1
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Yang S, Li Z. FBN2 pathogenic variants in congenital contractural arachnodactyly with severe cardiovascular manifestations. Connect Tissue Res 2024:1-12. [PMID: 38602424 DOI: 10.1080/03008207.2024.2340004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE Congenital contractural arachnodactyly (CCA) is an extremely rare autosomal dominant connective tissue genetic disorder caused by pathogenic variants in FBN2. CCA is characterized by arachnodactyly, camptodactyly, contracture of major joints, scoliosis, pectus deformities, and crumpled ears, but rarely with lethal cardiovascular manifestations as in Marfan syndrome. It is imperative to conduct a comprehensive analysis and review of the pathogenesis of CCA resulting from pathogenic variants in FBN2 gene. MATERIALS AND METHODS Using whole-exome sequencing and Sanger sequencing, we identified a novel pathogenic splice-altering variant (c.4472-3C>A) in intron 34 of FBN2 gene in a CCA pedigree. The transcriptional result of the splicing-altering variant was analyzed by RNA sequencing. We systematically analyzed the clinical manifestations of all reported cases of CCA caused by splicing-altering pathogenic variants and focused on all the pathogenic variants in FBN2 gene that are associated with severe cardiovascular manifestations. RESULTS The splice-altering variant (c.4472-3C>A) in FBN2 was demonstrated to result in the exon 35 skipping and cause an in-frame deletion. Furthermore, we identified exons 31 to 35 may be a hotspot region in FBN2 gene associated with severe cardiovascular phenotype. CONCLUSIONS This study enriched the pathogenic spectrum of CCA and identified a hotspot region in FBN2 gene associated with severe cardiovascular manifestations. We recommend that patients carrying pathogenic variants in exons 31 to 35 of FBN2 pay more attention to cardiac evaluation.
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Affiliation(s)
- Shulin Yang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zongzhe Li
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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2
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Suárez-Herrera N, Garanto A, Collin RWJ. Understanding and Rescuing the Splicing Defect Caused by the Frequent ABCA4 Variant c.4253+43G>A Underlying Stargardt Disease. Nucleic Acid Ther 2024; 34:73-82. [PMID: 38466963 DOI: 10.1089/nat.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Pathogenic variants in ABCA4 are the underlying molecular cause of Stargardt disease (STGD1), an autosomal recessive macular dystrophy characterized by a progressive loss of central vision. Among intronic ABCA4 variants, c.4253+43G>A is frequently detected in STGD1 cases and is classified as a hypomorphic allele, generally associated with late-onset cases. This variant was previously reported to alter splicing regulatory sequences, but the splicing outcome is not fully understood yet. In this study, we attempted to better understand its effect on splicing and to rescue the aberrant splicing via antisense oligonucleotides (AONs). Wild-type and c.4253+43G>A variant-harboring maxigene vectors revealed additional skipping events, which were not previously detected upon transfection in HEK293T cells. To restore exon inclusion, we designed a set of 27 AONs targeting either splicing silencer motifs or the variant region and screened these in maxigene-transfected HEK293T cells. Candidate AONs able to promote exon inclusion were selected for further testing in patient-derived photoreceptor precursor cells. Surprisingly, no robust splicing modulation was observed in this model system. Overall, this research helped to adequately characterize the splicing alteration caused by the c.4253+43G>A variant, although future development of AON-mediated exon inclusion therapy for ABCA4 is needed.
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Affiliation(s)
- Nuria Suárez-Herrera
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Lu J, Zhang M, Liu Z, Guo L, Huang P, Xia W, Li J, Lv J, Cheung HH, Ding C, Li H, Huang B. NSUN2-Mediated m 5C Methylation Impairs Endometrial Receptivity. J Transl Med 2024; 104:100327. [PMID: 38237738 DOI: 10.1016/j.labinv.2024.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/05/2023] [Accepted: 12/23/2023] [Indexed: 02/12/2024] Open
Abstract
Impaired endometrial decidualization is the primary cause of recurrent implantation failure (RIF). RNA methylation modification, especially NSUN family mediated m5C, is crucial for various physiological events, such as maternal-to-zygotic transition, gametogenesis, embryonic development, organismal lifespan, and cell cycle. However, the regulatory mechanisms between NSUN family mediated m5C modification and RIF remain unknown. We acquired NSUN2 expression data of 15 human endometrium samples at proliferative and secretory stages from reproductive cell atlas. The overall pattern of m5C sites and genes was elucidated through m5C-BS-seq, whereas the overall m5C levels in different groups were revealed by dot blot assay. BrdU and western blotting assays were carried out to evaluate the role of NSUN2 in proliferation and autophagy. The effects of NSUN2-mediated m5C modification on embryo attachment were evaluated by an in vitro model of a confluent monolayer of Ishikawa cells cocultured with BeWo spheroids, and its downstream targets were evaluated by real-time reverse-transcription PCR and western blotting in Ishikawa cells. The molecular mechanism for NSUN2 regulating its downstream targets' expression was determined by Cut&Tag and coimmunoprecipitation assays. NSUN2 was increased in SOX9+ cells and widespread in epithelial cell type at the proliferative stage by previous single-cell RNA sequencing data. NSUN2 overexpression (NSUN2OE) in the Ishikawa cell line elevated m5C levels and promoted cell proliferation and autophagy. NSUN2OE reduced attachment efficiency of BeWo cell spheres. Overexpressed NSUN2 was found to increase STAT1 and MMP14 mRNA expressions by inducing exon skipping. NSUN2 interacted with CLDN4 through m5C modification, and NSUN2OE or NSUN2 knockdown resulted in a similar variation tendency of CLDN4. Overexpression of NSUN2 increased CLDN4 H3K9ac modification by downregulating SIRT4 expression at the protein level, leading to the upregulation of CLDN4 mRNA expression. Our results uncovered a novel intricate regulatory mechanism between NSUN2-mediated m5C and RIF and suggested a potential new therapeutic strategy for RIF.
