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Batistatou N, Kritzer JA. Comparing Cell Penetration of Biotherapeutics across Human Cell Lines. ACS Chem Biol 2024; 19:1351-1365. [PMID: 38836425 DOI: 10.1021/acschembio.4c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
A major obstacle in biotherapeutics development is maximizing cell penetration. Ideally, assays would allow for optimization of cell penetration in the cell type of interest early in the drug development process. However, few assays exist to compare cell penetration across different cell types independent of drug function. In this work, we applied the chloroalkane penetration assay (CAPA) in seven mammalian cell lines as well as primary cells. Careful controls were used to ensure that data could be compared across cell lines. We compared the nuclear penetration of several peptides and drug-like oligonucleotides and saw significant differences among the cell lines. To help explain these differences, we quantified the relative activities of endocytosis pathways in these cell lines and correlated them with the penetration data. Based on these results, we knocked down clathrin in a cell line with an efficient permeability profile and observed reduced penetration of peptides but not oligonucleotides. Finally, we used small-molecule endosomal escape enhancers and observed enhancement of cell penetration of some oligonucleotides, but only in some of the cell lines tested. CAPA data provide valuable points of comparison among different cell lines, including primary cells, for evaluating the cell penetration of various classes of peptides and oligonucleotides.
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Affiliation(s)
- Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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2
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Yadav K, Gnanakani SPE, Sahu KK, Veni Chikkula CK, Vaddi PS, Srilakshmi S, Yadav R, Sucheta, Dubey A, Minz S, Pradhan M. Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review. Int J Biol Macromol 2024; 274:133244. [PMID: 38901506 DOI: 10.1016/j.ijbiomac.2024.133244] [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: 01/10/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.
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Affiliation(s)
- Krishna Yadav
- Rungta College of Pharmaceutical Sciences and Research, Kohka, Bhilai 490024, India
| | - S Princely E Gnanakani
- Department of Pharmaceutical Biotechnology, Parul Institute of Pharmacy, Parul University, Post Limda, Ta.Waghodia - 391760, Dist. Vadodara, Gujarat, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh 281406, India
| | - C Krishna Veni Chikkula
- Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, USA
| | - Poorna Sai Vaddi
- Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, USA
| | - S Srilakshmi
- Gitam School of Pharmacy, Department of Pharmaceutical Chemistry, Gitams University, Vishakhapatnam, India
| | - Renu Yadav
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana 122103, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana 122103, India
| | - Akhilesh Dubey
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangaluru 575018, Karnataka, India
| | - Sunita Minz
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak (M.P.), India
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3
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Miyoshi M, Shimosato T, Takaya T. Myogenic Anti-Nucleolin Aptamer iSN04 Inhibits Proliferation and Promotes Differentiation of Vascular Smooth Muscle Cells. Biomolecules 2024; 14:709. [PMID: 38927112 PMCID: PMC11201766 DOI: 10.3390/biom14060709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
De-differentiation and subsequent increased proliferation and inflammation of vascular smooth muscle cells (VSMCs) is one of the mechanisms of atherogenesis. Maintaining VSMCs in a contractile differentiated state is therefore a promising therapeutic strategy for atherosclerosis. We have reported the 18-base myogenetic oligodeoxynucleotide, iSN04, which serves as an anti-nucleolin aptamer and promotes skeletal and myocardial differentiation. The present study investigated the effect of iSN04 on VSMCs because nucleolin has been reported to contribute to VSMC de-differentiation under pathophysiological conditions. Nucleolin is localized in the nucleoplasm and nucleoli of both rat and human VSMCs. iSN04 without a carrier was spontaneously incorporated into VSMCs, indicating that iSN04 would serve as an anti-nucleolin aptamer. iSN04 treatment decreased the ratio of 5-ethynyl-2'-deoxyuridine (EdU)-positive proliferating VSMCs and increased the expression of α-smooth muscle actin, a contractile marker of VSMCs. iSN04 also suppressed angiogenesis of mouse aortic rings ex vivo, which is a model of pathological angiogenesis involved in plaque formation, growth, and rupture. These results demonstrate that antagonizing nucleolin with iSN04 preserves VSMC differentiation, providing a nucleic acid drug candidate for the treatment of vascular disease.
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MESH Headings
- Nucleolin
- Animals
- RNA-Binding Proteins/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Aptamers, Nucleotide/pharmacology
- Cell Proliferation/drug effects
- Phosphoproteins/metabolism
- Cell Differentiation/drug effects
- Humans
- Rats
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/cytology
- Mice
- Cells, Cultured
- Oligodeoxyribonucleotides/pharmacology
- Male
- Rats, Sprague-Dawley
- Mice, Inbred C57BL
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Affiliation(s)
- Mana Miyoshi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
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4
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Khabir M, Blanchet M, Angelo L, Loucif H, van Grevenynghe J, Bukong TN, Labonté P. Exosomes as Conduits: Facilitating Hepatitis B Virus-Independent Hepatitis D Virus Transmission and Propagation in Hepatocytes. Viruses 2024; 16:825. [PMID: 38932118 PMCID: PMC11209184 DOI: 10.3390/v16060825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
A number of research studies, including ours, have spotlighted exosomes as critical facilitators of viral dissemination. While hepatitis B virus (HBV) transmission through exosomes has been studied, the focus on its satellite virus, the hepatitis delta virus (HDV), has been unexplored in this context. HDV, although being a defective virus, can replicate its genome autonomously within hepatocytes, independently of HBV. Investigations on Huh7 cells revealed an intriguing phenomenon: the HDV proteins, S-HDAg and L-HDAg, are transmitted between cells without a complete viral structure. Detailed analysis further revealed that the expression of these proteins not only bolstered exosome secretion but also ensured their enrichment within these vesicles. Our experimental approach utilized transfection of various plasmids to examine the role of HDV RNA and proteins in the process. One salient finding was the differential propagation of the HDV proteins S-HDAg and L-HDAg, suggesting intricate molecular mechanisms behind their transmission. Notably, the purity of our exosome preparations was monitored using markers such as TSG101 and CD81. Importantly, these exosomes were found to carry both HDV RNA and proteins, highlighting their role in HDV dissemination. This novel study underscores the role of exosomes in mediating the transmission of HDV components between hepatocytes independent of HBV. These revelations about the exosomal pathway of HDV transmission provide a foundation for the development of innovative therapeutic strategies against HDV infections.
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Affiliation(s)
| | | | | | | | | | | | - Patrick Labonté
- INRS–Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (M.K.); (M.B.); (L.A.); (H.L.); (J.v.G.); (T.N.B.)
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Umezawa K, Ikeda R, Sakamoto T, Enomoto Y, Nihashi Y, Shinji S, Shimosato T, Kagami H, Takaya T. Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation. BIOTECH 2024; 13:11. [PMID: 38804293 PMCID: PMC11130974 DOI: 10.3390/biotech13020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5'-TTG GGT GGG GAA-3'), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and a computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadruplex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs.
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Affiliation(s)
- Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Rena Ikeda
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi 275-0016, Japan;
| | - Yuya Enomoto
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Centoral 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan;
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
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6
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Baylot V, Le TK, Taïeb D, Rocchi P, Colleaux L. Between hope and reality: treatment of genetic diseases through nucleic acid-based drugs. Commun Biol 2024; 7:489. [PMID: 38653753 PMCID: PMC11039704 DOI: 10.1038/s42003-024-06121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Rare diseases (RD) affect a small number of people compared to the general population and are mostly genetic in origin. The first clinical signs often appear at birth or in childhood, and patients endure high levels of pain and progressive loss of autonomy frequently associated with short life expectancy. Until recently, the low prevalence of RD and the gatekeeping delay in their diagnosis have long hampered research. The era of nucleic acid (NA)-based therapies has revolutionized the landscape of RD treatment and new hopes arise with the perspectives of disease-modifying drugs development as some NA-based therapies are now entering the clinical stage. Herein, we review NA-based drugs that were approved and are currently under investigation for the treatment of RD. We also discuss the recent structural improvements of NA-based therapeutics and delivery system, which overcome the main limitations in their market expansion and the current approaches that are developed to address the endosomal escape issue. We finally open the discussion on the ethical and societal issues that raise this new technology in terms of regulatory approval and sustainability of production.
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Affiliation(s)
- Virginie Baylot
- Aix Marseille Univ, CNRS, CINAM, ERL INSERM U 1326, CERIMED, Marseille, France.
| | - Thi Khanh Le
- Aix Marseille Univ, CNRS, CINAM, ERL INSERM U 1326, CERIMED, Marseille, France
| | - David Taïeb
- Aix Marseille Univ, CNRS, CINAM, ERL INSERM U 1326, CERIMED, Marseille, France
| | - Palma Rocchi
- Aix Marseille Univ, CNRS, CINAM, ERL INSERM U 1326, CERIMED, Marseille, France.
| | - Laurence Colleaux
- Aix Marseille Univ, CNRS, CINAM, ERL INSERM U 1326, CERIMED, Marseille, France
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7
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Mallette TL, Lidke DS, Lakin MR. Heterochiral modifications enhance robustness and function of DNA in living human cells. Chembiochem 2024; 25:e202300755. [PMID: 38228506 PMCID: PMC10923132 DOI: 10.1002/cbic.202300755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Oligonucleotide therapeutics are becoming increasingly important as more are approved by the FDA, both for treatment and vaccination. Similarly, dynamic DNA nanotechnology is a promising technique that can be used to sense exogenous input molecules or endogenous biomarkers and integrate the results of multiple sensing reactions in situ via a programmed cascade of reactions. The combination of these two technologies could be highly impactful in biomedicine by enabling smart oligonucleotide therapeutics that can autonomously sense and respond to a disease state. A particular challenge, however, is the limited lifetime of standard nucleic acid components in living cells and organisms due to degradation by endogenous nucleases. In this work, we address this challenge by incorporating mirror-image, ʟ-DNA nucleotides to produce heterochiral "gapmers". We use dynamic DNA nanotechnology to show that these modifications keep the oligonucleotide intact in living human cells for longer than an unmodified strand. To this end, we used a sequential transfection protocol for delivering multiple nucleic acids into living human cells while providing enhanced confidence that subsequent interactions are actually occurring within the cells. Taken together, this work advances the state of the art of ʟ-nucleic acid protection of oligonucleotides and DNA circuitry for applications in vivo.
