1
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Shin M, Krishnamurthy PM, Devi G, Watts JK. Quantification of Antisense Oligonucleotides by Splint Ligation and Quantitative Polymerase Chain Reaction. Nucleic Acid Ther 2021; 32:66-73. [PMID: 34928745 PMCID: PMC8817697 DOI: 10.1089/nat.2021.0040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Reliable detection and quantification of antisense oligonucleotides (ASOs) in experimental and clinical specimens are essential to understand the biological function of novel oligonucleotide-based therapeutics. In this study, we describe a method to detect and quantify ASOs in biological samples, whereby the ASO acts as a splint to direct the ligation of complementary probes and quantitative real-time PCR was used to monitor ligation products. Low levels of 2′-O-methoxyethyl (2′-O-MOE) gapmer ASO in serum, liver, kidney, lung, heart, muscle, and brain tissues can be detected over a 6-log linear range for detection using this method. This method allows quantification of various types of chemically modified ASOs, including phosphorothioate linkage, 2′-O-methyl, 2′-O-MOE, and locked nucleic acid, as well as siRNAs. This method does not require probe modifications, and can be performed using standard laboratory equipment; making it a fast, sensitive, and reliable technique that can be widely applied. This detection method may find potential applications in detection of therapeutic oligonucleotides in biological samples.
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Affiliation(s)
- Minwook Shin
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
| | | | - Gitali Devi
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
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2
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Evéquoz D, Verhaart IEC, van de Vijver D, Renner W, Aartsma-Rus A, Leumann CJ. 7',5'-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy. Nucleic Acids Res 2021; 49:12089-12105. [PMID: 34850138 PMCID: PMC8643641 DOI: 10.1093/nar/gkab1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 01/16/2023] Open
Abstract
Antisense oligonucleotides are small pieces of modified DNA or RNA, which offer therapeutic potential for many diseases. We report on the synthesis of 7′,5′-α-bc-DNA phosphoramidite building blocks, bearing the A, G, T and MeC nucleobases. Solid-phase synthesis was performed to construct five oligodeoxyribonucleotides containing modified thymidine residues, as well as five fully modified oligonucleotides. Incorporations of the modification inside natural duplexes resulted in strong destabilizing effects. However, fully modified strands formed very stable duplexes with parallel RNA complements. In its own series, 7′,5′-α-bc-DNA formed duplexes with a surprising high thermal stability. CD spectroscopy and extensive molecular modeling indicated the adoption by the homo-duplex of a ladder-like structure, while hetero-duplexes with DNA or RNA still form helical structure. The biological properties of this new modification were investigated in animal models for Duchenne muscular dystrophy and spinal muscular atrophy, where exon splicing modulation can restore production of functional proteins. It was found that the 7′,5′-α-bc-DNA scaffold confers a high biostability and a good exon splicing modulation activity in vitro and in vivo.
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Affiliation(s)
- Damien Evéquoz
- Alpha Anomeric, 140 Bis, Rue de Rennes, 75006 Paris, France
| | - Ingrid E C Verhaart
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Davy van de Vijver
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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3
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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: 37] [Impact Index Per Article: 9.3] [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.
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Affiliation(s)
- Qing Li
- Department of Function, ShiJiaZhuang Traditional Chinese Medical Hospital, ShiJiaZhuang, HeBei, China.
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4
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Datson NA, Bijl S, Janson A, Testerink J, van den Eijnde R, Weij R, Puoliväli J, Lehtimäki K, Bragge T, Ahtoniemi T, van Deutekom JC. Using a State-of-the-Art Toolbox to Evaluate Molecular and Functional Readouts of Antisense Oligonucleotide-Induced Exon Skipping in mdx Mice. Nucleic Acid Ther 2020; 30:50-65. [PMID: 31821107 PMCID: PMC7049912 DOI: 10.1089/nat.2019.0824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe childhood muscle disease primarily caused by the lack of functional dystrophin at the muscle fiber membranes. Multiple therapeutic approaches are currently in (pre)clinical development, aimed at restoring expression of (truncated) dystrophin. Key questions in this phase relate to route of drug administration, dose regimen, and levels of dystrophin required to improve muscle function. A series of studies applying antisense oligonucleotides (AONs) in the mdx mouse model for DMD has been reported over the last two decades, claiming a variable range of exon skipping and increased dystrophin levels correlated to some functional improvement. The aim of this study was to compare the efficacy of subcutaneous (SC) versus intravenous (IV) dosing routes of an mdx-specific AON at both the molecular and functional level, using state-of-the-art quantitative technologies, including digital droplet polymerase chain reaction, capillary Western immunoassay, magnetic resonance imaging, and automated kinematic analysis. The majority of all readouts we quantified, both molecular and functional, showed that IV dosing of the AON had a more pronounced beneficial effect than SC dosing in mdx mice. Last, but not least, the more quantitative molecular and functional data obtained in this study suggest that low levels of dystrophin protein of at least 2.5% of wild type may already have a beneficial effect on muscle leakiness and may improve motor performance of mdx mice.
