′OMe-RNA chemical modifications protect signal transduction
reactants and intermediates against RNase degradation while enabling
Dicer processing of signal transduction products. Because diverse
biological pathways interact with RNA, scRNAs that transduce between
detection of endogenous RNA inputs and production of biologically
active RNA outputs hold great promise as a synthetic regulatory paradigm.
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Affiliation(s)
| | | | | | - Niles A. Pierce
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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26
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Chernikov IV, Gladkikh DV, Meschaninova MI, Karelina UA, Ven'yaminova AG, Zenkova MA, Vlassov VV, Chernolovskaya EL. Fluorophore Labeling Affects the Cellular Accumulation and Gene Silencing Activity of Cholesterol-Modified siRNAs In Vitro. Nucleic Acid Ther 2018; 29:33-43. [PMID: 30562146 DOI: 10.1089/nat.2018.0745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The objective of this study was to analyze the effects of fluorophores on the intracellular accumulation and biological activity of small interfering RNA (siRNA) and its cholesterol conjugates. In this study, we used stem-loop real-time PCR and calibration curves to quantitate cellular siRNA accumulation. Attachment of fluorophores significantly affected both the accumulation and biological activity of siRNA conjugates. The severity of this effect depended significantly on the structure of the conjugate; fluorophores (Cy5.5 or Alexa-488) attached to siRNA, facing the side of the duplex opposite to cholesterol, enhanced the unproductive intracellular accumulation of the conjugate when delivered in carrier-free mode. Enhanced cellular accumulation of siRNA conjugates did not result in enhanced biological activity of the conjugate. Moreover, the attachment of a hydrophobic fluorophore, such as Cy5.5, to conventional siRNA also enhanced its apparent intracellular accumulation, but not its biological activity. Thus, the use of fluorescent labels for the study of the intracellular accumulation of siRNA and its conjugates formed with different molecules is possible only for a limited range of structures, and requires verification using alternative methods.
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Affiliation(s)
- Ivan V Chernikov
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Daniil V Gladkikh
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mariya I Meschaninova
- 2 Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Ulyana A Karelina
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alya G Ven'yaminova
- 2 Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina A Zenkova
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Valentin V Vlassov
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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27
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Connexin 43 (Cx43) in cancer: Implications for therapeutic approaches via gap junctions. Cancer Lett 2018; 442:439-444. [PMID: 30472182 DOI: 10.1016/j.canlet.2018.10.043] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/30/2018] [Accepted: 10/25/2018] [Indexed: 01/11/2023]
Abstract
Gap junctions are membrane channels found in all cells of the human body that are essential to cellular physiology. Gap junctions are formed from connexin proteins and are responsible for transfer of biologically active molecules, metabolites, and salts between neighboring cells or cells and their extracellular environment. Over the last few years, aberrant connexin 43 (Cx43) expression has been associated with cancer recurrence, metastatic spread, and poor survival. Here we provide an overview of the general structure and function of gap junctions and review their roles in different cancer types. We discuss new therapeutic approaches targeting Cx43 and potential new ways of exploiting gap junction transfer for drug delivery and anti-cancer treatment. The permeability of Cx43 channels to small molecules and macromolecules makes them highly attractive targets for delivering drugs directly into the cytoplasm. Cancer cells overexpressing Cx43 may be more permeable and sensitive to chemotherapeutics. Because Cx43 can either act as a tumor suppressor or oncogene, biomarker analysis and a better understanding of how Cx43 contextually mediates cancer phenotypes will be required to develop clinically viable Cx43-based therapies.
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28
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Design and development of a robust photo-responsive block copolymer framework for tunable nucleic acid delivery and efficient gene silencing. Polym J 2018. [DOI: 10.1038/s41428-018-0077-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Reversal of siRNA-mediated gene silencing in vivo. Nat Biotechnol 2018; 36:509-511. [PMID: 29786096 DOI: 10.1038/nbt.4136] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
We report rapid, potent reversal of GalNAc-siRNA-mediated RNA interference (RNAi) activity in vivo with short, synthetic, high-affinity oligonucleotides complementary to the siRNA guide strand. We found that 9-mers with five locked nucleic acids (LNAs) have the highest potency across several targets. Our modular, sequence-specific approach, named REVERSIR, may enhance the therapeutic profile of any long-acting GalNAc-siRNA (short interfering RNA) conjugate by enabling control of RNAi pharmacology.
