1
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Lu T, Zhang C, Li Z, Wei Y, Sadewasser A, Yan Y, Sun L, Li J, Wen Y, Lai S, Chen C, Zhong H, Jiménez MR, Klar R, Schell M, Raith S, Michel S, Ke B, Zheng H, Jaschinski F, Zhang N, Xiao H, Bachert C, Wen W. Human angiotensin-converting enzyme 2-specific antisense oligonucleotides reduce infection with SARS-CoV-2 variants. J Allergy Clin Immunol 2024:S0091-6749(24)00631-6. [PMID: 38909634 DOI: 10.1016/j.jaci.2024.06.007] [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: 10/22/2023] [Revised: 05/16/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND The Spike protein mutation severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to decreased protective effect of various vaccines and mAbs, suggesting that blocking SARS-CoV-2 infection by targeting host factors would make the therapy more resilient against virus mutations. Angiotensin-converting enzyme 2 (ACE2) is the host receptor of SARS-CoV-2 and its variants, as well as many other coronaviruses. Downregulation of ACE2 expression in the respiratory tract may prevent viral infection. Antisense oligonucleotides (ASOs) can be rationally designed on the basis of sequence data, require no delivery system, and can be administered locally. OBJECTIVE We sought to design ASOs that can block SARS-CoV-2 by downregulating ACE2 in human airway. METHODS ACE2-targeting ASOs were designed using a bioinformatic method and screened in cell lines. Human primary nasal epithelial cells cultured at the air-liquid interface and humanized ACE2 mice were used to detect the ACE2 reduction levels and the safety of ASOs. ASO-pretreated nasal epithelial cells and mice were infected and then used to detect the viral infection levels. RESULTS ASOs reduced ACE2 expression on mRNA and protein level in cell lines and in human nasal epithelial cells. Furthermore, they efficiently suppressed virus replication of 3 different SARS-CoV-2 variants in human nasal epithelial cells. In vivo, ASOs also downregulated human ACE2 in humanized ACE2 mice and thereby reduced viral load, histopathologic changes in lungs, and increased survival of mice. CONCLUSIONS ACE2-targeting ASOs can effectively block SARS-CoV-2 infection. Our study provides a new approach for blocking SARS-CoV-2 and other ACE2-targeting virus in high-risk populations.
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Affiliation(s)
- Tong Lu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Chengcheng Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Zhengqi Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Wei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | | | - Yan Yan
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Lin Sun
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Jian Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Yihui Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Shimin Lai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Changhui Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Hua Zhong
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Richard Klar
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Monika Schell
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Stefanie Raith
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | | | - Nan Zhang
- Upper Airways Research Laboratory, Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Claus Bachert
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Department of Otorhinolaryngology - Head and Neck Surgery, University Hospital of Münster, Münster, Germany; Upper Airways Research Laboratory, Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Department of Otolaryngology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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2
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Hill AC, Becker JP, Slominski D, Halloy F, Søndergaard C, Ravn J, Hall J. Peptide Conjugates of a 2'- O-Methoxyethyl Phosphorothioate Splice-Switching Oligonucleotide Show Increased Entrapment in Endosomes. ACS OMEGA 2023; 8:40463-40481. [PMID: 37929104 PMCID: PMC10620785 DOI: 10.1021/acsomega.3c05144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Antisense oligonucleotides (ASOs) are short, single-stranded nucleic acid molecules that alter gene expression. However, their transport into appropriate cellular compartments is a limiting factor in their potency. Here, we synthesized splice-switching oligonucleotides (SSOs) previously developed to treat the rare disease erythropoietic protoporphyria. Using chemical ligation-quantitative polymerase chain reaction (CL-qPCR), we quantified the SSOs in cells and subcellular compartments following free uptake. To drive nuclear localization, we covalently conjugated nuclear localization signal (NLS) peptides to a lead 2'-O-methoxyethyl phosphorothioate SSO using thiol-maleimide chemistry. The conjugates and parent SSO displayed similar RNA target-binding affinities. CL-qPCR quantification of the conjugates in cells and subcellular compartments following free uptake revealed one conjugate with better nuclear accumulation relative to the parent SSO. However, compared to the parent SSO, which altered the splicing of the target pre-mRNA, the conjugates were inactive at splice correction under free uptake conditions in vitro. Splice-switching activity could be conferred on the conjugates by delivering them into cells via cationic lipid-mediated transfection or by treating the cells into which the conjugates had been freely taken up with chloroquine, an endosome-disrupting agent. Our results identify the major barrier to the activity of the peptide-oligonucleotide conjugates as endosomal entrapment.
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Affiliation(s)
- Alyssa C. Hill
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - J. Philipp Becker
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - Daria Slominski
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - François Halloy
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | | | - Jacob Ravn
- Roche
Innovation Center Copenhagen (RICC), Hørsholm 2970, Denmark
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
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3
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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4
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Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R. Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides. Nucleic Acid Ther 2023; 33:117-131. [PMID: 36735581 PMCID: PMC10066784 DOI: 10.1089/nat.2022.0046] [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: 02/04/2023] Open
Abstract
Huntington's disease is a neurodegenerative, trinucleotide repeat (TNR) disorder affecting both males and females. It is caused by an abnormal increase in the length of CAG•CTG TNR in exon 1 of the Huntingtin gene (HTT). The resultant, mutant HTT mRNA and protein cause neuronal toxicity, suggesting that reduction of their levels would constitute a promising therapeutic approach. We previously reported a novel strategy in which chemically modified oligonucleotides (ONs) directly target chromosomal DNA. These anti-gene ONs were able to downregulate both HTT mRNA and protein. In this study, various locked nucleic acid (LNA)/DNA mixmer anti-gene ONs were tested to investigate the effects of varying ON length, LNA content, and fatty acid modification on HTT expression. Altering the length did not significantly influence the ON potency, while LNA content was critical for activity. Utilization of palmitoyl-modified LNA monomers enhanced the ON activity relatively to the corresponding nonmodified LNA under serum starvation conditions. Furthermore, the number of palmitoylated LNA monomers and their positioning greatly affected ON potency. In addition, we performed RNA sequencing analysis, which showed that the anti-gene ONs affect the "immune system process, mRNA processing, and neurogenesis." Furthermore, we observed that for repeat containing genes, there is a higher tendency for antisense off-targeting. Taken together, our findings provide an optimized design of anti-gene ONs that could potentially be developed as DNA-targeting therapeutics for this class of TNR-related diseases.
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Affiliation(s)
- Osama Saher
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Tea Umek
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Mathias B Danielsen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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5
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:ijms23137224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA’s fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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6
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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: 14] [Impact Index Per Article: 7.0] [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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7
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Sharma R, Dong Y, Hu Y, Ma VPY, Salaita K. Gene Regulation Using Nanodiscs Modified with HIF-1-α Antisense Oligonucleotides. Bioconjug Chem 2022; 33:279-293. [PMID: 35080855 PMCID: PMC9884500 DOI: 10.1021/acs.bioconjchem.1c00505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Delivery of nucleic acids can be hindered by multiple factors including nuclease susceptibility, endosome trapping, and clearance. Multiple nanotechnology scaffolds have offered promising solutions, and among these, lipid-based systems are advantageous because of their high biocompatibility and low toxicity. However, many lipid nanoparticle systems still have issues regarding stability, rapid clearance, and cargo leakage. Herein, we demonstrate the use of a synthetic nanodisc (ND) scaffold functionalized with an anti-HIF-1-α antisense oligonucleotide (ASO) to reduce HIF-1-α mRNA transcript levels. We prepared ND conjugates by using a mixture of phosphoglycerolipids with phosphocholine and phosphothioethanol headgroups that self-assemble into a ∼13 × 5 nm discoidal structure upon addition of a 22-amino-acid ApoA1 mimetic peptide. Optimized reaction conditions yield 15 copies of the anti-HIF-1-α ASO DNA covalently conjugated to the thiolated phospholipids using maleimide-thiol chemistry. We show that DNA-ND conjugates are active, nuclease resistant, and rapidly internalized into cells to regulate HIF-1-α mRNA levels without the use of transfection agents. DNA-ND uptake is partially mediated through Scavenger Receptor B1 and the ND conjugates show enhanced knockdown of HIF-1-α compared to that of the soluble ASOs in multiple cell lines. Our results demonstrate that covalently functionalized NDs may offer an improved platform for ASO therapeutics.