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Affiliation(s)
| | | | | | | | | | - Rudie Weij
- BioMarin Nederland BV, Leiden, the Netherlands
| | | | | | - Timo Bragge
- Charles River Discovery Research Services, Kuopio, Finland
| | - Toni Ahtoniemi
- Charles River Discovery Research Services, Kuopio, Finland
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5
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Bosgra S, Sipkens J, de Kimpe S, den Besten C, Datson N, van Deutekom J. The Pharmacokinetics of 2'- O-Methyl Phosphorothioate Antisense Oligonucleotides: Experiences from Developing Exon Skipping Therapies for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2019; 29:305-322. [PMID: 31429628 DOI: 10.1089/nat.2019.0805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Delivery to the target site and adversities related to off-target exposure have made the road to clinical success and approval of antisense oligonucleotide (AON) therapies challenging. Various classes of AONs have distinct chemical features and pharmacological properties. Understanding the similarities and differences in pharmacokinetics (PKs) among AON classes is important to make future development more efficient and may facilitate regulatory guidance of AON development programs. For the class of 2'-O-methyl phosphorothioate (2OMe PS) RNA AONs, most nonclinical and clinical PK data available today are derived from development of exon skipping therapies for Duchenne muscular dystrophy (DMD). While some publications have featured PK aspects of these AONs, no comprehensive overview is available to date. This article presents a detailed review of absorption, distribution, metabolism, and excretion of 2OMe PS AONs, compiled from publicly available data and previously unpublished internal data on drisapersen and related exon skipping candidates in preclinical species and DMD patients. Considerations regarding drug-drug interactions, toxicokinetics, and pharmacodynamics are also discussed. From the data presented, the picture emerges of consistent PK properties within the 2OMe PS class, predictable behavior across species, and a considerable overlap with other single-stranded PS AONs. A level of detail on muscle as a target tissue is provided, which was not previously available. Furthermore, muscle biopsy samples taken in DMD clinical trials allowed confirmation of the applicability of interspecies scaling approaches commonly applied in the absence of clinical target tissue data.
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6
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Echevarría L, Aupy P, Relizani K, Bestetti T, Griffith G, Blandel F, Komisarski M, Haeberli A, Svinartchouk F, Garcia L, Goyenvalle A. Evaluating the Impact of Variable Phosphorothioate Content in Tricyclo-DNA Antisense Oligonucleotides in a Duchenne Muscular Dystrophy Mouse Model. Nucleic Acid Ther 2019; 29:148-160. [PMID: 31009315 DOI: 10.1089/nat.2018.0773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Antisense oligonucleotides (ASOs) hold promise for therapeutic splice switching correction for genetic diseases, in particular for Duchenne muscular dystrophy (DMD), for which ASO-exon skipping represents one of the most advanced therapeutic strategies. We have previously reported the therapeutic potential of tricyclo-DNA (tcDNA) in mouse models of DMD, highlighting the unique pharmaceutical properties and unprecedented uptake in many tissues after systemic delivery, including the heart and central nervous system. TcDNA-ASOs demonstrate an encouraging safety profile and no particular class-related toxicity, however, when administered in high doses for several months, mild renal toxicity is observed secondary to predictable phosphorothioate (PS)-ASO accumulation in kidneys. In this study, we investigate the influence of the relative content of PS linkages in tcDNA-ASOs on exon skipping efficacy. Mdx mice were injected intravenously once weekly for 4 weeks with tcDNA carrying various amounts of PS linkages (0%, 25%, 33%, 50%, 67%, 83%, and 100%). The results indicate that levels of exon-23 skipping and dystrophin rescue increase with the number of PS linkages in most skeletal muscles except in the heart. As expected, plasma coagulation times are shortened with decreasing PS content, and tcDNA-protein binding in serum directly correlates with the number of PS linkages on the tcDNA backbone. Altogether, these data contribute in establishing the appropriate sulfur content within the tcDNA backbone for maximal efficacy and minimal toxicity of the oligonucleotide.
