51
|
Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock. Genes Dev 2021; 35:899-913. [PMID: 34016691 PMCID: PMC8168560 DOI: 10.1101/gad.343541.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/26/2021] [Indexed: 12/20/2022]
Abstract
In mammals, a set of core clock genes form transcription-translation feedback loops to generate circadian oscillations. We and others recently identified a novel transcript at the Period2 (Per2) locus that is transcribed from the antisense strand of Per2 This transcript, Per2AS, is expressed rhythmically and antiphasic to Per2 mRNA, leading to our hypothesis that Per2AS and Per2 mutually inhibit each other's expression and form a double negative feedback loop. By perturbing the expression of Per2AS, we found that Per2AS transcription, but not transcript, represses Per2 However, Per2 does not repress Per2AS, as Per2 knockdown led to a decrease in the Per2AS level, indicating that Per2AS forms a single negative feedback loop with Per2 and maintains the level of Per2 within the oscillatory range. Per2AS also regulates the amplitude of the circadian clock, and this function cannot be solely explained through its interaction with Per2, as Per2 knockdown does not recapitulate the phenotypes of Per2AS perturbation. Overall, our data indicate that Per2AS is an important regulatory molecule in the mammalian circadian clock machinery. Our work also supports the idea that antisense transcripts of core clock genes constitute a common feature of circadian clocks, as they are found in other organisms.
Collapse
|
52
|
El-Khoury R, Damha MJ. 2'-Fluoro-arabinonucleic Acid (FANA): A Versatile Tool for Probing Biomolecular Interactions. Acc Chem Res 2021; 54:2287-2297. [PMID: 33861067 DOI: 10.1021/acs.accounts.1c00125] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Account highlights the structural features that render 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology.The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2'F-H8(purine) pseudohydrogen bonding interactions. We have shown that FANA/RNA hybrids are substrates of RNase H and Ago2, both implicated in the mechanism of action of antisense oligonucleotides (ASOs) and siRNA, respectvely. This knowledge has helped us study the conformational preferences of ASOs and siRNA as well as crRNA in CRISPR-associated Cas9, thereby revealing structural features crucial to biochemical activity.Additionally, FANA is of particular use in stabilizing noncanonical DNA structures. For instance, we have taken advantage of the anti N-glycosidic bond conformation of FANA monomers to induce a parallel topology in telomeric G-quadruplexes. Subsequent single-molecule FRET studies elucidated the mechanism by which these parallel G-quadruplexes are recognized and extended by telomerase. Similarly, we have utilized FANA to stabilize elusive telomeric i-motifs in the presence of concomitant parallel G-quadruplexes and under physiological conditions, thereby reinforcing their potential relevance to telomere biology. In another study, we adapted microarray technology and used FANA substitutions to enhance the binding affinity of the G-quadruplex thrombin-binding aptamer to its thrombin target.Finally, we discovered that DNA polymerases can synthesize FANA strands from DNA templates. On the basis of this property, other groups demonstrated that FANA, like DNA, can store hereditary information. They did so by engineering polymerases to efficiently transfer genetic information from DNA to FANA and retrieve it back into DNA. Subsequent studies showed that FANA could be evolved to acquire ribozyme-like endonuclease or ligase activity and to form high-affinity aptamers.Overall, the implications of these studies are remarkable because they promise a deeper understanding of human biochemistry for innovative therapeutic avenues. This Account summarizes past achievements and provides an outlook for inspiring the increased use of FANA in biological applications and fostering interdisciplinary collaborations.
Collapse
Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
53
|
Hammond SM, Aartsma‐Rus A, Alves S, Borgos SE, Buijsen RAM, Collin RWJ, Covello G, Denti MA, Desviat LR, Echevarría L, Foged C, Gaina G, Garanto A, Goyenvalle AT, Guzowska M, Holodnuka I, Jones DR, Krause S, Lehto T, Montolio M, Van Roon‐Mom W, Arechavala‐Gomeza V. Delivery of oligonucleotide-based therapeutics: challenges and opportunities. EMBO Mol Med 2021; 13:e13243. [PMID: 33821570 PMCID: PMC8033518 DOI: 10.15252/emmm.202013243] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleic acid-based therapeutics that regulate gene expression have been developed towards clinical use at a steady pace for several decades, but in recent years the field has been accelerating. To date, there are 11 marketed products based on antisense oligonucleotides, aptamers and small interfering RNAs, and many others are in the pipeline for both academia and industry. A major technology trigger for this development has been progress in oligonucleotide chemistry to improve the drug properties and reduce cost of goods, but the main hurdle for the application to a wider range of disorders is delivery to target tissues. The adoption of delivery technologies, such as conjugates or nanoparticles, has been a game changer for many therapeutic indications, but many others are still awaiting their eureka moment. Here, we cover the variety of methods developed to deliver nucleic acid-based therapeutics across biological barriers and the model systems used to test them. We discuss important safety considerations and regulatory requirements for synthetic oligonucleotide chemistries and the hurdles for translating laboratory breakthroughs to the clinic. Recent advances in the delivery of nucleic acid-based therapeutics and in the development of model systems, as well as safety considerations and regulatory requirements for synthetic oligonucleotide chemistries are discussed in this review on oligonucleotide-based therapeutics.
Collapse
Affiliation(s)
| | | | - Sandra Alves
- Department of Human Genetics, Research and Development UnitNational Health Institute Doutor Ricardo JorgePortoPortugal
| | - Sven E Borgos
- Department of Biotechnology and NanomedicineSINTEF ASTrondheimNorway
| | - Ronald A M Buijsen
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
| | - Giuseppina Covello
- Department of BiologyUniversity of PadovaPadovaItaly
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM‐CSICCIBERER, IdiPazUniversidad Autónoma de MadridMadridSpain
| | | | - Camilla Foged
- Department of PharmacyFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen ØDenmark
| | - Gisela Gaina
- Victor Babes National Institute of PathologyBucharestRomania
- Department of Biochemistry and Molecular BiologyUniversity of BucharestBucharestRomania
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Department of PediatricsRadboud University Medical CenterNijmegenThe Netherlands
| | | | - Magdalena Guzowska
- Department of Physiological SciencesFaculty of Veterinary MedicineWarsaw University of Life Sciences – SGGWWarsawPoland
| | - Irina Holodnuka
- Institute of Microbiology and VirologyRiga Stradins UniversityRigaLatvia
| | | | - Sabine Krause
- Department of NeurologyFriedrich‐Baur‐InstituteLudwig‐Maximilians‐University of MunichMunichGermany
| | - Taavi Lehto
- Institute of TechnologyUniversity of TartuTartuEstonia
- Division of Biomolecular and Cellular MedicineDepartment of Laboratory MedicineKarolinska InstitutetHuddingeSweden
| | - Marisol Montolio
- Duchenne Parent Project EspañaMadridSpain
- Department of Cell Biology, Fisiology and ImmunologyFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Willeke Van Roon‐Mom
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Virginia Arechavala‐Gomeza
- Neuromuscular Disorders GroupBiocruces Bizkaia Health Research InstituteBarakaldoSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| |
Collapse
|
54
|
Kizhakeyil A, Fazil MHUT, Verma NK. Targeted Gene Silencing in Malignant Hematolymphoid Cells Using GapmeR. Methods Mol Biol 2021; 2176:209-219. [PMID: 32865793 DOI: 10.1007/978-1-0716-0771-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Delivery of conventional antisense oligonucleotides or small interfering RNA (siRNA) molecules into hematolymphoid cells for targeted gene silencing has been proven to be difficult. Here, we describe a simple protocol to knockdown specific gene(s) in malignant hematolymphoid cells using "GapmeR." This protocol could be applicable to a wide range of cell-types and thus solves an important problem for researchers working with cell lines or primary cells derived from patients with hematolymphoid malignancies.
Collapse
Affiliation(s)
- Atish Kizhakeyil
- Lee Kong Chain School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | | | - Navin Kumar Verma
- Lee Kong Chain School of Medicine, Nanyang Technological University, Singapore, Singapore.,Skin Research Institute of Singapore, Singapore, Singapore
| |
Collapse
|
55
|
Wada F, Hori SI, Obika S, Yamamoto T. Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility. Methods Mol Biol 2021; 2176:141-154. [PMID: 32865788 DOI: 10.1007/978-1-0716-0771-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Oligonucleotide drugs (ODs) have gained increasing attention owing to their promising therapeutic potential. One major obstacle that ODs have been facing is the lack of appropriate in vitro validation systems that can predict in vivo activity and toxicity. We have devised a transfection method called CEM (Ca2+-enrichment method), where the simple enrichment of calcium ion with calcium chloride in culture medium potentiates the activity of various types of naked oligonucleotides including gapmers, siRNA, and phosphorodiamidate morpholino antisense oligonucleotides (PMO) in many cultured cell lines with limited cytotoxicity. We here describe a precise procedure of the method. Besides the benefit of the CEM's predictive power to accurately estimate in vivo activity of ODs of your interest in drug discovery and development settings, this cost-efficient, easy-to-access method can be a robust laboratory technique to modulate gene expressions with ODs with a variety of mechanisms of action.