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Affiliation(s)
- Jiafeng Lu
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Ming Zhang
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Zhenxing Liu
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Ling Guo
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Peng Huang
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Wenjuan Xia
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jincheng Li
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jinghuan Lv
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Hoi-Hung Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR
| | - Chenyue Ding
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Hong Li
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
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4
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Li C, Zhang R, Pan F, Xin Q, Shi X, Guo W, Qiao D, Wang Z, Zhang Y, Liu X, Zhang Y, Shao L. Functional analysis of the CTNS gene exonic variants predicted to affect splicing. Clin Genet 2024; 105:323-328. [PMID: 38009794 DOI: 10.1111/cge.14460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Cystinosis is a severe, monogenic systemic disease caused by variants in CTNS gene. Currently, there is growing evidence that exonic variants in many diseases can affect pre-mRNA splicing. The impact of CTNS gene exonic variants on splicing regulation may be underestimated due to the lack of routine studies at the RNA level. Here, we analyzed 59 exonic variants in the CTNS gene using bioinformatics tools and identified candidate variants that may induce splicing alterations by minigene assays. We identified six exonic variants that induce splicing alterations by disrupting the ratio of exonic splicing enhancers/exonic splicing silencers (ESEs/ESSs) or by interfering with the recognition of classical splice sites, or both. Our results help in the correct molecular characterization of variants in cystinosis and inform emerging therapies. Furthermore, our work suggests that the combination of in silico and in vitro assays facilitates to assess the effects of DNA variants driving rare genetic diseases on splicing regulation and will enhance the clinical utility of variant functional annotation.
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Affiliation(s)
- Changying Li
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Emergency, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Fengjiao Pan
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Qing Xin
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Wencong Guo
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Dan Qiao
- Department of Nephrology, Dalian Medical University, Dalian, China
| | - Zhi Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yiyin Zhang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xuyan Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yan Zhang
- Department of Nephrology, Weifang Medical University, Weifang, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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Kiianitsa K, Lukes ME, Hayes BJ, Brutman J, Valdmanis PN, Bird TD, Raskind WH, Korvatska O. TREM2 variants that cause early dementia and increase Alzheimer's disease risk affect gene splicing. Brain 2024:awae014. [PMID: 38226698 DOI: 10.1093/brain/awae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Loss-of-function variants in the triggering receptor expressed on myeloid cells 2 (TREM2) are responsible for a spectrum of neurodegenerative disorders. In the homozygous state, they cause severe pathologies with early onset dementia, such as Nasu-Hakola disease (NHD) and behavioral variants of frontotemporal dementia (FTD), whereas heterozygous variants increase the risk of late-onset Alzheimer's disease (AD) and FTD. For over half of TREM2 variants found in families with recessive early onset dementia, the defect occurs at the transcript level via premature termination codons or aberrant splicing. The remaining variants are missense alterations thought to affect the protein; however, the underlying pathogenic mechanism is less clear. In this work, we tested whether these disease-associated TREM2 variants contribute to the pathology via altered splicing. Variants scored by SpliceAI algorithm were tested by a full-size TREM2 splicing reporter assay in different cell lines. The effect of variants was quantified by qRT-/RT-PCR and western blots. Nanostring nCounter was used to measure TREM2 RNA in the brains of NHD patients who carried spliceogenic variants. Exon skipping events were analyzed from brain RNA-Seq datasets available through the Accelerating Medicines Partnership for Alzheimer's Disease Consortium (AMP-AD). We found that for some NHD and early onset FTD-causing variants, splicing defects were the primary cause (D134G) or likely contributor to pathogenicity (V126G and K186N). Similar but milder effects on splicing of exons 2 and 3 were demonstrated for A130V, L133L and R136W enriched in patients with dementia. Moreover, the two most frequent missense variants associated with AD/FTD risk in European and African ancestries (R62H, 1% in Caucasians, and T96K, 12% in Africans) had splicing defects via excessive skipping of exon 2 and overproduction of a potentially antagonistic TREM2 protein isoform. The effect of R62H on exon 2 skipping was confirmed in three independent brain RNA-seq datasets. Our findings revealed an unanticipated complexity of pathogenic variation in TREM2, in which effects on post-transcriptional gene regulation and protein function often coexist. This necessitates the inclusion of computational and experimental analyses of splicing and mRNA processing for a better understanding of genetic variation in disease.