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Affiliation(s)
- Tracy L Mallette
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| | - Diane S Lidke
- Department of Pathology and Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, 87131, USA
| | - Matthew R Lakin
- Department of Computer Science, Department of Chemical & Biological Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
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8
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Martins ASG, Reis SD, Benson E, Domingues MM, Cortinhas J, Vidal Silva JA, Santos SD, Santos NC, Pêgo AP, Moreno PMD. Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2309140. [PMID: 38342712 DOI: 10.1002/smll.202309140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/22/2023] [Indexed: 02/13/2024]
Abstract
The successful translation of therapeutic nucleic acids (NAs) for the treatment of neurological disorders depends on their safe and efficient delivery to neural cells, in particular neurons. DNA nanostructures can be a promising NAs delivery vehicle. Nonetheless, the potential of DNA nanostructures for neuronal cell delivery of therapeutic NAs is unexplored. Here, tetrahedral DNA nanostructures (TDN) as siRNA delivery scaffolds to neuronal cells, exploring the influence of functionalization with two different reported neuronal targeting ligands: C4-3 RNA aptamer and Tet1 peptide are investigated. Nanostructures are characterized in vitro, as well as in silico using molecular dynamic simulations to better understand the overall TDN structural stability. Enhancement of neuronal cell uptake of TDN functionalized with the C4-3 Aptamer (TDN-Apt), not only in neuronal cell lines but also in primary neuronal cell cultures is demonstrated. Additionally, TDN and TDN-Apt nanostructures carrying siRNA are shown to promote silencing in a process aided by chloroquine-induced endosomal disruption. This work presents a thorough workflow for the structural and functional characterization of the proposed TDN as a nano-scaffold for neuronal delivery of therapeutic NAs and for targeting ligands evaluation, contributing to the future development of new neuronal drug delivery systems based on DNA nanostructures.
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Affiliation(s)
- Ana S G Martins
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, s/n, Porto, 4200-465, Portugal
| | - Sara D Reis
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Erik Benson
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Tomtebodavägen 23, Solna, 171 65, Sweden
| | - Marco M Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - João Cortinhas
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Joana A Vidal Silva
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Sofia D Santos
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - Ana P Pêgo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto, 4050-313, Portugal
| | - Pedro M D Moreno
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
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Bogen O, Araldi D, Sucher A, Kober K, Ohara PT, Levine JD. Isolectin B4 (IB4)-conjugated streptavidin for the selective knockdown of proteins in IB4-positive (+) nociceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572242. [PMID: 38260446 PMCID: PMC10802253 DOI: 10.1101/2023.12.18.572242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In vivo analysis of protein function in nociceptor subpopulations using antisense oligonucleotides and short interfering RNAs is limited by their non-selective cellular uptake. To address the need for selective transfection methods, we covalently linked isolectin B4 (IB4) to streptavidin and analyzed whether it could be used to study protein function in IB4(+)-nociceptors. Rats treated intrathecally with IB4-conjugated streptavidin complexed with biotinylated antisense oligonucleotides for protein kinase C epsilon (PKCε) mRNA were found to have: a) less PKCε in dorsal root ganglia (DRG), b) reduced PKCε expression in IB4(+) but not IB4(-) DRG neurons, and c) fewer transcripts of the PKCε gene in the DRG. This knockdown in PKCε expression in IB4(+) DRG neurons is sufficient to reverse hyperalgesic priming, a rodent model of chronic pain that is dependent on PKCε in IB4(+)-nociceptors. These results establish that IB4-streptavidin can be used to study protein function in a defined subpopulation of nociceptive C-fiber afferents.
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10
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Bogen O, Araldi D, Sucher A, Kober K, Ohara PT, Levine JD. Isolectin B4 (IB4)-conjugated streptavidin for the selective knockdown of proteins in IB4-positive (+) nociceptors. Mol Pain 2024; 20:17448069241230419. [PMID: 38246917 PMCID: PMC10851726 DOI: 10.1177/17448069241230419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
In vivo analysis of protein function in nociceptor subpopulations using antisense oligonucleotides and short interfering RNAs is limited by their non-selective cellular uptake. To address the need for selective transfection methods, we covalently linked isolectin B4 (IB4) to streptavidin and analyzed whether it could be used to study protein function in IB4(+)-nociceptors. Rats treated intrathecally with IB4-conjugated streptavidin complexed with biotinylated antisense oligonucleotides for protein kinase C epsilon (PKCε) mRNA were found to have: (a) less PKCε in dorsal root ganglia (DRG), (b) reduced PKCε expression in IB4(+) but not IB4(-) DRG neurons, and (c) fewer transcripts of the PKCε gene in the DRG. This knockdown in PKCε expression in IB4(+) DRG neurons is sufficient to reverse hyperalgesic priming, a rodent model of chronic pain that is dependent on PKCε in IB4(+)-nociceptors. These results establish that IB4-streptavidin can be used to study protein function in a defined subpopulation of nociceptive C-fiber afferents.
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Affiliation(s)
- Oliver Bogen
- Department of Oral & Maxillofacial Surgery, UCSF Pain and Addiction Research Center, University of California, San Francisco, CA, USA
| | - Dionéia Araldi
- Department of Oral & Maxillofacial Surgery, UCSF Pain and Addiction Research Center, University of California, San Francisco, CA, USA
| | - Anatol Sucher
- School of Nursing, University of California, San Francisco, CA, USA
| | - Kord Kober
- School of Nursing, University of California, San Francisco, CA, USA
| | - Peter T Ohara
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Jon D Levine
- Department of Oral & Maxillofacial Surgery, UCSF Pain and Addiction Research Center, University of California, San Francisco, CA, USA
- Division of Neuroscience, Department of Medicine, University of California, San Francisco, CA, USA
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11
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Jadhav SG, Setten RL, Medina C, Cui XS, Dowdy SF. Design, Synthesis, and Biochemical Analysis of a Molecule Designed to Enhance Endosomal Escape. AAPS J 2023; 26:10. [PMID: 38133698 DOI: 10.1208/s12248-023-00876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
RNA therapeutics, including siRNAs, ASOs, and PMOs, have great potential to treat human disease. However, RNA therapeutics are too large, too charged, and/or too hydrophilic to cross the cellular membrane and are instead taken up into cells by endocytosis. Unfortunately, the vast majority of RNA therapeutics remain trapped inside endosomes (≥ 99%), which is the sole reason preventing their use to treat cancer, COVID, and other diseases. In contrast, enveloped viruses, such as influenza, also have an endosomal escape problem, but have evolved a highly efficient endosomal escape mechanism using trimeric hemagglutinin (HA) fusogenic protein. HA contains an outer hydrophilic domain (HA1) that masks an inner hydrophobic fusogenic/endosomal escape domain (HA2). Once inside endosomes, HA1 is shed to expose HA2 that, due to hydrophobicity, buries itself into the endosomal lipid bilayer, driving escape into the cytoplasm in a non-toxic fashion. To begin to address the RNA therapeutics rate-limiting endosomal escape problem, we report here a first step in the design and synthesis of a universal endosomal escape domain (uEED) that biomimics the enveloped virus escape mechanism. uEED contains an outer hydrophilic mask covalently attached to an inner hydrophobic escape domain. In plasma, uEED is inert and highly metabolically stable; however, when placed in endo/lysosomal conditions, uEED is activated by enzymatic removal of the hydrophilic mask, followed by self-immolation of the linker resulting in exposure of the hydrophobic indole ring domain in the absence of any hydrophilic tags. Thus, uEED is a synthetic biomimetic of the highly efficient viral endosomal escape mechanism.
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Affiliation(s)
- Satish G Jadhav
- Department of Cellular & Molecular Medicine, UCSD School of Medicine, 9500 Gilman Dr, MC0686, La Jolla, California, 92093-0686, USA
- Ionis Pharmaceuticals, Carlsbad, California, 92008, USA
| | - Ryan L Setten
- Department of Cellular & Molecular Medicine, UCSD School of Medicine, 9500 Gilman Dr, MC0686, La Jolla, California, 92093-0686, USA
- , San Diego, California, USA
| | - Carlos Medina
- Department of Cellular & Molecular Medicine, UCSD School of Medicine, 9500 Gilman Dr, MC0686, La Jolla, California, 92093-0686, USA
- Genedit, South San Francisco, California, USA
| | - Xian-Shu Cui
- Department of Cellular & Molecular Medicine, UCSD School of Medicine, 9500 Gilman Dr, MC0686, La Jolla, California, 92093-0686, USA
| | - Steven F Dowdy
- Department of Cellular & Molecular Medicine, UCSD School of Medicine, 9500 Gilman Dr, MC0686, La Jolla, California, 92093-0686, USA.