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8
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Kapustin AN, Davey P, Longmire D, Matthews C, Linnane E, Rustogi N, Stavrou M, Devine PWA, Bond NJ, Hanson L, Sonzini S, Revenko A, MacLeod AR, Ross S, Chiarparin E, Puri S. Antisense oligonucleotide activity in tumour cells is influenced by intracellular LBPA distribution and extracellular vesicle recycling. Commun Biol 2021; 4:1241. [PMID: 34725463 PMCID: PMC8560811 DOI: 10.1038/s42003-021-02772-0] [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] [Received: 10/01/2019] [Accepted: 10/08/2021] [Indexed: 12/18/2022] Open
Abstract
Next generation modified antisense oligonucleotides (ASOs) are commercially approved new therapeutic modalities, yet poor productive uptake and endosomal entrapment in tumour cells limit their broad application. Here we compare intracellular traffic of anti KRAS antisense oligonucleotide (AZD4785) in tumour cell lines PC9 and LK2, with good and poor productive uptake, respectively. We find that the majority of AZD4785 is rapidly delivered to CD63+late endosomes (LE) in both cell lines. Importantly, lysobisphosphatidic acid (LBPA) that triggers ASO LE escape is presented in CD63+LE in PC9 but not in LK2 cells. Moreover, both cell lines recycle AZD4785 in extracellular vesicles (EVs); however, AZD4785 quantification by advanced mass spectrometry and proteomic analysis reveals that LK2 recycles more AZD4785 and RNA-binding proteins. Finally, stimulating LBPA intracellular production or blocking EV recycling enhances AZD4785 activity in LK2 but not in PC9 cells thus offering a possible strategy to enhance ASO potency in tumour cells with poor productive uptake of ASOs. Kapustin et al. investigate the intracellular trafficking of anti-KRAS antisense oligonucleotides. They show that the oligonucleotide AZD4785 is recycled via late endosomes in extracellular vesicles in both cells with poor and good oligo productive uptake, and that inducing lysobisphosphatidic acid in late endosomes or blocking EV recycling enhance AZD4785 activity in cells with poor productive uptake, potentially offering improved treatment strategies.
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Affiliation(s)
- Alexander N Kapustin
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
| | - Paul Davey
- Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - David Longmire
- Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Carl Matthews
- Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Emily Linnane
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Nitin Rustogi
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Maria Stavrou
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Paul W A Devine
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Lyndsey Hanson
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Alderley Park, UK
| | - Silvia Sonzini
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Sarah Ross
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Sanyogitta Puri
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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9
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Overcoming the challenges of tissue delivery for oligonucleotide therapeutics. Trends Pharmacol Sci 2021; 42:588-604. [PMID: 34020790 DOI: 10.1016/j.tips.2021.04.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/07/2021] [Accepted: 04/20/2021] [Indexed: 12/19/2022]
Abstract
Synthetic therapeutic oligonucleotides (STO) represent the third bonafide platform for drug discovery in the pharmaceutical industry after small molecule and protein therapeutics. So far, thirteen STOs have been approved by regulatory agencies and over one hundred of them are in different stages of clinical trials. STOs hybridize to their target RNA or DNA in cells via Watson-Crick base pairing to exert their pharmacological effects. This unique class of therapeutic agents has the potential to target genes and gene products that are considered undruggable by other therapeutic platforms. However, STOs must overcome several extracellular and intracellular obstacles to interact with their biological RNA targets inside cells. These obstacles include degradation by extracellular nucleases, scavenging by the reticuloendothelial system, filtration by the kidney, traversing the capillary endothelium to access the tissue interstitium, cell-surface receptor-mediated endocytic uptake, and escape from endolysosomal compartments to access the nuclear and/or cytoplasmic compartments where their targets reside. In this review, we present the recent advances in this field with a specific focus on antisense oligonucleotides (ASOs) and siRNA therapeutics.
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10
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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11
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Ochaba J, Powers AF, Tremble KA, Greenlee S, Post NM, Matson JE, MacLeod AR, Guo S, Aghajan M. A novel and translational role for autophagy in antisense oligonucleotide trafficking and activity. Nucleic Acids Res 2020; 47:11284-11303. [PMID: 31612951 PMCID: PMC6868497 DOI: 10.1093/nar/gkz901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 01/26/2023] Open
Abstract
Endocytosis is a mechanism by which cells sense their environment and internalize various nutrients, growth factors and signaling molecules. This process initiates at the plasma membrane, converges with autophagy, and terminates at the lysosome. It is well-established that cellular uptake of antisense oligonucleotides (ASOs) proceeds through the endocytic pathway; however, only a small fraction escapes endosomal trafficking while the majority are rendered inactive in the lysosome. Since these pathways converge and share common molecular machinery, it is unclear if autophagy-related trafficking participates in ASO uptake or whether modulation of autophagy affects ASO activity and localization. To address these questions, we investigated the effects of autophagy modulation on ASO activity in cells and mice. We found that enhancing autophagy through small-molecule mTOR inhibition, serum-starvation/fasting, and ketogenic diet, increased ASO-mediated target reduction in vitro and in vivo. Additionally, autophagy activation enhanced the localization of ASOs into autophagosomes without altering intracellular concentrations or trafficking to other compartments. These results support a novel role for autophagy and the autophagosome as a previously unidentified compartment that participates in and contributes to enhanced ASO activity. Further, we demonstrate non-chemical methods to enhance autophagy and subsequent ASO activity using translatable approaches such as fasting or ketogenic diet.
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Affiliation(s)
- Joseph Ochaba
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | | | | | | | - Noah M Post
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - John E Matson
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | | | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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12
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Herkt M, Foinquinos A, Batkai S, Thum T, Pich A. Pharmacokinetic Studies of Antisense Oligonucleotides Using MALDI-TOF Mass Spectrometry. Front Pharmacol 2020; 11:220. [PMID: 32269522 PMCID: PMC7109322 DOI: 10.3389/fphar.2020.00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 11/21/2022] Open
Abstract
Cardiac diseases are the most frequent causes of death in industrialized countries. Pathological remodeling of the heart muscle is caused by several etiologies such as prolonged hypertension or injuries that can lead to myocardial infarction and in serious cases also the death of the patient. The micro-RNA miR-132 has been identified as a master-switch in the development of cardiac hypertrophy and adverse remodeling. In this study, MALDI-TOF mass spectrometry (MS) was utilized to establish a robust and fast method to sensitively detect and accurately quantify anti-microRNA (antimiR) oligonucleotides in blood plasma. An antimiR oligonucleotide isolation protocol containing an ethanol precipitation step with glycogen as oligonucleotide carrier as well as a robust and reproducible MS-analysis procedure has been established. Proteinase K treatment was crucial for releasing antimiR oligonucleotides from plasma- as well as cellular proteins and reducing background derived from biological matrices. AntimiR oligonucleotide detection was achieved from samples of studies in different animal models such as mouse and pig where locked nucleic acids-(LNA)-modified antimiR oligonucleotides have been used to generate pharmacokinetic data.
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Affiliation(s)
- Markus Herkt
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Ariana Foinquinos
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Sandor Batkai
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Thomas Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Andreas Pich
- Hannover Medical School, Institute for Toxicology - Core Unit Proteomics, Hanover, Germany
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13
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Christou M, Wengel J, Sokratous K, Kyriacou K, Nikolaou G, Phylactou LA, Mastroyiannopoulos NP. Systemic Evaluation of Chimeric LNA/2'-O-Methyl Steric Blockers for Myotonic Dystrophy Type 1 Therapy. Nucleic Acid Ther 2019; 30:80-93. [PMID: 31873063 PMCID: PMC7133450 DOI: 10.1089/nat.2019.0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited, multisystemic disorder characterized clinically by delayed muscle relaxation and weakness. The disease is caused by a CTG repeat expansion in the 3′ untranslated region (3′ UTR) of the DMPK gene, which leads to the expression of a toxic gain-of-function mRNA. The expanded CUG repeat mRNA sequesters the MBNL1 splicing regulator in nuclear-retained foci structures, resulting in loss of protein function and disruption of alternative splicing homeostasis. In this study, we used CAG repeat antisense oligonucleotides (ASOs), composed of locked nucleic acid (LNA)- and 2′-O-methyl (2′OMe)-modified bases in a chimeric design, to alleviate CUGexpanded-mediated toxicity. Chimeric 14–18mer LNA/2′OMe oligonucleotides, exhibiting an LNA incorporation of ∼33%, significantly ameliorated the misregulated alternative splicing of Mbnl1-dependent exons in primary DM1 mouse myoblasts and tibialis anterior muscles of DM1 mice. Subcutaneous delivery of 14mer and 18mer LNA/2′OMe chimeras in DM1 mice resulted in high levels of accumulation in all tested skeletal muscles, as well as in the diaphragm and heart tissue. Despite the efficient delivery, chimeric LNA/2′OMe oligonucleotides were not able, even at a high-dosage regimen (400 mg/kg/week), to correct the misregulated splicing of Serca1 exon 22 in skeletal muscles. Nevertheless, oligonucleotide doses were well-tolerated as determined by histological and plasma biochemistry analyses. Our results provide proof of concept that inhibition of MBNL1 sequestration by systemic delivery of a steric-blocking ASO is extremely challenging, considering the large number of target sites that need to be occupied per RNA molecule. Although not suitable for DM1 therapy, chimeric LNA/2′OMe oligonucleotides could prove to be highly beneficial for other diseases, such as Duchenne muscular dystrophy, that require inhibition of a single target site per RNA molecule.