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Affiliation(s)
- Kostantin Kiianitsa
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maria E Lukes
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Brian J Hayes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Julianna Brutman
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Paul N Valdmanis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
- Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, WA 98108, USA
| | - Wendy H Raskind
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
- Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Medical Center, Seattle, WA 98108, USA
| | - Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
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6
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Ali G, Shin KC, Habbab W, Alkhadairi G, AbdelAleem A, AlShaban FA, Park Y, Stanton LW. Characterization of a loss-of-function NSF attachment protein beta mutation in monozygotic triplets affected with epilepsy and autism using cortical neurons from proband-derived and CRISPR-corrected induced pluripotent stem cell lines. Front Neurosci 2024; 17:1302470. [PMID: 38260021 PMCID: PMC10801733 DOI: 10.3389/fnins.2023.1302470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
We investigated whether a homozygous recessive genetic variant of NSF attachment protein beta (NAPB) gene inherited by monozygotic triplets contributed to their phenotype of early-onset epilepsy and autism. Induced pluripotent stem cell (iPSC) lines were generated from all three probands and both parents. The NAPB genetic variation was corrected in iPSC lines from two probands by CRISPR/Cas9 gene editing. Cortical neurons were produced by directed, in vitro differentiation from all iPSC lines. These cell line-derived neurons enabled us to determine that the genetic variation in the probands causes exon skipping and complete absence of NAPB protein. Electrophysiological and transcriptomic comparisons of cortical neurons derived from parents and probands cell lines indicate that loss of NAPB function contributes to alterations in neuronal functions and likely contributed to the impaired neurodevelopment of the triplets.
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Affiliation(s)
- Gowher Ali
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Wesal Habbab
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ghaneya Alkhadairi
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Alice AbdelAleem
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Fouad A. AlShaban
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
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7
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Saad FA, Saad JF, Siciliano G, Merlini L, Angelini C. Duchenne Muscular Dystrophy Gene Therapy. Curr Gene Ther 2024; 24:17-28. [PMID: 36411557 DOI: 10.2174/1566523223666221118160932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022]
Abstract
Duchenne and Becker muscular dystrophies are allelic X-linked recessive neuromuscular diseases affecting both skeletal and cardiac muscles. Therefore, owing to their single X chromosome, the affected boys receive pathogenic gene mutations from their unknowing carrier mothers. Current pharmacological drugs are palliative that address the symptoms of the disease rather than the genetic cause imbedded in the Dystrophin gene DNA sequence. Therefore, alternative therapies like gene drugs that could address the genetic cause of the disease at its root are crucial, which include gene transfer/implantation, exon skipping, and gene editing. Presently, it is possible through genetic reprogramming to engineer AAV vectors to deliver certain therapeutic cargos specifically to muscle or other organs regardless of their serotype. Similarly, it is possible to direct the biogenesis of exosomes to carry gene editing constituents or certain therapeutic cargos to specific tissue or cell type like brain and muscle. While autologous exosomes are immunologically inert, it is possible to camouflage AAV capsids, and lipid nanoparticles to evade the immune system recognition. In this review, we highlight current opportunities for Duchenne muscular dystrophy gene therapy, which has been known thus far as an incurable genetic disease. This article is a part of Gene Therapy of Rare Genetic Diseases thematic issue.
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Affiliation(s)
- Fawzy A Saad
- Department of Biology, Padua University School of Medicine, Via Trieste 75, Padova 35121, Italy
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Jasen F Saad
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Pisa University School of Medicine, Pisa, Italy
| | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, Bologna University School of Medicine, 40126 Bologna, Italy
| | - Corrado Angelini
- Department Neurosciences, Padova University School of Medicine, Padova, Italy
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Yavas A, van Putten M, Aartsma-Rus A. Antisense Oligonucleotide-Mediated Downregulation of IGFBPs Enhances IGF-1 Signaling. J Neuromuscul Dis 2024; 11:299-314. [PMID: 38189760 DOI: 10.3233/jnd-230118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Insulin-like growth factor-1 (IGF-1) has been considered as a therapeutic agent for muscle wasting conditions including Duchenne muscular dystrophy as it stimulates muscle regeneration, growth and function. Several preclinical and clinical studies have been conducted to show the therapeutic potential of IGF-1, however, delivery issues, short half-life and isoform complexity have impose challenges. Antisense oligonucleotides (AONs) are able to downregulate target proteins by interfering with their transcripts. Here, we investigated the feasibility of enhancing IGF-1 signaling by downregulation of IGF-binding proteins. We observed that out of frame exon skipping of Igfbp1 and Igfbp3 downregulated their protein expression, which increased Akt phosphorylation on the downstream IGF-1 signaling in vitro. 3'RNA sequencing analysis revealed the related transcriptome in C2C12 cells in response to IGFBP3 downregulation. The AONs did however not induce any exon skipping or protein knockdown in mdx mice after 6 weeks of systemic treatment. We conclude that IGFBP downregulation could be a good strategy to increase IGF-1 signaling but alternative tools are needed for efficient delivery and knockdown in vivo.