Collapse
Affiliation(s)
- Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Shin-Ichiro Hori
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Medicinal Chemistry Research Laboratory for Medium Molecular Drug Discovery, Shionogi & Co., Ltd., Osaka, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan. .,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
| |
Collapse
|
56
|
Abstract
Antisense oligonucleotides (ASOs) are widely used for the identification of gene functions and regulation of genes involved in different diseases for therapeutic purposes. For in vitro evaluation of the knockdown activity of gapmer ASOs, we often use lipofection or electroporation to deliver gapmer ASOs into the cells. Here, we describe a method for evaluating the knockdown activity of gapmer ASOs by a cell-free uptake mechanism, termed as gymnosis, using MALAT1 gapmer ASOs modified with 2'-O-methoxyethyl RNA (2'-MOE) or 2'-O,4'-C-ethylene-bridged nucleic acid (ENA). This method is robust because it does not involve the use of any transfection reagent and has minimal effects on cell growth. Further, we describe a convenient technique for performing one-step reverse transcription and real-time qPCR using cell lysates without RNA extraction. Data for up to 96 samples can be obtained following these methods.
Collapse
|
57
|
Albumin-Binding Fatty Acid-Modified Gapmer Antisense Oligonucleotides for Modulation of Pharmacokinetics. Methods Mol Biol 2021; 2176:163-174. [PMID: 32865790 DOI: 10.1007/978-1-0716-0771-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Prolonged circulation and modulation of the pharmacokinetic profile are important to improve the clinical potential of antisense oligonucleotides (ASOs). Gapmer ASOs demonstrate excellent nuclease stability and robust gene silencing activity without the requirement of transfection agents. A major challenge for in vivo applications, however, is the short blood circulatory half-life. This work describes utilization of the long circulation of serum albumin to increase the blood residence time of gapmer ASOs. The method introduces fatty acid modifications into the gapmer ASOs design to exploit the binding and transport property of serum albumin for endogenous ligands. The level of albumin-gapmer ASOs interaction, blood circulatory half-life and biodistribution was dependent on number, position, and fatty acid type (palmitic or myristic acid) within the gapmer ASO sequence and either phosphorothioate or phosphodiester backbone modifications. This work offers a strategy to optimize gapmer ASO pharmacokinetics by a proposed endogenous assembly process with serum albumin that can be tuned by gapmer ASO design modifications.
Collapse
|
58
|
Design and Application of a Short (16-mer) Locked Nucleic Acid Splice-Switching Oligonucleotide for Dystrophin Production in Duchenne Muscular Dystrophy Myotubes. Methods Mol Biol 2021; 2161:37-50. [PMID: 32681504 DOI: 10.1007/978-1-0716-0680-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Splice-switching oligonucleotides (SSOs) have been used to modulate gene expression by interfering with pre-mRNA splicing with the intent to treat disease. For Duchenne muscular dystrophy, splicing modulation has been used to induce the skipping of exon 51 of the dystrophin transcript, allowing the production of a truncated but functional protein. Although oligonucleotide-based therapies are promising, the rapid degradation of oligonucleotides (ONs) by intracellular nucleases has been a major obstacle. Locked nucleic acid (LNA) substitution in SSOs protects oligonucleotides from nuclease degradation and enhances the hybridization properties of the oligo. However, the best optimum size of the oligo depends on the LNA substitution rate. Here we show that 16-mer DNA SSOs with 60% LNA substitution and full phosphorothioate (PS) linkage backbone efficiently induce exon 51 skipping in myogenic cells derived from a DMD patient, allowing expression of the dystrophin protein.
Collapse
|
59
|
Nishikawa M, Yanagawa N. Knockdown of Nuclear lncRNAs by Locked Nucleic Acid (LNA) Gapmers in Nephron Progenitor Cells. Methods Mol Biol 2021; 2161:29-36. [PMID: 32681503 DOI: 10.1007/978-1-0716-0680-3_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite recent advance in our understanding on the role of long noncoding RNAs (lncRNAs), the function of the vast majority of lncRNAs remains poorly understood. To characterize the function of lncRNAs, knockdown studies are essential. However, the conventional silencing methods for mRNA, such as RNA interference (RNAi), may not be as efficient against lncRNAs, partly due to the mismatch of the localization of lncRNAs and RNAi machinery. To circumvent such limitation, a new technique has recently been developed, i.e., locked nucleic acid (LNA) gapmers. This system utilizes RNase H that distributes evenly in both nucleus and cytoplasm and is expected to knock down lncRNAs of interest more consistently regardless of their localization in the cell. In this chapter, we describe the procedure with tips to silence lncRNAs by LNA gapmers, by using mouse nephron progenitor cells as an example.
Collapse
Affiliation(s)
- Masaki Nishikawa
- School of Engineering, Chemical System Engineering, University of Tokyo, Tokyo, Japan.
| | - Norimoto Yanagawa
- Medical and Research Services, Greater Los Angeles Veterans Affairs Healthcare System at Sepulveda, North Hills, CA, USA.
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
60
|
Cribbs AP, Filippakopoulos P, Philpott M, Wells G, Penn H, Oerum H, Valge-Archer V, Feldmann M, Oppermann U. Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function. Front Immunol 2021; 12:626255. [PMID: 33717143 PMCID: PMC7953504 DOI: 10.3389/fimmu.2021.626255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that play a pivotal role in the immune surveillance and elimination of transformed or virally infected cells. Using a chemo-genetic approach, we identify BET bromodomain containing proteins BRD2 and BRD4 as central regulators of NK cell functions, including direct cytokine secretion, NK cell contact-dependent inflammatory cytokine secretion from monocytes as well as NK cell cytolytic functions. We show that both BRD2 and BRD4 control inflammatory cytokine production in NK cells isolated from healthy volunteers and from rheumatoid arthritis patients. In contrast, knockdown of BRD4 but not of BRD2 impairs NK cell cytolytic responses, suggesting BRD4 as critical regulator of NK cell mediated tumor cell elimination. This is supported by pharmacological targeting where the first-generation pan-BET bromodomain inhibitor JQ1(+) displays anti-inflammatory effects and inhibit tumor cell eradication, while the novel bivalent BET bromodomain inhibitor AZD5153, which shows differential activity towards BET family members, does not. Given the important role of both cytokine-mediated inflammatory microenvironment and cytolytic NK cell activities in immune-oncology therapies, our findings present a compelling argument for further clinical investigation.
Collapse
Affiliation(s)
- Adam P Cribbs
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | | | - Martin Philpott
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Graham Wells
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Henry Penn
- Arthritis Centre, Northwick Park Hospital, Harrow, United Kingdom
| | - Henrik Oerum
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Viia Valge-Archer
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Marc Feldmann
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom.,Freiburg Institute of Advanced Studies, Freiburg, Germany.,Oxford Centre for Translational Myeloma Research, Oxford, United Kingdom
| |
Collapse
|
61
|
Egorova KS, Posvyatenko AV, Larin SS, Ananikov V. Ionic liquids: prospects for nucleic acid handling and delivery. Nucleic Acids Res 2021; 49:1201-1234. [PMID: 33476366 PMCID: PMC7897475 DOI: 10.1093/nar/gkaa1280] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.
Collapse
Affiliation(s)
- Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
| | - Alexandra V Posvyatenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Valentine P Ananikov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
| |
Collapse
|
62
|
Fumoto S, Yamamoto T, Okami K, Maemura Y, Terada C, Yamayoshi A, Nishida K. Understanding In Vivo Fate of Nucleic Acid and Gene Medicines for the Rational Design of Drugs. Pharmaceutics 2021; 13:159. [PMID: 33530309 PMCID: PMC7911509 DOI: 10.3390/pharmaceutics13020159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid and genetic medicines are increasingly being developed, owing to their potential to treat a variety of intractable diseases. A comprehensive understanding of the in vivo fate of these agents is vital for the rational design, discovery, and fast and straightforward development of the drugs. In case of intravascular administration of nucleic acids and genetic medicines, interaction with blood components, especially plasma proteins, is unavoidable. However, on the flip side, such interaction can be utilized wisely to manipulate the pharmacokinetics of the agents. In other words, plasma protein binding can help in suppressing the elimination of nucleic acids from the blood stream and deliver naked oligonucleotides and gene carriers into target cells. To control the distribution of these agents in the body, the ligand conjugation method is widely applied. It is also important to understand intracellular localization. In this context, endocytosis pathway, endosomal escape, and nuclear transport should be considered and discussed. Encapsulated nucleic acids and genes must be dissociated from the carriers to exert their activity. In this review, we summarize the in vivo fate of nucleic acid and gene medicines and provide guidelines for the rational design of drugs.
Collapse
Affiliation(s)
- Shintaro Fumoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan; (T.Y.); (K.O.); (Y.M.); (C.T.); (A.Y.); (K.N.)
| | | | | | | | | | | | | |
Collapse
|
63
|
Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
Collapse
Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| |
Collapse
|
64
|
Taiana E, Favasuli V, Ronchetti D, Morelli E, Tassone P, Viglietto G, Munshi NC, Neri A, Amodio N. In Vitro Silencing of lncRNAs Using LNA GapmeRs. Methods Mol Biol 2021; 2348:157-166. [PMID: 34160805 DOI: 10.1007/978-1-0716-1581-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Despite substantial advancements have been achieved in the identification of long noncoding RNA (lncRNA) molecules, many challenges still remain into their functional characterization. Loss-of-function approaches are needed to study oncogenic lncRNAs, which appear more difficult to knock down by RNA interference as compared to mRNAs. In this chapter, we present a protocol based on the use of a novel class of antisense oligonucleotides, named locked nucleic acid (LNA) GapmeRs, to inhibit the oncogenic lncRNA NEAT1 in multiple myeloma cells. Overall, this approach holds many advantages, including its possible independence from delivery reagents as well as the capability to knock down lncRNAs even in hard-to-transfect suspension cells, like hematopoietic cells.