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30
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Jaiprasart P, Yeung BZ, Lu Z, Wientjes MG, Cui M, Hsieh CM, Woo S, Au JLS. Quantitative contributions of processes by which polyanion drugs reduce intracellular bioavailability and transfection efficiency of cationic siRNA lipoplex. J Control Release 2018; 270:101-113. [PMID: 29203416 DOI: 10.1016/j.jconrel.2017.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 11/07/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022]
Abstract
RNA Interference (RNAi) is a potentially useful tool to correct the detrimental effects of faulty genes; several RNAi are undergoing clinical evaluation in various diseases. The present study identified the relative contributions of three mechanisms by which polyanion drugs reduced the gene silencing activity of Lipoplex, a complex of small interfering RNA (siRNA) and cationic liposomes. The study used a siRNA against the chemoresistance gene survivin and two model polyanion drugs (suramin, heparin). Products of Lipoplex destabilization were separated, identified, and/or quantified using ultrafiltration, gel electrophoresis, and RT-qPCR (quantitative reverse transcription polymerase chain reaction). Cell binding and endocytosis of fluorescence-labeled Lipoplex and the amount of siRNA at its site of action RISC (RNA-induced silencing complex) were evaluated using endocytosis markers, confocal microscopy, quantitative image analysis, immunoprecipitation, and RT-qPCR. The results show suramin and heparin exerted multiple concentration-dependent effects. First, these agents altered several Lipoplex properties (i.e., reduced particle size, changed surface charge, modified composition of protein biocorona). Second, both caused Lipoplex destabilization to release double- and single-strand siRNA and/or smaller siRNA-lipid complexes with reduced siRNA cargo. Third, both prevented the cell surface binding and internalization of Lipoplex, diminished the siRNA concentration in RISC, and retarded the mRNA knockdown. Suramin and heparin yielded qualitatively and quantitatively different results. Analysis of the experimental results of suramin using quantitative pharmacology (QP) modeling indicated the major cause of gene silencing activity loss depended on drug concentration, changing from inhibition of endocytosis at lower concentration (accounting for 60% loss at ~9μM) to inhibition of cell surface binding and loss of siRNA cargo at higher concentrations (accounting for 64% and 27%, respectively, at 70μM). In summary, the present study demonstrates the complex and dynamic interactions between polyanions and Lipoplex, and the use of QP modeling to delineate the contributions of three mechanisms to the eventual loss of gene silencing activity.
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Affiliation(s)
- Pharavee Jaiprasart
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, United States
| | - Bertrand Z Yeung
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, United States; Optimum Therapeutics LLC, Carlsbad, CA 92008, United States
| | - Ze Lu
- Optimum Therapeutics LLC, Carlsbad, CA 92008, United States; Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, United States
| | - M Guillaume Wientjes
- Optimum Therapeutics LLC, Carlsbad, CA 92008, United States; Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, United States
| | - Minjian Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, United States; Optimum Therapeutics LLC, Carlsbad, CA 92008, United States; Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, United States
| | - Chien-Ming Hsieh
- College of Pharmacy, Taipei Medical University, Taipei, Taiwan, ROC
| | - Sukyung Woo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, United States
| | - Jessie L-S Au
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, United States; Optimum Therapeutics LLC, Carlsbad, CA 92008, United States; Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, United States; College of Pharmacy, Taipei Medical University, Taipei, Taiwan, ROC.
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31
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Nair JK, Attarwala H, Sehgal A, Wang Q, Aluri K, Zhang X, Gao M, Liu J, Indrakanti R, Schofield S, Kretschmer P, Brown CR, Gupta S, Willoughby JLS, Boshar JA, Jadhav V, Charisse K, Zimmermann T, Fitzgerald K, Manoharan M, Rajeev KG, Akinc A, Hutabarat R, Maier MA. Impact of enhanced metabolic stability on pharmacokinetics and pharmacodynamics of GalNAc-siRNA conjugates. Nucleic Acids Res 2017; 45:10969-10977. [PMID: 28981809 PMCID: PMC5737438 DOI: 10.1093/nar/gkx818] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023] Open
Abstract
Covalent attachment of a synthetic triantennary N-acetylagalactosamine (GalNAc) ligand to chemically modified siRNA has enabled asialoglycoprotein (ASGPR)-mediated targeted delivery of therapeutically active siRNAs to hepatocytes in vivo. This approach has become transformative for the delivery of RNAi therapeutics as well as other classes of investigational oligonucleotide therapeutics to the liver. For efficient functional delivery of intact drug into the desired subcellular compartment, however, it is critical that the nucleic acids are stabilized against nucleolytic degradation. Here, we compared two siRNAs of the same sequence but with different modification pattern resulting in different degrees of protection against nuclease activity. In vitro stability studies in different biological matrices show that 5'-exonuclease is the most prevalent nuclease activity in endo-lysosomal compartments and that additional stabilization in the 5'-regions of both siRNA strands significantly enhances the overall metabolic stability of GalNAc-siRNA conjugates. In good agreement with in vitro findings, the enhanced stability translated into substantially improved liver exposure, gene silencing efficacy and duration of effect in mice. Follow-up studies with a second set of conjugates targeting a different transcript confirmed the previous results, provided additional insights into kinetics of RISC loading and demonstrated excellent translation to non-human primates.