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Affiliation(s)
- Alper Yavas
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike van Putten
- Department of Human Genetics, 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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Yoshimoto R, Nakayama Y, Nomura I, Yamamoto I, Nakagawa Y, Tanaka S, Kurihara M, Suzuki Y, Kobayashi T, Kozuka-Hata H, Oyama M, Mito M, Iwasaki S, Yamazaki T, Hirose T, Araki K, Nakagawa S. 4.5SH RNA counteracts deleterious exonization of SINE B1 in mice. Mol Cell 2023; 83:4479-4493.e6. [PMID: 38096826 DOI: 10.1016/j.molcel.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/09/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
4.5SH RNA is a highly abundant, small rodent-specific noncoding RNA that localizes to nuclear speckles enriched in pre-mRNA-splicing regulators. To investigate the physiological functions of 4.5SH RNA, we have created mutant mice that lack the expression of 4.5SH RNA. The mutant mice exhibited embryonic lethality, suggesting that 4.5SH RNA is an essential species-specific noncoding RNA in mice. RNA-sequencing analyses revealed that 4.5SH RNA protects the transcriptome from abnormal exonizations of the antisense insertions of the retrotransposon SINE B1 (asB1), which would otherwise introduce deleterious premature stop codons or frameshift mutations. Mechanistically, 4.5SH RNA base pairs with complementary asB1-containing exons via the target recognition region and recruits effector proteins including Hnrnpm via its 5' stem loop region. The modular organization of 4.5SH RNA allows us to engineer a programmable splicing regulator to induce the skipping of target exons of interest. Our results also suggest the general existence of splicing regulatory noncoding RNAs.
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Affiliation(s)
- Rei Yoshimoto
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan.
| | - Yuta Nakayama
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ikuko Nomura
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ikuko Yamamoto
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Yumeka Nakagawa
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan
| | - Shigeyuki Tanaka
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan
| | - Misuzu Kurihara
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Yu Suzuki
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tomohiro Yamazaki
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan; Center for Metabolic Regulation of Healthy Aging, Kumamoto University, 1-1-1, Honjo, Kumamoto 860-8556, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan.
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Gushchina LV, Bradley AJ, Vetter TA, Lay JW, Rohan NL, Frair EC, Wein N, Flanigan KM. Persistence of exon 2 skipping and dystrophin expression at 18 months after U7snRNA-mediated therapy in the Dup2 mouse model. Mol Ther Methods Clin Dev 2023; 31:101144. [PMID: 38027058 PMCID: PMC10679948 DOI: 10.1016/j.omtm.2023.101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive X-linked disease caused by mutations in the DMD gene that prevent the expression of a functional dystrophin protein. Exon duplications represent 6%-11% of mutations, and duplications of exon 2 (Dup2) are the most common (∼11%) of duplication mutations. An exon-skipping strategy for Dup2 mutations presents a large therapeutic window. Skipping one exon copy results in full-length dystrophin expression, whereas skipping of both copies (Del2) activates an internal ribosomal entry site (IRES) in exon 5, inducing the expression of a highly functional truncated dystrophin isoform. We have previously confirmed the therapeutic efficacy of AAV9.U7snRNA-mediated skipping in the Dup2 mouse model and showed the absence of off-target splicing effects and lack of toxicity in mice and nonhuman primates. Here, we report long-term dystrophin expression data following the treatment of 3-month-old Dup2 mice with the scAAV9.U7.ACCA vector. Significant exon 2 skipping and robust dystrophin expression in the muscles and hearts of treated mice persist at 18 months after treatment, along with the partial rescue of muscle function. These data extend our previous findings and show that scAAV9.U7.ACCA provides long-term protection by restoring the disrupted dystrophin reading frame in the context of exon 2 duplications.
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Affiliation(s)
- Liubov V. Gushchina
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Adrienne J. Bradley
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Tatyana A. Vetter
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Jacob W. Lay
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Natalie L. Rohan
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Emma C. Frair
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Kevin M. Flanigan
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Department of Neurology, The Ohio State University, Columbus, OH, USA
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11
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Watanabe N, Tone Y, Nagata T, Masuda S, Saito T, Motohashi N, Takagaki K, Aoki Y, Takeda S. Exon 44 skipping in Duchenne muscular dystrophy: NS-089/NCNP-02, a dual-targeting antisense oligonucleotide. Mol Ther Nucleic Acids 2023; 34:102034. [PMID: 37854955 PMCID: PMC10579524 DOI: 10.1016/j.omtn.2023.102034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/15/2023] [Indexed: 10/20/2023]
Abstract
Exon-skipping therapy mediated by antisense oligonucleotides is expected to provide a therapeutic option for Duchenne muscular dystrophy. Antisense oligonucleotides for exon skipping reported so far target a single continuous sequence in or around the target exon. In the present study, we investigated antisense oligonucleotides for exon 44 skipping (applicable to approximately 6% of all Duchenne muscular dystrophy patients) to improve activity by using a novel antisense oligonucleotide design incorporating two connected sequences. Phosphorodiamidate morpholino oligomers targeting two separate sequences in exon 44 were created to target two splicing regulators in exon 44 simultaneously, and their exon 44 skipping was measured. NS-089/NCNP-02 showed the highest skipping activity among the oligomers. NS-089/NCNP-02 also induced exon 44 skipping and dystrophin protein expression in cells from a Duchenne muscular dystrophy patient to whom exon 44 skipping is applicable. We also assessed the in vivo activity of NS-089/NCNP-02 by intravenous administration to cynomolgus monkeys. NS-089/NCNP-02 induced exon 44 skipping in skeletal and cardiac muscle of cynomolgus monkeys. In conclusion, NS-089/NCNP-02, an antisense oligonucleotide with a novel connected-sequence design, showed highly efficient exon skipping both in vitro and in vivo.