Collapse
Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Vanessa Favasuli
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Domenica Ronchetti
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Eugenio Morelli
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy.
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| |
Collapse
|
65
|
Hulot JS, Masurkar N. miRNA-Based Therapeutics for Heart Failure: Why Not? J Am Coll Cardiol 2020; 75:1801-1803. [PMID: 32299592 DOI: 10.1016/j.jacc.2020.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Jean-Sébastien Hulot
- Université de Paris, PARCC, INSERM, Paris, France; CIC1418 and DMU CARTE, Assistance Publique - Hôpitaux de Paris, Hôpital Européen Georges-Pompidou, Paris, France.
| | | |
Collapse
|
66
|
Cerrato CP, Kivijärvi T, Tozzi R, Lehto T, Gestin M, Langel Ü. Intracellular delivery of therapeutic antisense oligonucleotides targeting mRNA coding mitochondrial proteins by cell-penetrating peptides. J Mater Chem B 2020; 8:10825-10836. [PMID: 33174901 DOI: 10.1039/d0tb01106a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cell-penetrating peptides are a promising therapeutic strategy for a wide variety of degenerative diseases, ageing, and cancer. Among the multitude of cell-penetrating peptides, PepFect14 has been preferentially used in our laboratory for oligonucleotide delivery into cells and in vivo mouse models. However, this activity has mainly been reported towards cytoplasm and nuclei, while the mentioned disorders have been linked to mitochondrial defects. Here, we report a library generated from a combinatorial covalent fusion of a mitochondrial-penetrating peptide, mtCPP1, and PepFect14 in order to deliver therapeutic biomolecules to influence mitochondrial protein expression. The non-covalent complexation of these peptides with oligonucleotides resulted in nano-complexes affecting biological functions in the cytoplasm and on mitochondria. This delivery system proved to efficiently target mitochondrial genes, providing a framework for the development of mitochondrial peptide-based oligonucleotide technologies with the potential to be used as a treatment for patients with mitochondrial disorders.
Collapse
Affiliation(s)
- Carmine Pasquale Cerrato
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691 Stockholm, Sweden.
| | | | | | | | | | | |
Collapse
|
67
|
Knutson SD, Sanford AA, Swenson CS, Korn MM, Manuel BA, Heemstra JM. Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging. J Am Chem Soc 2020; 142:17766-17781. [PMID: 33017148 DOI: 10.1021/jacs.0c08996] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Controlling the structure and activity of nucleic acids dramatically expands their potential for application in therapeutics, biosensing, nanotechnology, and biocomputing. Several methods have been developed to impart responsiveness of DNA and RNA to small-molecule and light-based stimuli. However, heat-triggered control of nucleic acids has remained largely unexplored, leaving a significant gap in responsive nucleic acid technology. Moreover, current technologies have been limited to natural nucleic acids and are often incompatible with polymerase-generated sequences. Here we show that glyoxal, a well-characterized compound that covalently attaches to the Watson-Crick-Franklin face of several nucleobases, addresses these limitations by thermoreversibly modulating the structure and activity of virtually any nucleic acid scaffold. Using a variety of DNA and RNA constructs, we demonstrate that glyoxal modification is easily installed and potently disrupts nucleic acid structure and function. We also characterize the kinetics of decaging and show that activity can be restored via tunable thermal removal of glyoxal adducts under a variety of conditions. We further illustrate the versatility of this approach by reversibly caging a 2'-O-methylated RNA aptamer as well as synthetic threose nucleic acid (TNA) and peptide nucleic acid (PNA) scaffolds. Glyoxal caging can also be used to reversibly disrupt enzyme-nucleic acid interactions, and we show that caging of guide RNA allows for tunable and reversible control over CRISPR-Cas9 activity. We also demonstrate glyoxal caging as an effective method for enhancing PCR specificity, and we cage a biostable antisense oligonucleotide for time-release activation and titration of gene expression in living cells. Together, glyoxalation is a straightforward and scarless method for imparting reversible thermal responsiveness to theoretically any nucleic acid architecture, addressing a significant need in synthetic biology and offering a versatile new tool for constructing programmable nucleic acid components in medicine, nanotechnology, and biocomputing.
Collapse
Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aimee A Sanford
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Megan M Korn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Brea A Manuel
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
68
|
Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
Collapse
Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| |
Collapse
|
69
|
The stem cell-specific long noncoding RNA HOXA10-AS in the pathogenesis of KMT2A-rearranged leukemia. Blood Adv 2020; 3:4252-4263. [PMID: 31867596 DOI: 10.1182/bloodadvances.2019032029] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 11/18/2019] [Indexed: 01/10/2023] Open
Abstract
HOX genes are highly conserved, and their precisely controlled expression is crucial for normal hematopoiesis. Accordingly, deregulation of HOX genes can cause leukemia. However, despite of intensive research on the coding HOX genes, the role of the numerous long noncoding RNAs (lncRNAs) within the HOX clusters during hematopoiesis and their contribution to leukemogenesis are incompletely understood. Here, we show that the lncRNA HOXA10-AS, located antisense to HOXA10 and mir-196b in the HOXA cluster, is highly expressed in hematopoietic stem cells (HSCs) as well as in KMT2A-rearranged and NPM1 mutated acute myeloid leukemias (AMLs). Using short hairpin RNA- and locked nucleic acid-conjugated chimeric antisense oligonucleotide (LNA-GapmeR)-mediated HOXA10-AS-knockdown and CRISPR/Cas9-mediated excision in vitro, we demonstrate that HOXA10-AS acts as an oncogene in KMT2A-rearranged AML. Moreover, HOXA10-AS knockdown severely impairs the leukemic growth of KMT2A-rearranged patient-derived xenografts in vivo, while high HOXA10-AS expression can serve as a marker of poor prognosis in AML patients. Lentiviral expression of HOXA10-AS blocks normal monocytic differentiation of human CD34+ hematopoietic stem and progenitor cells. Mechanistically, we show that HOXA10-AS localizes in the cytoplasm and acts in trans to induce NF-κB target genes. In total, our data imply that the normally HSC-specific HOXA10-AS is an oncogenic lncRNA in KMT2A-r AML. Thus, it may also represent a potential therapeutic target in KMT2A-rearranged AML.
Collapse
|
70
|
Lazar S, Wurtzel JGT, Chen X, Ma P, Goldfinger LE. High-efficiency unassisted transfection of platelets with naked double-stranded miRNAs modulates signal-activated translation and platelet function. Platelets 2020; 32:794-806. [PMID: 32838617 DOI: 10.1080/09537104.2020.1809642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We sought novel approaches to improve transfection efficiencies of microRNAs (miRNAs) in platelets, and to apply these approaches to investigate the roles of miRNAs in regulating signal-activated protein translation and functional effects. We found that ex vivo human platelets support gymnosis---internalization of ectopic miRNAs following co-incubation in the absence of conventional transfection reagents or schemes---and subsequently incorporate transfected miRNA into ARGONAUTE2 (AGO2)-based RNA-induced silencing complexes (RISC). Thrombin/fibrinogen stimulation activated translation of miR-223-3p target SEPTIN2, which was suppressed by miR-223-3p transfection in an AGO2/RISC-dependent manner. Thrombin/fibrinogen-induced exosome and microvesicle generation was inhibited by miR-223-3p transfection, and this effect was reversed with a RISC inhibitor. Platelet gymnosis of naked miRNAs appeared to be mediated in part by endocytic pathways including clathrin-dependent and fluid-phase endocytosis and caveolae. These results demonstrate the ability of ex vivo platelets to internalize ectopic miRNAs by unassisted transfection, and utilize them to modulate signal-activated translation and platelet function. Our results identify new roles for miR-223-3p in extracellular vesicle generation in stimulated platelets. High-efficiency gymnotic transfection of miRNAs in ex vivo platelets may be a broadly useful tool for exploring molecular genetic regulation of platelet function.
Collapse
Affiliation(s)
- Sophia Lazar
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeremy G T Wurtzel
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xi Chen
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peisong Ma
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lawrence E Goldfinger
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
71
|
Soung YH, Chung H, Yan C, Fesler A, Kim H, Oh ES, Ju J, Chung J. Therapeutic Potential of Chemically Modified miR-489 in Triple-Negative Breast Cancers. Cancers (Basel) 2020; 12:E2209. [PMID: 32784600 PMCID: PMC7463492 DOI: 10.3390/cancers12082209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancers (TNBCs) lack ER, PR and her2 receptors that are targets of common breast cancer therapies with poor prognosis due to their high rates of metastasis and chemoresistance. Based on our previous studies that epigenetic silencing of a potential metastasis suppressor, arrestin domain-containing 3 (ARRDC3), is linked to the aggressive nature of TNBCs, we identified a sub-group of tumor suppressing miRNAs whose expressions were significantly up-regulated by ARRDC3 over-expression in TNBC cells. Among these tumor suppressing miRs, we found that miR-489 is most anti-proliferative in TNBC cells. miR-489 also blocked DNA damaging responses (DDRs) in TNBC cells. To define the mechanism by which miR-489 inhibits TNBC cell functions, we screened the potential target genes of miR-489 and identified MDC-1 and SUZ-12 as novel target genes of miR-489 in TNBC cells. To further exploit the therapeutic potentials of miR-489 in TNBC models, we chemically modified the guide strand of miR-489 (CMM489) by replacing Uracil with 5-fluorouracil (5-FU) so that tumor suppressor (miR-489) and DNA damaging (5-FU) components are combined into a single agent as a novel drug candidate for TNBCs. Our studies demonstrated that CMM489 shows superior effects over miR-489 or 5-FU in inhibition of TNBC cell proliferation and tumor progression, suggesting its therapeutic efficacy in TNBC models.
