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Zhu A, Chiba S, Shimizu Y, Kunitake K, Okuno Y, Aoki Y, Yokota T. Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping. Pharmaceutics 2023; 15:1808. [PMID: 37513994 PMCID: PMC10384346 DOI: 10.3390/pharmaceutics15071808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine-learning-based computational methods, such as eSkip-Finder, have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce the computational burden and improve the prediction performance by using feature selection within machine-learning algorithms and ensemble-learning techniques. We evaluated our approach using a dataset of experimentally validated exon-skipping events, dividing it into training and testing sets. Our results demonstrate that using a three-way-voting approach with random forest, gradient boosting, and XGBoost can significantly reduce the computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2'-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.
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Affiliation(s)
- Alex Zhu
- Phillips Academy, Andover, MA 01810, USA
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shuntaro Chiba
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Yuki Shimizu
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Yasushi Okuno
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Zheng Z, Song Y, Tan X. Deciphering hERG Mutation in Long QT Syndrome Type 2 Using Antisense Oligonucleotide-Mediated Techniques: Lessons from Cystic Fibrosis. Heart Rhythm 2023:S1547-5271(23)02180-X. [PMID: 37121422 DOI: 10.1016/j.hrthm.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/02/2023]
Abstract
Long QT syndrome type 2 (LQT2) is a genetic disorder caused by mutations in the KCNH2 gene, also known as the human ether-a-go-go-related gene (hERG). Over 30% of hERG mutations result in a premature termination codon (PTC) that triggers a process called nonsense-mediated mRNA decay (NMD), where the mRNA transcript is degraded. NMD is a quality control mechanism that removes faulty mRNA to prevent the translation of truncated proteins. Recent advances in antisense oligonucleotide (ASO) technology in the field of cystic fibrosis (CF) have yielded significant progress, including the ASO-mediated comprehensive characterization of key NMD factors and exon-skipping therapy. These advances have contributed to our understanding of the role of PTC-containing mutations in disease phenotypes and have also led to the development of potentially useful therapeutic strategies. Historically, studies of CF have provided valuable insights for the research on LQT2, particularly concerning increasing the expression of hERG. In this article, we outline the current state of knowledge regarding ASO, NMD, and hERG and discuss the introduction of ASO technology in the CF to elucidate the pathogenic mechanisms through targeting NMD. We also discuss the potential clinical therapeutic benefits and limitations of ASO for the management of LQT2. By drawing on lessons learned from CF research, we explore the potential translational values of these advances into LQT2 studies.
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Affiliation(s)
- Zequn Zheng
- Department of Cardiology, Shantou University Medical College, Shantou, China; Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, China; Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, China.
| | - Yongfei Song
- Ningbo Institute for Medicine &Biomedical Engineering Combined Innovation, Ningbo, China
| | - Xuerui Tan
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, China; Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, China.
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3
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Wang X, You B, Yin F, Chen C, He H, Liu F, Pan Z, Ni X, Pang N, Peng J. A presumed missense variant in the U2AF2 gene causes exon skipping in neurodevelopmental diseases. J Hum Genet 2023; 68:375-382. [PMID: 36747105 DOI: 10.1038/s10038-023-01128-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/14/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an indispensable pre-mRNA splicing factor in the early process of splicing. Recently, U2AF2 was reported as a novel candidate gene associated with neurodevelopmental disorders. Herein, we report a patient with a novel presumed heterozygous missense variant in the U2AF2 gene (c.603G>T), who has a similar clinical phenotype as the patient reported before, including epilepsy, intellectual disability, language delay, microcephaly, and hypoplastic corpus callosum. We reviewed the phenotypic and genetic spectrum of patients with U2AF2-related neurological diseases, both newly diagnosed and previously reported. To investigate the possible pathogenesis, EBV-immortalized lymphoblastoid cells were derived from the peripheral blood obtained from the patient and control groups. Furthermore, according to the results of WB, RT-PCR, Q-PCR, and cDNA sequencing of RT-PCR products, the presumed missense variant c.603G>T caused exon 6 skipping in the U2AF2 mRNA transcript and led to a truncated protein (p.E163_E201del). Cell Counting Kit-8 (CCK-8) and cell cycle detection demonstrated that the variant c.603G>T inhibited the proliferation of patient lymphocyte cells compared with the control group. This study is aimed at expanding the phenotypic and genetic spectrum of U2AF2-related neurodevelopmental diseases and investigating the potential effects. This is the first report of the possible pathogenesis of a U2AF2 gene pathogenic variant in a patient with neurodevelopmental diseases and shows that a novel presumed missense variant in the U2AF2 gene causes exon skipping.