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Affiliation(s)
- Naoki Watanabe
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Yuichiro Tone
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
- Department of Neurology and Neurological Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Masuda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Takashi Saito
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Norio Motohashi
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Kazuchika Takagaki
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Shin’ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
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12
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Doisy M, Vacca O, Fergus C, Gileadi T, Verhaeg M, Saoudi A, Tensorer T, Garcia L, Kelly VP, Montanaro F, Morgan JE, van Putten M, Aartsma-Rus A, Vaillend C, Muntoni F, Goyenvalle A. Networking to Optimize Dmd exon 53 Skipping in the Brain of mdx52 Mouse Model. Biomedicines 2023; 11:3243. [PMID: 38137463 PMCID: PMC10741439 DOI: 10.3390/biomedicines11123243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene that disrupt the open reading frame and thus prevent production of functional dystrophin proteins. Recent advances in DMD treatment, notably exon skipping and AAV gene therapy, have achieved some success aimed at alleviating the symptoms related to progressive muscle damage. However, they do not address the brain comorbidities associated with DMD, which remains a critical aspect of the disease. The mdx52 mouse model recapitulates one of the most frequent genetic pathogenic variants associated with brain involvement in DMD. Deletion of exon 52 impedes expression of two brain dystrophins, Dp427 and Dp140, expressed from distinct promoters. Interestingly, this mutation is eligible for exon skipping strategies aimed at excluding exon 51 or 53 from dystrophin mRNA. We previously showed that exon 51 skipping can restore partial expression of internally deleted yet functional Dp427 in the brain following intracerebroventricular (ICV) injection of antisense oligonucleotides (ASO). This was associated with a partial improvement of anxiety traits, unconditioned fear response, and Pavlovian fear learning and memory in the mdx52 mouse model. In the present study, we investigated in the same mouse model the skipping of exon 53 in order to restore expression of both Dp427 and Dp140. However, in contrast to exon 51, we found that exon 53 skipping was particularly difficult in mdx52 mice and a combination of multiple ASOs had to be used simultaneously to reach substantial levels of exon 53 skipping, regardless of their chemistry (tcDNA, PMO, or 2'MOE). Following ICV injection of a combination of ASO sequences, we measured up to 25% of exon 53 skipping in the hippocampus of treated mdx52 mice, but this did not elicit significant protein restoration. These findings indicate that skipping mouse dystrophin exon 53 is challenging. As such, it has not yet been possible to answer the pertinent question whether rescuing both Dp427 and Dp140 in the brain is imperative to more optimal treatment of neurological aspects of dystrophinopathy.
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Affiliation(s)
- Mathilde Doisy
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; (M.D.); (O.V.); (A.S.)
| | - Ophélie Vacca
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; (M.D.); (O.V.); (A.S.)
| | - Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (C.F.)
| | - Talia Gileadi
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford Street, London WC1N 1EH, UK; (T.G.); (F.M.); (J.E.M.); (F.M.)
- National Institute for Health Research, Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Minou Verhaeg
- Department of Human Genetics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.V.); (M.v.P.); (A.A.-R.)
| | - Amel Saoudi
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; (M.D.); (O.V.); (A.S.)
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France;
| | - Thomas Tensorer
- SQY Therapeutics-Synthena, UVSQ, 78180 Montigny le Bretonneux, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; (M.D.); (O.V.); (A.S.)
| | - Vincent P. Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (C.F.)
| | - Federica Montanaro
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford Street, London WC1N 1EH, UK; (T.G.); (F.M.); (J.E.M.); (F.M.)
- National Institute for Health Research, Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Jennifer E. Morgan
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford Street, London WC1N 1EH, UK; (T.G.); (F.M.); (J.E.M.); (F.M.)
- National Institute for Health Research, Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.V.); (M.v.P.); (A.A.-R.)
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.V.); (M.v.P.); (A.A.-R.)
| | - Cyrille Vaillend
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France;
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford Street, London WC1N 1EH, UK; (T.G.); (F.M.); (J.E.M.); (F.M.)
- National Institute for Health Research, Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; (M.D.); (O.V.); (A.S.)
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13
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Vasterling ME, Maitski RJ, Davis BA, Barnes JE, Kelkar RA, Klapper RJ, Patel H, Ahmadzadeh S, Shekoohi S, Kaye AD, Varrassi G. AMONDYS 45 (Casimersen), a Novel Antisense Phosphorodiamidate Morpholino Oligomer: Clinical Considerations for Treatment in Duchenne Muscular Dystrophy. Cureus 2023; 15:e51237. [PMID: 38283433 PMCID: PMC10821770 DOI: 10.7759/cureus.51237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
AMONDYS 45 (casimersen) is an antisense oligonucleotide therapy used to treat Duchenne muscular dystrophy (DMD), a rare genetic disorder characterized by a mutation in the DMD gene. Symptoms include progressive muscle weakness, respiratory and cardiac complications, and premature death. Casimersen targets a specific mutation in the DMD gene that results in the absence of dystrophin protein, a key structural component of muscle fibers. While there is currently no cure for DMD, exon-skipping therapy works by restoring the reading frame of the mutated gene, allowing the production of a partially functional dystrophin protein. Clinical trials of casimersen have shown promising results in increasing dystrophin production, as measured by polymerase chain reaction (PCR) droplets when compared to placebo. In a randomized double-blind trial, patients who received casimersen had significantly higher dystrophin levels when compared to those who received placebo. Casimersen therapy is administered through repeated intravenous infusions, although the optimal dosage and duration of treatment are still under investigation. Based on the completed and ongoing clinical trials, casimersen has been well tolerated, with most adverse events being mild and unrelated to casimersen. In 2021, AMONDYS 45 (casimersen) received approval from the US Food and Drug Administration (FDA) for the treatment of Duchene muscular dystrophy in patients with a mutation of the DMD gene that is amenable to exon 45 skipping. These collective findings indicate that casimersen has the potential to elicit functional changes in individuals with DMD, although further studies are necessary to comprehensively evaluate the specific functional improvements. Regardless, the FDA approval and ongoing clinic trials mark a significant milestone in the development of DMD treatments and offer hope for those affected by this debilitating disease.