Collapse
Affiliation(s)
- Young Hwa Soung
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
| | - Heesung Chung
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea;
| | - Cecilia Yan
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
| | - Andrew Fesler
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
| | - Hyungjin Kim
- Department of Pharmacological Sciences, Stony Brook Medicine, Stony Brook, NY 11794, USA;
| | - Eok-Soo Oh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea;
| | - Jingfang Ju
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
| | - Jun Chung
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA; (Y.H.S.); (H.C.); (C.Y.); (A.F.); (J.J.)
| |
Collapse
|
72
|
Coskun FS, Srivastava S, Raj P, Dozmorov I, Belkaya S, Mehra S, Golden NA, Bucsan AN, Chapagain ML, Wakeland EK, Kaushal D, Gumbo T, van Oers NSC. sncRNA-1 Is a Small Noncoding RNA Produced by Mycobacterium tuberculosis in Infected Cells That Positively Regulates Genes Coupled to Oleic Acid Biosynthesis. Front Microbiol 2020; 11:1631. [PMID: 32849337 PMCID: PMC7399025 DOI: 10.3389/fmicb.2020.01631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Nearly one third of the world’s population is infected with Mycobacterium tuberculosis (Mtb). While much work has focused on the role of different Mtb encoded proteins in pathogenesis, recent studies have revealed that Mtb also transcribes many noncoding RNAs whose functions remain poorly characterized. We performed RNA sequencing and identified a subset of Mtb H37Rv-encoded small RNAs (<30 nts in length) that were produced in infected macrophages. Designated as smaller noncoding RNAs (sncRNAs), three of these predominated the read counts. Each of the three, sncRNA-1, sncRNA-6, and sncRNA-8 had surrounding sequences with predicted stable secondary RNA stem loops. Site-directed mutagenesis of the precursor sequences suggest the existence of a hairpin loop dependent RNA processing mechanism. A functional assessment of sncRNA-1 suggested that it positively regulated two mycobacterial transcripts involved in oleic acid biosynthesis. Complementary loss- and gain- of-function approaches revealed that sncRNA-1 positively supports Mtb growth and survival in nutrient-depleted cultures as well as in infected macrophages. Overall, the findings reveal that Mtb produces sncRNAs in infected cells, with sncRNA-1 modulating mycobacterial gene expression including genes coupled to oleic acid biogenesis.
Collapse
Affiliation(s)
- Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Serkan Belkaya
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Smriti Mehra
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Nadia A Golden
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Allison N Bucsan
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Deepak Kaushal
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States.,Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
73
|
Festag J, Thelemann T, Schell M, Raith S, Michel S, Jaschinski F, Klar R. Preventing ATP Degradation by ASO-Mediated Knockdown of CD39 and CD73 Results in A2aR-Independent Rescue of T Cell Proliferation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:656-669. [PMID: 32739778 PMCID: PMC7393471 DOI: 10.1016/j.omtn.2020.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 01/09/2023]
Abstract
The adenosine axis contributes to the suppression of antitumor immune responses. The ectonucleotidase CD39 degrades extracellular adenosine triphosphate (ATP) to adenosine monophosphate (AMP), which is degraded to adenosine by CD73. Adenosine binds to, e.g., the A2a receptor (A2aR), which reportedly suppresses effector immune cells. We investigated effects of ATP, AMP, and adenosine analogs on T cell proliferation, apoptosis, and proinflammatory cytokine secretion. CD39 and CD73 expression were suppressed using antisense oligonucleotides (ASOs), and A2aR was blocked using small molecules. Addition of ATP to T cells reduced proliferation and induced apoptosis. Intriguingly, those effects were reverted by suppression of CD39 and/or CD73 expression but not A2aR inhibition. Adenosine analogs did not suppress proliferation but inhibited secretion of proinflammatory cytokines. Here, we suggest that suppression of T cell proliferation is not directly mediated by A2aR but by intracellular downstream metabolites of adenosine, as blockade of the equilibrative nucleoside transporter (ENT) or adenosine kinase rescued proliferation and prevented induction of apoptosis. In conclusion, adenosine might primarily affect cytokine secretion directly via adenosine receptors, whereas adenosine metabolites might impair T cell proliferation and induce apoptosis. Therefore, inhibition of CD39 and/or CD73 has evident advantages over A2aR blockade to fully revert suppression of antitumor immune responses by the adenosine axis.
Collapse
Affiliation(s)
- Julia Festag
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Tamara Thelemann
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Monika Schell
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Stefanie Raith
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Frank Jaschinski
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany
| | - Richard Klar
- Secarna Pharmaceuticals GmbH & Co. KG, 82152 Planegg/Martinsried, Germany.
| |
Collapse
|
74
|
Funder ED, Albæk N, Moisan A, Sewing S, Koch T. Refining LNA safety profile by controlling phosphorothioate stereochemistry. PLoS One 2020; 15:e0232603. [PMID: 32530964 PMCID: PMC7292364 DOI: 10.1371/journal.pone.0232603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/17/2020] [Indexed: 01/01/2023] Open
Abstract
Drug discovery with phosphorothioate oligonucleotides is an area of intensive research. In this study we have controlled the stereochemistry of the phosphorothioate backbone of LNA oligonucleotides to investigate the differences in safety profile, target mRNA knock down, and cellular uptake in vitro. The study reveals that controlling only four stereocenters in an isomeric phosphorothioate mixture can improve the therapeutic index significantly by improving safety without compromising activity.
Collapse
Affiliation(s)
| | - Nanna Albæk
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Annie Moisan
- Roche Innovation Center Basel, Basel, Switzerland
| | | | - Troels Koch
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| |
Collapse
|
75
|
Aguti S, Bolduc V, Ala P, Turmaine M, Bönnemann CG, Muntoni F, Zhou H. Exon-Skipping Oligonucleotides Restore Functional Collagen VI by Correcting a Common COL6A1 Mutation in Ullrich CMD. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:205-216. [PMID: 32585628 PMCID: PMC7321786 DOI: 10.1016/j.omtn.2020.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 11/19/2022]
Abstract
Collagen VI-related congenital muscular dystrophies (COL6-CMDs) are the second most common form of congenital muscular dystrophy. Currently, there is no effective treatment available. COL6-CMDs are caused by recessive or dominant mutations in one of the three genes encoding for the α chains of collagen type VI (COL6A1, COL6A2, and COL6A3). One of the most common mutations in COL6-CMD patients is a de novo deep intronic c.930+189C > T mutation in COL6A1 gene. This mutation creates a cryptic donor splice site and induces incorporation of a novel in-frame pseudo-exon in the mature transcripts. In this study, we systematically evaluated the splice switching approach using antisense oligonucleotides (ASOs) to correct this mutation. Fifteen ASOs were designed using the RNA-tiling approach to target the misspliced pseudo-exon and its flanking sequences. The efficiency of ASOs was evaluated at RNA, protein, and structural levels in skin fibroblasts established from four patients carrying the c.930+189C > T mutation. We identified two additional lead ASO candidates that efficiently induce pseudo-exon exclusion from the mature transcripts, thus allowing for the restoration of a functional collagen VI microfibrillar matrix. Our findings provide further evidence for ASO exon skipping as a therapeutic approach for COL6-CMD patients carrying this common intronic mutation.
Collapse
Affiliation(s)
- Sara Aguti
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Pierpaolo Ala
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Mark Turmaine
- Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.
| | - Haiyan Zhou
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK; Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.
| |
Collapse
|
76
|
Glazier DA, Liao J, Roberts BL, Li X, Yang K, Stevens CM, Tang W. Chemical Synthesis and Biological Application of Modified Oligonucleotides. Bioconjug Chem 2020; 31:1213-1233. [PMID: 32227878 DOI: 10.1021/acs.bioconjchem.0c00060] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA plays a myriad of roles in the body including the coding, decoding, regulation, and expression of genes. RNA oligonucleotides have garnered significant interest as therapeutics via antisense oligonucleotides or small interfering RNA strategies for the treatment of diseases ranging from hyperlipidemia, HCV, and others. Additionally, the recently developed CRISPR-Cas9 mediated gene editing strategy also relies on Cas9-associated RNA strands. However, RNA presents numerous challenges as both a synthetic target and a potential therapeutic. RNA is inherently unstable, difficult to deliver into cells, and potentially immunogenic by itself or upon modification. Despite these challenges, with the help of chemically modified oligonucleotides, multiple RNA-based drugs have been approved by the FDA. The progress is made possible due to the nature of chemically modified oligonucleotides bearing advantages of nuclease stability, stronger binding affinity, and some other unique properties. This review will focus on the chemical synthesis of RNA and its modified versions. How chemical modifications of the ribose units and of the phosphatediester backbone address the inherent issues with using native RNA for biological applications will be discussed along the way.