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Affiliation(s)
- Lucía Echevarría
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France.,2 SQY Therapeutics, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Philippine Aupy
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | - Karima Relizani
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France.,2 SQY Therapeutics, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Thomas Bestetti
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | - Graziella Griffith
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France.,2 SQY Therapeutics, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Florence Blandel
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | | | | | - Fedor Svinartchouk
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France.,2 SQY Therapeutics, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Luis Garcia
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | - Aurélie Goyenvalle
- 1 Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
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7
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van Putten M, Tanganyika-de Winter C, Bosgra S, Aartsma-Rus A. Nonclinical Exon Skipping Studies with 2'-O-Methyl Phosphorothioate Antisense Oligonucleotides in mdx and mdx-utrn-/- Mice Inspired by Clinical Trial Results. Nucleic Acid Ther 2019; 29:92-103. [PMID: 30672725 PMCID: PMC6461150 DOI: 10.1089/nat.2018.0759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Duchenne muscular dystrophy is a severe, progressive muscle-wasting disease that is caused by mutations that abolish the production of functional dystrophin protein. The exon skipping approach aims to restore the disrupted dystrophin reading frame, to allow the production of partially functional dystrophins, such as found in the less severe Becker muscular dystrophy. Exon skipping is achieved by antisense oligonucleotides (AONs). Several chemical modifications have been tested in nonclinical and clinical trials. The morpholino phosphorodiamidate oligomer eteplirsen has been approved by the Food and Drug Administration, whereas clinical development with the 2'-O-methyl phosphorothioate (2OMePS) AON drisapersen was recently stopped. In this study, we aimed to study various aspects of 2OMePS AONs in nonclinical animal studies. We show that while efficiency of exon skipping restoration is comparable in young and older C57BL/10ScSn-Dmdmdx/J (mdx/BL10) mice, functional improvement was only observed for younger treated mice. Muscle quality did not affect exon skipping efficiency as exon skip and dystrophin levels were similar between mdx/BL10 and more severely affected, age-matched D2-mdx mice. We further report that treadmill running increases AON uptake and dystrophin levels in mdx/BL10 mice. Finally, we show that even low levels of exon skipping and dystrophin restoration are sufficient to significantly increase the survival of mdx-utrn-/- mice from 70 to 97 days.
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Affiliation(s)
- Maaike van Putten
- 1 Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Sieto Bosgra
- 2 Biomarin Nederland BV, Leiden, the Netherlands
| | - Annemieke Aartsma-Rus
- 1 Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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8
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Suppression of prostate tumor cell survival by antisense oligonucleotide-mediated inhibition of AR-V7 mRNA synthesis. Oncogene 2019; 38:3696-3709. [PMID: 30664691 PMCID: PMC6756119 DOI: 10.1038/s41388-019-0696-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 12/19/2022]
Abstract
One of the mechanisms by which advanced prostate cancer develops resistance to androgen deprivation therapy is the elevated expression of C-terminally truncated androgen receptor (AR) variants. These variants, such as AR-V7, originate from aberrant splicing of the AR pre-mRNA and the inclusion of a cryptic exon containing a premature stop codon in the mRNA. The resulting loss of the ligand-binding domain allows AR-V7 to act as a constitutively active transcription factor. Here, we designed two antisense oligonucleotides (AONs) directed against cryptic splicing signals within the AR pre-mRNA. These two AONs, AON-ISE and AON-ESE, demonstrated high efficiency in silencing AR-V7 splicing without affecting full-length AR expression. The subsequent downregulation of AR-V7-target gene UBE2C was accompanied by inhibition of androgen-independent cell proliferation and induction of apoptosis in castration-resistant prostate cancer (CRPC)-derived cell line models 22Rv1, DuCaP, and VCaP. Our results show that splicing-directed AONs can efficiently prevent expression of AR-V7, providing an attractive new therapeutic option for the treatment of CRPC.