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Affiliation(s)
| | | | | | - Qianfan Wang
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | | | - Xuemei Zhang
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | - Minggeng Gao
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | - Ju Liu
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | | | | | | | | | - Swati Gupta
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
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32
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Mihaila R, Ruhela D, Keough E, Cherkaev E, Chang S, Galinski B, Bartz R, Brown D, Howell B, Cunningham JJ. Mathematical Modeling: A Tool for Optimization of Lipid Nanoparticle-Mediated Delivery of siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624200 PMCID: PMC5415968 DOI: 10.1016/j.omtn.2017.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipid nanoparticles (LNPs) have been used to successfully deliver small interfering RNAs (siRNAs) to target cells in both preclinical and clinical studies and currently are the leading systems for in vivo delivery. Here, we propose the use of an ordinary differential equation (ODE)-based model as a tool for optimizing LNP-mediated delivery of siRNAs. As a first step, we have used a combination of experimental and computational approaches to develop and validate a mathematical model that captures the critical features for efficient siRNA-LNP delivery in vitro. This model accurately predicts mRNA knockdown resulting from novel combinations of siRNAs and LNPs in vitro. As demonstrated, this model can be effectively used as a screening tool to select the most efficacious LNPs, which can then further be evaluated in vivo. The model serves as a starting point for the future development of next generation models capable of capturing the additional complexity of in vivo delivery.
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Affiliation(s)
- Radu Mihaila
- Sirna Therapeutics, 1700 Owens Street, Fourth Floor, San Francisco, CA 94158, USA.
| | - Dipali Ruhela
- Sirna Therapeutics, 1700 Owens Street, Fourth Floor, San Francisco, CA 94158, USA
| | - Edward Keough
- Department of RNA Therapeutics, Merck Sharp & Dohme Corp., West Point, PA 19486, USA
| | - Elena Cherkaev
- Department of Mathematics, University of Utah, Salt Lake City, UT 84112, USA
| | - Silvia Chang
- Sirna Therapeutics, 1700 Owens Street, Fourth Floor, San Francisco, CA 94158, USA
| | - Beverly Galinski
- Sirna Therapeutics, 1700 Owens Street, Fourth Floor, San Francisco, CA 94158, USA
| | - René Bartz
- Department of RNA Therapeutics, Merck Sharp & Dohme Corp., West Point, PA 19486, USA
| | - Duncan Brown
- Sirna Therapeutics, 1700 Owens Street, Fourth Floor, San Francisco, CA 94158, USA
| | - Bonnie Howell
- Department of RNA Therapeutics, Merck Sharp & Dohme Corp., West Point, PA 19486, USA
| | - James J Cunningham
- Department of RNA Therapeutics, Merck Sharp & Dohme Corp., West Point, PA 19486, USA
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33
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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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34
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Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 2017; 35:238-248. [PMID: 28244990 PMCID: PMC5517098 DOI: 10.1038/nbt.3765] [Citation(s) in RCA: 725] [Impact Index Per Article: 103.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
After nearly 40 years of development, oligonucleotide therapeutics are nearing meaningful clinical productivity. One of the key advantages of oligonucleotide drugs is that their delivery and potency are derived primarily from the chemical structure of the oligonucleotide whereas their target is defined by the base sequence. Thus, as oligonucleotides with a particular chemical design show appropriate distribution and safety profiles for clinical gene silencing in a particular tissue, this will open the door to the rapid development of additional drugs targeting other disease-associated genes in the same tissue. To achieve clinical productivity, the chemical architecture of the oligonucleotide needs to be optimized with a combination of sugar, backbone, nucleobase, and 3'- and 5'-terminal modifications. A portfolio of chemistries can be used to confer drug-like properties onto the oligonucleotide as a whole, with minor chemical changes often translating into major improvements in clinical efficacy. One outstanding challenge in oligonucleotide chemical development is the optimization of chemical architectures to ensure long-term safety. There are multiple designs that enable effective targeting of the liver, but a second challenge is to develop architectures that enable robust clinical efficacy in additional tissues.