Collapse
Affiliation(s)
- Daniel A Glazier
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Brett L Roberts
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaolei Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ka Yang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Christopher M Stevens
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
77
|
Delivery of Antisense Oligonucleotides Mediated by a Hydrogel System: In Vitro and In Vivo Application in the Context of Spinal Cord Injury. Methods Mol Biol 2020; 2036:205-219. [PMID: 31410799 DOI: 10.1007/978-1-4939-9670-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Biomaterials-based hydrogels are attractive drug-eluting vehicles in the context of RNA therapeutics, such as those utilizing antisense oligonucleotide or RNA interference based drugs, as they can potentially reduce systemic toxicity and enhance in vivo efficacy by increasing in situ concentrations. Here we describe the preparation of antisense oligonucleotide-loaded fibrin hydrogels exploring their applications in the context of the nervous system utilizing an organotypic dorsal root ganglion explant in vitro system and an in vivo model of spinal cord injury.
Collapse
|
78
|
Li Q. Nusinersen as a Therapeutic Agent for Spinal Muscular Atrophy. Yonsei Med J 2020; 61:273-283. [PMID: 32233169 PMCID: PMC7105407 DOI: 10.3349/ymj.2020.61.4.273] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 01/02/2023] Open
Abstract
The reduction of survival motor neuron (SMN) protein causes spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease. Nusinersen is an antisense oligonucleotide, approved by the FDA, which specifically binds to the repressor within SMN2 exon 7 to enhance exon 7 inclusion and augment production of functional SMN protein. Nusinersen is the first new oligonucleotide-based drug targeting the central nervous system for the treatment of SMA. This review of nusinersen will discuss its action mechanism, cellular uptake, trafficking mechanisms, and administration approaches to cross the blood-brain barrier. Furthermore, nusinersen clinical trials will be assessed in terms of pharmacokinetics, tolerability and safety, the clinical outcomes of multiple intrathecal doses, and a discussion on the primary and secondary endpoints.
Collapse
Affiliation(s)
- Qing Li
- Department of Function, ShiJiaZhuang Traditional Chinese Medical Hospital, ShiJiaZhuang, HeBei, China.
| |
Collapse
|
79
|
Scharner J, Ma WK, Zhang Q, Lin KT, Rigo F, Bennett CF, Krainer AR. Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res 2020; 48:802-816. [PMID: 31802121 PMCID: PMC6954394 DOI: 10.1093/nar/gkz1132] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/03/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Splice-switching antisense oligonucleotides (ASOs), which bind specific RNA-target sequences and modulate pre-mRNA splicing by sterically blocking the binding of splicing factors to the pre-mRNA, are a promising therapeutic modality to treat a range of genetic diseases. ASOs are typically 15–25 nt long and considered to be highly specific towards their intended target sequence, typically elements that control exon definition and/or splice-site recognition. However, whether or not splice-modulating ASOs also induce hybridization-dependent mis-splicing of unintended targets has not been systematically studied. Here, we tested the in vitro effects of splice-modulating ASOs on 108 potential off-targets predicted on the basis of sequence complementarity, and identified 17 mis-splicing events for one of the ASOs tested. Based on analysis of data from two overlapping ASO sequences, we conclude that off-target effects are difficult to predict, and the choice of ASO chemistry influences the extent of off-target activity. The off-target events caused by the uniformly modified ASOs tested in this study were significantly reduced with mixed-chemistry ASOs of the same sequence. Furthermore, using shorter ASOs, combining two ASOs, and delivering ASOs by free uptake also reduced off-target activity. Finally, ASOs with strategically placed mismatches can be used to reduce unwanted off-target splicing events.
Collapse
Affiliation(s)
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | | |
Collapse
|
80
|
Antisense Oligonucleotide in LNA-Gapmer Design Targeting TGFBR2-A Key Single Gene Target for Safe and Effective Inhibition of TGFβ Signaling. Int J Mol Sci 2020; 21:ijms21061952. [PMID: 32178467 PMCID: PMC7139664 DOI: 10.3390/ijms21061952] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/13/2022] Open
Abstract
Antisense Oligonucleotides (ASOs) are an emerging drug class in gene modification. In our study we developed a safe, stable, and effective ASO drug candidate in locked nucleic acid (LNA)-gapmer design, targeting TGFβ receptor II (TGFBR2) mRNA. Discovery was performed as a process using state-of-the-art library development and screening. We intended to identify a drug candidate optimized for clinical development, therefore human specificity and gymnotic delivery were favored by design. A staggered process was implemented spanning in-silico-design, in-vitro transfection, and in-vitro gymnotic delivery of small batch syntheses. Primary in-vitro and in-vivo toxicity studies and modification of pre-lead candidates were also part of this selection process. The resulting lead compound NVP-13 unites human specificity and highest efficacy with lowest toxicity. We particularly focused at attenuation of TGFβ signaling, addressing both safety and efficacy. Hence, developing a treatment to potentially recondition numerous pathological processes mediated by elevated TGFβ signaling, we have chosen to create our data in human lung cell lines and human neuronal stem cell lines, each representative for prospective drug developments in pulmonary fibrosis and neurodegeneration. We show that TGFBR2 mRNA as a single gene target for NVP-13 responds well, and that it bears great potential to be safe and efficient in TGFβ signaling related disorders.
Collapse
|
81
|
Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism. Proc Natl Acad Sci U S A 2020; 117:6056-6066. [PMID: 32123118 PMCID: PMC7084125 DOI: 10.1073/pnas.1919893117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
T cells control many immune functions, with Th17 cells critical in regulating inflammation. Following activation, T cells undergo metabolic reprogramming and utilize glycolysis to increase the ATP availability. Epigenetic mechanisms controlling metabolic functions in T cells are currently not well-defined. Here, we establish an epigenetic link between the histone H3K27me3 demethylases KDM6A/B and the coordination of a metabolic response. Inhibition of KDM6A/B leads to global increases in the repressive H3K27me3 histone mark, resulting in down-regulation of key transcription factors, followed by metabolic reprogramming and anergy. This work suggests a critical role of H3K27 demethylase enzymes in maintaining Th17 functions by controlling metabolic switches. Short-term treatment with KDM6 enzyme inhibitors may be useful in the therapy of chronic inflammatory diseases. T helper (Th) cells are CD4+ effector T cells that play a critical role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations. Using a combined chemico-genetic approach, we identify histone H3K27 demethylases KDM6A and KDM6B as central regulators of human Th subsets. The prototypic KDM6 inhibitor GSK-J4 increases genome-wide levels of the repressive H3K27me3 chromatin mark and leads to suppression of the key transcription factor RORγt during Th17 differentiation. In mature Th17 cells, GSK-J4 induces an altered transcriptional program with a profound metabolic reprogramming and concomitant suppression of IL-17 cytokine levels and reduced proliferation. Single-cell analysis reveals a specific shift from highly inflammatory cell subsets toward a resting state upon demethylase inhibition. The root cause of the observed antiinflammatory phenotype in stimulated Th17 cells is reduced expression of key metabolic transcription factors, such as PPRC1. Overall, this leads to reduced mitochondrial biogenesis, resulting in a metabolic switch with concomitant antiinflammatory effects. These data are consistent with an effect of GSK-J4 on Th17 T cell differentiation pathways directly related to proliferation and include regulation of effector cytokine profiles. This suggests that inhibiting KDM6 demethylases may be an effective, even in the short term, therapeutic target for autoimmune diseases, including ankylosing spondylitis.
Collapse
|
82
|
Pendergraff H, Schmidt S, Vikeså J, Weile C, Øverup C, W. Lindholm M, Koch T. Nuclear and Cytoplasmatic Quantification of Unconjugated, Label-Free Locked Nucleic Acid Oligonucleotides. Nucleic Acid Ther 2020; 30:4-13. [PMID: 31618108 PMCID: PMC6987631 DOI: 10.1089/nat.2019.0810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022] Open
Abstract
Methods for the quantification of antisense oligonucleotides (AONs) provide insightful information on biodistribution and intracellular trafficking. However, the established methods have not provided information on the absolute number of molecules in subcellular compartments or about how many AONs are needed for target gene reduction for unconjugated AONs. We have developed a new method for nuclear AON quantification that enables us to determine the absolute number of AONs per nucleus without relying on AON conjugates such as fluorophores that may alter AON distribution. This study describes an alternative and label-free method using subcellular fractionation, nucleus counting, and locked nucleic acid (LNA) sandwich enzyme-linked immunosorbent assay to quantify absolute numbers of oligonucleotides in nuclei. Our findings show compound variability (diversity) by which 247,000-693,000 LNAs/nuclei results in similar target reduction for different compounds. This method can be applied to any antisense drug discovery platform providing information on specific and clinically relevant AONs. Finally, this method can directly compare nuclear entry of AON with target gene knockdown for any compound design and nucleobase sequence, gene target, and phosphorothioate stereochemistry.
Collapse
Affiliation(s)
- Hannah Pendergraff
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Jonas Vikeså
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Christian Weile
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Marie W. Lindholm
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Troels Koch
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| |
Collapse
|
83
|
Zhou Y, Zang C, Wang H, Li J, Cui Z, Li Q, Guo F, Yan Z, Wen X, Xi Z, Zhou C. 4'-C-Trifluoromethyl modified oligodeoxynucleotides: synthesis, biochemical studies, and cellular uptake properties. Org Biomol Chem 2020; 17:5550-5560. [PMID: 31112186 DOI: 10.1039/c9ob00765b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Herein, we report the synthesis of 4'-C-trifluoromethyl (4'-CF3) thymidine (T4'-CF3) and its incorporation into oligodeoxynucleotides (ODNs) through solid-supported DNA synthesis. The 4'-CF3 modification leads to a marginal effect on the deoxyribose conformation and a local helical structure perturbation for ODN/RNA duplexes. This type of modification slightly decreases the thermal stability of ODN/RNA duplexes (-1 °C/modification) and leads to improved nuclease resistance. Like the well-known phosphorothioate (PS) modification, heavy 4'-CF3 modifications enable direct cellular uptake of the modified ODNs without any delivery reagents. This work highlights that 4'-CF3 modified ODNs are promising candidates for antisense-based therapeutics, which will, in turn, inspire us to develop more potent modifications for antisense ODNs and siRNAs.