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9
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Ultrasensitive Hybridization-Based ELISA Method for the Determination of Phosphorodiamidate Morpholino Oligonucleotides in Biological samples. Methods Mol Biol 2018; 1565:265-277. [PMID: 28364250 DOI: 10.1007/978-1-4939-6817-6_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Determining the concentration of oligonucleotide in biological samples such as tissue lysate and serum is essential for determining the biodistribution and pharmacokinetic profile, respectively. ELISA-based assays have shown far greater sensitivities compared to other methods such as HPLC and LC/MS. Here, we describe a novel ultrasensitive hybridization-based ELISA method for quantitating morpholino oligonucleotides in mouse tissue lysate and serum samples. The assay has a linear detection range of 5-250 pM (R2 > 0.99).
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10
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González-Barriga A, Nillessen B, Kranzen J, van Kessel IDG, Croes HJE, Aguilera B, de Visser PC, Datson NA, Mulders SAM, van Deutekom JCT, Wieringa B, Wansink DG. Intracellular Distribution and Nuclear Activity of Antisense Oligonucleotides After Unassisted Uptake in Myoblasts and Differentiated Myotubes In Vitro. Nucleic Acid Ther 2017; 27:144-158. [PMID: 28375678 PMCID: PMC5467152 DOI: 10.1089/nat.2016.0641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Clinical efficacy of antisense oligonucleotides (AONs) for the treatment of neuromuscular disorders depends on efficient cellular uptake and proper intracellular routing to the target. Selection of AONs with highest in vitro efficiencies is usually based on chemical or physical methods for forced cellular delivery. Since these methods largely bypass existing natural mechanisms for membrane passage and intracellular trafficking, spontaneous uptake and distribution of AONs in cells are still poorly understood. Here, we report on the unassisted uptake of naked AONs, so-called gymnosis, in muscle cells in culture. We found that gymnosis works similarly well for proliferating myoblasts as for terminally differentiated myotubes. Cell biological analyses combined with microscopy imaging showed that a phosphorothioate backbone promotes efficient gymnosis, that uptake is clathrin mediated and mainly results in endosomal-lysosomal accumulation. Nuclear localization occurred at a low level, but the gymnotically delivered AONs effectively modulated the expression of their nuclear RNA targets. Chloroquine treatment after gymnotic delivery helped increase nuclear AON levels. In sum, we demonstrate that gymnosis is feasible in proliferating and non-proliferating muscle cells and we confirm the relevance of AON chemistry for uptake and intracellular trafficking with this method, which provides a useful means for bio-activity screening of AONs in vitro.
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Affiliation(s)
- Anchel González-Barriga
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands .,2 BioMarin Nederland B.V., Leiden, the Netherlands
| | - Bram Nillessen
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Julia Kranzen
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Ingeborg D G van Kessel
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Huib J E Croes
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | | | | | | | | | | | - Bé Wieringa
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Derick G Wansink
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
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11
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Oligonucleotide therapies for disorders of the nervous system. Nat Biotechnol 2017; 35:249-263. [PMID: 28244991 DOI: 10.1038/nbt.3784] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022]
Abstract
Oligonucleotide therapies are currently experiencing a resurgence driven by advances in backbone chemistry and discoveries of novel therapeutic pathways that can be uniquely and efficiently modulated by the oligonucleotide drugs. A quarter of a century has passed since oligonucleotides were first applied in living mammalian brain to modulate gene expression. Despite challenges in delivery to the brain, multiple oligonucleotide-based compounds are now being developed for treatment of human brain disorders by direct delivery inside the blood brain barrier (BBB). Notably, the first new central nervous system (CNS)-targeted oligonucleotide-based drug (nusinersen/Spinraza) was approved by US Food and Drug Administration (FDA) in late 2016 and several other compounds are in advanced clinical trials. Human testing of brain-targeted oligonucleotides has highlighted unusual pharmacokinetic and pharmacodynamic properties of these compounds, including complex active uptake mechanisms, low systemic exposure, extremely long half-lives, accumulation and gradual release from subcellular depots. Further work on oligonucleotide uptake, development of formulations for delivery across the BBB and relevant disease biology studies are required for further optimization of the oligonucleotide drug development process for brain applications.