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Affiliation(s)
- Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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35
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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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36
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Ly S, Navaroli DM, Didiot MC, Cardia J, Pandarinathan L, Alterman JF, Fogarty K, Standley C, Lifshitz LM, Bellve KD, Prot M, Echeverria D, Corvera S, Khvorova A. Visualization of self-delivering hydrophobically modified siRNA cellular internalization. Nucleic Acids Res 2017; 45:15-25. [PMID: 27899655 PMCID: PMC5224471 DOI: 10.1093/nar/gkw1005] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 10/07/2016] [Accepted: 10/24/2016] [Indexed: 01/07/2023] Open
Abstract
siRNAs are a new class of therapeutic modalities with promising clinical efficacy that requires modification or formulation for delivery to the tissue and cell of interest. Conjugation of siRNAs to lipophilic groups supports efficient cellular uptake by a mechanism that is not well characterized. Here we study the mechanism of internalization of asymmetric, chemically stabilized, cholesterol-modified siRNAs (sd-rxRNAs®) that efficiently enter cells and tissues without the need for formulation. We demonstrate that uptake is rapid with significant membrane association within minutes of exposure followed by the formation of vesicular structures and internalization. Furthermore, sd-rxRNAs are internalized by a specific class of early endosomes and show preferential association with epidermal growth factor (EGF) but not transferrin (Tf) trafficking pathways as shown by live cell TIRF and structured illumination microscopy (SIM). In fixed cells, we observe ∼25% of sd-rxRNA co-localizing with EGF and <5% with Tf, which is indicative of selective endosomal sorting. Likewise, preferential sd-rxRNA co-localization was demonstrated with EEA1 but not RBSN-containing endosomes, consistent with preferential EGF-like trafficking through EEA1-containing endosomes. sd-rxRNA cellular uptake is a two-step process, with rapid membrane association followed by internalization through a selective, saturable subset of the endocytic process. However, the mechanistic role of EEA1 is not yet known. This method of visualization can be used to better understand the kinetics and mechanisms of hydrophobic siRNA cellular uptake and will assist in further optimization of these types of compounds for therapeutic intervention.
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Affiliation(s)
- Socheata Ly
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Deanna M Navaroli
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Marie-Cécile Didiot
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | | | - Julia F Alterman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kevin Fogarty
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Clive Standley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Lawrence M Lifshitz
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl D Bellve
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Matthieu Prot
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Dimas Echeverria
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Anastasia Khvorova
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
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37
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Hydroxychloroquine-conjugated gold nanoparticles for improved siRNA activity. Biomaterials 2016; 90:62-71. [DOI: 10.1016/j.biomaterials.2016.02.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/13/2016] [Accepted: 02/19/2016] [Indexed: 12/21/2022]
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Parmar R, Willoughby JLS, Liu J, Foster DJ, Brigham B, Theile CS, Charisse K, Akinc A, Guidry E, Pei Y, Strapps W, Cancilla M, Stanton MG, Rajeev KG, Sepp-Lorenzino L, Manoharan M, Meyers R, Maier MA, Jadhav V. 5'-(E)-Vinylphosphonate: A Stable Phosphate Mimic Can Improve the RNAi Activity of siRNA-GalNAc Conjugates. Chembiochem 2016; 17:985-9. [PMID: 27121751 DOI: 10.1002/cbic.201600130] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 11/08/2022]
Abstract
Small interfering RNA (siRNA)-mediated silencing requires siRNA loading into the RNA-induced silencing complex (RISC). Presence of 5'-phosphate (5'-P) is reported to be critical for efficient RISC loading of the antisense strand (AS) by anchoring it to the mid-domain of the Argonaute2 (Ago2) protein. Phosphorylation of exogenous duplex siRNAs is thought to be accomplished by cytosolic Clp1 kinase. However, although extensive chemical modifications are essential for siRNA-GalNAc conjugate activity, they can significantly impair Clp1 kinase activity. Here, we further elucidated the effect of 5'-P on the activity of siRNA-GalNAc conjugates. Our results demonstrate that a subset of sequences benefit from the presence of exogenous 5'-P. For those that do, incorporation of 5'-(E)-vinylphosphonate (5'-VP), a metabolically stable phosphate mimic, results in up to 20-fold improved in vitro potency and up to a threefold benefit in in vivo activity by promoting Ago2 loading and enhancing metabolic stability.
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Affiliation(s)
- Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | - Jingxuan Liu
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Donald J Foster
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Benjamin Brigham
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Akin Akinc
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Erin Guidry
- Merck and Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Yi Pei
- Merck and Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Walter Strapps
- Merck and Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Mark Cancilla
- Merck and Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | | | | | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Rachel Meyers
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Martin A Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Vasant Jadhav
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA.