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Affiliation(s)
- Melina Christou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense M, Denmark
| | - Kleitos Sokratous
- Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Georgios Nikolaou
- Veterinary Diagnostic Laboratory, Vet Ex Machina Ltd, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nikolaos P Mastroyiannopoulos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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14
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Buntz A, Killian T, Schmid D, Seul H, Brinkmann U, Ravn J, Lindholm M, Knoetgen H, Haucke V, Mundigl O. Quantitative fluorescence imaging determines the absolute number of locked nucleic acid oligonucleotides needed for suppression of target gene expression. Nucleic Acids Res 2019; 47:953-969. [PMID: 30462278 PMCID: PMC6344898 DOI: 10.1093/nar/gky1158] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Locked nucleic acid based antisense oligonucleotides (LNA-ASOs) can reach their intracellular RNA targets without delivery modules. Functional cellular uptake involves vesicular accumulation followed by translocation to the cytosol and nucleus. However, it is yet unknown how many LNA-ASO molecules need to be delivered to achieve target knock down. Here we show by quantitative fluorescence imaging combined with LNA-ASO microinjection into the cytosol or unassisted uptake that ∼105 molecules produce >50% knock down of their targets, indicating that a substantial amount of LNA-ASO escapes from endosomes. Microinjected LNA-ASOs redistributed within minutes from the cytosol to the nucleus and remained bound to nuclear components. Together with the fact that RNA levels for a given target are several orders of magnitude lower than the amounts of LNA-ASO, our data indicate that only a minor fraction is available for RNase H1 mediated reduction of target RNA. When non-specific binding sites were blocked by co-administration of non-related LNA-ASOs, the amount of target LNA-ASO required was reduced by an order of magnitude. Therefore, dynamic processes within the nucleus appear to influence the distribution and activity of LNA-ASOs and may represent important parameters for improving their efficacy and potency.
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Affiliation(s)
- Annette Buntz
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Tobias Killian
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Daniela Schmid
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Heike Seul
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Ulrich Brinkmann
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Jacob Ravn
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Marie Lindholm
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Hendrik Knoetgen
- Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Volker Haucke
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin 13125, Germany
| | - Olaf Mundigl
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
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15
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Breuel S, Vorm M, Bräuer AU, Owczarek-Lipska M, Neidhardt J. Combining Engineered U1 snRNA and Antisense Oligonucleotides to Improve the Treatment of a BBS1 Splice Site Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:123-130. [PMID: 31541798 PMCID: PMC6796732 DOI: 10.1016/j.omtn.2019.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 08/01/2019] [Indexed: 12/23/2022]
Abstract
Manipulation of pre-mRNA processing is a promising approach toward overcoming disease-causing mutations and treating human diseases. We show that a combined treatment applying two splice-manipulating technologies improves therapeutic efficacies to correct mutation-induced splice defects. Previously, we identified a family affected by retinitis pigmentosa caused by the homozygous BBS1 splice donor site mutation c.479G > A. The mutation leads to both exon 5 skipping and intron 5 retention. We developed a therapeutic approach applying lentivirus-mediated gene delivery of engineered U1 small nuclear RNA (U1), which resulted in increased levels of correctly spliced BBS1. Herein, we show that the therapeutic effect of the engineered U1 efficiently reverted exon skipping but failed to reduce the intron retention. To complement the engineered U1 treatment, we identified four different antisense oligonucleotides (AONs) that block intron 5 retention in BBS1 transcripts. A treatment using engineered U1 in combination with AONs showed the highest therapeutic efficacy and increased the amount of correctly spliced BBS1 transcripts. We did not detect elevated levels of apoptotic cell death in AON-treated cell lines. In conclusion, engineered U1 or AONs provide efficient therapies with complementary effects and can be combined to increase efficacy of therapeutic approaches to correct splice defects.
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Affiliation(s)
- Saskia Breuel
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Mariann Vorm
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Anja U Bräuer
- Anatomy, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Germany
| | - Marta Owczarek-Lipska
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Germany; Joint research training group of the Faculty of Medicine and Health Sciences, University of Oldenburg, Germany and the University Medical Center Groningen, Groningen, Netherlands.
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16
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Chen Z, Li H, Zhang L, Lee CK, Ho LWC, Chan CKW, Yang H, Choi CHJ. Specific Delivery of Oligonucleotides to the Cell Nucleus via Gentle Compression and Attachment of Polythymidine. ACS APPLIED MATERIALS & INTERFACES 2019; 11:27624-27640. [PMID: 31303000 DOI: 10.1021/acsami.9b11391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nonviral delivery of nucleic acids to the cell nucleus typically requires chemical methods that do not guarantee specific delivery (e.g., transfection agent) or physical methods that may require extensive fabrication (e.g., microfluidics) or an elevated pressure (e.g., 105 Pa for microneedles). We report a method of delivering oligonucleotides to the nucleus with high specificity (relative to the cytosol) by synergistically combining chemical and physical approaches. Particularly, we demonstrate that DNA oligonucleotides appended with a polythymidine [poly(T)] segment (chemical) profusely accumulate inside the nucleus when the cells are under gentle compression imposed by the weight of a single glass coverslip (physical; ∼2.2 Pa). Our "compression-cum-poly(T)" delivery method is simple, can be generalizable to three "hard-to-transfect" cell types, and does not induce significant levels of cytotoxicity or long-term oxidative stress to the treated cells when provided the use of suitable compression times and oligonucleotide concentrations. In bEnd.3 endothelial cells, compression-aided intranuclear delivery of poly(T) is primarily mediated by importin β and nucleoporin 62. Our method significantly enhances the intranuclear delivery of antisense oligonucleotides to bEnd.3 endothelioma cells and the inhibition of two target genes, including a reporter gene encoding the enhanced green fluorescent protein and an intranuclear lncRNA oncogene (metastasis-associated lung adenocarcinoma transcript 1), when compared with delivery without gentle compression or poly(T) attachment. Our data underscore the critical roles of pressure and nucleotide sequence on the intranuclear delivery of nucleic acids.
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17
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Wang S, Allen N, Prakash TP, Liang XH, Crooke ST. Lipid Conjugates Enhance Endosomal Release of Antisense Oligonucleotides Into Cells. Nucleic Acid Ther 2019; 29:245-255. [PMID: 31158063 DOI: 10.1089/nat.2019.0794] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides modified with phosphorothioate linkages (PS-ASOs) can enter cells via endocytic pathways and must escape from membraned organelles to reach target RNAs. We recently found that membrane destabilization induced by different lipid species contributes to PS-ASO release from late endosomes (LEs). In this study, we characterized intracellular uptake, trafficking, and activities of PS-ASOs conjugated with different lipid species. We found that palmitic acid-, tocopherol-, and cholesterol-conjugated PS-ASOs have increased protein binding and enhanced intracellular uptake compared to unconjugated PS-ASOs. Similar to the parental PS-ASO, the lipid-conjugated PS-ASOs traffic from early to LEs without incorporation into lipid droplets. Unlike parental PS-ASOs, the lipid-conjugated PS-ASOs tend to remain associated with plasma or endosomal membranes, and this appears to influence their release from endosomes. The lipid-conjugated PS-ASOs were released more rapidly than parental PS-ASO. These results suggest that lipid conjugation enhances the interactions of PS-ASOs with proteins or membranes, in turn facilitating intracellular trafficking and endosomal release.
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Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Nickolas Allen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
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18
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Laikova KV, Oberemok VV, Krasnodubets AM, Gal'chinsky NV, Useinov RZ, Novikov IA, Temirova ZZ, Gorlov MV, Shved NA, Kumeiko VV, Makalish TP, Bessalova EY, Fomochkina II, Esin AS, Volkov ME, Kubyshkin AV. Advances in the Understanding of Skin Cancer: Ultraviolet Radiation, Mutations, and Antisense Oligonucleotides as Anticancer Drugs. Molecules 2019; 24:E1516. [PMID: 30999681 PMCID: PMC6514765 DOI: 10.3390/molecules24081516] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022] Open
Abstract
Skin cancer has always been and remains the leader among all tumors in terms of occurrence. One of the main factors responsible for skin cancer, natural and artificial UV radiation, causes the mutations that transform healthy cells into cancer cells. These mutations inactivate apoptosis, an event required to avoid the malignant transformation of healthy cells. Among these deadliest of cancers, melanoma and its 'younger sister', Merkel cell carcinoma, are the most lethal. The heavy toll of skin cancers stems from their rapid progression and the fact that they metastasize easily. Added to this is the difficulty in determining reliable margins when excising tumors and the lack of effective chemotherapy. Possibly the biggest problem posed by skin cancer is reliably detecting the extent to which cancer cells have spread throughout the body. The initial tumor is visible and can be removed, whereas metastases are invisible to the naked eye and much harder to eliminate. In our opinion, antisense oligonucleotides, which can be used in the form of targeted ointments, provide real hope as a treatment that will eliminate cancer cells near the tumor focus both before and after surgery.
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Affiliation(s)
- Kateryna V Laikova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
- Research Institute of Agriculture of Crimea, Kiyevskaya St. 150, 295493, Simferopol, Crimea.
| | - Volodymyr V Oberemok
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Av. 4, 295007 Simferopol, Crimea.