Collapse
Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
84
|
Metelev VG, Bogdanov AA. Synthesis and applications of theranostic oligonucleotides carrying multiple fluorine atoms. Theranostics 2020; 10:1391-1414. [PMID: 31938071 PMCID: PMC6956824 DOI: 10.7150/thno.37936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
The use of various oligonucleotide (ON) syntheses and post-synthetic strategies for targeted chemical modification enables improving their efficacy as potent modulators of gene expression levels in eukaryotic cells. However, the search still continues for new approaches designed for increasing internalization, lysosomal escape, and tissue specific delivery of ON. In this review we emphasized all aspects related to the synthesis and properties of ON derivatives carrying multifluorinated (MF) groups. These MF groups have unique physico-chemical properties because of their simultaneous hydrophobicity and lipophobicity. Such unusual combination of properties results in the overall modification of ON mode of interaction with the cells and making multi-fluorination highly relevant to the goal of improving potency of ON as components of new therapies. The accumulated evidence so far is pointing to high potential of ON probes, RNAi components and ON imaging beacons carrying single or multiple MF groups for improving the stability, specificity of interaction with biological targets and delivery of ONs in vitro and potentially in vivo.
Collapse
Affiliation(s)
- Valeriy G. Metelev
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, Worcester MA, USA
- Department of Chemistry, Moscow State University, Moscow, Russian Federation
| | - Alexei A. Bogdanov
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, Worcester MA, USA
- Laboratory of Molecular Imaging, A.N. Bakh Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow
| |
Collapse
|
85
|
Abewe H, Deshmukh S, Mukim A, Beliakova-Bethell N. Use of GapmeRs for gene expression knockdowns in human primary resting CD4+ T cells. J Immunol Methods 2020; 476:112674. [PMID: 31629740 PMCID: PMC6939142 DOI: 10.1016/j.jim.2019.112674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Human primary resting CD4+ T cells are difficult to transfect while preserving viability. The present study evaluated gymnotic delivery and RNase H1-dependent gene expression knockdown mediated by antisense oligonucleotides, called GapmeRs. Exposure of primary resting CD4+ T cells to GapmeRs did not cause cell activation or affect cell viability. Gene expression knockdowns were stable at least up to 48 h after removal of GapmeRs from culture. Exposure to GapmeRs resulted in comparable levels of degradation along the entire transcript, which could be important when studying function of regulatory long non-coding RNAs. Efficiency of transcript degradation was not solely dependent on the dose of GapmeR, RNA target and its localization. When using GapmeRs, some optimization is required, and all targets have to be individually tested; however, using GapmeRs is advantageous in experiments where preservation of the resting state of the human primary CD4+ T cells and targeting nuclear RNAs are desired. In certain cases, combining GapmeR with siRNA for the same target may improve knockdown efficiency.
Collapse
Affiliation(s)
- Hosiana Abewe
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; University of California San Diego, La Jolla, CA 92093, USA
| | - Savitha Deshmukh
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Amey Mukim
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Nadejda Beliakova-Bethell
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
86
|
Chemical Diversity of Locked Nucleic Acid-Modified Antisense Oligonucleotides Allows Optimization of Pharmaceutical Properties. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:706-717. [PMID: 31951854 PMCID: PMC6965521 DOI: 10.1016/j.omtn.2019.12.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/21/2023]
Abstract
The identification of molecules that can modulate RNA or protein function and the subsequent chemical and structural optimization to refine such molecules into drugs is a key activity in drug discovery. Here, we explored the extent to which chemical and structural differences in antisense oligonucleotides, designed as gapmers and capable of recruiting RNase H for target RNA cleavage, can affect their functional properties. To facilitate structure-activity learning, we analyzed two sets of iso-sequential locked nucleic acid (LNA)-modified gapmers, where we systematically varied the number and positions of LNA modifications in the flanks. In total, we evaluated 768 different and architecturally diverse gapmers in HeLa cells for target knockdown activity and cytotoxic potential and found widespread differences in both of these properties. Binding affinity between gapmer and RNA target, as well as the presence of certain short sequence motifs in the gap region, can explain these differences, and we propose statistical and machine-learning models that can be used to predict region-specific, optimal LNA-modification architectures. Once accessible regions in the target of interest have been identified, our results show how to refine and optimize LNA gapmers with improved pharmacological profiles targeting such regions.
Collapse
|
87
|
Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| |
Collapse
|
88
|
Klar R, Michel S, Schell M, Hinterwimmer L, Zippelius A, Jaschinski F. A highly efficient modality to block the degradation of tryptophan for cancer immunotherapy: locked nucleic acid-modified antisense oligonucleotides to inhibit human indoleamine 2,3-dioxygenase 1/tryptophan 2,3-dioxygenase expression. Cancer Immunol Immunother 2019; 69:57-67. [PMID: 31802183 DOI: 10.1007/s00262-019-02438-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022]
Abstract
Tumors can utilize a diverse repertoire of immunosuppressive mechanisms to evade attack by the immune system. Despite promising success with blockade of immune checkpoints like PD-1 the majority of patients does not respond to current immunotherapies. The degradation of tryptophan into immunosuppressive kynurenine is an important immunosuppressive pathway. Recent attempts to target the key enzymes of this pathway-IDO1 and TDO2-have so far failed to show therapeutic benefit in the clinic, potentially caused by insufficient target engagement. We, therefore, sought to add an alternative, highly efficient approach to block the degradation of tryptophan by inhibiting the expression of IDO1 and TDO2 using locked nucleic acid (LNA)-modified antisense oligonucleotides (ASOs). We show that LNA-modified ASOs can profoundly inhibit the expression of IDO1 and TDO2 in cancer cells in vitro without using a transfection reagent with IC50 values in the sub-micromolar range. We furthermore measured kynurenine production by ASO-treated cancer cells in vitro and observed potently reduced kynurenine levels. Accordingly, inhibiting IDO1 expression in cancer cells in an in vitro system leads to increased proliferation of activated T cells in coculture. We furthermore show that combined treatment of cancer cells in vitro with IDO1-specific ASOs and small molecule inhibitors can reduce the production of kynurenine by cancer cells in a synergistic manner. In conclusion, we propose that a combination of LNA-modified ASOs and small molecule inhibitors should be considered as a strategy for efficient blockade of the degradation of tryptophan into kynurenine in cancer immunotherapy.
Collapse
Affiliation(s)
- Richard Klar
- Secarna Pharmaceuticals GmbH & Co. KG, Am Klopferspitz 19, 82152, Planegg, Germany.
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co. KG, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Monika Schell
- Secarna Pharmaceuticals GmbH & Co. KG, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Lisa Hinterwimmer
- Secarna Pharmaceuticals GmbH & Co. KG, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Frank Jaschinski
- Secarna Pharmaceuticals GmbH & Co. KG, Am Klopferspitz 19, 82152, Planegg, Germany.
| |
Collapse
|
89
|
Jin SJ, Jin MZ, Xia BR, Jin WL. Long Non-coding RNA DANCR as an Emerging Therapeutic Target in Human Cancers. Front Oncol 2019; 9:1225. [PMID: 31799189 PMCID: PMC6874123 DOI: 10.3389/fonc.2019.01225] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators of numerous biological processes, especially in cancer development. Aberrantly expressed and specifically located in tumor cells, they exert distinct functions in different cancers via regulating multiple downstream targets such as chromatins, RNAs, and proteins. Differentiation antagonizing non-protein coding RNA (DANCR) is a cytoplasmic lncRNA that generally works as a tumor promoter. Mechanically, DANCR promotes the functions of vital components in the oncogene network by sponging their corresponding microRNAs or by interacting with various regulating proteins. DANCR's distinct expression in tumor cells and collective involvement in pro-tumor pathways make it a promising therapeutic target for broad cancer treatment. Herein, we summarize the functions and molecular mechanism of DANCR in human cancers. Furthermore, we introduce the use of CRISPR/Cas9, antisense oligonucleotides and small interfering RNAs as well as viral, lipid, or exosomal vectors for onco-lncRNA targeted treatment. Conclusively, DANCR is a considerable promoter of cancers with a bright prospect in targeted therapy.