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Berman CL, Barros SA, Galloway SM, Kasper P, Oleson FB, Priestley CC, Sweder KS, Schlosser MJ, Sobol Z. OSWG Recommendations for Genotoxicity Testing of Novel Oligonucleotide-Based Therapeutics. Nucleic Acid Ther 2016; 26:73-85. [PMID: 26978711 DOI: 10.1089/nat.2015.0534] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Oligonucleotide Safety Working Group subcommittee on genotoxicity testing considers therapeutic oligonucleotides (ONs) unlikely to be genotoxic based on their properties and on the negative results for ONs tested to date. Nonetheless, the subcommittee believes that genotoxicity testing of new ONs is warranted because modified monomers could be liberated from a metabolized ON and incorporated into DNA and could hypothetically cause chain termination, miscoding, and/or faulty replication or repair. The standard test battery as described in Option 1 of International Conference on Harmonisation S2(R1) is generally adequate to assess such potential. However, for the in vitro assay for gene mutations, mammalian cells are considered more relevant than bacteria for most ONs due to their known responsiveness to nucleosides and their greater potential for ON uptake; on the other hand, bacterial assays may be more appropriate for ONs containing non-ON components. Testing is not recommended for ONs with only naturally occurring chemistries or for ONs with chemistries for which there is documented lack of genotoxicity in systems with demonstrated cellular uptake. Testing is recommended for ONs that contain non-natural chemical modifications and use of the complete drug product (including linkers, conjugates, and liposomes) is suggested to provide the most clinically relevant assessment. Documentation of uptake into cells comparable to those used for genotoxicity testing is proposed because intracellular exposure cannot be assumed for these large molecules. ONs could also hypothetically cause mutations through triple helix formation with genomic DNA and no tests are available for detection of such sequence-specific mutations across the entire genome. However, because the potential for triplex formation by therapeutic ONs is extremely low, this potential can be assessed adequately by sequence analysis.
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Affiliation(s)
| | | | | | - Peter Kasper
- 4 Federal Institute for Drugs and Medical Devices (BfArM) , Bonn, Germany
| | | | | | - Kevin S Sweder
- 7 Forensic and National Security Sciences Institute, Syracuse University , Syracuse, New York
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Yeung BZ, Lu Z, Wientjes GM, Au JLS. High Sensitivity RT-qPCR Assay of Nonlabeled siRNA in Small Blood Volume for Pharmacokinetic Studies: Application to Survivin siRNA. AAPS JOURNAL 2015; 17:1475-82. [PMID: 26286676 DOI: 10.1208/s12248-015-9812-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/02/2015] [Indexed: 11/30/2022]
Abstract
RNAi therapeutics provide an opportunity to correct faulty genes, and several RNAi have entered clinical evaluation. The existing quantification methods typically use radioactivity- or fluorescence-labeled RNAi, require large blood volumes, and/or have a limited dynamic detection range. We established a quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) assay to measure RNAi; the model analyte was survivin siRNA (siSurvivin). A second siRNA was used as the internal standard. The three major steps were (a) extraction of the two siRNAs from blood or water, (b) synthesis of their cDNA by poly-A extension, and (c) qPCR of cDNA. Standard curves were established. Utility of the assay was demonstrated in a pharmacokinetic study where all 12 samples for the blood concentration-time profile were obtained from a single mouse given an intravenous dose of 1 nmole siSurvivin (prepared as lipoplex with pegylated cationic liposomes). The RT-qPCR assay was sensitive (lower detection limit of 100 fM) and had a 5 × 107-fold dynamic range and low sample volume requirement (10 μL). The 16-point standard curves constructed using whole blood samples were linear (R (2) > 0.98). The intraday and interday variations for the slopes were ≤6%, although the variations for accuracy and precision at individual concentrations were substantially higher (58-145%). Standard curves prepared with water in place of blood showed similar results (<6% difference), indicating water may be used when blood is not available. The current RT-qPCR assay enabled the measurement of nonlabeled siRNA in small volume of blood samples.
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Affiliation(s)
- Bertrand Z Yeung
- Department of Pharmaceutical Sciences, University of Oklahoma, Oklahoma City, Oklahoma, 73117, USA
| | - Ze Lu
- Optimum Therapeutics LLC, 1815 Aston Ave, Suite 107, Carlsbad, California, 92008, USA
| | - Guillaume M Wientjes
- Optimum Therapeutics LLC, 1815 Aston Ave, Suite 107, Carlsbad, California, 92008, USA
| | - Jessie L-S Au
- Department of Pharmaceutical Sciences, University of Oklahoma, Oklahoma City, Oklahoma, 73117, USA. .,Optimum Therapeutics LLC, 1815 Aston Ave, Suite 107, Carlsbad, California, 92008, USA. .,Taipei Medical University, Taipei, Taiwan, Republic of China.