- Nikita Botanical Gardens ⁻ National Scientific Centre RAS, Nikitsky spusk 52, vil. Nikita, 298648 Yalta, Crimea.
| | - Alisa M Krasnodubets
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Av. 4, 295007 Simferopol, Crimea.
| | - Nikita V Gal'chinsky
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Av. 4, 295007 Simferopol, Crimea.
| | - Refat Z Useinov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Av. 4, 295007 Simferopol, Crimea.
| | - Ilya A Novikov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Av. 4, 295007 Simferopol, Crimea.
| | - Zenure Z Temirova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
| | - Mikhail V Gorlov
- D. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia.
| | - Nikita A Shved
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Sukhanova St. 8, 690090 Vladivostok, Russia.
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Palchevsky St. 17, 690041 Vladivostok, Russia.
| | - Vadim V Kumeiko
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Sukhanova St. 8, 690090 Vladivostok, Russia.
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Palchevsky St. 17, 690041 Vladivostok, Russia.
| | - Tatiana P Makalish
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
| | - Evgeniya Y Bessalova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
| | - Iryna I Fomochkina
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
| | - Andrey S Esin
- D. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia.
| | - Mikhail E Volkov
- Ltd "NPF Syntol", Тimiryazevskaya St. 42, 127434 Moscow, Russia.
| | - Anatoly V Kubyshkin
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Boulevard 5/7, 295051 Simferopol, Crimea.
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19
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Seth PP, Swayze EE. The Medicinal Chemistry of RNase H-activating Antisense Oligonucleotides. ADVANCES IN NUCLEIC ACID THERAPEUTICS 2019. [DOI: 10.1039/9781788015714-00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review focuses on the properties that an RNase H-activating antisense oligonucleotide (ASO) drug must have to function effectively in animals, as well as on medicinal chemistry strategies to achieve these properties. The biochemistry and structural requirements for activating RNase H are briefly summarized, as well as chemical modifications that can effect activation of RNase H when an ASO is bound to target RNA. The key modifications available to the medicinal chemist to engineer desired properties of the ASO are briefly reviewed, as are ASO design strategies to achieve optimal activity in animal systems. Lastly, the interactions of ASOs with proteins and strategies to control these interactions to improve the profile of ASOs are discussed.
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Affiliation(s)
- Punit P. Seth
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
| | - Eric E. Swayze
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
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20
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Seth PP, Tanowitz M, Bennett CF. Selective tissue targeting of synthetic nucleic acid drugs. J Clin Invest 2019; 129:915-925. [PMID: 30688661 DOI: 10.1172/jci125228] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are chemically synthesized nucleic acid analogs designed to bind to RNA by Watson-Crick base pairing. Following binding to the targeted RNA, the ASO perturbs RNA function by promoting selective degradation of the targeted RNA, altering RNA intermediary metabolism, or disrupting function of the RNA. Most antisense drugs are chemically modified to enhance their pharmacological properties and for passive targeting of the tissues of therapeutic interest. Recent advances in selective tissue targeting have resulted in a newer generation of ASO drugs that are more potent and better tolerated than previous generations, spawning renewed interest in identifying selective ligands that enhance targeted delivery of ASOs to tissues.
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21
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Liang XH, Sun H, Nichols JG, Allen N, Wang S, Vickers TA, Shen W, Hsu CW, Crooke ST. COPII vesicles can affect the activity of antisense oligonucleotides by facilitating the release of oligonucleotides from endocytic pathways. Nucleic Acids Res 2018; 46:10225-10245. [PMID: 30239896 PMCID: PMC6212795 DOI: 10.1093/nar/gky841] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
RNase H1-dependent, phosphorothioate-modified antisense oligonucleotides (PS-ASOs) can enter cells through endocytic pathways and need to be released from the membrane-enclosed organelles, a limiting step for antisense activity. Accumulating evidence has suggested that productive PS-ASO release mainly occurs from late endosomes (LEs). However, how PS-ASOs escape from LEs is not well understood. Here, we report that upon PS-ASO incubation, COPII vesicles, normally involved in ER-Golgi transport, can re-locate to PS-ASO-containing LEs. Reduction of COPII coat proteins significantly decreased PS-ASO activity, without affecting the levels of PS-ASO uptake and early-to-late endosome transport, but caused slower PS-ASO release from LEs. COPII co-localization with PS-ASOs at LEs does not require de novo assembly of COPII at ER. Interestingly, reduction of STX5 and P115, proteins involved in tethering and fusion of COPII vesicles with Golgi membranes, impaired COPII re-localization to LEs and decreased PS-ASO activity. STX5 can re-locate to LEs upon PS-ASO incubation, can bind PS-ASOs, and the binding appears to be required for this pathway. Our study reveals a novel release pathway in which PS-ASO incubation causes LE re-localization of STX5, which mediates the recruitment of COPII vesicles to LEs to facilitate endosomal PS-ASO release, and identifies another key PS-ASO binding protein.
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Affiliation(s)
- Xue-hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Nickolas Allen
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Shiyu Wang
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Chih-Wei Hsu
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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22
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Lu X, Zhang K. PEGylation of therapeutic oligonucletides: From linear to highly branched PEG architectures. NANO RESEARCH 2018; 11:5519-5534. [PMID: 30740197 PMCID: PMC6366847 DOI: 10.1007/s12274-018-2131-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 05/12/2023]
Abstract
PEGylation, the attachment of poly(ethylene glycol) (PEG), has been adopted to improve the pharmacokinetic properties of oligonucleotide therapeutics for nearly 30 years. Prior efforts mainly focused on the investigation of linear or slightly branched PEG having different molecular weights, terminal functional groups, and possible oligonucleotide sites for functionalization. Recent studies on highly branched PEG (including brush, star, and micellar structures) indicate superior properties in several areas including cellular uptake, gene regulation efficacy, reduction of side effects, and biodistribution. This review focuses on comparing the effects of PEG architecture on the physiochemical and biological properties of the PEGylated oligonucleotide.
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Affiliation(s)
- Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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23
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Miller CM, Tanowitz M, Donner AJ, Prakash TP, Swayze EE, Harris EN, Seth PP. Receptor-Mediated Uptake of Phosphorothioate Antisense Oligonucleotides in Different Cell Types of the Liver. Nucleic Acid Ther 2018; 28:119-127. [PMID: 29425080 DOI: 10.1089/nat.2017.0709] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide therapeutics have emerged as a third distinct platform for drug discovery within the pharmaceutical industry. Five oligonucleotide-based drugs have been approved by the US FDA and over 100 oligonucleotides drugs are currently at different stages of human trials. Several of these oligonucleotide drugs are modified using the phosphorothioate (PS) backbone modification where one of the nonbridging oxygen atoms of the phosphodiester linkage is replaced with sulfur. In this review, we summarize our knowledge on receptor-mediated uptake of PS antisense oligonucleotides (ASOs) within different cell types of the liver-a privileged organ for the discovery of oligonucleotide-based therapeutics.
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Affiliation(s)
- Colton M Miller
- 1 Department of Biochemistry, University of Nebraska , Lincoln, Nebraska
| | | | | | | | | | - Edward N Harris
- 1 Department of Biochemistry, University of Nebraska , Lincoln, Nebraska
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24
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Tanowitz M, Hettrick L, Revenko A, Kinberger GA, Prakash TP, Seth PP. Asialoglycoprotein receptor 1 mediates productive uptake of N-acetylgalactosamine-conjugated and unconjugated phosphorothioate antisense oligonucleotides into liver hepatocytes. Nucleic Acids Res 2017; 45:12388-12400. [PMID: 29069408 PMCID: PMC5716100 DOI: 10.1093/nar/gkx960] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/11/2017] [Indexed: 01/13/2023] Open
Abstract
Antisense oligonucleotide (ASO) therapeutics show tremendous promise for the treatment of previously intractable human diseases but to exert their effects on cellular RNA processing they must first cross the plasma membrane by endocytosis. The conjugation of ASOs to a receptor ligand can dramatically increase their entry into certain cells and tissues, as demonstrated by the implementation of N-acetylgalactosamine (GalNAc)-conjugated ASOs for Asialoglycoprotein Receptor (ASGR)-mediated uptake into liver hepatocytes. We compared the internalization and activity of GalNAc-conjugated ASOs and their parents in endogenous ASGR-expressing cells and were able to recapitulate hepatocyte ASO uptake and activity in cells engineered to heterologously express the receptor. We found that the minor receptor subunit, ASGR2, is not required for effective in vitro or in vivo uptake of GalNAc-conjugated ASO and that the major subunit, ASGR1, plays a small but significant role in the uptake of unconjugated phosphorothioate ASOs into hepatocytes. Moreover, our data demonstrates there is a large excess capacity of liver ASGR for the effective uptake of GalNAc–ASO conjugates, suggesting broad opportunities to exploit receptors with relatively moderate levels of expression.