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12
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Verheul RC, van Deutekom JCT, Datson NA. Digital Droplet PCR for the Absolute Quantification of Exon Skipping Induced by Antisense Oligonucleotides in (Pre-)Clinical Development for Duchenne Muscular Dystrophy. PLoS One 2016; 11:e0162467. [PMID: 27612288 PMCID: PMC5017733 DOI: 10.1371/journal.pone.0162467] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/15/2023] Open
Abstract
Antisense oligonucleotides (AONs) in clinical development for Duchenne muscular dystrophy (DMD) aim to induce skipping of a specific exon of the dystrophin transcript during pre-mRNA splicing. This results in restoration of the open reading frame and consequently synthesis of a dystrophin protein with a shorter yet functional central rod domain. To monitor the molecular therapeutic effect of exon skip-inducing AONs in clinical studies, accurate quantification of pre- and post-treatment exon skip levels is required. With the recent introduction of 3rd generation digital droplet PCR (ddPCR), a state-of-the-art technology became available which allows absolute quantification of transcript copy numbers with and without specific exon skip with high precision, sensitivity and reproducibility. Using Taqman assays with probes targeting specific exon-exon junctions, we here demonstrate that ddPCR reproducibly quantified cDNA fragments with and without exon 51 of the DMD gene over a 4-log dynamic range. In a comparison of conventional nested PCR, qPCR and ddPCR using cDNA constructs with and without exon 51 mixed in different molar ratios using, ddPCR quantification came closest to the expected outcome over the full range of ratios (0–100%), while qPCR and in particular nested PCR overestimated the relative percentage of the construct lacking exon 51. Highest accuracy was similarly obtained with ddPCR in DMD patient-derived muscle cells treated with an AON inducing exon 51 skipping. We therefore recommend implementation of ddPCR for quantification of exon skip efficiencies of AONs in (pre)clinical development for DMD.
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13
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Havens MA, Hastings ML. Splice-switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Res 2016; 44:6549-63. [PMID: 27288447 PMCID: PMC5001604 DOI: 10.1093/nar/gkw533] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/02/2016] [Indexed: 01/09/2023] Open
Abstract
Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipulate protein production from a gene. Splicing modulation is particularly valuable in cases of disease caused by mutations that lead to disruption of normal splicing or when interfering with the normal splicing process of a gene transcript may be therapeutic. SSOs offer an effective and specific way to target and alter splicing in a therapeutic manner. Here, we discuss the different approaches used to target and alter pre-mRNA splicing with SSOs. We detail the modifications to the nucleic acids that make them promising therapeutics and discuss the challenges to creating effective SSO drugs. We highlight the development of SSOs designed to treat Duchenne muscular dystrophy and spinal muscular atrophy, which are currently being tested in clinical trials.
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Affiliation(s)
- Mallory A Havens
- Department of Biology, Lewis University, Romeoville, IL 60446, USA
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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14
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Burki U, Keane J, Blain A, O'Donovan L, Gait MJ, Laval SH, Straub V. Development and Application of an Ultrasensitive Hybridization-Based ELISA Method for the Determination of Peptide-Conjugated Phosphorodiamidate Morpholino Oligonucleotides. Nucleic Acid Ther 2015; 25:275-84. [PMID: 26176274 DOI: 10.1089/nat.2014.0528] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotide (AON)-induced exon skipping is one of the most promising strategies for treating Duchenne muscular dystrophy (DMD) and other rare monogenic conditions. Phosphorodiamidate morpholino oligonucleotides (PMOs) and 2'-O-methyl phosphorothioate (2'OMe) are two of the most advanced AONs in development. The next generation of peptide-conjugated PMO (P-PMO) is also showing great promise, but to advance these therapies it is essential to determine the pharmacokinetic and biodistribution (PK/BD) profile using a suitable method to detect AON levels in blood and tissue samples. An enzyme-linked immunosorbent assay (ELISA)-based method, which shows greater sensitivity than the liquid chromatography-mass spectrometry method, is the method of choice for 2'OMe detection in preclinical and clinical studies. However, no such assay has been developed for PMO/P-PMO detection, and we have, therefore, developed an ultrasensitive hybridization-based ELISA for this purpose. The assay has a linear detection range of 5-250 pM (R(2)>0.99) in mouse serum and tissue lysates. The sensitivity was sufficient for determining the 24-h PK/BD profile of PMO and P-PMO injected at standard doses (12.5 mg/kg) in mdx mice, the dystrophin-deficient mouse model for DMD. The assay demonstrated an accuracy approaching 100% with precision values under 12%. This provides a powerful cost-effective assay for the purpose of accelerating the development of these emerging therapeutic agents.