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12
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González-Martínez I, Cerro-Herreros E, Moreno N, García-Rey A, Espinosa-Espinosa J, Carrascosa-Sàez M, Piqueras-Losilla D, Arzumanov A, Seoane-Miraz D, Jad Y, Raz R, Wood MJ, Varela MA, Llamusí B, Artero R. Peptide-conjugated antimiRs improve myotonic dystrophy type 1 phenotypes by promoting endogenous MBNL1 expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102024. [PMID: 37744174 PMCID: PMC10514136 DOI: 10.1016/j.omtn.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by a CTG repeat expansion in the DMPK gene that generates toxic RNA with a myriad of downstream alterations in RNA metabolism. A key consequence is the sequestration of alternative splicing regulatory proteins MBNL1/2 by expanded transcripts in the affected tissues. MBNL1/2 depletion interferes with a developmental alternative splicing switch that causes the expression of fetal isoforms in adults. Boosting the endogenous expression of MBNL proteins by inhibiting the natural translational repressors miR-23b and miR-218 has previously been shown to be a promising therapeutic approach. We designed antimiRs against both miRNAs with a phosphorodiamidate morpholino oligonucleotide (PMO) chemistry conjugated to cell-penetrating peptides (CPPs) to improve delivery to affected tissues. In DM1 cells, CPP-PMOs significantly increased MBNL1 levels. In some candidates, this was achieved using concentrations less than two orders of magnitude below the median toxic concentration, with up to 5.38-fold better therapeutic window than previous antagomiRs. In HSALR mice, intravenous injections of CPP-PMOs improve molecular, histopathological, and functional phenotypes, without signs of toxicity. Our findings place CPP-PMOs as promising antimiR candidates to overcome the treatment delivery challenge in DM1 therapy.
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Affiliation(s)
- Irene González-Martínez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Estefanía Cerro-Herreros
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Nerea Moreno
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Andrea García-Rey
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
- Group of Emerging and Neglected Diseases, Ecoepidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito 170521, Ecuador
| | - Marc Carrascosa-Sàez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Diego Piqueras-Losilla
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Andrey Arzumanov
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - David Seoane-Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Yahya Jad
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Richard Raz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Matthew J. Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Miguel A. Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Beatriz Llamusí
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
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13
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Gao X, Diep JK, Norris DA, Yu RZ, Geary RS. Predicting the pharmacokinetics and pharmacodynamics of antisense oligonucleotides: an overview of various approaches and opportunities for PBPK/PD modelling. Expert Opin Drug Metab Toxicol 2023; 19:979-990. [PMID: 37970635 DOI: 10.1080/17425255.2023.2283524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
INTRODUCTION Advances in research and development (R&D) have enabled many approvals of antisense oligonucleotides (ASOs). Its administration expanded from systemic to local for treating various diseases, where predicting target tissue exposures and pharmacokinetics (PK) and pharmacodynamics (PD) in human can be critical. AREAS COVERED A literature search for PBPK/PD models of ASOs was conducted using PubMed and Embase (to 1 April 2023). ASO PK and PD in animals and humans and modeling approaches including physiologically based (PB) are summarized; and relevance and impacts of PBPK/PD modeling are assessed. EXPERT OPINION Allometric scaling and compartmental PK/PD modeling have been successful to predict human ASO PK/PD, addressing most R&D needs. Understanding tissue distribution of ASOs can be crucial for their efficacy and safety especially for intrathecal (IT), pulmonary, or other local routes. PBPK/PD modeling is expected to improve such understanding, for which, efforts have been sporadic. However, developing a PBPK/PD model requires careful review of known biology/pharmacology and thoughtful experimental designs. Resulting models have the potential to predict target/specified tissue exposures and responses in human adults and pediatrics. Ultimately, a PBPK/PD modeling approach can lead to more efficient and rational clinical development, resulting in well-informed decision making and a shortened timeline.
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Affiliation(s)
- Xiang Gao
- Preclinical Development, Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - John K Diep
- Preclinical Development, Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - Daniel A Norris
- Preclinical Development, Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - Rosie Z Yu
- Preclinical Development, Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - Richard S Geary
- Preclinical Development, Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
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14
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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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15
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Ozeri-Galai E, Friedman L, Barchad-Avitzur O, Markovetz MR, Boone W, Rouillard KR, Stampfer CD, Oren YS, Hill DB, Kerem B, Hart G. Delivery Characterization of SPL84 Inhaled Antisense Oligonucleotide Drug for 3849 + 10 kb C- > T Cystic Fibrosis Patients. Nucleic Acid Ther 2023; 33:306-318. [PMID: 37643307 DOI: 10.1089/nat.2023.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Recent advances in the therapeutic potential of RNA-related treatments, specifically for antisense oligonucleotide (ASO)-based drugs, have led to increased numbers of ASO regulatory approvals. In this study, we focus on SPL84, an inhaled ASO-based drug, developed for the treatment of the pulmonary disease cystic fibrosis (CF). Pulmonary drug delivery is challenging, due to a variety of biological, physical, chemical, and structural barriers, especially when targeting the cell nucleus. The distribution of SPL84 throughout the lungs, penetration into the epithelial cells and nucleus, and structural stability are critical parameters that will impact drug efficacy in a clinical setting. In this study, we demonstrate broad distribution, as well as cell and nucleus penetration of SPL84 in mouse and monkey lungs. In vivo and in vitro studies confirmed the stability of our inhaled drug in CF patient-derived mucus and in lung lysosomal extracts. The mobility of SPL84 through hyperconcentrated mucus was also demonstrated. Our results, supported by a promising preclinical pharmacological effect of full restoration of cystic fibrosis transmembrane conductance regulator channel activity, emphasize the high potential of SPL84 as an effective drug for the treatment of CF patients. In addition, successfully tackling the lung distribution of SPL84 offers immense opportunities for further development of SpliSense's inhaled ASO-based drugs for unmet needs in pulmonary diseases.
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Affiliation(s)
| | - Lital Friedman
- SpliSense, Biohouse Labs, Haddasah Ein Kerem, Jerusalem, Israel
| | | | | | - William Boone
- Marsico Lung Institute, UNC Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Yifat S Oren
- SpliSense, Biohouse Labs, Haddasah Ein Kerem, Jerusalem, Israel
| | - David B Hill
- Marsico Lung Institute, UNC Chapel Hill, Chapel Hill, North Carolina, USA
- Joint Department of Biomedical Engineering, UNC Chapel Hill, Chapel Hill, North Carolina, USA
| | - Batsheva Kerem
- SpliSense, Biohouse Labs, Haddasah Ein Kerem, Jerusalem, Israel
- Department of Genetics, The Hebrew University, Jerusalem, Israel
| | - Gili Hart
- SpliSense, Biohouse Labs, Haddasah Ein Kerem, Jerusalem, Israel
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16
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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17
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Roca Suarez AA, Batbold E, Bartosch B, Dashdorj N, Testoni B, Zoulim F. Emerging anti-HDV drugs and HBV cure strategies with anti-HDV activity. Liver Int 2023; 43 Suppl 1:87-95. [PMID: 37017060 DOI: 10.1111/liv.15417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 04/06/2023]
Abstract
Hepatitis delta virus (HDV) is a satellite RNA virus that requires the presence of hepatitis B virus (HBV) for its replication. HDV/HBV co-infection is often associated with a faster disease progression of chronic hepatitis in comparison to HBV mono-infection. Therefore, the development of novel antiviral therapies targeting HDV represents a high priority and an urgent medical need. In this review, we summarize the ongoing efforts to evaluate promising HDV-specific drugs, such as lonafarnib (LNF), pegylated interferon lambda (PEG-IFN-λ) and their use as a combination therapy. Furthermore, we review the most recent developments in the area of anti-HBV drugs with potential effects against HDV, including therapeutic agents targeting hepatitis B surface antigen (HBsAg) expression, secretion and function. Finally, we consider the important insights that have emerged from the development of these potential antiviral strategies, as well as the intriguing questions that remain to be elucidated in this rapidly changing field.
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Affiliation(s)
- Armando A Roca Suarez
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | | | - Birke Bartosch
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | | | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
- Hospices Civils de Lyon (HCL), Lyon, France
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18
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Dowdy SF. Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem? RNA (NEW YORK, N.Y.) 2023; 29:396-401. [PMID: 36669888 PMCID: PMC10019367 DOI: 10.1261/rna.079507.122] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/09/2023] [Indexed: 05/15/2023]
Abstract
With over 15 FDA approved drugs on the market and numerous ongoing clinical trials, RNA therapeutics, such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs), have shown great potential to treat human disease. Their mechanism of action is based entirely on the sequence of validated disease-causing genes without the prerequisite knowledge of protein structure, activity or cellular location. In contrast to small molecule therapeutics that passively diffuse across the cell membrane's lipid bilayer, RNA therapeutics are too large, too charged, and/or too hydrophilic to passively diffuse across the cellular membrane and instead are taken up into cells by endocytosis. However, endosomes are also composed of a lipid bilayer barrier that results in endosomal capture and retention of 99% of RNA therapeutics with 1% or less entering the cytoplasm. Although this very low level of endosomal escape has proven sufficient for liver and some CNS disorders, it is insufficient for the vast majority of extra-hepatic diseases. Unfortunately, there are currently no acceptable solutions to the endosomal escape problem. Consequently, before RNA therapeutics can be used to treat widespread human disease, the rate-limiting delivery problem of endosomal escape must be solved in a nontoxic manner.