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Affiliation(s)
- Michael Tanowitz
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Lisa Hettrick
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Alexey Revenko
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Garth A Kinberger
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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25
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Wang S, Sun H, Tanowitz M, Liang XH, Crooke ST. Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides. Nucleic Acids Res 2017; 45:5309-5322. [PMID: 28379543 PMCID: PMC5605259 DOI: 10.1093/nar/gkx231] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/27/2017] [Indexed: 12/12/2022] Open
Abstract
Antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages are broadly used as research tools and therapeutic agents. Chemically modified PS-ASOs can mediate efficient target reduction by site-specific cleavage of RNA through RNase H1. PS-ASOs are known to be internalized via a number of endocytotic pathways and are released from membrane-enclosed endocytotic organelles, mainly late endosomes (LEs). This study was focused on the details of PS-ASO trafficking through endocytic pathways. It was found that lysobisphosphatidic acid (LBPA) is required for release of PS-ASOs from LEs. PS-ASOs exited early endosomes (EEs) rapidly after internalization and became co-localized with LBPA by 2 hours in LEs. Inside LEs, PS-ASOs and LBPA were co-localized in punctate, dot-like structures, likely intraluminal vesicles (ILVs). Deactivation of LBPA using anti-LBPA antibody significantly decreased PS-ASO activities without affecting total PS-ASO uptake. Reduction of Alix also substantially decreased PS-ASO activities without affecting total PS-ASO uptake. Furthermore, Alix reduction decreased LBPA levels and limited co-localization of LBPA with PS-ASOs at ILVs inside LEs. Thus, the fusion properties of ILVs, which are supported by LBPA, contribute to PS-ASO intracellular release from LEs.
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Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Tanowitz
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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26
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Bohr HG, Shim I, Stein C, Ørum H, Hansen HF, Koch T. Electronic Structures of LNA Phosphorothioate Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:428-441. [PMID: 28918042 PMCID: PMC5537454 DOI: 10.1016/j.omtn.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023]
Abstract
Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.
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Affiliation(s)
- Henrik G Bohr
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Irene Shim
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Cy Stein
- Department of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Henrik Ørum
- Anemonevej 4, Hareskov, 3500 Værløse, Denmark
| | - Henrik F Hansen
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
| | - Troels Koch
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
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27
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Enhancing the cytotoxicity of chemoradiation with radiation-guided delivery of anti-MGMT morpholino oligonucleotides in non-methylated solid tumors. Cancer Gene Ther 2017; 24:348-357. [PMID: 28752860 PMCID: PMC5605678 DOI: 10.1038/cgt.2017.27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 01/25/2023]
Abstract
The DNA repair enzyme O6-methylguanine DNA methyltransferase (MGMT) is epigenetically silenced in some tumors by MGMT gene promoter methylation. MGMT-hypermethylated solid tumors have enhanced susceptibility to the cytotoxic effects of alkylating chemotherapy such as temozolomide, compared with non-methylated tumors. In glioblastoma, subjects with MGMT hypermethylation have significantly longer survival rates after chemoradiotherapy. We report the first successful use of a non-ablative dose of ionizing radiation to prime human cancer cells to enhance the uptake of unmodified anti-MGMT morpholino oligonucleotide (AMON) sequences. We demonstrate >40% reduction in the in vitro proliferation index and cell viability in radiation-primed MGMT-expressing human solid tumor cells treated with a single dose of AMONs and temozolomide. We further demonstrate the feasibility of using a non-ablative dose of radiation in vivo to guide and enhance the delivery of intravenously administered AMONs to achieve 50% MGMT knockdown only at radiation-primed tumor sites in a subcutaneous tumor model. Local upregulation of physiological endocytosis after radiation may have a role in radiation-guided uptake of AMONs. This approach holds direct translational significance in glioblastoma and brain metastases where radiation is part of the standard of care; our approach to silence MGMT could overcome the significant problem of MGMT-mediated chemoresistance.
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28
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Donner AJ, Wancewicz EV, Murray HM, Greenlee S, Post N, Bell M, Lima WF, Swayze EE, Seth PP. Co-Administration of an Excipient Oligonucleotide Helps Delineate Pathways of Productive and Nonproductive Uptake of Phosphorothioate Antisense Oligonucleotides in the Liver. Nucleic Acid Ther 2017; 27:209-220. [PMID: 28448194 DOI: 10.1089/nat.2017.0662] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phosphorothioate (PS) modified antisense oligonucleotides (ASOs) have progressed rapidly in the clinic for treating a variety of disease indications. We previously demonstrated that the activity of PS ASOs in the liver can be enhanced by co-infusion of an excipient oligonucleotide (EON). It was posited that the EON saturates a nonproductive uptake pathway(s) thereby permitting accumulation of the PS ASO in a productive tissue compartment. In this report, we measured PS ASO activity following administration by bolus, infusion or co-fusion with EON within hepatocytes and nonparenchymal cells (NPCs), of the liver. This revealed that while ASOs accumulate preferentially in NPCs, they are intrinsically more active in hepatocytes. Furthermore, we show that the EON enhances ASO potency when infused up to 72 h before or after administration of the active ASO suggesting that the EON can saturate and displace the ASO from nonproductive to productive compartments. Physical presence of the EON in tissues was required for optimal potentiation suggesting that there is a dynamic distribution of the ASO and EON between the compartments. Lastly, using a candidate approach, we confirmed Stabilin-2 as a molecular pathway for ASO uptake in sinusoidal endothelial cells and the ASGR as a pathway for ASO uptake into hepatocytes in the liver.
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Affiliation(s)
| | | | | | | | - Noah Post
- Ionis Pharmaceuticals , Carlsbad, California
| | | | - Walt F Lima
- Ionis Pharmaceuticals , Carlsbad, California
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29
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Sprangers AJ, Hao L, Banga RJ, Mirkin CA. Liposomal Spherical Nucleic Acids for Regulating Long Noncoding RNAs in the Nucleus. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201602753. [PMID: 28026123 PMCID: PMC5343594 DOI: 10.1002/smll.201602753] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/21/2016] [Indexed: 05/22/2023]
Abstract
Emerging evidence indicates that long noncoding RNAs (lncRNAs) are actively involved in a number of developmental and tumorigenic processes. Here, the authors describe the first successful use of spherical nucleic acids as an effective nanoparticle platform for regulating lncRNAs in cells; specifically, for the targeted knockdown of the nuclear-retained metastasis associated lung adenocarcinoma transcript 1 (Malat1), a key oncogenic lncRNA involved in metastasis of several cancers. Utilizing the liposomal spherical nucleic acid (LSNA) constructs, the authors first explored the delivery of antisense oligonucleotides to the nucleus. A dose-dependent inhibition of Malat1 upon LSNA treatment as well as the consequent up-regulation of tumor suppressor messenger RNA associated with Malat1 knockdown are shown. These findings reveal the biologic and therapeutic potential of a LSNA-based antisense strategy in targeting disease-associated, nuclear-retained lncRNAs.
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Affiliation(s)
- Anthony J Sprangers
- Department of Biomedical Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Liangliang Hao
- Interdisciplinary Biological Sciences, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Resham J Banga
- Department of Chemical and Biological Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Biomedical Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
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30
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Cellular uptake and trafficking of antisense oligonucleotides. Nat Biotechnol 2017; 35:230-237. [PMID: 28244996 DOI: 10.1038/nbt.3779] [Citation(s) in RCA: 379] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
Abstract
Antisense oligonucleotides (ASOs) modified with phosphorothioate (PS) linkages and different 2' modifications can be used either as drugs (e.g., to treat homozygous familial hypercholesterolemia and spinal muscular atrophy) or as research tools to alter gene expression. PS-ASOs can enter cells without additional modification or formulation and can be designed to mediate sequence-specific cleavage of different types of RNA (including mRNA and non-coding RNA) targeted by endogenous RNase H1. Although PS-ASOs function in both the cytoplasm and nucleus, localization to different subcellular regions can affect their therapeutic potency. Cellular uptake and intracellular distribution of PS ASOs are mediated by protein interactions. The main proteins involved in these processes have been identified, and intracellular sites in which PS ASOs are active, or inactive, cataloged.
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31
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Abstract
The discovery of an ever-expanding plethora of coding and non-coding RNAs with nodal and causal roles in the regulation of lung physiology and disease is reinvigorating interest in the clinical utility of the oligonucleotide therapeutic class. This is strongly supported through recent advances in nucleic acids chemistry, synthetic oligonucleotide delivery and viral gene therapy that have succeeded in bringing to market at least three nucleic acid-based drugs. As a consequence, multiple new candidates such as RNA interference modulators, antisense, and splice switching compounds are now progressing through clinical evaluation. Here, manipulation of RNA for the treatment of lung disease is explored, with emphasis on robust pharmacological evidence aligned to the five pillars of drug development: exposure to the appropriate tissue, binding to the desired molecular target, evidence of the expected mode of action, activity in the relevant patient population and commercially viable value proposition.