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Affiliation(s)
- Umar Burki
- 1 The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Jonathan Keane
- 1 The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Alison Blain
- 1 The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Liz O'Donovan
- 2 Laboratory of Molecular Biology , Medical Research Council, Cambridge, United Kingdom
| | - Michael John Gait
- 2 Laboratory of Molecular Biology , Medical Research Council, Cambridge, United Kingdom
| | - Steven H Laval
- 1 The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Volker Straub
- 1 The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University , Newcastle upon Tyne, United Kingdom
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Functional correction in mouse models of muscular dystrophy using exon-skipping tricyclo-DNA oligomers. Nat Med 2015; 21:270-5. [PMID: 25642938 DOI: 10.1038/nm.3765] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/30/2014] [Indexed: 12/27/2022]
Abstract
Antisense oligonucleotides (AONs) hold promise for therapeutic correction of many genetic diseases via exon skipping, and the first AON-based drugs have entered clinical trials for neuromuscular disorders. However, despite advances in AON chemistry and design, systemic use of AONs is limited because of poor tissue uptake, and recent clinical reports confirm that sufficient therapeutic efficacy has not yet been achieved. Here we present a new class of AONs made of tricyclo-DNA (tcDNA), which displays unique pharmacological properties and unprecedented uptake by many tissues after systemic administration. We demonstrate these properties in two mouse models of Duchenne muscular dystrophy (DMD), a neurogenetic disease typically caused by frame-shifting deletions or nonsense mutations in the gene encoding dystrophin and characterized by progressive muscle weakness, cardiomyopathy, respiratory failure and neurocognitive impairment. Although current naked AONs do not enter the heart or cross the blood-brain barrier to any substantial extent, we show that systemic delivery of tcDNA-AONs promotes a high degree of rescue of dystrophin expression in skeletal muscles, the heart and, to a lesser extent, the brain. Our results demonstrate for the first time a physiological improvement of cardio-respiratory functions and a correction of behavioral features in DMD model mice. This makes tcDNA-AON chemistry particularly attractive as a potential future therapy for patients with DMD and other neuromuscular disorders or with other diseases that are eligible for exon-skipping approaches requiring whole-body treatment.
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Correlating In Vitro Splice Switching Activity With Systemic In Vivo Delivery Using Novel ZEN-modified Oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e212. [PMID: 25423116 PMCID: PMC4459549 DOI: 10.1038/mtna.2014.63] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/20/2014] [Indexed: 01/16/2023]
Abstract
Splice switching oligonucleotides (SSOs) induce alternative splicing of pre-mRNA and typically employ chemical modifications to increase nuclease resistance and binding affinity to target pre-mRNA. Here we describe a new SSO non-base modifier (a naphthyl-azo group, "ZEN™") to direct exon exclusion in mutant dystrophin pre-mRNA to generate functional dystrophin protein. The ZEN modifier is placed near the ends of a 2'-O-methyl (2'OMe) oligonucleotide, increasing melting temperature and potency over unmodified 2'OMe oligonucleotides. In cultured H2K cells, a ZEN-modified 2'OMe phosphorothioate (PS) oligonucleotide delivered by lipid transfection greatly enhanced dystrophin exon skipping over the same 2'OMePS SSO lacking ZEN. However, when tested using free gymnotic uptake in vitro and following systemic delivery in vivo in dystrophin deficient mdx mice, the same ZEN-modified SSO failed to enhance potency. Importantly, we show for the first time that in vivo activity of anionic SSOs is modelled in vitro only when using gymnotic delivery. ZEN is thus a novel modifier that enhances activity of SSOs in vitro but will require improved delivery methods before its in vivo clinical potential can be realized.