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Affiliation(s)
- Xiaole Wang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Baiyang You
- Department of Physical Medicine & Rehabilitation, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Hailan He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Fangyun Liu
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Zou Pan
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Xiaoyuan Ni
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China. .,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Changsha, China.
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4
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Vester K, Preußner M, Holton N, Feng S, Schultz C, Heyd F, Wahl MC. Recruitment of a splicing factor to the nuclear lamina for its inactivation. Commun Biol 2022; 5:736. [PMID: 35869234 PMCID: PMC9307855 DOI: 10.1038/s42003-022-03689-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Precursor messenger RNA splicing is a highly regulated process, mediated by a complex RNA-protein machinery, the spliceosome, that encompasses several hundred proteins and five small nuclear RNAs in humans. Emerging evidence suggests that the spatial organization of splicing factors and their spatio-temporal dynamics participate in the regulation of splicing. So far, methods to manipulate the spatial distribution of splicing factors in a temporally defined manner in living cells are missing. Here, we describe such an approach that takes advantage of a reversible chemical dimerizer, and outline the requirements for efficient, reversible re-localization of splicing factors to selected sub-nuclear compartments. In a proof-of-principle study, the partial re-localization of the PRPF38A protein to the nuclear lamina in HEK293T cells induced a moderate increase in intron retention. Our approach allows fast and reversible re-localization of splicing factors, has few side effects and can be applied to many splicing factors by fusion of a protein tag through genome engineering. Apart from the systematic analysis of the spatio-temporal aspects of splicing regulation, the approach has a large potential for the fast induction and reversal of splicing switches and can reveal mechanisms of splicing regulation in native nuclear environments. Through the use of a reversible chemical dimerizer, the splicing factor PRPF38A is re-localized to the nuclear lamina, paving the way for a systematic analysis of spatio-temporal splicing regulation.
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Luo M, Lee LKC, Peng B, Choi CHJ, Tong WY, Voelcker NH. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201740. [PMID: 35851766 PMCID: PMC9475540 DOI: 10.1002/advs.202201740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/19/2022] [Indexed: 06/01/2023]
Abstract
Central Nervous System (CNS) diseases, such as Alzheimer's diseases (AD), Parkinson's Diseases (PD), brain tumors, Huntington's disease (HD), and stroke, still remain difficult to treat by the conventional molecular drugs. In recent years, various gene therapies have come into the spotlight as versatile therapeutics providing the potential to prevent and treat these diseases. Despite the significant progress that has undoubtedly been achieved in terms of the design and modification of genetic modulators with desired potency and minimized unwanted immune responses, the efficient and safe in vivo delivery of gene therapies still poses major translational challenges. Various non-viral nanomedicines have been recently explored to circumvent this limitation. In this review, an overview of gene therapies for CNS diseases is provided and describes recent advances in the development of nanomedicines, including their unique characteristics, chemical modifications, bioconjugations, and the specific applications that those nanomedicines are harnessed to deliver gene therapies.