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32
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Miller CM, Harris EN. Antisense Oligonucleotides: Treatment Strategies and Cellular Internalization. RNA & DISEASE 2016; 3:e1393. [PMID: 28374018 PMCID: PMC5376066 DOI: 10.14800/rd.1393] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The clinical applicaton of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific non-targeted ASO internalization within cells.
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Affiliation(s)
- Colton M. Miller
- Department of Biochemistry, University of Nebraska - Lincoln, 1901 Vine St. Lincoln NE 68588 USA
| | - Edward N. Harris
- Department of Biochemistry, University of Nebraska - Lincoln, 1901 Vine St. Lincoln NE 68588 USA
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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34
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Wang S, Sun H, Tanowitz M, Liang XH, Crooke ST. Annexin A2 facilitates endocytic trafficking of antisense oligonucleotides. Nucleic Acids Res 2016; 44:7314-30. [PMID: 27378781 PMCID: PMC5009748 DOI: 10.1093/nar/gkw595] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/16/2016] [Indexed: 02/01/2023] Open
Abstract
Chemically modified antisense oligonucleotides (ASOs) designed to mediate site-specific cleavage of RNA by RNase H1 are used as research tools and as therapeutics. ASOs modified with phosphorothioate (PS) linkages enter cells via endocytotic pathways. The mechanisms by which PS-ASOs are released from membrane-enclosed endocytotic organelles to reach target RNAs remain largely unknown. We recently found that annexin A2 (ANXA2) co-localizes with PS-ASOs in late endosomes (LEs) and enhances ASO activity. Here, we show that co-localization of ANXA2 with PS-ASO is not dependent on their direct interactions or mediated by ANXA2 partner protein S100A10. Instead, ANXA2 accompanies the transport of PS-ASOs to LEs, as ANXA2/PS-ASO co-localization was observed inside LEs. Although ANXA2 appears not to affect levels of PS-ASO internalization, ANXA2 reduction caused significant accumulation of ASOs in early endosomes (EEs) and reduced localization in LEs and decreased PS-ASO activity. Importantly, the kinetics of PS-ASO activity upon free uptake show that target mRNA reduction occurs at least 4 hrs after PS-ASOs exit from EEs and is coincident with release from LEs. Taken together, our results indicate that ANXA2 facilitates PS-ASO trafficking from early to late endosomes where it may also contribute to PS-ASO release.
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Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Tanowitz
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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35
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Liu CB, Xu JQ, Xu BX, Zhang JM, Chen YM, Wang RM, Tian JH. Can Carrier-Mediated Delivery System Promote the Development of Antisense Imaging? Mol Imaging Biol 2016; 17:625-32. [PMID: 25666290 DOI: 10.1007/s11307-015-0827-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PURPOSE We aimed to explore the feasibility of transfection methods for antisense imaging. PROCEDURES Antisense oligonucleotides (ASON) targeted to the mRNA of hTERT gene were synthesized and labeled with Technetium-99m and fluorescein isothiocyanate (FITC), respectively. Then, ASON was combined with transfection reagent Lipofectamine 2000 and Xfect(TM), named Lipo-ASON and Xfect-ASON, respectively. After transfection, the labeled ASON was characterized in hNPCs-G3 and hRPE cells. Reverse transcription polymerase chain reaction (RT-PCR) and Western blotting were performed to assay the hTERT mRNA and protein levels after hNPCs-G3 cells were incubated with Lipo-ASON, Xfect-ASON, and naked ASON. In addition, Lipo-ASON, Xfect-ASON, and naked ASON were injected into tumor-bearing mice, and the biodistribution in vivo was performed. RESULTS The presence of two transfection reagents significantly increased intracellular uptake of radiolabeled ASON in both cell lines compared with naked ASON (p < 0.05). However, there was no significant difference in cellular uptake rates of Lipo-ASON and Xfect-ASON between hNPCs-G3 and hRPE cells. In comparison with naked ASON, the fluorescence intensity was strongly enhanced after binding to transfection reagents. Furthermore, the levels of hTERT mRNA and protein were significantly reduced in cells treated with Lipo-ASON and Xfect-ASON (p < 0.05), but naked ASON had no significant effect on hTERT expression level. The biodistribution study indicated that tumor radioactivity uptake of radiolabeled ASON for naked ASON, Lipo-ASON, and Xfect-ASON group was low and shown no significant difference in vivo. CONCLUSIONS Lipofectamine transfection and Xfect(TM) transfection were not effective delivery methods of ASON for antisense imaging.
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Affiliation(s)
- Chang-bin Liu
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China
| | - Jun-qing Xu
- Department Of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Bai-xuan Xu
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China
| | - Jin-ming Zhang
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China
| | - Ying-mao Chen
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China
| | - Rui-min Wang
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China
| | - Jia-he Tian
- Department of Nuclear Medicine, The Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, People's Republic of China.
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36
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St-Pierre G, Pal S, Østergaard ME, Zhou T, Yu J, Tanowitz M, Seth PP, Hanessian S. Synthesis and biological evaluation of sialyl-oligonucleotide conjugates targeting leukocyte B trans-membranal receptor CD22 as delivery agents for nucleic acid drugs. Bioorg Med Chem 2016; 24:2397-2409. [PMID: 27117693 DOI: 10.1016/j.bmc.2016.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/16/2016] [Accepted: 03/27/2016] [Indexed: 01/27/2023]
Abstract
Antisense oligonucleotides (ASOs) modified with ligands which target cell surface receptors have the potential to significantly improve potency in the target tissue. This has recently been demonstrated using triantennary N-acetyl d-galactosamine conjugated ASOs. CD22 is a cell surface receptor expressed exclusively on B cells thus presenting an attractive target for B cell specific delivery of drugs. Herein, we reported the synthesis of monovalent and trivalent ASO conjugates with biphenylcarbonyl (BPC) modified sialic acids and their study as ASO delivery agents into B cells. CD22 positive cells exhibited reduced potency when treated with ligand modified ASOs and mechanistic examination suggested reduced uptake into cells potentially as a result of sequestration of ASO by other cell-surface proteins.
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Affiliation(s)
- Gabrielle St-Pierre
- Department of Chemistry, Université de Montréal, PO Box 6128, Succ., Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Sudip Pal
- Department of Chemistry, Université de Montréal, PO Box 6128, Succ., Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Michael E Østergaard
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Tianyuan Zhou
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Jinghua Yu
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Michael Tanowitz
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Punit P Seth
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States.
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, PO Box 6128, Succ., Centre-ville, Montréal, Québec H3C 3J7, Canada.
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37
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Shemesh CS, Yu RZ, Gaus HJ, Seth PP, Swayze EE, Bennett FC, Geary RS, Henry SP, Wang Y. Pharmacokinetic and Pharmacodynamic Investigations of ION-353382, a Model Antisense Oligonucleotide: Using Alpha-2-Macroglobulin and Murinoglobulin Double-Knockout Mice. Nucleic Acid Ther 2016; 26:223-35. [PMID: 27031383 DOI: 10.1089/nat.2016.0607] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the pharmacokinetics (PKs) and pharmacodynamics (PDs) for ION-353382, an antisense oligonucleotide (ASO) targeting scavenger receptor class B type I (SRB1) mRNA, using alpha-2-macroglobulin (A2M), murinoglobulin double-knockout (DKO), and wild-type mice. Wild-type and DKO homozygous mice were administered a single subcutaneous injection of ION-353382 at 0, 5, 15, 30, and 60 mg/kg. Mice were sacrificed at 72 h with plasma and organs harvested. Both liquid chromatography-mass spectrometry (LC-MS) and enzyme-linked immunosorbent assay (ELISA) were used to determine ASO exposure with real-time PCR for SRB1 expression. Immunohistochemistry was evaluated to explore hepatic uptake of ASOs. The total plasma protein binding and profiling was assessed. Finally, two-dimensional gel electrophoresis identified protein expression differences. PK exposures were comparable between wild-type and DKO mice in plasma, liver, and kidney, yet a near twofold reduction in EC50 was revealed for DKO mice based on an inhibitory effect liver exposure response model. Total plasma protein binding and profiling revealed no major dissimilarities between both groups. Plasma proteome fingerprinting confirmed protein expression variations related to A2M. Histological examination revealed enhanced ASO distribution into hepatocytes and less nonparenchymal uptake for DKO mice compared to wild-type mice. Knocking out A2M showed improved PD activities without an effect on total plasma and tissue exposure kinetics. Binding to A2M could mediate ASOs to nonproductive compartments, and thus, decreased binding of ASOs to A2M could potentially improve ASO pharmacology.