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Affiliation(s)
- Steven F Dowdy
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, USA
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19
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Finicle B, Eckenstein K, Revenko A, Anderson B, Wan W, McCracken A, Gil D, Fruman D, Hanessian S, Seth P, Edinger A. Simultaneous inhibition of endocytic recycling and lysosomal fusion sensitizes cells and tissues to oligonucleotide therapeutics. Nucleic Acids Res 2023; 51:1583-1599. [PMID: 36727438 PMCID: PMC9976930 DOI: 10.1093/nar/gkad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Inefficient endosomal escape remains the primary barrier to the broad application of oligonucleotide therapeutics. Liver uptake after systemic administration is sufficiently robust that a therapeutic effect can be achieved but targeting extrahepatic tissues remains challenging. Prior attempts to improve oligonucleotide activity using small molecules that increase the leakiness of endosomes have failed due to unacceptable toxicity. Here, we show that the well-tolerated and orally bioavailable synthetic sphingolipid analog, SH-BC-893, increases the activity of antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) up to 200-fold in vitro without permeabilizing endosomes. SH-BC-893 treatment trapped endocytosed oligonucleotides within extra-lysosomal compartments thought to be more permeable due to frequent membrane fission and fusion events. Simultaneous disruption of ARF6-dependent endocytic recycling and PIKfyve-dependent lysosomal fusion was necessary and sufficient for SH-BC-893 to increase non-lysosomal oligonucleotide levels and enhance their activity. In mice, oral administration of SH-BC-893 increased ASO potency in the liver by 15-fold without toxicity. More importantly, SH-BC-893 enabled target RNA knockdown in the CNS and lungs of mice treated subcutaneously with cholesterol-functionalized duplexed oligonucleotides or unmodified ASOs, respectively. Together, these results establish the feasibility of using a small molecule that disrupts endolysosomal trafficking to improve the activity of oligonucleotides in extrahepatic tissues.
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Affiliation(s)
- Brendan T Finicle
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Kazumi H Eckenstein
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | | | | | - W Brad Wan
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | | | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | | | - Aimee L Edinger
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
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20
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Oligonucleotide Enhancing Compound Increases Tricyclo-DNA Mediated Exon-Skipping Efficacy in the Mdx Mouse Model. Cells 2023; 12:cells12050702. [PMID: 36899837 PMCID: PMC10001065 DOI: 10.3390/cells12050702] [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: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Nucleic acid-based therapeutics hold great promise for the treatment of numerous diseases, including neuromuscular disorders, such as Duchenne muscular dystrophy (DMD). Some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA for DMD, but the potential of this therapy is still limited by several challenges, including the poor distribution of ASOs to target tissues, but also the entrapment of ASO in the endosomal compartment. Endosomal escape is a well recognized limitation that prevents ASO from reaching their target pre-mRNA in the nucleus. Small molecules named oligonucleotide-enhancing compounds (OEC) have been shown to release ASO from endosomal entrapment, thus increasing ASO nuclear concentration and ultimately correcting more pre-mRNA targets. In this study, we evaluated the impact of a therapy combining ASO and OEC on dystrophin restoration in mdx mice. Analysis of exon-skipping levels at different time points after the co-treatment revealed improved efficacy, particularly at early time points, reaching up to 4.4-fold increase at 72 h post treatment in the heart compared to treatment with ASO alone. Significantly higher levels of dystrophin restoration were detected two weeks after the end of the combined therapy, reaching up to 2.7-fold increase in the heart compared to mice treated with ASO alone. Moreover, we demonstrated a normalization of cardiac function in mdx mice after a 12-week-long treatment with the combined ASO + OEC therapy. Altogether, these findings indicate that compounds facilitating endosomal escape can significantly improve the therapeutic potential of exon-skipping approaches offering promising perspectives for the treatment of DMD.
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21
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Zhao JC, Saleh A, Crooke ST. SIDT2 Inhibits Phosphorothioate Antisense Oligonucleotide Activity by Regulating Cellular Localization of Lysosomes. Nucleic Acid Ther 2022; 33:108-116. [PMID: 36576400 DOI: 10.1089/nat.2022.0055] [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: 12/29/2022] Open
Abstract
Phosphorothioate (PS)-modified antisense oligonucleotide (ASO) drugs enter cells through endocytic pathways where a majority are entrapped within membrane-bound endosomes and lysosomes, representing a limiting step for antisense activity. While late endosomes have been identified as a major site for productive PS-ASO release, how lysosomes regulate PS-ASO activity beyond macromolecule degradation remains not fully understood. In this study, we reported that SID1 transmembrane family, member 2 (SIDT2), a lysosome transmembrane protein, can robustly regulate PS-ASO activity. We showed that SIDT2 is required for the proper colocalization between PS-ASO and lysosomes, suggesting an important role of SIDT2 in the entrapment of PS-ASOs in lysosomes. Mechanistically, we revealed that SIDT2 regulates lysosome cellular location. Lysosome location is largely determined by its movement along microtubules. Interestingly, we also observed an enrichment of proteins involved in microtubule function among SIDT2-binding proteins, suggesting that SIDT2 regulates lysosome location via its interaction with microtubule-related proteins. Overall, our data suggest that lysosome protein SIDT2 inhibits PS-ASO activity potentially through its interaction with microtubule-related proteins to place lysosomes at perinuclear regions, thus, facilitating PS-ASO's localization to lysosomes for degradation.
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Affiliation(s)
- Jing Crystal Zhao
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Aurian Saleh
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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22
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Zhang L, Liang Y, Liang G, Tian Z, Zhang Y, Liu Z, Ji X. The therapeutic prospects of N-acetylgalactosamine-siRNA conjugates. Front Pharmacol 2022; 13:1090237. [PMID: 36588695 PMCID: PMC9794871 DOI: 10.3389/fphar.2022.1090237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
RNA interference has become increasingly used for genetic therapy following the rapid development of oligonucleotide drugs. Significant progress has been made in its delivery system and implementation in the treatment of target organs. After a brief introduction of RNA interference technology and siRNA, the efficiency and stability of GalNAc-siRNA conjugates are highlighted since several oligonucleotide drugs of GalNAc have been approved for clinical use in recent years. The structure and features of GalNAc-siRNA conjugates are studied and the clinical efficiency and limitations of oligonucleotide-based drugs are summarized and investigated. Furthermore, another delivery system, lipid nanoparticles, that confer many advantages, is concluded, includ-ing stability and mass production, compared with GalNAc-siRNA conjugates. Importantly, developing new approaches for the use of oligonucleotide drugs brings hope to genetic therapy.
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Affiliation(s)
- Lei Zhang
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yayu Liang
- School of Stomatology, Henan University, Kaifeng, China
| | - Guohui Liang
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Zhili Tian
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Yue Zhang
- Department of Obstetrics and Gynecology, Zhengzhou, China
| | - Zhihui Liu
- Department of General Practice, Henan Provincial People’s Hospital, Zhengzhou University, Zhengzhou, China,*Correspondence: Zhihui Liu, ; Xinying Ji,
| | - Xinying Ji
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China,*Correspondence: Zhihui Liu, ; Xinying Ji,
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23
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Shah AM, Giacca M. Small non-coding RNA therapeutics for cardiovascular disease. Eur Heart J 2022; 43:4548-4561. [PMID: 36106499 PMCID: PMC9659475 DOI: 10.1093/eurheartj/ehac463] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/07/2023] Open
Abstract
Novel bio-therapeutic agents that harness the properties of small, non-coding nucleic acids hold great promise for clinical applications. These include antisense oligonucleotides that inhibit messenger RNAs, microRNAs (miRNAs), or long non-coding RNAs; positive effectors of the miRNA pathway (short interfering RNAs and miRNA mimics); or small RNAs that target proteins (i.e. aptamers). These new therapies also offer exciting opportunities for cardiovascular diseases and promise to move the field towards more precise approaches based on disease mechanisms. There have been substantial advances in developing chemical modifications to improve the in vivo pharmacological properties of antisense oligonucleotides and reduce their immunogenicity. Carrier methods (e.g. RNA conjugates, polymers, and lipoplexes) that enhance cellular uptake of RNA therapeutics and stability against degradation by intracellular nucleases are also transforming the field. A number of small non-coding RNA therapies for cardiovascular indications are now approved. Moreover, there is a large pipeline of therapies in clinical development and an even larger list of putative therapies emerging from pre-clinical studies. Progress in this area is reviewed herein along with the hurdles that need to be overcome to allow a broader clinical translation.