Collapse
Affiliation(s)
- Shi-Jia Jin
- Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, Department of Instrument Science and Engineering, Shanghai Engineering Center for Intelligent Diagnosis and Treatment Instrument, School of Electronic Information and Electronic Engineering, Institute of Nano Biomedicine and Engineering, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Zhu Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bai-Rong Xia
- Department of Gynecology, The Affiliated Tumor Hospital, Harbin Medical University, Harbin, China
| | - Wei-Lin Jin
- Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, Department of Instrument Science and Engineering, Shanghai Engineering Center for Intelligent Diagnosis and Treatment Instrument, School of Electronic Information and Electronic Engineering, Institute of Nano Biomedicine and Engineering, Shanghai Jiao Tong University, Shanghai, China.,National Center for Translational Medicine, Collaborative Innovational Center for System Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
90
|
Crespo D, Assis LHC, van de Kant HJG, de Waard S, Safian D, Lemos MS, Bogerd J, Schulz RW. Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: follicle-stimulating hormone, retinoic acid and androgens. Development 2019; 146:dev.178665. [PMID: 31597660 DOI: 10.1242/dev.178665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/01/2019] [Indexed: 01/07/2023]
Abstract
Retinoic acid (RA) is crucial for mammalian spermatogonia differentiation, and stimulates Stra8 expression, a gene required for meiosis. Certain fish species, including zebrafish, have lost the stra8 gene. While RA still seems important for spermatogenesis in fish, it is not known which stage(s) respond to RA or whether its effects are integrated into the endocrine regulation of spermatogenesis. In zebrafish, RA promoted spermatogonia differentiation, supported androgen-stimulated meiosis, and reduced spermatocyte and spermatid apoptosis. Follicle-stimulating hormone (Fsh) stimulated RA production. Expressing a dominant-negative RA receptor variant in germ cells clearly disturbed spermatogenesis but meiosis and spermiogenesis still took place, although sperm quality was low in 6-month-old adults. This condition also activated Leydig cells. Three months later, spermatogenesis apparently had recovered, but doubling of testis weight demonstrated hypertrophy, apoptosis/DNA damage among spermatids was high and sperm quality remained low. We conclude that RA signaling is important for zebrafish spermatogenesis but is not of crucial relevance. As Fsh stimulates androgen and RA production, germ cell-mediated, RA-dependent reduction of Leydig cell activity may form a hitherto unknown intratesticular negative-feedback loop.
Collapse
Affiliation(s)
- Diego Crespo
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Luiz H C Assis
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Henk J G van de Kant
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Sjors de Waard
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Diego Safian
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Moline S Lemos
- Laboratory of Cellular Biology, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jan Bogerd
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Rüdiger W Schulz
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands .,Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen NO-5817, Norway
| |
Collapse
|
91
|
García-García P, Ruiz M, Reyes R, Delgado A, Évora C, Riancho JA, Rodríguez-Rey JC, Pérez-Campo FM. Smurf1 Silencing Using a LNA-ASOs/Lipid Nanoparticle System to Promote Bone Regeneration. Stem Cells Transl Med 2019; 8:1306-1317. [PMID: 31631568 PMCID: PMC6877774 DOI: 10.1002/sctm.19-0145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
Despite the great advance of bone tissue engineering in the last few years, repair of bone defects remains a major problem. Low cell engraftment and dose‐dependent side effects linked to the concomitant administration of bone morphogenetic proteins (BMPs) are the main problems currently hindering the clinical use of mesenchymal stem cell (MSC)‐based therapies in this field. We have managed to bypass these drawbacks by combining the silencing the Smurf1 ubiquitin ligase in MSCs with the use of a scaffold that sustainably releases low doses of BMP‐2. In this system, Smurf1 silencing is achieved by using GapmeRs, a clinically safe method that avoids the use of viral vectors, facilitating its translation to the clinic. Here, we show that a single transient transfection with a small quantity of a Smurf1‐specific GapmeR is able to induce a significant level of silencing of the target gene, enough to prime MSCs for osteogenic differentiation. Smurf1 silencing highly increases MSCs responsiveness to BMP‐2, allowing a dramatic reduction of the dose needed to achieve the desired therapeutic effect. The combination of these primed cells with alginate scaffolds designed to sustainably and locally release low doses of BMP‐2 to the defect microenvironment is able to induce the formation of a mature bone matrix both in an osteoporotic rat calvaria system and in a mouse ectopic model. Importantly, this approach also enhances osteogenic differentiation in MSCs from osteoporotic patients, characterized by a reduced bone‐forming potential, even at low BMP doses, underscoring the regenerative potential of this system. stem cells translational medicine2019;8:1306&1317 The BMP‐Smad signaling cascade is an effective therapeutic target to promote bone formation. Silencing of Smurf1, a known BMP signaling inhibitor, increases the responsiveness of Mesenchymal stem cells to BMP, allowing a dramatic reduction of the doses used in the clinic to promote bone formation and therefore, avoiding secondary effects associated to the use of these factors.![]()
Collapse
Affiliation(s)
- Patricia García-García
- Department of Chemical Engineering and Pharmaceutical Technology, Institute of Biomedical Technologies (ITB), University of La Laguna, La Laguna, Spain
| | - Mario Ruiz
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria, IDIVAL, Santander, Spain
| | - Ricardo Reyes
- Department of Biochemistry, Microbiology, Cellular Biology and Genetics, Institute of Biomedical Technologies (ITB), University of La Laguna, La Laguna, Spain
| | - Araceli Delgado
- Department of Chemical Engineering and Pharmaceutical Technology, Institute of Biomedical Technologies (ITB), University of La Laguna, La Laguna, Spain
| | - Carmen Évora
- Department of Chemical Engineering and Pharmaceutical Technology, Institute of Biomedical Technologies (ITB), University of La Laguna, La Laguna, Spain
| | - José Antonio Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - José Carlos Rodríguez-Rey
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria, IDIVAL, Santander, Spain
| | - Flor María Pérez-Campo
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria, IDIVAL, Santander, Spain
| |
Collapse
|
92
|
Systematic Approach to Developing Splice Modulating Antisense Oligonucleotides. Int J Mol Sci 2019; 20:ijms20205030. [PMID: 31614438 PMCID: PMC6834167 DOI: 10.3390/ijms20205030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
The process of pre-mRNA splicing is a common and fundamental step in the expression of most human genes. Alternative splicing, whereby different splice motifs and sites are recognised in a developmental and/or tissue-specific manner, contributes to genetic plasticity and diversity of gene expression. Redirecting pre-mRNA processing of various genes has now been validated as a viable clinical therapeutic strategy, providing treatments for Duchenne muscular dystrophy (inducing specific exon skipping) and spinal muscular atrophy (promoting exon retention). We have designed and evaluated over 5000 different antisense oligonucleotides to alter splicing of a variety of pre-mRNAs, from the longest known human pre-mRNA to shorter, exon-dense primary gene transcripts. Here, we present our guidelines for designing, evaluating and optimising splice switching antisense oligomers in vitro. These systematic approaches assess several critical factors such as the selection of target splicing motifs, choice of cells, various delivery reagents and crucial aspects of validating assays for the screening of antisense oligonucleotides composed of 2′-O-methyl modified bases on a phosphorothioate backbone.
Collapse
|
93
|
Leitner S, Grijalvo S, Solans C, Eritja R, García-Celma MJ, Calderó G. Ethylcellulose nanoparticles as a new "in vitro" transfection tool for antisense oligonucleotide delivery. Carbohydr Polym 2019; 229:115451. [PMID: 31826509 DOI: 10.1016/j.carbpol.2019.115451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 02/06/2023]
Abstract
Oil-in-water nano-emulsions have been obtained in the HEPES 20 mM buffer solution / [Alkylamidoammonium:Kolliphor EL = 1:1] / [6 wt% ethylcellulose in ethyl acetate] system over a wide oil-to-surfactant range and above 35 wt% aqueous component at 25 °C. The nano-emulsion with an oil-to-surfactant ratio of 70/30 and 95 wt% aqueous component was used for nanoparticles preparation. These nanoparticles (mean diameter around 90 nm and zeta potential of +22 mV) were non-toxic to HeLa cells up to a concentration of 3 mM of cationic species. Successful complexation with an antisense phosphorothioate oligonucleotide targeting Renilla luciferase mRNA was achieved at cationic/anionic charge ratios above 16, as confirmed by zeta potential measurements and an electrophoretic mobility shift assay, provided that no Fetal Bovine Serum is present in the cell culture medium. Importantly, Renilla luciferase gene inhibition shows an optimum efficiency (40%) for the cationic/anionic ratio 28, which makes these complexes promising for "in vitro" cell transfection.
Collapse
Affiliation(s)
- S Leitner
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - S Grijalvo
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - C Solans
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - R Eritja
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - M J García-Celma
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain; Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, Univ. de Barcelona, IN2UB, Unitat Associada d'I+D al CSIC, Av Joan XXIII, s/n, 08028 Barcelona, Spain
| | - G Calderó
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
| |
Collapse
|
94
|
Grinman E, Espadas I, Puthanveettil SV. Emerging roles for long noncoding RNAs in learning, memory and associated disorders. Neurobiol Learn Mem 2019; 163:107034. [DOI: 10.1016/j.nlm.2019.107034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/03/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022]
|
95
|
Buntz A, Killian T, Schmid D, Seul H, Brinkmann U, Ravn J, Lindholm M, Knoetgen H, Haucke V, Mundigl O. Quantitative fluorescence imaging determines the absolute number of locked nucleic acid oligonucleotides needed for suppression of target gene expression. Nucleic Acids Res 2019; 47:953-969. [PMID: 30462278 PMCID: PMC6344898 DOI: 10.1093/nar/gky1158] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Locked nucleic acid based antisense oligonucleotides (LNA-ASOs) can reach their intracellular RNA targets without delivery modules. Functional cellular uptake involves vesicular accumulation followed by translocation to the cytosol and nucleus. However, it is yet unknown how many LNA-ASO molecules need to be delivered to achieve target knock down. Here we show by quantitative fluorescence imaging combined with LNA-ASO microinjection into the cytosol or unassisted uptake that ∼105 molecules produce >50% knock down of their targets, indicating that a substantial amount of LNA-ASO escapes from endosomes. Microinjected LNA-ASOs redistributed within minutes from the cytosol to the nucleus and remained bound to nuclear components. Together with the fact that RNA levels for a given target are several orders of magnitude lower than the amounts of LNA-ASO, our data indicate that only a minor fraction is available for RNase H1 mediated reduction of target RNA. When non-specific binding sites were blocked by co-administration of non-related LNA-ASOs, the amount of target LNA-ASO required was reduced by an order of magnitude. Therefore, dynamic processes within the nucleus appear to influence the distribution and activity of LNA-ASOs and may represent important parameters for improving their efficacy and potency.