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van Putten M, Young C, van den Berg S, Pronk A, Hulsker M, Karnaoukh TG, Vermue R, van Dijk KW, de Kimpe S, Aartsma-Rus A. Preclinical studies on intestinal administration of antisense oligonucleotides as a model for oral delivery for treatment of duchenne muscular dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e211. [PMID: 25405468 PMCID: PMC4459548 DOI: 10.1038/mtna.2014.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/01/2014] [Indexed: 01/03/2023]
Abstract
Antisense oligonucleotides (AONs) used to reframe dystrophin mRNA transcripts for Duchenne muscular dystrophy (DMD) patients are tested in clinical trials. Here, AONs are administered subcutaneously and intravenously, while the less invasive oral route would be preferred. Oral delivery of encapsulated AONs supplemented with a permeation enhancer, sodium caprate, has been successfully used to target tumor necrosis factor (TNF)-α expression in liver. To test the feasibility of orally delivered AONs for DMD, we applied 2′-O-methyl phosphorothioate AONs (with or without sodium caprate supplementation) directly to the intestine of mdx mice and compared pharmacokinetics and -dynamics with intravenous, intraperitoneal, and subcutaneous delivery. Intestinally infused AONs were taken up, but resulted in lower plasma levels compared to other delivery routes, although bioavailability could be largely improved by supplementation of sodium caprate. After intestinal infusion, AON levels in all tissues were lower than for other administration routes, as were the ratios of target versus nontarget organ levels, except for diaphragm and heart where comparable levels and ratios were observed. For each administration route, low levels of exon skipping in triceps was observed 3 hours post-AON administration. These data suggest that oral administration of naked 2′-O-methyl phosphorothioate AONs may be feasible, but only when high AON concentrations are used in combination with sodium caprate.
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Affiliation(s)
- Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Courtney Young
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sjoerd van den Berg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Amanda Pronk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet Hulsker
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Rick Vermue
- Prosensa Therapeutics BV, Leiden, the Netherlands
| | - Ko Willems van Dijk
- 1] Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands [2] Department of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Jeong J, Shin K, Lee SB, Lee DR, Kwon H. Patient-tailored application for Duchene muscular dystrophy on mdx mice based induced mesenchymal stem cells. Exp Mol Pathol 2014; 97:253-8. [PMID: 25102299 DOI: 10.1016/j.yexmp.2014.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/01/2014] [Indexed: 12/11/2022]
Abstract
Mesenchymal stem cells (MSCs) may be used as powerful tools for the repair and regeneration of damaged tissues. However, isolating tissue specific-derived MSCs may cause pain and increased infection rates in patients, and repetitive isolations may be required. To overcome these difficulties, we have examined alternative methods for MSC production. Here, we show that induced pluripotent stem cells (iPSCs) may be differentiated into mesenchymal stem cells (iMSCs) following exposure to SB431542. Purified iMSCs were administered to mdx mice to study skeletal muscle regeneration in a murine model of muscular dystrophy. Purified iMSCs displayed fibroblast-like morphology, formed three-dimensional spheroid structures, and expressed characteristic mesenchymal stem cell surface markers such as CD29, CD33, CD73, CD90, and CD105. Moreover, iMSCs were capable of differentiating into adipogenic, osteogenic, and chondrogenic lineages. Transplanting iMSC cells to tibialis anterior skeletal muscle tissue in mdx mice lowered oxidative damage as evidenced by a reduction in nitrotyrosine levels, and normal dystrophin expression levels were restored. This study demonstrates the therapeutic potential of purified iMSCs in skeletal muscle regeneration in mdx mice, and suggests that iPSCs are a viable alternate source for deriving MSCs as needed.