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Affiliation(s)
- Ajay M Shah
- King’s College London, British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Mauro Giacca
- King’s College London, British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
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24
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Shetty K, Yasaswi S, Dutt S, Yadav KS. Multifunctional nanocarriers for delivering siRNA and miRNA in glioblastoma therapy: advances in nanobiotechnology-based cancer therapy. 3 Biotech 2022; 12:301. [PMID: 36276454 PMCID: PMC9525514 DOI: 10.1007/s13205-022-03365-2] [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: 03/08/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most lethal cancer due to poor diagnosis and rapid resistance developed towards the drug. Genes associated to cancer-related overexpression of proteins, enzymes, and receptors can be suppressed using an RNA silencing technique. This assists in obtaining tumour targetability, resulting in less harm caused to the surrounding healthy cells. RNA interference (RNAi) has scientific basis for providing potential therapeutic applications in improving GBM treatment. However, the therapeutic application of RNAi is challenging due to its poor permeability across blood-brain barrier (BBB). Nanobiotechnology has evolved the use of nanocarriers such as liposomes, polymeric nanoparticles, gold nanoparticles, dendrimers, quantum dots and other nanostructures in encasing the RNAi entities like siRNA and miRNA. The review highlights the role of these carriers in encasing siRNA and miRNA and promising therapy in delivering them to the glioma cells.
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Affiliation(s)
- Karishma Shetty
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM’S NMIMS (Deemed to be University), Mumbai, India
| | - Soma Yasaswi
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM’S NMIMS (Deemed to be University), Mumbai, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085 India
| | - Khushwant S. Yadav
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM’S NMIMS (Deemed to be University), Mumbai, India
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25
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Nohira N, Shinji S, Nakamura S, Nihashi Y, Shimosato T, Takaya T. Myogenetic Oligodeoxynucleotides as Anti-Nucleolin Aptamers Inhibit the Growth of Embryonal Rhabdomyosarcoma Cells. Biomedicines 2022; 10:2691. [PMID: 36359210 PMCID: PMC9687923 DOI: 10.3390/biomedicines10112691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Embryonal rhabdomyosarcoma (ERMS) is the muscle-derived tumor retaining myogenic ability. iSN04 and AS1411, which are myogenetic oligodeoxynucleotides (myoDNs) serving as anti-nucleolin aptamers, have been reported to inhibit the proliferation and induce the differentiation of myoblasts. The present study investigated the effects of iSN04 and AS1411 in vitro on the growth of multiple patient-derived ERMS cell lines, ERMS1, KYM1, and RD. RT-PCR and immunostaining revealed that nucleolin was abundantly expressed and localized in nucleoplasm and nucleoli in all ERMS cell lines, similar to myoblasts. Both iSN04 and AS1411 at final concentrations of 10-30 μM significantly decreased the number of all ERMS cells; however, their optimal conditions were different among the cell lines. In all ERMS cell lines, iSN04 at a final concentration of 10 μM markedly reduced the ratio of EdU+ cells, indicating the inhibition of cell proliferation. Quantitative RT-PCR or immunostaining of phosphorylated histone H3 and myosin heavy chain demonstrated that iSN04 suppressed the cell cycle and partially promoted myogenesis but did not induce apoptosis in ERMS cells. Finally, both iSN04 and AS1411 at final concentrations of 10-30 μM disrupted the formation and outgrowth of RD tumorspheres in three-dimensional culture mimicking in vivo tumorigenesis. In conclusion, ERMS cells expressed nucleolin, and their growth was inhibited by the anti-nucleolin aptamers, iSN04 and AS1411, which modulates several cell cycle-related and myogenic gene expression. The present study provides evidence that anti-nucleolin aptamers can be used as nucleic acid drugs for chemotherapy against ERMS.
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Affiliation(s)
- Naoki Nohira
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Shunichi Nakamura
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
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26
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Dowdy SF, Setten RL, Cui XS, Jadhav SG. Delivery of RNA Therapeutics: The Great Endosomal Escape! Nucleic Acid Ther 2022; 32:361-368. [PMID: 35612432 PMCID: PMC9595607 DOI: 10.1089/nat.2022.0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
RNA therapeutics, including siRNAs, antisense oligonucleotides, and other oligonucleotides, have great potential to selectively treat a multitude of human diseases, from cancer to COVID to Parkinson's disease. RNA therapeutic activity is mechanistically driven by Watson-Crick base pairing to the target gene RNA without the requirement of prior knowledge of the protein structure, function, or cellular location. However, before widespread use of RNA therapeutics becomes a reality, we must overcome a billion years of evolutionary defenses designed to keep invading RNAs from entering cells. Unlike small-molecule therapeutics that are designed to passively diffuse across the cell membrane, macromolecular RNA therapeutics are too large, too charged, and/or too hydrophilic to passively diffuse across the cellular membrane and are instead taken up into cells by endocytosis. However, similar to the cell membrane, endosomes comprise a lipid bilayer that entraps 99% or more of RNA therapeutics, even in semipermissive tissues such as the liver, central nervous system, and muscle. Consequently, before RNA therapeutics can achieve their ultimate clinical potential to treat widespread human disease, the rate-limiting delivery problem of endosomal escape must be solved in a clinically acceptable manner.
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Affiliation(s)
- Steven F. Dowdy
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Ryan L. Setten
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Xian-Shu Cui
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Satish G. Jadhav
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
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27
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Migliorati JM, Liu S, Liu A, Gogate A, Nair S, Bahal R, Rasmussen TP, Manautou JE, Zhong XB. Absorption, Distribution, Metabolism, and Excretion of US Food and Drug Administration-Approved Antisense Oligonucleotide Drugs. Drug Metab Dispos 2022; 50:888-897. [PMID: 35221287 PMCID: PMC11022858 DOI: 10.1124/dmd.121.000417] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/22/2022] [Indexed: 04/19/2024] Open
Abstract
Absorption, distribution, metabolism, and excretion (ADME) are the key biologic processes for determination of a drug's pharmacokinetic parameters, which have direct impacts on efficacy and adverse drug reactions (ADRs). The chemical structures, dosage forms, and sites and routes of administration are the principal determinants of ADME profiles and consequent impacts on their efficacy and ADRs. Newly developed large molecule biologic antisense oligonucleotide (ASO) drugs have completely unique ADME that is not fully defined. ASO-based drugs are single-stranded synthetic antisense nucleic acids with diverse modes of drug actions from induction of mRNA degradation, exon skipping and restoration, and interactions with proteins. ASO drugs have a great potential to treat certain human diseases that have remained untreatable with small molecule-based drugs. The ADME of ASO drugs contributes to their unique set of ADRs and toxicity. In this review, to better understand their ADME, the 10 US Food and Drug Administration (FDA)-approved ASO drugs were selected: fomivirsen, pegaptanib, mipomersen, nusinersen, inotersen, defibrotide, eteplirsen, golodirsen, viltolarsen, and casimersen. A meta-analysis was conducted on their formulation, dosage, sites of administration, local and systematic distribution, metabolism, degradation, and excretion. Membrane permeabilization through endocytosis and nucleolytic degradation by endonucleases and exonucleases are major ADME features of the ASO drugs that differ from small-molecule drugs. The information summarized here provides comprehensive ADME characteristics of FDA-approved ASO drugs, leading to a better understanding of their therapeutic efficacy and their potential ADRs and toxicity. Numerous knowledge gaps, particularly on cellular uptake and subcellular trafficking and distribution, are identified, and future perspectives and directions are discussed. SIGNIFICANCE STATEMENT: Through a systematic analysis of the existing information of absorption, distribution, metabolism, and excretion (ADME) parameters for 10 US Food and Drug Administration (FDA)-approved antisense oligonucleotide (ASO) drugs, this review provides an overall view of the unique ADME characteristics of ASO drugs, which are distinct from small chemical drug ADME. This knowledge is useful for discovery and development of new ASO drugs as well as clinical use of current FDA-approved ASO drugs.
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Affiliation(s)
- Julia M Migliorati
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Sunna Liu
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Anna Liu
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Anagha Gogate
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Sreenidhi Nair
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy (J.M.M., S.L., A.L., A.G., R.B., T.P.R., J.E.M., X.Z.) and Department of Molecular and Cell Biology (S.N.), University of Connecticut, Storrs, Connecticut
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28
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PDL1-binding peptide/anti-miRNA21 conjugate as a therapeutic modality for PD-L1high tumors and TAMs. J Control Release 2022; 345:62-74. [DOI: 10.1016/j.jconrel.2022.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/19/2022]
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29
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Kay E, Stulz R, Becquart C, Lovric J, Tängemo C, Thomen A, Baždarević D, Najafinobar N, Dahlén A, Pielach A, Fernandez-Rodriguez J, Strömberg R, Ämmälä C, Andersson S, Kurczy M. NanoSIMS Imaging Reveals the Impact of Ligand-ASO Conjugate Stability on ASO Subcellular Distribution. Pharmaceutics 2022; 14:pharmaceutics14020463. [PMID: 35214195 PMCID: PMC8876276 DOI: 10.3390/pharmaceutics14020463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023] Open
Abstract
The delivery of antisense oligonucleotides (ASOs) to specific cell types via targeted endocytosis is challenging due to the low cell surface expression of target receptors and inefficient escape of ASOs from the endosomal pathway. Conjugating ASOs to glucagon-like peptide 1 (GLP1) leads to efficient target knockdown, specifically in pancreatic β-cells. It is presumed that ASOs dissociate from GLP1 intracellularly to enable an ASO interaction with its target RNA. It is unknown where or when this happens following GLP1-ASO binding to GLP1R and endocytosis. Here, we use correlative nanoscale secondary ion mass spectroscopy (NanoSIMS) and transmission electron microscopy to explore GLP1-ASO subcellular trafficking in GLP1R overexpressing HEK293 cells. We isotopically label both eGLP1 and ASO, which do not affect the eGLP1-ASO conjugate function. We found that the eGLP1 peptide and ASO are not detected at the same level in the same endosomes, within 30 min of GLP1R-HEK293 cell exposure to eGLP1-ASO. When we utilized different linker chemistry to stabilize the GLP1-ASO conjugate, we observed more ASO located with GLP1 compared to cell incubation with the less stable conjugate. Overall, our work suggests that the ASO separates from GLP1 relatively early in the endocytic pathway, and that linker chemistry might impact the GLP1-ASO function.