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Affiliation(s)
- Meihua Luo
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and Nanotechnologythe University of QueenslandSt LuciaQLD4072Australia
| | - Leo Kit Cheung Lee
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Bo Peng
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Frontiers Science Center for Flexible ElectronicsXi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical materials & EngineeringNorthwestern Polytechnical UniversityXi'an710072China
| | - Chung Hang Jonathan Choi
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Wing Yin Tong
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)ClaytonVIC3168Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClaytonVIC3168Australia
- Materials Science and EngineeringMonash University14 Alliance LaneClaytonVIC3800Australia
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6
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Fuentes-Fayos AC, Pérez-Gómez JM, G-García ME, Jiménez-Vacas JM, Blanco-Acevedo C, Sánchez-Sánchez R, Solivera J, Breunig JJ, Gahete MD, Castaño JP, Luque RM. SF3B1 inhibition disrupts malignancy and prolongs survival in glioblastoma patients through BCL2L1 splicing and mTOR/ß-catenin pathways imbalances. J Exp Clin Cancer Res 2022; 41:39. [PMID: 35086552 PMCID: PMC8793262 DOI: 10.1186/s13046-022-02241-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glioblastoma is one of the most devastating cancer worldwide based on its locally aggressive behavior and because it cannot be cured by current therapies. Defects in alternative splicing process are frequent in cancer. Recently, we demonstrated that dysregulation of the spliceosome is directly associated with glioma development, progression, and aggressiveness. METHODS Different human cohorts and a dataset from different glioma mouse models were analyzed to determine the mutation frequency as well as the gene and protein expression levels between tumor and control samples of the splicing-factor-3B-subunit-1 (SF3B1), an essential and druggable spliceosome component. SF3B1 expression was also explored at the single-cell level across all cell subpopulations and transcriptomic programs. The association of SF3B1 expression with relevant clinical data (e.g., overall survival) in different human cohorts was also analyzed. Different functional (proliferation/migration/tumorspheres and colonies formation/VEGF secretion/apoptosis) and mechanistic (gene expression/signaling pathways) assays were performed in three different glioblastomas cell models (human primary cultures and cell lines) in response to SF3B1 blockade (using pladienolide B treatment). Moreover, tumor progression and formation were monitored in response to SF3B1 blockade in two preclinical xenograft glioblastoma mouse models. RESULTS Our data provide novel evidence demonstrating that the splicing-factor-3B-subunit-1 (SF3B1, an essential and druggable spliceosome component) is low-frequency mutated in human gliomas (~ 1 %) but widely overexpressed in glioblastoma compared with control samples from the different human cohorts and mouse models included in the present study, wherein SF3B1 levels are associated with key molecular and clinical features (e.g., overall survival, poor prognosis and/or drug resistance). Remarkably, in vitro and in vivo blockade of SF3B1 activity with pladienolide B drastically altered multiple glioblastoma pathophysiological processes (i.e., reduction in proliferation, migration, tumorspheres formation, VEGF secretion, tumor initiation and increased apoptosis) likely by suppressing AKT/mTOR/ß-catenin pathways, and an imbalance of BCL2L1 splicing. CONCLUSIONS Together, we highlight SF3B1 as a potential diagnostic and prognostic biomarker and an efficient pharmacological target in glioblastoma, offering a clinically relevant opportunity worth to be explored in humans.
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Affiliation(s)
- Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Jesús M Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Miguel E G-García
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Cristóbal Blanco-Acevedo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Department of Neurosurgery, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Pathology Service, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Juan Solivera
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Department of Neurosurgery, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain.
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From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies. Biomedicines 2021; 9:biomedicines9050550. [PMID: 34068948 PMCID: PMC8156014 DOI: 10.3390/biomedicines9050550] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.
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8
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Halloy F, Iyer PS, Ćwiek P, Ghidini A, Barman-Aksözen J, Wildner-Verhey van Wijk N, Theocharides APA, Minder EI, Schneider-Yin X, Schümperli D, Hall J. Delivery of oligonucleotides to bone marrow to modulate ferrochelatase splicing in a mouse model of erythropoietic protoporphyria. Nucleic Acids Res 2020; 48:4658-4671. [PMID: 32313951 PMCID: PMC7229840 DOI: 10.1093/nar/gkaa229] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/25/2020] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Erythropoietic protoporphyria (EPP) is a rare genetic disease in which patients experience acute phototoxic reactions after sunlight exposure. It is caused by a deficiency in ferrochelatase (FECH) in the heme biosynthesis pathway. Most patients exhibit a loss-of-function mutation in trans to an allele bearing a SNP that favors aberrant splicing of transcripts. One viable strategy for EPP is to deploy splice-switching oligonucleotides (SSOs) to increase FECH synthesis, whereby an increase of a few percent would provide therapeutic benefit. However, successful application of SSOs in bone marrow cells is not described. Here, we show that SSOs comprising methoxyethyl-chemistry increase FECH levels in cells. We conjugated one SSO to three prototypical targeting groups and administered them to a mouse model of EPP in order to study their biodistribution, their metabolic stability and their FECH splice-switching ability. The SSOs exhibited distinct distribution profiles, with increased accumulation in liver, kidney, bone marrow and lung. However, they also underwent substantial metabolism, mainly at their linker groups. An SSO bearing a cholesteryl group increased levels of correctly spliced FECH transcript by 80% in the bone marrow. The results provide a promising approach to treat EPP and other disorders originating from splicing dysregulation in the bone marrow.
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Affiliation(s)
- François Halloy
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Pavithra S Iyer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Paulina Ćwiek
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Alice Ghidini
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | | | | | - Alexandre P A Theocharides
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | | | | | - Daniel Schümperli
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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