Collapse
Affiliation(s)
- Annette Buntz
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Tobias Killian
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Daniela Schmid
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Heike Seul
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Ulrich Brinkmann
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Jacob Ravn
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Marie Lindholm
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Hendrik Knoetgen
- Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Volker Haucke
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin 13125, Germany
| | - Olaf Mundigl
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| |
Collapse
|
96
|
Wang Y, Shen W, Liang XH, Crooke ST. Phosphorothioate Antisense Oligonucleotides Bind P-Body Proteins and Mediate P-Body Assembly. Nucleic Acid Ther 2019; 29:343-358. [PMID: 31429620 DOI: 10.1089/nat.2019.0806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) regulate gene expression by binding to complementary target RNA, and ASOs can be designed to take advantage of a growing array of post RNA binding molecular mechanisms. Intracellular trafficking of ASOs influences their efficacy. We have identified a number of membrane-less structures in the nucleus, nucleolus, and cytoplasm where phosphorothioate-modified ASOs (PS-ASOs) accumulate and have shown that PS-ASOs can induce the formation of new nuclear structures such as PS-bodies and paraspeckle-like structures. In this study, we report that PS-ASOs can localize to cytoplasmic processing bodies (P-bodies) and increase the number of P-bodies in cells. The antisense activity of PS-ASOs was not affected by the absence of essential P-body assembly proteins DDX6 and LSm14A. Moreover, the effects of PS-ASOs on P-body assembly were independent of their antisense activities. The phosphorothioate modification stabilizes the association between ASOs and cellular proteins and is essential for the P-body localization of ASOs. Since PS-ASOs bind to major P-body components, PS-ASOs may serve as scaffolds for P-body formation. Taken together, these results indicate that interactions of PS-ASO with proteins, rather than antisense activities, are essential for the dynamic interplay between PS-ASOs and P-bodies.
Collapse
Affiliation(s)
- Ying Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| |
Collapse
|
97
|
Fazil MHUT, Ong ST, Chalasani MLS, Kizhakeyil A, Verma NK. GapmeR-Mediated Gene Silencing in Motile T-Cells. Methods Mol Biol 2019; 1930:67-73. [PMID: 30610600 DOI: 10.1007/978-1-4939-9036-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Gene silencing is an important method to study gene functions in health and diseases. While there are various techniques that are applied to knockdown specific gene(s) of interest, they have certain limitations in application to T-lymphocytes. T-cells are "hard-to-transfect" cells and are recalcitrant to transfection reagents. Here, we describe the use of novel cell-permeating antisense molecules, called "GapmeR", to knockdown specific gene(s) in human primary T-cells.
Collapse
Affiliation(s)
| | - Seow Theng Ong
- Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Madhavi Latha Somaraju Chalasani
- Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore.,Autoimmunity and Inflammation Program, Hospital for Special Surgery, NY, USA
| | - Atish Kizhakeyil
- Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Navin Kumar Verma
- Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| |
Collapse
|
98
|
Costales MG, Suresh B, Vishnu K, Disney MD. Targeted Degradation of a Hypoxia-Associated Non-coding RNA Enhances the Selectivity of a Small Molecule Interacting with RNA. Cell Chem Biol 2019; 26:1180-1186.e5. [PMID: 31130520 PMCID: PMC6697612 DOI: 10.1016/j.chembiol.2019.04.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/24/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
Small-molecule targeted recruitment of nucleases to RNA is a powerful method to affect RNA biology. Inforna, a sequence-based design approach to target RNA, enables the design of small molecules that bind to and cleave RNA in a selective and substoichiometric manner. Here, we investigate the ability of RNA-targeted degradation to improve the selectivity of small molecules targeting RNA. The microRNA-210 hairpin precursor (pre-miR-210) is overexpressed in hypoxic cancers. Previously, a small molecule (Targapremir-210 [TGP-210]) targeted this RNA in cells, but with a 5-fold window for DNA binding. Appendage of a nuclease recruitment module onto TGP-210 locally recruited ribonuclease L onto pre-miR-210, triggering its degradation. The chimera has enhanced selectivity compared with TGP-210 with nanomolar binding to the pre-miR-210, but no DNA binding, and is broadly selective for affecting RNA function in cells. Importantly, it cleaved pre-miR-210 substoichiometrically and induced apoptosis in breast cancer cells.
Collapse
Affiliation(s)
| | - Blessy Suresh
- Department of Chemistry, Scripps Research, Jupiter, FL 33458, USA
| | | | - Matthew D Disney
- Department of Chemistry, Scripps Research, Jupiter, FL 33458, USA.
| |
Collapse
|
99
|
Chen Z, Li H, Zhang L, Lee CK, Ho LWC, Chan CKW, Yang H, Choi CHJ. Specific Delivery of Oligonucleotides to the Cell Nucleus via Gentle Compression and Attachment of Polythymidine. ACS APPLIED MATERIALS & INTERFACES 2019; 11:27624-27640. [PMID: 31303000 DOI: 10.1021/acsami.9b11391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nonviral delivery of nucleic acids to the cell nucleus typically requires chemical methods that do not guarantee specific delivery (e.g., transfection agent) or physical methods that may require extensive fabrication (e.g., microfluidics) or an elevated pressure (e.g., 105 Pa for microneedles). We report a method of delivering oligonucleotides to the nucleus with high specificity (relative to the cytosol) by synergistically combining chemical and physical approaches. Particularly, we demonstrate that DNA oligonucleotides appended with a polythymidine [poly(T)] segment (chemical) profusely accumulate inside the nucleus when the cells are under gentle compression imposed by the weight of a single glass coverslip (physical; ∼2.2 Pa). Our "compression-cum-poly(T)" delivery method is simple, can be generalizable to three "hard-to-transfect" cell types, and does not induce significant levels of cytotoxicity or long-term oxidative stress to the treated cells when provided the use of suitable compression times and oligonucleotide concentrations. In bEnd.3 endothelial cells, compression-aided intranuclear delivery of poly(T) is primarily mediated by importin β and nucleoporin 62. Our method significantly enhances the intranuclear delivery of antisense oligonucleotides to bEnd.3 endothelioma cells and the inhibition of two target genes, including a reporter gene encoding the enhanced green fluorescent protein and an intranuclear lncRNA oncogene (metastasis-associated lung adenocarcinoma transcript 1), when compared with delivery without gentle compression or poly(T) attachment. Our data underscore the critical roles of pressure and nucleotide sequence on the intranuclear delivery of nucleic acids.
Collapse
|
100
|
Werner TR, Kunze AC, Stenzig J, Eschenhagen T, Hirt MN. Blockade of miR-140-3p prevents functional deterioration in afterload-enhanced engineered heart tissue. Sci Rep 2019; 9:11494. [PMID: 31391475 PMCID: PMC6686025 DOI: 10.1038/s41598-019-46818-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 07/02/2019] [Indexed: 12/11/2022] Open
Abstract
Afterload enhancement (AE) of rat engineered heart tissue (EHT) in vitro leads to a multitude of changes that in vivo are referred to as pathological cardiac hypertrophy: e.g., cardiomyocyte hypertrophy, contractile dysfunction, reactivation of fetal genes and fibrotic changes. Moreover AE induced the upregulation of 22 abundantly expressed microRNAs. Here, we aimed at evaluating the functional effect of inhibiting 7 promising microRNAs (miR-21-5p, miR-146b-5p, miR-31a-5p, miR-322-5p, miR-450a-5p, miR-140-3p and miR-132-3p) in a small-range screen. Singular transfection of locked nucleic acid (LNA)-based anti-miRs at 100 nM (before the one week AE-procedure) led to a powerful reduction of the targeted microRNAs. Pretreatment with anti-miR-146b-5p, anti-miR-322-5p or anti-miR-450a-5p did not alter the AE-induced contractile decline, while anti-miR-31a-5p-pretreatment even worsened it. Anti-miR-21-5p and anti-miR-132-3p partially attenuated the AE-effect, confirming previous reports. LNA-anti-miR against miR-140-3p, a microRNA recently identified as a prognostic biomarker of cardiovascular disease, also attenuated the AE-effect. To simplify future in vitro experiments and to create an inhibitor for in vivo applications, we designed shorter miR-140-3p-inhibitors and encountered variable efficiency. Only the inhibitor that effectively repressed miR-140-3p was also protective against the AE-induced contractile decline. In summary, in a small-range functional screen, miR-140-3p evolved as a possible new target for the attenuation of afterload-induced pathological cardiac hypertrophy.
Collapse
Affiliation(s)
- Tessa R Werner
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Ann-Cathrin Kunze
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Justus Stenzig
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Marc N Hirt
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.
| |
Collapse
|