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Affiliation(s)
- Emma Kay
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden; (R.S.); (R.S.)
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
| | - Cécile Becquart
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 412 96 Gothenburg, Sweden;
| | - Jelena Lovric
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
| | - Carolina Tängemo
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Aurélien Thomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 412 96 Gothenburg, Sweden;
| | - Dženita Baždarević
- Bioscience, Early Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Neda Najafinobar
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
| | - Anna Pielach
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; (A.P.); (J.F.-R.)
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; (A.P.); (J.F.-R.)
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden; (R.S.); (R.S.)
| | - Carina Ämmälä
- Bioscience, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
| | - Michael Kurczy
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
- Correspondence:
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30
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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31
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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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32
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Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
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Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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Liang XH, Nichols JG, Tejera D, Crooke ST. Perinuclear positioning of endosomes can affect PS-ASO activities. Nucleic Acids Res 2021; 49:12970-12985. [PMID: 34878127 PMCID: PMC8682747 DOI: 10.1093/nar/gkab1198] [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: 08/24/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphorothioate (PS) modified antisense oligonucleotide (ASO) drugs that act on cellular RNAs must enter cells and be released from endocytic organelles to elicit antisense activity. It has been shown that PS-ASOs are mainly released by late endosomes. However, it is unclear how endosome movement in cells contributes to PS-ASO activity. Here, we show that PS-ASOs in early endosomes display Brownian type motion and migrate only short distances, whereas PS-ASOs in late endosomes (LEs) move linearly along microtubules with substantial distances. In cells with normal microtubules and LE movement, PS-ASO-loaded LEs tend to congregate perinuclearly. Disruption of perinuclear positioning of LEs by reduction of dynein 1 decreased PS-ASO activity, without affecting PS-ASO cellular uptake. Similarly, disruption of perinuclear positioning of PS-ASO-LE foci by reduction of ER tethering proteins RNF26, SQSTM1 and UBE2J1, or by overexpression of P50 all decreased PS-ASO activity. However, enhancing perinuclear positioning through reduction of USP15 or over-expression of RNF26 modestly increased PS-ASO activity, indicating that LE perinuclear positioning is required for ensuring efficient PS-ASO release. Together, these observations suggest that LE movement along microtubules and perinuclear positioning affect PS-ASO productive release.
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Affiliation(s)
- Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Dario Tejera
- Neurology, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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34
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Coelho F, Botelho C, Paris JL, Marques EF, Silva BF. Influence of the media ionic strength on the formation and in vitro biological performance of polycation-DNA complexes. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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35
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Khosravi HM, Jantsch MF. Site-directed RNA editing: recent advances and open challenges. RNA Biol 2021; 18:41-50. [PMID: 34569891 PMCID: PMC8677011 DOI: 10.1080/15476286.2021.1983288] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022] Open
Abstract
RNA editing by cytosine and adenosine deaminases changes the identity of the edited bases. While cytosines are converted to uracils, adenines are converted to inosines. If coding regions of mRNAs are affected, the coding potential of the RNA can be changed, depending on the codon affected. The recoding potential of nucleotide deaminases has recently gained attention for their ability to correct genetic mutations by either reverting the mutation itself or by manipulating processing steps such as RNA splicing. In contrast to CRISPR-based DNA-editing approaches, RNA editing events are transient in nature, therefore reducing the risk of long-lasting inadvertent side-effects. Moreover, some RNA-based therapeutics are already FDA approved and their use in targeting multiple cells or organs to restore genetic function has already been shown. In this review, we provide an overview on the current status and technical differences of site-directed RNA-editing approaches. We also discuss advantages and challenges of individual approaches.
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Affiliation(s)
- Hamid Mansouri Khosravi
- Center of Anatomy & Cell Biology Division of Cell & Developmental Biology Medical, Unviersity of Vienna SchwarzspanierstrasseVienna, Austria
| | - Michael F. Jantsch
- Center of Anatomy & Cell Biology Division of Cell & Developmental Biology Medical, Unviersity of Vienna SchwarzspanierstrasseVienna, Austria
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36
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RNAi-Based Approaches for Pancreatic Cancer Therapy. Pharmaceutics 2021; 13:pharmaceutics13101638. [PMID: 34683931 PMCID: PMC8541396 DOI: 10.3390/pharmaceutics13101638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/17/2023] Open
Abstract
Pancreatic cancer is one of the most lethal forms of cancer, predicted to be the second leading cause of cancer-associated death by 2025. Despite intensive research for effective treatment strategies and novel anticancer drugs over the past decade, the overall patient survival rate remains low. RNA interference (RNAi) is capable of interfering with expression of specific genes and has emerged as a promising approach for pancreatic cancer because genetic aberrations and dysregulated signaling are the drivers for tumor formation and the stromal barrier to conventional therapy. Despite its therapeutic potential, RNA-based drugs have remaining hurdles such as poor tumor delivery and susceptibility to serum degradation, which could be overcome with the incorporation of nanocarriers for clinical applications. Here we summarize the use of small interfering RNA (siRNA) and microRNA (miRNA) in pancreatic cancer therapy in preclinical reports with approaches for targeting either the tumor or tumor microenvironment (TME) using various types of nanocarriers. In these studies, inhibition of oncogene expression and induction of a tumor suppressive response in cancer cells and surrounding immune cells in TME exhibited a strong anticancer effect in pancreatic cancer models. The review discusses the remaining challenges and prospective strategies suggesting the potential of RNAi-based therapeutics for pancreatic cancer.
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37
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Rodriguez FD. Targeting Epigenetic Mechanisms to Treat Alcohol Use Disorders (AUD). Curr Pharm Des 2021; 27:3252-3272. [PMID: 33535943 PMCID: PMC8778698 DOI: 10.2174/1381612827666210203142539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND The impact of abusive alcohol consumption on human health is remarkable. According to the World Health Organization (WHO), approximately 3.3 million people die annually because of harmful alcohol consumption (the figure represents around 5.9% of global deaths). Alcohol Use Disorder (AUD) is a chronic disease where individuals exhibit compulsive alcohol drinking and present negative emotional states when they do not drink. In the most severe manifestations of AUD, the individuals lose control over intake despite a decided will to stop drinking. Given the multiple faces and the specific forms of this disease, the term AUD often appears in the plural (AUDs). Since only a few approved pharmacological treatments are available to treat AUD and they do not apply to all individuals or AUD forms, the search for compounds that may help to eliminate the burden of the disease and complement other therapeutical approaches is necessary. METHODS This work reviews recent research focused on the involvement of epigenetic mechanisms in the pathophysiology of AUD. Excessive drinking leads to chronic and compulsive consumption that eventually damages the organism. The central nervous system is a key target and is the focus of this study. The search for the genetic and epigenetic mechanisms behind the intricated dysregulation induced by ethanol will aid researchers in establishing new therapy approaches. CONCLUSION Recent findings in the field of epigenetics are essential and offer new windows for observation and research. The study of small molecules that inhibit key epienzymes involved in nucleosome architecture dynamics is necessary in order to prove their action and specificity in the laboratory and to test their effectivity and safety in clinical trials with selected patients bearing defined alterations caused by ethanol.
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Affiliation(s)
- F. David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemistry, University of Salamanca and Group GIR BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
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38
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Bost JP, Barriga H, Holme MN, Gallud A, Maugeri M, Gupta D, Lehto T, Valadi H, Esbjörner EK, Stevens MM, El-Andaloussi S. Delivery of Oligonucleotide Therapeutics: Chemical Modifications, Lipid Nanoparticles, and Extracellular Vesicles. ACS NANO 2021; 15:13993-14021. [PMID: 34505766 PMCID: PMC8482762 DOI: 10.1021/acsnano.1c05099] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 05/04/2023]
Abstract
Oligonucleotides (ONs) comprise a rapidly growing class of therapeutics. In recent years, the list of FDA-approved ON therapies has rapidly expanded. ONs are small (15-30 bp) nucleotide-based therapeutics which are capable of targeting DNA and RNA as well as other biomolecules. ONs can be subdivided into several classes based on their chemical modifications and on the mechanisms of their target interactions. Historically, the largest hindrance to the widespread usage of ON therapeutics has been their inability to effectively internalize into cells and escape from endosomes to reach their molecular targets in the cytosol or nucleus. While cell uptake has been improved, "endosomal escape" remains a significant problem. There are a range of approaches to overcome this, and in this review, we focus on three: altering the chemical structure of the ONs, formulating synthetic, lipid-based nanoparticles to encapsulate the ONs, or biologically loading the ONs into extracellular vesicles. This review provides a background to the design and mode of action of existing FDA-approved ONs. It presents the most common ON classifications and chemical modifications from a fundamental scientific perspective and provides a roadmap of the cellular uptake pathways by which ONs are trafficked. Finally, this review delves into each of the above-mentioned approaches to ON delivery, highlighting the scientific principles behind each and covering recent advances.