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Affiliation(s)
- Megan E Vasterling
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Rebecca J Maitski
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Brice A Davis
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Julie E Barnes
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Rucha A Kelkar
- School of Medicine, Medical University of South Carolina, Charleston, USA
| | - Rachel J Klapper
- Radiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Hirni Patel
- Anesthesiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Shahab Ahmadzadeh
- Anesthesiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Sahar Shekoohi
- Anesthesiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Alan D Kaye
- Anesthesiology, Louisiana State University Health Sciences Center, Shreveport, USA
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14
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Engelbeen S, O'Reilly D, Van De Vijver D, Verhaart I, van Putten M, Hariharan V, Hassler M, Khvorova A, Damha MJ, Aartsma-Rus A. Challenges of Assessing Exon 53 Skipping of the Human DMD Transcript with Locked Nucleic Acid-Modified Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2023; 33:348-360. [PMID: 38010230 DOI: 10.1089/nat.2023.0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Antisense oligonucleotide (AON)-mediated exon skipping is a promising therapeutic approach for Duchenne muscular dystrophy (DMD) patients to restore dystrophin expression by reframing the disrupted open reading frame of the DMD transcript. However, the treatment efficacy of the already conditionally approved AONs remains low. Aiming to optimize AON efficiency, we assessed exon 53 skipping of the DMD transcript with different chemically modified AONs, all with a phosphorothioate backbone: 2'-O-methyl (2'OMe), locked nucleic acid (LNA)-2'OMe, 2'-fluoro (FRNA), LNA-FRNA, αLNA-FRNA, and FANA-LNA-FRNA. Efficient exon 53 skipping was observed with the FRNA, LNA-FRNA, and LNA-2'OMe AONs in human control myoblast cultures. Weekly subcutaneous injections (50 mg/kg AON) for a duration of 6 weeks were well tolerated by hDMDdel52/mdx males. Treatment with the LNA-FRNA and LNA-2'OMe AONs resulted in pronounced exon 53 skip levels in skeletal muscles and heart up to 90%, but no dystrophin restoration was observed. This discrepancy was mainly ascribed to the strong binding nature of LNA modifications to RNA, thereby interfering with the amplification of the unskipped product resulting in artificial overamplification of the exon 53 skip product. Our study highlights that treatment effect on RNA and protein level should both be considered when assessing AON efficiency.
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Affiliation(s)
- Sarah Engelbeen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel O'Reilly
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, Massachusetts, USA
- Department of Chemistry, McGill University, Montreal, Canada
| | - Davy Van De Vijver
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid Verhaart
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Vignesh Hariharan
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, Massachusetts, USA
| | - Matthew Hassler
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, Massachusetts, USA
| | - Anastasia Khvorova
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, Massachusetts, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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15
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Bizot F, Tensorer T, Garcia L, Goyenvalle A. Impact of the Inhibition of Organic Anion Transporter on Tricyclo-DNA-Mediated Exon Skipping in the mdx Mouse Model. Nucleic Acid Ther 2023; 33:374-380. [PMID: 37967388 DOI: 10.1089/nat.2023.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023] Open
Abstract
Antisense-mediated exon skipping is one of the most promising therapeutic strategies for Duchenne muscular dystrophy (DMD) and some antisense oligonucleotide (ASO) drugs have already been approved by the U.S. FDA for DMD. The potential of this therapy is still limited by several challenges including the poor distribution of ASOs to target tissues. Indeed, most of them accumulate in the kidney and tend to be rapidly eliminated after systemic delivery. We hypothesized here that preventing renal clearance of ASO using organic anion transporter (OAT) inhibitor could increase the bioavailability of ASOs and thus their distribution to target tissues and ultimately their efficacy in muscles. Mdx mice were, therefore, treated with ASO with or without the OAT inhibitor named probenecid. Our findings indicate that OAT inhibition, or at least using probenecid, does not improve the therapeutic potential of ASO-mediated exon-skipping approaches for the treatment of DMD.