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Ragelle H, Colombo S, Pourcelle V, Vanvarenberg K, Vandermeulen G, Bouzin C, Marchand-Brynaert J, Feron O, Foged C, Préat V. Intracellular siRNA delivery dynamics of integrin-targeted, PEGylated chitosan–poly(ethylene imine) hybrid nanoparticles: A mechanistic insight. J Control Release 2015; 211:1-9. [DOI: 10.1016/j.jconrel.2015.05.274] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 12/20/2022]
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42
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Gilleron J, Paramasivam P, Zeigerer A, Querbes W, Marsico G, Andree C, Seifert S, Amaya P, Stöter M, Koteliansky V, Waldmann H, Fitzgerald K, Kalaidzidis Y, Akinc A, Maier MA, Manoharan M, Bickle M, Zerial M. Identification of siRNA delivery enhancers by a chemical library screen. Nucleic Acids Res 2015. [PMID: 26220182 PMCID: PMC4652771 DOI: 10.1093/nar/gkv762] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Most delivery systems for small interfering RNA therapeutics depend on endocytosis and release from endo-lysosomal compartments. One approach to improve delivery is to identify small molecules enhancing these steps. It is unclear to what extent such enhancers can be universally applied to different delivery systems and cell types. Here, we performed a compound library screen on two well-established siRNA delivery systems, lipid nanoparticles and cholesterol conjugated-siRNAs. We identified fifty-one enhancers improving gene silencing 2–5 fold. Strikingly, most enhancers displayed specificity for one delivery system only. By a combination of quantitative fluorescence and electron microscopy we found that the enhancers substantially differed in their mechanism of action, increasing either endocytic uptake or release of siRNAs from endosomes. Furthermore, they acted either on the delivery system itself or the cell, by modulating the endocytic system via distinct mechanisms. Interestingly, several compounds displayed activity on different cell types. As proof of principle, we showed that one compound enhanced siRNA delivery in primary endothelial cells in vitro and in the endocardium in the mouse heart. This study suggests that a pharmacological approach can improve the delivery of siRNAs in a system-specific fashion, by exploiting distinct mechanisms and acting upon multiple cell types.
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Affiliation(s)
- Jerome Gilleron
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Nice, France; Université de Nice Sophia-Antipolis, Nice, France
| | - Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Anja Zeigerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | | | - Giovanni Marsico
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Cordula Andree
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Pablo Amaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Victor Koteliansky
- Lomonosov Moscow State University, Chemistry Department, Leninskie Gory, 1/3, Moscow 119991, Russia Skolkovo Institute of Science and Technology, 100 Novaya str., Skolkovo, Odinsovsky district, Moscow 143025, Russia
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | | | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
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43
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Abrams MT, Koser M, Burchard J, Strapps W, Mehmet H, Gindy M, Zaller D, Sepp-Lorenzino L, Stickens D. A Single Dose of EGLN1 siRNA Yields Increased Erythropoiesis in Nonhuman Primates. Nucleic Acid Ther 2014; 24:405-12. [PMID: 25272050 DOI: 10.1089/nat.2014.0495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | - Martin Koser
- Merck Research Laboratories, West Point, Pennsylvania
| | | | | | | | - Marian Gindy
- Merck Research Laboratories, West Point, Pennsylvania
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44
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Colombo S, Zeng X, Ragelle H, Foged C. Complexity in the therapeutic delivery of RNAi medicines: an analytical challenge. Expert Opin Drug Deliv 2014; 11:1481-95. [DOI: 10.1517/17425247.2014.927439] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abstract
RNA interference (RNAi) therapeutics appear to offer substantial opportunities for future therapy. However, post-administration RNAi effectors are typically unable to reach disease target cells in vivo without the assistance of a delivery system or vector. The main focus of this review is on lipid-based nanoparticle (LNP) delivery systems in current research and development that have at least been shown to act as effective delivery systems for functional delivery of RNAi effectors to disease target cells in vivo. The potential utility of these LNP delivery systems is growing rapidly, and LNPs are emerging as the preferred synthetic delivery systems in preclinical studies and current nonviral RNAi effector clinical trials. Moreover, studies on LNP-mediated delivery in vivo are leading to the emergence of useful biophysical parameters and physical organic chemistry rules that provide a framework for understanding in vivo delivery behaviors and outcomes. These same parameters and rules should also suggest ways and means to develop next generations of LNPs with genuine utility and long-term clinical viability.
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Affiliation(s)
- Andrew D Miller
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Waterloo Campus, 150 Stamford Street, London SE1 9NH , UK and GlobalAcorn Limited , London , UK
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46
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Abstract
For several decades extensive research has been conducted into the development of fusogenic lipid nanoparticles (LNPs) capable of introducing large, charged molecules into the cytoplasm of target cells. The majority of this work has focused on cationic LNPs encapsulating nucleic acids ranging from small oligonucleotides to large plasmid constructs thousands of bases long. However, since the introduction of siRNA payloads this quest for a non-viral, intracellular delivery systems has advanced significantly. Of particular importance was the demonstration that LNPs containing ionizable, dialkylamino lipids, enable potent hepatic gene silencing across species including humans. This review focuses on the evolution of this delivery system, summarizes the promising data now emerging from clinical trials and considers future directions for the platform.