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Affiliation(s)
- Jeremy P. Bost
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Hanna Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Margaret N. Holme
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Audrey Gallud
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Marco Maugeri
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Dhanu Gupta
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Taavi Lehto
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Hadi Valadi
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Elin K. Esbjörner
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Department
of Materials, Department of Bioengineering, Institute of Biomedical
Engineering, Imperial College London, London SW7 2BU, United Kingdom
| | - Samir El-Andaloussi
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
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Kwak G, Kim H, Park J, Kim EH, Jang H, Han G, Wang SY, Yang Y, Chan Kwon I, Kim SH. A Trojan-Horse Strategy by In Situ Piggybacking onto Endogenous Albumin for Tumor-Specific Neutralization of Oncogenic MicroRNA. ACS NANO 2021; 15:11369-11384. [PMID: 34191497 DOI: 10.1021/acsnano.1c00799] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), a recently discovered class of noncoding RNAs, play pivotal roles in regulating fundamental biological processes by suppressing the expression of target genes. Aberrant miRNA expression is commonly correlated with human diseases, including cancers. Anti-miRNA oligonucleotides provide an innovative therapeutic strategy for silencing disease-associated miRNAs. However, the clinical application of anti-miRNA therapy has been limited by formulation challenges and physiological delivery barriers. Here, to provide the safe and effective tumor-targeted delivery of anti-miRNAs, we designed carrier-free maleimide-functionalized anti-miRNAs (MI-Anti-miRNAs) that enable "piggybacking" onto albumin in vivo. These functionalized MI-Anti-miRNAs covalently bind to cysteine-34 of endogenous albumin within minutes. In addition to resulting in a markedly extended blood circulation lifetime, this strategy allows MI-Anti-miRNAs to "hitchhike" to the tumor site. Importantly, in situ-generated albumin-Anti-miRNAs are capable of intracellularly internalizing highly negatively charged anti-miRNA molecules and knocking down target miRNAs. In particular, MI-Anti-miRNAs that targeted miRNA-21, which is involved in tumor initiation, progression, invasion, and metastasis in several types of cancer, successfully repressed miRNA-21 activity, resulting in a superior antitumor activity in both solid and metastatic tumor models without causing systemic toxicity. This endogenous albumin-piggybacking approach using MI-Anti-miRNAs provides a simple and broadly applicable platform strategy for the systemic delivery of anti-miRNA therapeutics.
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Affiliation(s)
- Gijung Kwak
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hyosuk Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jooho Park
- Department of Biomedical & Health Science, Konkuk University, 268 Chungwon-daero, Chungju 27478, Republic of Korea
| | - Eun Hye Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hochung Jang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Geonhee Han
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sun Young Wang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Yoosoo Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Ick Chan Kwon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- KIST-DFCI On-Site-Lab, Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts 02215, United States
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
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Nihashi Y, Shinji S, Umezawa K, Shimosato T, Ono T, Kagami H, Takaya T. Myogenetic oligodeoxynucleotide complexed with berberine promotes differentiation of chicken myoblasts. Anim Sci J 2021; 92:e13597. [PMID: 34309956 DOI: 10.1111/asj.13597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Myoblasts are myogenic precursors that develop into myotubes during muscle formation. Improving efficiency of myoblast differentiation is important for advancing meat production by domestic animals. We recently identified novel oligodeoxynucleotides (ODNs) termed myogenetic ODNs (myoDNs) that promote the differentiation of mammalian myoblasts. An isoquinoline alkaloid, berberine, forms a complex with one of the myoDNs, iSN04, and enhances its activities. This study investigated the effects of myoDNs on chicken myoblasts to elucidate their species-specific actions. Seven myoDNs (iSN01-iSN07) were found to facilitate the differentiation of chicken myoblasts into myosin heavy chain (MHC)-positive myotubes. The iSN04-berberine complex exhibited a higher myogenetic activity than iSN04 alone, which was shown to enhance the differentiation of myoblasts into myotubes and the upregulation of myogenic gene expression (MyoD, myogenin, MHC, and myomaker). These data indicate that myoDNs promoting chicken myoblast differentiation may be used as potential feed additives in broiler diets.
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Affiliation(s)
- Yuma Nihashi
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan.,Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Takeshi Shimosato
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan.,Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan.,Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan.,Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Tamao Ono
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Tomohide Takaya
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan.,Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan.,Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan.,Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
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41
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Nanoparticles-Based Oligonucleotides Delivery in Cancer: Role of Zebrafish as Animal Model. Pharmaceutics 2021; 13:pharmaceutics13081106. [PMID: 34452067 PMCID: PMC8400075 DOI: 10.3390/pharmaceutics13081106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/29/2022] Open
Abstract
Oligonucleotide (ON) therapeutics are molecular target agents composed of chemically synthesized DNA or RNA molecules capable of inhibiting gene expression or protein function. How ON therapeutics can efficiently reach the inside of target cells remains a problem still to be solved in the majority of potential clinical applications. The chemical structure of ON compounds could affect their capability to pass through the plasma membrane. Other key factors are nuclease degradation in the extracellular space, renal clearance, reticulo-endothelial system, and at the target cell level, the endolysosomal system and the possible export via exocytosis. Several delivery platforms have been proposed to overcome these limits including the use of lipidic, polymeric, and inorganic nanoparticles, or hybrids between them. The possibility of evaluating the efficacy of the proposed therapeutic strategies in useful in vivo models is still a pivotal need, and the employment of zebrafish (ZF) models could expand the range of possibilities. In this review, we briefly describe the main ON therapeutics proposed for anticancer treatment, and the different strategies employed for their delivery to cancer cells. The principal features of ZF models and the pros and cons of their employment in the development of ON-based therapeutic strategies are also discussed.
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42
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Michel S, Klar R, Jaschinski F. Investigation of the Activity of Antisense Oligonucleotides Targeting Multiple Genes by RNA-Sequencing. Nucleic Acid Ther 2021; 31:427-435. [PMID: 34251864 DOI: 10.1089/nat.2020.0932] [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: 11/12/2022] Open
Abstract
Locked nucleic acid-modified antisense oligonucleotides (ASOs) can achieve strongly different degrees of target knockdown despite having similar biophysical properties and 100% homology with their target. The determinants for this observation remain largely unknown. We used multi-specific ASOs that have 100% sequence complementarity with a common target (IDO1) and a different number of diverse targets and investigated their effect on gene expression in a cell line by RNA-sequencing. We observed a significant higher chance for downregulation of long genes compared to short genes, of genes with high compared to lower expression, and of genes that have more than one binding site for the respective ASO. By investigating the expression of genes that have binding sites for more than one ASO we identified the individual binding site being an important determinant for activity. Under the selected experimental conditions we have not seen indications that availability of RNase H is a limiting factor as the number of degraded target RNA molecules correlated significantly with the number of predicted target RNA molecules. Taken together, by using multi-specific ASOs as tool compounds we identified determinants for ASO activity that can be taken into consideration to improve the selection process of highly potent and selective ASOs in the future.
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Affiliation(s)
- Sven Michel
- ISecarna Pharmaceuticals, GmbH & Co. KG, Planegg, Germany
| | - Richard Klar
- ISecarna Pharmaceuticals, GmbH & Co. KG, Planegg, Germany
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43
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Liang XH, Nichols JG, De Hoyos CL, Sun H, Zhang L, Crooke ST. Golgi-58K can re-localize to late endosomes upon cellular uptake of PS-ASOs and facilitates endosomal release of ASOs. Nucleic Acids Res 2021; 49:8277-8293. [PMID: 34244781 PMCID: PMC8373082 DOI: 10.1093/nar/gkab599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/14/2022] Open
Abstract
Phosphorothioate (PS) modified antisense oligonucleotide (ASO) drugs can trigger RNase H1 cleavage of cellular target RNAs to modulate gene expression. Internalized PS-ASOs must be released from membraned endosomal organelles, a rate limiting step that is not well understood. Recently we found that M6PR transport between Golgi and late endosomes facilitates productive release of PS-ASOs, raising the possibility that Golgi-mediated transport may play important roles in PS-ASO activity. Here we further evaluated the involvement of Golgi in PS-ASO activity by examining additional Golgi proteins. Reduction of certain Golgi proteins, including Golgi-58K, GCC1 and TGN46, decreased PS-ASO activity, without substantial effects on Golgi integrity. Upon PS-ASO cellular uptake, Golgi-58K was recruited to late endosomes where it colocalized with PS-ASOs. Reduction of Golgi-58K caused slower PS-ASO release from late endosomes, decreased GCC2 late endosome relocalization, and led to slower retrograde transport of M6PR from late endosomes to trans-Golgi. Late endosome relocalization of Golgi-58K requires Hsc70, and is most likely mediated by PS-ASO-protein interactions. Together, these results suggest a novel function of Golgi-58K in mediating Golgi-endosome transport and indicate that the Golgi apparatus plays an important role in endosomal release of PS-ASO, ensuring antisense activity.