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Affiliation(s)
- Colby S Shemesh
- 1 Department of Pharmacokinetics and Clinical Pharmacology, Ionis Pharmaceuticals , Carlsbad, California
| | - Rosie Z Yu
- 1 Department of Pharmacokinetics and Clinical Pharmacology, Ionis Pharmaceuticals , Carlsbad, California
| | - Hans J Gaus
- 2 Department of Structural Biology, Ionis Pharmaceuticals , Carlsbad, California
| | - Punit P Seth
- 3 Department of Medicinal Chemistry, Ionis Pharmaceuticals , Carlsbad, California
| | - Eric E Swayze
- 3 Department of Medicinal Chemistry, Ionis Pharmaceuticals , Carlsbad, California
| | - Frank C Bennett
- 4 Department of Research Biology, Ionis Pharmaceuticals , Carlsbad, California
| | - Richard S Geary
- 5 Department of Clinical Development, Ionis Pharmaceuticals , Carlsbad, California
| | - Scott P Henry
- 6 Department of Toxicology, Ionis Pharmaceuticals , Carlsbad, California
| | - Yanfeng Wang
- 1 Department of Pharmacokinetics and Clinical Pharmacology, Ionis Pharmaceuticals , Carlsbad, California
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38
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Protein Kinase C-α is a Critical Protein for Antisense Oligonucleotide-mediated Silencing in Mammalian Cells. Mol Ther 2016; 24:1117-1125. [PMID: 26961407 DOI: 10.1038/mt.2016.54] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/18/2016] [Indexed: 01/08/2023] Open
Abstract
We have identified the existence of a productive, PKC-α-dependent endocytotic silencing pathway that leads gymnotically-delivered locked nucleic acid (LNA)-gapmer phosphorothioate antisense oligonucleotides (ASOs) into late endosomes. By blocking the maturation of early endosomes to late endosomes, silencing the expression of PKC-α results in the potent reduction of ASO silencing ability in the cell. We have also demonstrated that silencing of gene expression in the cytoplasm is vitiated when PKC-α expression is reduced. Restoring PKC-α expression via a reconstitution experiment reinstates the ability of ASOs to silence. These results advance our understanding of intracellular ASO trafficking and activity following gymnotic delivery, and further demonstrate the existence of two distinct silencing pathways in mammalian cells, one in the cytoplasmic and the other in the nuclear compartment.
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Kremlitzka M, Mácsik-Valent B, Erdei A. Syk is indispensable for CpG-induced activation and differentiation of human B cells. Cell Mol Life Sci 2015; 72:2223-36. [PMID: 25543269 PMCID: PMC11113211 DOI: 10.1007/s00018-014-1806-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/21/2014] [Accepted: 12/15/2014] [Indexed: 12/11/2022]
Abstract
B cells are efficiently activated by CpG oligodeoxynucleotides (ODNs) to produce pro-inflammatory cytokines and antibody (Ab). Here, we describe a so far unidentified, spleen tyrosine kinase (Syk)-dependent pathway, which is indispensable for CpG-induced human B cell activation. We show that triggering of B cells by CpG results in Syk and src kinase phosphorylation, proliferation, as well as cytokine and Ab production independent of the BCR. Notably, all these functions are abrogated when Syk is inhibited. We demonstrate that CpG-induced Syk activation originates from the cell surface in a TLR9-dependent manner. While inhibition of Syk does not influence the uptake of CpG ODNs, activation of the kinase is a prerequisite for the delivery of CpG into TLR9-containing endolysosomes and for the CpG-induced up-regulation of TLR9 expression. Our results reveal an alternative, Syk-dependent pathway of CpG-induced B cell stimulation, which is initiated at the plasma membrane and seems to be an upstream requirement for endosomal TLR9-driven B cell proliferation and differentiation.
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Affiliation(s)
| | - Bernadett Mácsik-Valent
- Department of Immunology, Eötvös Loránd University, 1117 Budapest Pázmány s. 1/c, Budapest, Hungary
| | - Anna Erdei
- Department of Immunology, Eötvös Loránd University, 1117 Budapest Pázmány s. 1/c, Budapest, Hungary
- MTA-ELTE Immunology Research Group, Budapest, Hungary
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40
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Venuganti VVK, Saraswathy M, Dwivedi C, Kaushik RS, Perumal OP. Topical gene silencing by iontophoretic delivery of an antisense oligonucleotide-dendrimer nanocomplex: the proof of concept in a skin cancer mouse model. NANOSCALE 2015; 7:3903-3914. [PMID: 25436837 DOI: 10.1039/c4nr05241b] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The study was aimed at investigating the feasibility of using a poly (amidoamine) (PAMAM) dendrimer as a carrier for topical iontophoretic delivery of an antisense oligonucleotide (ASO). Bcl-2, an anti-apoptotic protein implicated in skin cancer, was used as the model target protein to demonstrate the topical gene silencing approach. Confocal laser scanning microscopy studies demonstrated that the iontophoretically delivered ASO-dendrimer complex can reach the viable epidermis in porcine skin. In contrast, passively delivered free or dendrimer complexed ASO was mainly localized to the stratum corneum. The cell uptake of ASO was significantly enhanced by the dendrimer complex and the complex suppressed Bcl-2 levels in the cell. In the skin cancer mouse model, the iontophoretically delivered ASO-dendrimer complex reduced the tumor volume by 45% and was consistent with the reduction in Bcl-2 protein levels. The iontophoretically delivered ASO-dendrimer complex caused significant apoptosis in skin tumor. Overall, the findings from this study demonstrate that dendrimers are promising nanocarriers for developing topical gene silencing approaches for skin diseases.
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Affiliation(s)
- Venkata Vamsi K Venuganti
- Department of Pharmaceutical Sciences, College of Pharmacy, South Dakota State University, Brookings, SD 57007, USA.
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41
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Liang XH, Sun H, Shen W, Crooke ST. Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages. Nucleic Acids Res 2015; 43:2927-45. [PMID: 25712094 PMCID: PMC4357732 DOI: 10.1093/nar/gkv143] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although the RNase H-dependent mechanism of inhibition of gene expression by chemically modified antisense oligonucleotides (ASOs) has been well characterized, little is known about the interactions between ASOs and intracellular proteins that may alter cellular localization and/or potency of ASOs. Here, we report the identification of 56 intracellular ASO-binding proteins using multi-step affinity selection approaches. Many of the tested proteins had no significant effect on ASO activity; however, some proteins, including La/SSB, NPM1, ANXA2, VARS and PC4, appeared to enhance ASO activities, likely through mechanisms related to subcellular distribution. VARS and ANXA2 co-localized with ASOs in endocytic organelles, and reduction in the level of VARS altered lysosome/ASO localization patterns, implying that these proteins may facilitate ASO release from the endocytic pathway. Depletion of La and NPM1 reduced nuclear ASO levels, suggesting potential roles in ASO nuclear accumulation. On the other hand, Ku70 and Ku80 proteins inhibited ASO activity, most likely by competition with RNase H1 for ASO/RNA duplex binding. Our results demonstrate that phosphorothioate-modified ASOs bind a set of cellular proteins that affect ASO activity via different mechanisms.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
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42
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Bryzgunova O, Laktionov P. Generation of blood circulating DNA: the sources, peculiarities of circulation and structure. ACTA ACUST UNITED AC 2015; 61:409-26. [DOI: 10.18097/pbmc20156104409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extracellular nucleic acids (exNA) were described in blood of both healthy and illness people as early as in 1948, but staied overlooked until middle 60-th. Starting from the beginning of new millennium and mainly in the last 5 years exNA are intensively studied. Main attention is directed to investigation of exNA as the source of diagnostic material whereas the mechanisms of their generation, as well as mechanisms to providing long-term circulation of exNA in the bloodstream are not established unambiguously. According to some authors, the main source of circulating nucleic acids in blood are the processes of apoptosis and necrosis, while others refer to the possible nucleic acid secretion by healthy and tumor cells. Circulating DNA were found to be stable in the blood for a long time, escaping from the action of DNA hydrolyzing enzymes and are apparently packed in different supramolecular complexes. This review presents the opinions of various authors and evidence in favor of all the theories describingappearance of extracellular DNA, the features of the circulation and structure of the extracellular DNA and factors affecting the time of DNA circulation in blood
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Affiliation(s)
- O.E. Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - P.P. Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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43
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Efficient Delivery of Therapeutic Agents by Using Targeted Albumin Nanoparticles. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 98:121-43. [DOI: 10.1016/bs.apcsb.2014.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Bryzgunova OE, Laktionov PP. Generation of blood circulating DNAs: Sources, features of struction and circulation. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s1990750814030020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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45
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Koch T, Shim I, Lindow M, Ørum H, Bohr HG. Quantum mechanical studies of DNA and LNA. Nucleic Acid Ther 2014; 24:139-48. [PMID: 24491259 DOI: 10.1089/nat.2013.0465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies of the electrostatic potentials were compared among model oligonucleotides, and it was observed that small structural modifications induce global changes in the molecular structure and surface potentials. Since ligand structure and electrostatic potential complementarity with a receptor is a determinant for the bonding pattern between molecules, minor chemical modifications may have profound changes in the interaction profiles of oligonucleotides, possibly leading to changes in pharmacological properties. The QM modeling data can be used to understand earlier observations of antisense oligonucleotide properties, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize the exhibited property diversity of oligonucleotides to produce improved antisense drugs.