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Abstract
Small non-coding RNA (ncRNA) therapeutics make use of small ncRNA effectors for desired therapeutic purposes that are essentially short (10–20 kD) RNA segments. These small ncRNA effectors are potentially tremendously powerful therapeutic agents, but are typically unable to reach disease target cells in vivo without the assistance of a delivery system or vector. The main focus of this review is the use of lipid-based nanoparticles (LNPs) for the functional delivery of small ncRNA effectors in vivo. LNPs appear to be amongst the most effective delivery systems currently available for this purpose. Moreover, studies on LNP-mediated delivery in vivo are leading to the emergence of useful biophysical parameters and physical organic chemistry rules that provide a framework for understanding LNP-mediated in vivo delivery behaviors and outcomes. These same parameters and rules should also suggest ways and means to develop next generations of LNPs with genuine utility and long-term clinical viability.
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48
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Xu Y, Ou M, Keough E, Roberts J, Koeplinger K, Lyman M, Fauty S, Carlini E, Stern M, Zhang R, Yeh S, Mahan E, Wang Y, Slaughter D, Gindy M, Raab C, Thompson C, Hochman J. Quantitation of physiological and biochemical barriers to siRNA liver delivery via lipid nanoparticle platform. Mol Pharm 2014; 11:1424-34. [PMID: 24588618 DOI: 10.1021/mp400584h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Effective delivery of small interfering RNA (siRNA) requires efficient cellular uptake and release into cytosol where it forms an active complex with RNAi induced silencing complex (RISC). Despite rapid developments in RNAi therapeutics, improvements in delivery efficiency of siRNA are needed to realize the full potential of this modality in broad therapeutic applications. We evaluated potential physiological and biochemical barrier(s) to the effective liver delivery of siRNA formulated in lipid nanoparticle (LNP) delivery vehicles. The comparative siRNA delivery performance of three LNPs was investigated in rats. They were assembled with either C14- or C18-anchored PEG-lipid(s), cationic lipid(s), and various helper lipid(s) and contained the same siRNA duplex. These LNPs demonstrated differentiated potency with ED50's ranging from 0.02 to 0.25 mg/kg. The two C14-PEG-LNPs had comparable siRNA exposure in plasma and liver, while the C18-PEG-LNP demonstrated a higher plasma siRNA exposure and a slower but sustained liver uptake. RISC bound siRNA within the liver, a more proximal measure of the pharmacologically active siRNA species, displayed loading kinetics that paralleled the target mRNA knockdown profile, with greater RISC loading associated with more potent LNPs. Liver perfusion and hepatocyte isolation experiments were performed following treatment of rats with LNPs containing VivoTag-fluorescently labeled siRNA. One hour after dosing a majority of the siRNA within the liver was associated with hepatocytes and was internalized (within small subcellular vesicles) with no significant cell surface association, indicating good liver tissue penetration, hepatocellular distribution, and internalization. Comparison of siRNA amounts in hepatocytes and subcellular fractions of the three LNPs suggests that endosomal escape is a significant barrier to siRNA delivery where cationic lipid seems to have a great impact. Quantitation of Ago-2 associated siRNA revealed that after endosomal escape further loss of siRNA occurs prior to RISC loading. This quantitative assessment of LNP-mediated siRNA delivery has highlighted potential barriers with respect to endosomal escape and incomplete RISC loading for delivery optimization efforts.
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Affiliation(s)
- Yan Xu
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, ‡RNA Discovery Biology, ∥Laboratory Animal Resources, and #Pharmaceutical Sciences, Merck Research Laboratories, Merck & Co., Inc. , 770 Sumneytown Pike, West Point, Pennsylvania 19446, United States
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49
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Wu SY, Yang X, Gharpure KM, Hatakeyama H, Egli M, McGuire MH, Nagaraja AS, Miyake TM, Rupaimoole R, Pecot CV, Taylor M, Pradeep S, Sierant M, Rodriguez-Aguayo C, Choi HJ, Previs RA, Armaiz-Pena GN, Huang L, Martinez C, Hassell T, Ivan C, Sehgal V, Singhania R, Han HD, Su C, Kim JH, Dalton HJ, Kovvali C, Keyomarsi K, McMillan NAJ, Overwijk WW, Liu J, Lee JS, Baggerly KA, Lopez-Berestein G, Ram PT, Nawrot B, Sood AK. 2'-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity. Nat Commun 2014; 5:3459. [PMID: 24619206 DOI: 10.1038/ncomms4459] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/17/2014] [Indexed: 12/19/2022] Open
Abstract
Improving small interfering RNA (siRNA) efficacy in target cell populations remains a challenge to its clinical implementation. Here, we report a chemical modification, consisting of phosphorodithioate (PS2) and 2'-O-Methyl (2'-OMe) MePS2 on one nucleotide that significantly enhances potency and resistance to degradation for various siRNAs. We find enhanced potency stems from an unforeseen increase in siRNA loading to the RNA-induced silencing complex, likely due to the unique interaction mediated by 2'-OMe and PS2. We demonstrate the therapeutic utility of MePS2 siRNAs in chemoresistant ovarian cancer mouse models via targeting GRAM domain containing 1B (GRAMD1B), a protein involved in chemoresistance. GRAMD1B silencing is achieved in tumours following MePS2-modified siRNA treatment, leading to a synergistic anti-tumour effect in combination with paclitaxel. Given the previously limited success in enhancing siRNA potency with chemically modified siRNAs, our findings represent an important advance in siRNA design with the potential for application in numerous cancer types.