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Affiliation(s)
| | | | | | - Hong Sun
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Lingdi Zhang
- Core Antisense Research, Carlsbad, CA 92010, USA
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44
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Nilsson JR, Baladi T, Gallud A, Baždarević D, Lemurell M, Esbjörner EK, Wilhelmsson LM, Dahlén A. Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics. Sci Rep 2021; 11:11365. [PMID: 34059711 PMCID: PMC8166847 DOI: 10.1038/s41598-021-90629-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dženita Baždarević
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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45
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From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies. Biomedicines 2021; 9:biomedicines9050550. [PMID: 34068948 PMCID: PMC8156014 DOI: 10.3390/biomedicines9050550] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.
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46
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Chemical Manipulation of the Endosome Trafficking Machinery: Implications for Oligonucleotide Delivery. Biomedicines 2021; 9:biomedicines9050512. [PMID: 34063104 PMCID: PMC8148136 DOI: 10.3390/biomedicines9050512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides (ASOs), siRNA and splice switching oligonucleotides (SSOs) all have immense potential as therapeutic agents, potential that is now being validated as oligonucleotides enter the clinic. However, progress in oligonucleotide-based therapeutics has been limited by the difficulty in delivering these complex molecules to their sites of action in the cytosol or nucleus of cells within specific tissues. There are two aspects to the delivery problem. The first is that most types of oligonucleotides have poor uptake into non-hepatic tissues. The second is that much of the oligonucleotide that is taken up by cells is entrapped in endosomes where it is pharmacologically inert. It has become increasingly recognized that endosomal trapping is a key constraint on oligonucleotide therapeutics. Thus, many approaches have been devised to address this problem, primarily ones based on various nanoparticle technologies. However, recently an alternative approach has emerged that employs small molecules to manipulate intracellular trafficking processes so as to enhance oligonucleotide actions. This review presents the current status of this chemical biology approach to oligonucleotide delivery and seeks to point out possible paths for future development.
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47
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Verbeke R, Lentacker I, De Smedt SC, Dewitte H. The dawn of mRNA vaccines: The COVID-19 case. J Control Release 2021; 333:511-520. [PMID: 33798667 PMCID: PMC8008785 DOI: 10.1016/j.jconrel.2021.03.043] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023]
Abstract
In less than one year since the outbreak of the COVID-19 pandemic, two mRNA-based vaccines, BNT162b2 and mRNA-1273, were granted the first historic authorization for emergency use, while another mRNA vaccine, CVnCoV, progressed to phase 3 clinical testing. The COVID-19 mRNA vaccines represent a new class of vaccine products, which consist of synthetic mRNA strands encoding the SARS-CoV-2 Spike glycoprotein, packaged in lipid nanoparticles to deliver mRNA to cells. This review digs deeper into the scientific breakthroughs of the last decades that laid the foundations for the rapid rise of mRNA vaccines during the COVID-19 pandemic. As well as providing momentum for mRNA vaccines, SARS-CoV-2 represents an ideal case study allowing to compare design-activity differences between the different mRNA vaccine candidates. Therefore, a detailed overview of the composition and (pre)clinical performance of the three most advanced mRNA vaccines is provided and the influence of choices in their structural design on to their immunogenicity and reactogenicity profile is discussed in depth. In addition to the new fundamental insights in the mRNA vaccines' mode of action highlighted here, we also point out which unknowns remain that require further investigation and possibly, optimization in future mRNA vaccine development.
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Affiliation(s)
- Rein Verbeke
- Ghent Research Group on Nanomedicines, Faculty of Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Ine Lentacker
- Ghent Research Group on Nanomedicines, Faculty of Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Faculty of Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium.
| | - Heleen Dewitte
- Ghent Research Group on Nanomedicines, Faculty of Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
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48
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de la Fuente IF, Sawant SS, Tolentino MQ, Corrigan PM, Rouge JL. Viral Mimicry as a Design Template for Nucleic Acid Nanocarriers. Front Chem 2021; 9:613209. [PMID: 33777893 PMCID: PMC7987652 DOI: 10.3389/fchem.2021.613209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Therapeutic nucleic acids hold immense potential in combating undruggable, gene-based diseases owing to their high programmability and relative ease of synthesis. While the delivery of this class of therapeutics has successfully entered the clinical setting, extrahepatic targeting, endosomal escape efficiency, and subcellular localization. On the other hand, viruses serve as natural carriers of nucleic acids and have acquired a plethora of structures and mechanisms that confer remarkable transfection efficiency. Thus, understanding the structure and mechanism of viruses can guide the design of synthetic nucleic acid vectors. This review revisits relevant structural and mechanistic features of viruses as design considerations for efficient nucleic acid delivery systems. This article explores how viral ligand display and a metastable structure are central to the molecular mechanisms of attachment, entry, and viral genome release. For comparison, accounted for are details on the design and intracellular fate of existing nucleic acid carriers and nanostructures that share similar and essential features to viruses. The review, thus, highlights unifying themes of viruses and nucleic acid delivery systems such as genome protection, target specificity, and controlled release. Sophisticated viral mechanisms that are yet to be exploited in oligonucleotide delivery are also identified as they could further the development of next-generation nonviral nucleic acid vectors.
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Affiliation(s)
| | | | | | | | - Jessica L. Rouge
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
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49
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Knerr L, Prakash TP, Lee R, Drury Iii WJ, Nikan M, Fu W, Pirie E, Maria LD, Valeur E, Hayen A, Ölwegård-Halvarsson M, Broddefalk J, Ämmälä C, Østergaard ME, Meuller J, Sundström L, Andersson P, Janzén D, Jansson-Löfmark R, Seth PP, Andersson S. Glucagon Like Peptide 1 Receptor Agonists for Targeted Delivery of Antisense Oligonucleotides to Pancreatic Beta Cell. J Am Chem Soc 2021; 143:3416-3429. [PMID: 33626278 DOI: 10.1021/jacs.0c12043] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The extra hepatic delivery of antisense oligonucleotides (ASOs) remains a challenge and hampers the widespread application of this powerful class of therapeutic agents. In that regard, pancreatic beta cells are a particularly attractive but challenging cell type because of their pivotal role in diabetes and the fact that they are refractory to uptake of unconjugated ASOs. To circumvent this, we have expanded our understanding of the structure activity relationship of ASOs conjugated to Glucagon Like Peptide 1 Receptor (GLP1R) agonist peptide ligands. We demonstrate the key role of the linker chemistry and its optimization to design maleimide based conjugates with improved in vivo efficacy. In addition, truncation studies and scoping of a diverse set of GLP1R agonists proved fruitful to identify additional targeting ligands efficacious in vivo including native hGLP1(7-36)NH2. Variation of the carrier peptide also shed some light on the dramatic impact of subtle sequence differences on the corresponding ASO conjugate performance in vivo, an area which clearly warrant further investigations. We have confirmed the remarkable potential of GLP1R agonist conjugation for the delivery of ASOs to pancreatic beta cell by effectively knocking down islet amyloid polypeptide (IAPP) mRNA, a potential proapoptotic target, in mice.
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Affiliation(s)
- Laurent Knerr
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Richard Lee
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - William J Drury Iii
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mehran Nikan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Wuxia Fu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Elaine Pirie
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ahlke Hayen
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maria Ölwegård-Halvarsson
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Broddefalk
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina Ämmälä
- Bioscience, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael E Østergaard
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Johan Meuller
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Sundström
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Patrik Andersson
- Respiratory and Immunology Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Janzén
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rasmus Jansson-Löfmark
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Shalini Andersson
- Research and early Development, Discovery Sciences,, AstraZeneca, Gothenburg, Sweden
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50
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Liang XH, Nichols JG, Hsu CW, Crooke ST. Hsc70 Facilitates Mannose-6-Phosphate Receptor-Mediated Intracellular Trafficking and Enhances Endosomal Release of Phosphorothioate-Modified Antisense Oligonucleotides. Nucleic Acid Ther 2021; 31:284-297. [PMID: 33567234 DOI: 10.1089/nat.2020.0920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phosphorothioate-modified antisense oligonucleotide (PS-ASO) drugs are commonly used to modulate gene expression through RNase H1-mediated cleavage of target RNAs. Upon internalization through endocytic pathways into cells, PS-ASOs must be released from membraned endosomal organelles to act on target RNAs, a limiting step of PS-ASO activity. Here we report that Hsc70 protein mediates productive release of PS-ASOs from endosomes. Hsc70 protein was enriched in endosome fractions shortly after PS-ASO incubation with cells. Reduction of Hsc70 significantly decreased the activities of PS-ASOs in reducing target RNAs. PS-ASO uptake and transport from early endosomes to late endosomes (LEs) were not affected upon Hsc70 reduction; however, endosomal release of PS-ASOs was impaired. Reduction of Hsc70 led to more scattered mannose-6-phosphate receptor (M6PR) localization at LEs in the cytoplasm, in contrast to the perinuclear localization at trans-Golgi network (TGN) in control cells, suggesting that retrograde transport of M6PR from LEs to TGN was affected. Consistently, reduction of Hsc70 increased colocalization of M6PR and PS-ASOs at LEs, and also delayed M6PR antibody transport from LE to TGN. Together, these results suggest that Hsc70 protein is involved in M6PR vesicle escape from LEs and may thus enhance PS-ASO release from LEs.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Chih-Wei Hsu
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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