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46
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Costa JA, Leal-Pinto E, Henderson SC, Zabel T, Hawkins ME, Hanss B. Use of a Pteridine Moiety to Track DNA Uptake in Cells. Pteridines 2014; 23:81-89. [PMID: 24465092 DOI: 10.1515/pteridines.2012.23.1.81] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fluorescence labeled oligonucleotides have a long history of being used to monitor nucleic acid transport and uptake. However, it is not known if the fluorescent moiety itself physically limits the number of pathways that can be used by the cell due to steric, hydrophobic, or other chemical characteristics. Here, we report a method for comparing the uptake kinetics of oligonucleotides labeled either with the fluorescent pteridine, 3-methyl-8-(2-deoxy-β-D-ribofuranosyl) isoxanthopterin (3MI), or the common fluorophore 5-carboxyfluorescein (5-FAM). We use a multiphoton microscopic technique to monitor nucleic acid uptake LLC-PK1, a pig renal tubular cell line that is known to have multiple uptake pathways. We find that the two fluorophores enter the cells at different rates, suggesting that choice of fluorescent moiety influences the uptake pathway used by a cell. Finally, we reconstituted an LLC-PK1 membrane channel that is selective for nucleic acids in planar lipid bilayers, and tested the ability of the labeled nucleic acids to permeate the channel. We find that 3MI, and not 5-FAM labeled oligonucleotides can traverse the plasma membrane through the channel. These results have implications for future studies aimed at delivering pteridine moieties to cells and for tracking nucleic acid transport into tissues.
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Affiliation(s)
- Justin A Costa
- Division of Nephrology, Department of Medicine, Mt. Sinai School of Medicine, New York, NY
| | - Edgar Leal-Pinto
- Department of Physiology and Biophysics, Virginia Commonwealth University Medical Center, Richmond, VA
| | - Scott C Henderson
- Department of Anatomy and Neurobiology, Virginia Commonwealth University Medical Center, Richmond, VA
| | | | - Mary E Hawkins
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD
| | - Basil Hanss
- Division of Nephrology, Department of Medicine, Mt. Sinai School of Medicine, New York, NY
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47
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Moseman AP, Moseman EA, Schworer S, Smirnova I, Volkova T, von Andrian U, Poltorak A. Mannose receptor 1 mediates cellular uptake and endosomal delivery of CpG-motif containing oligodeoxynucleotides. THE JOURNAL OF IMMUNOLOGY 2013; 191:5615-24. [PMID: 24184555 DOI: 10.4049/jimmunol.1301438] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recognition of microbial components is critical for activation of TLRs, subsequent innate immune signaling, and directing adaptive immune responses. The DNA sensor TLR9 traffics from the endoplasmic reticulum to endolysosomal compartments where it is cleaved by resident proteases to generate a competent receptor. Activation of TLR9 by CpG-motif containing oligodeoxynucleotides (CpG ODNs) is preceded by agonist endocytosis and delivery into the endolysosomes. The events that dictate this process remain largely unknown; furthermore, it is unclear whether the receptors involved in mediating uptake of exogenous DNA are conserved for both naturally derived pathogenic DNA and synthetic ODNs. In this study, we report that peritoneal macrophages from a wild-derived inbred mouse strain, MOLF/Ei, are hyporesponsive to CpG ODN but are fully responsive to bacterial DNA, thus implying that microbial recognition is not fully recapitulated by a synthetic analog. To identify the gene responsible for the CpG ODN defect, we have performed genome-wide linkage analysis. Using N2 backcross mice, we mapped the trait with high resolution to a single locus containing Mrc1 as the gene conferring the trait. We show that mannose receptor 1 (MRC1; CD206) is involved in CpG ODN uptake and trafficking in wild-derived MOLF/Ei peritoneal macrophages. Furthermore, we show that other strains of wild-derived mice also require MRC1 for CpG-induced cytokine responses. These findings reveal novel functions for MRC1 and demonstrate that wild-derived mice are important and indispensable model for understanding naturally occurring regulators of inflammatory responses in innate immune pathways.
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Affiliation(s)
- Annie Park Moseman
- Graduate Program in Immunology, Sackler School of Biomedical Sciences, Tufts University, Boston, MA 02111
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48
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Liu CH, Ren J, Liu CM, Liu PK. Intracellular gene transcription factor protein-guided MRI by DNA aptamers in vivo. FASEB J 2013; 28:464-73. [PMID: 24115049 DOI: 10.1096/fj.13-234229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The mechanisms by which transcription factor (TF) protein AP-1 modulates amphetamine's effects on gene transcription in living brains are unclear. We describe here the first part of our studies to investigate these mechanisms, specifically, our efforts to develop and validate aptamers containing the binding sequence of TF AP-1 (5ECdsAP1), in order to elucidate its mechanism of action in living brains. This AP-1-targeting aptamer, as well as a random sequence aptamer with no target (5ECdsRan) as a control, was partially phosphorothioate modified and tagged with superparamagnetic iron oxide nanoparticles (SPIONs), gold, or fluorescein isothiothianate contrast agent for imaging. Optical and transmission electron microscopy studies revealed that 5ECdsAP1 is taken up by endocytosis and is localized in the neuronal endoplasmic reticulum. The results of magnetic resonance imaging (MRI) with SPION-5ECdsAP1 revealed that neuronal AP-1 TF protein levels were elevated in neurons of live male C57black6 mice after amphetamine exposure; however, pretreatment with SCH23390, a dopaminergic receptor antagonist, suppressed this elevation. As studies in transgenic mice with neuronal dominant-negative A-FOS mutant protein, which has no binding affinity for the AP-1 sequence, showed a completely null MRI signal in the striatum, we can conclude that the MR signal reflects specific binding between the 5ECdsAP1 aptamer and endogenous AP-1 protein. Together, these data lend support to the application of 5ECdsAP1 aptamer for intracellular protein-guided imaging and modulation of gene transcription, which will thus allow investigation of the mechanisms of signal transduction in living brains.
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Affiliation(s)
- Christina H Liu
- 3Massachusetts General Hospital, CNY149 (2301) Thirteenth St., Charlestown, MA 02129, USA.
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49
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Leifer CA, Rose WA, Botelho F. Traditional biochemical assays for studying toll-like receptor 9. J Immunoassay Immunochem 2013; 34:1-15. [PMID: 23323977 DOI: 10.1080/15321819.2012.666222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Understanding the mechanistic basis of receptor activation and regulation can offer therapeutic targets for disease treatment. Evidence is emerging for a role of the normally foreign responsive Toll-like receptors (TLRs) in the development of autoimmunity through response to self-patterns. Regulatory mechanisms governing this class of receptors are poorly understood, and failures within this system likely contribute to development of autoimmunity. In this article, we review biochemical assays used to study one of the self-pattern responsive TLRs, TLR9, and suggest that these studies are critical for development of new targets for autoimmune therapies.
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Affiliation(s)
- Cynthia A Leifer
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
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50
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Liu CH, Yang J, Ren JQ, Liu CM, You Z, Liu PK. MRI reveals differential effects of amphetamine exposure on neuroglia in vivo. FASEB J 2012; 27:712-24. [PMID: 23150521 DOI: 10.1096/fj.12-220061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
How amphetamine affects the neuroglia in living brains is not well understood. In an effort to elucidate this effect, we investigated neuroglia in response to amphetamine exposure using antisense (AS) or sense (S) phosphorothioate-modified oligodeoxynucleotide (sODN) sequences that correspond to glial fibrillary acidic protein (GFAP) mRNA (AS-gfap or S-gfap, respectively) expression. The control is a random-sequence sODN (Ran). Using cyanine 5.5-superparamagnetic iron oxide nanoparticle (Cy5.5-SPION) labeling and fluorescent microscopy, we demonstrated that living neural progenitor cells (PC-12.1), as well as the cells in fresh brain slices and intact brains of male C57BL6 mice, exhibited universal uptake of all of the sODNs but rapidly excluded all sODN-Ran and most S-gfap. Moreover, transmission electron microscopy revealed electron-dense nanoparticles only in the neuroglia of normal or transgenic mice [B6;DBA-Tg(Fos-tTA, Fos-EGFP*)1MmayTg(tetO-lacZ,tTA*)1Mmay/J] that had been administered AS-gfap or Cy5.5-SPION-gfap. Subtraction R2* maps from mice with acute and chronic amphetamine exposure demonstrated, validated by postmortem immunohistochemistry, a reduction in striatal neuroglia, with gliogenesis in the subventricular zone and the somatosensory cortex in vivo. The sensitivity of our unique gene transcript targeted MRI was illustrated by a positive linear correlation (r(2)=1.0) between in vivo MRI signal changes and GFAP mRNA copy numbers determined by ex vivo quantitative RT-PCR. The study provides direct evidence for targeting neuroglia by antisense DNA-based SPION-gfap that enables in vivo MRI of inaccessible tissue with PCR sensitivity. The results enable us to conclude that amphetamine induces toxicity to neuroglia in vivo, which may cause remodeling or reconnectivity of neuroglia.
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Affiliation(s)
- Christina H Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
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