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Affiliation(s)
- Sherry Y Wu
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2]
| | - Xianbin Yang
- 1] AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, USA [2]
| | - Kshipra M Gharpure
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Hiroto Hatakeyama
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
| | - Michael H McGuire
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Archana S Nagaraja
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Takahito M Miyake
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rajesha Rupaimoole
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chad V Pecot
- Division of Cancer Medicine, MDACC, Houston, Texas 77054, USA
| | - Morgan Taylor
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Cristian Rodriguez-Aguayo
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Hyun J Choi
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rebecca A Previs
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Guillermo N Armaiz-Pena
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Li Huang
- Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Tom Hassell
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Cristina Ivan
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Vasudha Sehgal
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Richa Singhania
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Centre for Biomolecular Sciences, School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Hee-Dong Han
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Immunology Laboratory, School of Medicine, Konkuk University, Chungju 380-701, South Korea
| | - Chang Su
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Ji Hoon Kim
- 1] Department of Systems Biology, MDACC, Houston, Texas 77054, USA [2] Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul 136-701, Korea
| | - Heather J Dalton
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chandra Kovvali
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, MDACC, Houston, Texas 77054, USA
| | - Nigel A J McMillan
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Griffith Health Institute and School of Medical Sciences, Griffith University, Southport, Queensland 4222, Australia
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, MDACC, Houston, Texas 77054, USA
| | - Jinsong Liu
- Department of Pathology, MDACC, Houston, Texas 77054, USA
| | - Ju-Seog Lee
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | | | - Gabriel Lopez-Berestein
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Prahlad T Ram
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Anil K Sood
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
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50
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Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet 2013; 9:e1003821. [PMID: 24086155 PMCID: PMC3784563 DOI: 10.1371/journal.pgen.1003821] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/24/2013] [Indexed: 12/31/2022] Open
Abstract
Argonaute proteins are often credited for their cytoplasmic activities in which they function as central mediators of the RNAi platform and microRNA (miRNA)-mediated processes. They also facilitate heterochromatin formation and establishment of repressive epigenetic marks in the nucleus of fission yeast and plants. However, the nuclear functions of Ago proteins in mammalian cells remain elusive. In the present study, we combine ChIP-seq (chromatin immunoprecipitation coupled with massively parallel sequencing) with biochemical assays to show that nuclear Ago1 directly interacts with RNA Polymerase II and is widely associated with chromosomal loci throughout the genome with preferential enrichment in promoters of transcriptionally active genes. Additional analyses show that nuclear Ago1 regulates the expression of Ago1-bound genes that are implicated in oncogenic pathways including cell cycle progression, growth, and survival. Our findings reveal the first landscape of human Ago1-chromosomal interactions, which may play a role in the oncogenic transcriptional program of cancer cells. Argonaute (Ago) proteins are an evolutionarily conserved family of proteins indispensable for a gene regulation mechanism known as RNA interference (RNAi) which is mediated by small RNA including microRNA (miRNA) and small interfering RNA (siRNA) and occurs mainly in the cytoplasm. In mammalian cells, however, the function of Agos in the nucleus is largely unknown despite a few examples in which Agos are shown to be involved in regulating gene transcription and alternative splicing. In this study, by taking a genome-wide approach, we found that human Ago1, but not Ago2, is pervasively associated with gene regulatory sequences known as promoter and interacts with the core component of the gene transcription machinery to exert positive impact on gene expression in cancer cells. Strikingly, the genes bound and regulated by Ago1 are mostly genes that stimulate cell growth and survival, and are known to be involved in the development of cancer. The findings from our study unveil an unexpected role of nuclear Ago1 in regulating gene expression which may be important both in normal cellular processes and in disease such as cancer.
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