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Affiliation(s)
- Flavien Bizot
- Université de Versailles Saint Quentin en Yveline, Inserm, END-ICAP, Université Paris-Saclay, Versailles, France
| | | | - Luis Garcia
- Université de Versailles Saint Quentin en Yveline, Inserm, END-ICAP, Université Paris-Saclay, Versailles, France
| | - Aurélie Goyenvalle
- Université de Versailles Saint Quentin en Yveline, Inserm, END-ICAP, Université Paris-Saclay, Versailles, France
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16
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Qiu H, Li G, Yuan J, Yang D, Ma Y, Wang F, Dai Y, Chang X. Efficient exon skipping by base-editor-mediated abrogation of exonic splicing enhancers. Cell Rep 2023; 42:113340. [PMID: 37906593 DOI: 10.1016/j.celrep.2023.113340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disease caused by the loss of the dystrophin protein. Exon skipping is a promising strategy to treat DMD by restoring truncated dystrophin. Here, we demonstrate that base editors (e.g., targeted AID-mediated mutagenesis [TAM]) are able to efficiently induce exon skipping by disrupting functional redundant exonic splicing enhancers (ESEs). By developing an unbiased and high-throughput screening to interrogate exonic sequences, we successfully identify novel ESEs in DMD exons 51 and 53. TAM-CBE (cytidine base editor) induces near-complete skipping of the respective exons by targeting these ESEs in patients' induced pluripotent stem cell (iPSC)-derived cardiomyocytes. Combined with strategies to disrupt splice sites, we identify suitable single guide RNAs (sgRNAs) with TAM-CBE to efficiently skip most DMD hotspot exons without substantial double-stranded breaks. Our study thus expands the repertoire of potential targets for CBE-mediated exon skipping in treating DMD and other RNA mis-splicing diseases.
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Affiliation(s)
- Han Qiu
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Geng Li
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Juanjuan Yuan
- Shunde Hospital, Southern Medical University, Foshan 528308, Guangdong, China
| | - Dian Yang
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Yunqing Ma
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Feng Wang
- Department of Laboratory Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo 315040, Zhejiang, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - Xing Chang
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China.
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17
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Zhao B, Nguyen MA, Woo S, Kim J, Yu TW, Lee EA. Contribution and therapeutic implications of retroelement insertions in ataxia telangiectasia. Am J Hum Genet 2023; 110:1976-1982. [PMID: 37802069 PMCID: PMC10645548 DOI: 10.1016/j.ajhg.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
Certain classes of genetic variation still escape detection in clinical sequencing analysis. One such class is retroelement insertion, which has been reported as a cause of Mendelian diseases and may offer unique therapeutic implications. Here, we conducted retroelement profiling on whole-genome sequencing data from a cohort of 237 individuals with ataxia telangiectasia (A-T). We found 15 individuals carrying retroelement insertions in ATM, all but one of which integrated in noncoding regions. Systematic functional characterization via RNA sequencing, RT-PCR, and/or minigene splicing assays showed that 12 out of 14 intronic insertions led or contributed to ATM loss of function by exon skipping or activating cryptic splice sites. We also present proof-of-concept antisense oligonucleotides that suppress cryptic exonization caused by a deep intronic retroelement insertion. These results provide an initial systematic estimate of the contribution of retroelements to the genetic architecture of recessive Mendelian disorders as ∼2.1%-5.5%. Our study highlights the importance of retroelement insertions as causal variants and therapeutic targets in genetic diseases.
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Affiliation(s)
- Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Minh A Nguyen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Sijae Woo
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jinkuk Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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18
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Pascal C, Zonszain J, Hameiri O, Gargi-Levi C, Lev-Maor G, Tammer L, Levy T, Tarabeih A, Roy VR, Ben-Salmon S, Elbaz L, Eid M, Hakim T, Abu Rabe'a S, Shalev N, Jordan A, Meshorer E, Ast G. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation. Mol Cell 2023; 83:3801-3817.e8. [PMID: 37922872 DOI: 10.1016/j.molcel.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.
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Affiliation(s)
- Corina Pascal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Zonszain
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Gargi-Levi
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Levy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anan Tarabeih
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stav Ben-Salmon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liraz Elbaz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mireille Eid
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Hakim
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Salima Abu Rabe'a
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nana Shalev
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Albert Jordan
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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19
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Rok M, Wong TWY, Maino E, Ahmed A, Yang G, Hyatt E, Lindsay K, Fatehi S, Marks R, Delgado-Olguín P, Ivakine EA, Cohn RD. Prevention of early-onset cardiomyopathy in Dmd exon 52-54 deletion mice by CRISPR-Cas9-mediated exon skipping. Mol Ther Methods Clin Dev 2023; 30:246-258. [PMID: 37545481 PMCID: PMC10403712 DOI: 10.1016/j.omtm.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a disease with a life-threatening trajectory resulting from mutations in the dystrophin gene, leading to degeneration of skeletal muscle and fibrosis of cardiac muscle. The overwhelming majority of mutations are multiexonic deletions. We previously established a dystrophic mouse model with deletion of exons 52-54 in Dmd that develops an early-onset cardiac phenotype similar to DMD patients. Here we employed CRISPR-Cas9 delivered intravenously by adeno-associated virus (AAV) vectors to restore functional dystrophin expression via excision or skipping of exon 55. Exon skipping with a solitary guide significantly improved editing outcomes and dystrophin recovery over dual guide excision. Some improvements to genomic and transcript editing levels were observed when the guide dose was enhanced, but dystrophin restoration did not improve considerably. Editing and dystrophin recovery were restricted primarily to cardiac tissue. Remarkably, our exon skipping approach completely prevented onset of the cardiac phenotype in treated mice up to 12 weeks. Thus, our results demonstrate that intravenous delivery of a single-cut CRISPR-Cas9-mediated exon skipping therapy can prevent heart dysfunction in DMD in vivo.