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Affiliation(s)
- Jaemin Jeong
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea; BK21 Plus Project, Yonsei University College of Dentistry, Seoul 120-752, South Korea.
| | - Kyungshin Shin
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea; Research Center for Radio-Senescence, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea
| | - Seung Bum Lee
- National Radiation Emergency Medical Center, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea
| | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul 135-081, South Korea
| | - Heechung Kwon
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea; Research Center for Radio-Senescence, Korea Institute of Radiological and Medical Sciences, Seoul 139-706, South Korea.
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19
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The Dynamics of Compound, Transcript, and Protein Effects After Treatment With 2OMePS Antisense Oligonucleotides in mdx Mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e148. [PMID: 24549299 PMCID: PMC3950770 DOI: 10.1038/mtna.2014.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/24/2013] [Indexed: 12/28/2022]
Abstract
Antisense-mediated exon skipping is currently in clinical development for Duchenne muscular dystrophy (DMD) to amend the consequences of the underlying genetic defect and restore dystrophin expression. Due to turnover of compound, transcript, and protein, chronic treatment with effector molecules (antisense oligonucleotides) will be required. To investigate the dynamics and persistence of antisense 2′-O-methyl phosphorothioate oligonucleotides, exon skipping, and dystrophin expression after dosing was concluded, mdx mice were treated subcutaneously for 8 weeks with 100 mg/kg oligonucleotides twice weekly. Thereafter, mice were sacrificed at different time points after the final injection (36 hours–24 weeks). Oligonucleotide half-life was longer in heart (~65 days) compared with that in skeletal muscle, liver, and kidney (~35 days). Exon skipping half-lives varied between 33 and 53 days, whereas dystrophin protein showed a long half-life (>100 days). Oligonucleotide and exon-skipping levels peaked in the first week and declined thereafter. By contrast, dystrophin expression peaked after 3–8 weeks and then slowly declined, remaining detectable after 24 weeks. Concordance between levels of oligonucleotides, exon skipping, and proteins was observed, except in heart, wherein high oligonucleotide levels but low exon skipping and dystrophin expression were seen. Overall, these results enhance our understanding of the pharmacokinetics and pharmacodynamics of 2′-O-methyl phosphorothioate oligos used for the treatment of DMD.
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Jirka SMG, Heemskerk H, Tanganyika-de Winter CL, Muilwijk D, Pang KH, de Visser PC, Janson A, Karnaoukh TG, Vermue R, 't Hoen PAC, van Deutekom JCT, Aguilera B, Aartsma-Rus A. Peptide conjugation of 2'-O-methyl phosphorothioate antisense oligonucleotides enhances cardiac uptake and exon skipping in mdx mice. Nucleic Acid Ther 2013; 24:25-36. [PMID: 24320790 DOI: 10.1089/nat.2013.0448] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antisense oligonucleotide (AON)-mediated exon skipping is a promising therapeutic approach for Duchenne muscular dystrophy that is currently being tested in various clinical trials. This approach is based on restoring the open reading frame of dystrophin transcripts resulting in shorter but partially functional dystrophin proteins as found in patients with Becker muscular dystrophy. After systemic administration, a large proportion of AONs ends up in the liver and kidneys. Therefore, enhancing AON uptake by skeletal and cardiac muscle would improve the AONs' therapeutic effect. For phosphorodiamidate morpholino oligomer, AONs use nonspecific positively charged cell penetrating peptides to enhance efficacy. However, this is challenging for negatively charged 2'-O-methyl phosphorothioate oligomer. Therefore, we screened a 7-mer phage display peptide library to identify muscle and heart homing peptides in vivo in the mdx mouse model and found a promising candidate peptide capable of binding muscle cells in vitro and in vivo. Upon systemic administration in dystrophic mdx mice, conjugation of a 2'-O-methyl phosphorothioate AON to this peptide indeed improved uptake in skeletal and cardiac muscle, and resulted in higher exon skipping levels with a significant difference in heart and diaphragm. Based on these results, peptide conjugation represents an interesting strategy to enhance the therapeutic effect of exon skipping with 2'-O-methyl phosphorothioate AONs for Duchenne muscular dystrophy.
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Affiliation(s)
- Silvana M G Jirka
- 1 Department of Human Genetics, Leiden University Medical Center , Leiden, The Netherlands
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