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Affiliation(s)
- Matthew Rok
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tatianna Wai Ying Wong
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eleonora Maino
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Abdalla Ahmed
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Grace Yang
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Elzbieta Hyatt
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Kyle Lindsay
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Sina Fatehi
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ryan Marks
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Paul Delgado-Olguín
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Heart & Stroke Richard Lewar Centre of Excellence, Toronto, ON, Canada
| | - Evgueni A. Ivakine
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Ronald D. Cohn
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
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20
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Kita Y, Okuzaki Y, Naoe Y, Lee J, Bang U, Okawa N, Ichiki A, Jonouchi T, Sakurai H, Kojima Y, Hotta A. Dual CRISPR-Cas3 system for inducing multi- exon skipping in DMD patient-derived iPSCs. Stem Cell Reports 2023; 18:1753-1765. [PMID: 37625413 PMCID: PMC10545483 DOI: 10.1016/j.stemcr.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
To restore dystrophin protein in various mutation patterns of Duchenne muscular dystrophy (DMD), the multi-exon skipping (MES) approach has been investigated. However, only limited techniques are available to induce a large deletion to cover the target exons spread over several hundred kilobases. Here, we utilized the CRISPR-Cas3 system for MES induction and showed that dual crRNAs could induce a large deletion at the dystrophin exon 45-55 region (∼340 kb), which can be applied to various types of DMD patients. We developed a two-color SSA-based reporter system for Cas3 to enrich the genome-edited cell population and demonstrated that MES induction restored dystrophin protein in DMD-iPSCs with three distinct mutations. Whole-genome sequencing and distance analysis detected no significant off-target deletion near the putative crRNA binding sites. Altogether, dual CRISPR-Cas3 is a promising tool to induce a gigantic genomic deletion and restore dystrophin protein via MES induction.
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Affiliation(s)
- Yuto Kita
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuya Okuzaki
- Nagoya University Graduate School of Bioagricultural Sciences, Avian Bioscience Research Center, Furo-cho, Chikusa-ku, Nagoya, Aishi 464-8601, Japan
| | - Youichi Naoe
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Joseph Lee
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Uikyu Bang
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Natsumi Okawa
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akane Ichiki
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tatsuya Jonouchi
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yusuke Kojima
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa 251-8555, Japan.
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21
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Gapinske M, Winter J, Swami D, Gapinske L, Woods WS, Shirguppe S, Miskalis A, Busza A, Joulani D, Kao CJ, Kostan K, Bigot A, Bashir R, Perez-Pinera P. Targeting Duchenne muscular dystrophy by skipping DMD exon 45 with base editors. Mol Ther Nucleic Acids 2023; 33:572-586. [PMID: 37637209 PMCID: PMC10448430 DOI: 10.1016/j.omtn.2023.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Duchenne muscular dystrophy is an X-linked monogenic disease caused by mutations in the dystrophin gene (DMD) characterized by progressive muscle weakness, leading to loss of ambulation and decreased life expectancy. Since the current standard of care for Duchenne muscular dystrophy is to merely treat symptoms, there is a dire need for treatment modalities that can correct the underlying genetic mutations. While several gene replacement therapies are being explored in clinical trials, one emerging approach that can directly correct mutations in genomic DNA is base editing. We have recently developed CRISPR-SKIP, a base editing strategy to induce permanent exon skipping by introducing C > T or A > G mutations at splice acceptors in genomic DNA, which can be used therapeutically to recover dystrophin expression when a genomic deletion leads to an out-of-frame DMD transcript. We now demonstrate that CRISPR-SKIP can be adapted to correct some forms of Duchenne muscular dystrophy by disrupting the splice acceptor in human DMD exon 45 with high efficiency, which enables open reading frame recovery and restoration of dystrophin expression. We also demonstrate that AAV-delivered split-intein base editors edit the splice acceptor of DMD exon 45 in cultured human cells and in vivo, highlighting the therapeutic potential of this strategy.
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Affiliation(s)
- Michael Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Devyani Swami
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauren Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick J. Holonyak Micro and Nano Technology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shraddha Shirguppe
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Angelo Miskalis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna Busza
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dana Joulani
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin J. Kao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kurt Kostan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick J. Holonyak Micro and Nano Technology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Champaign, IL 61820, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Champaign, IL 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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22
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Michaud V, Sequeira A, Mercier E, Lasseaux E, Plaisant C, Hadj-Rabia S, Whalen S, Bonneau D, Dieux-Coeslier A, Morice-Picard F, Coursimault J, Arveiler B, Javerzat S. Unsuspected consequences of synonymous and missense variants in OCA2 can be detected in blood cell RNA samples of patients with albinism. Pigment Cell Melanoma Res 2023. [PMID: 37650133 DOI: 10.1111/pcmr.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Oculocutaneous albinism type 2 (OCA2) is the second most frequent form of albinism and represents about 30% of OCA worldwide. As with all types of OCA, patients present with hypopigmentation of hair and skin, as well as severe visual abnormalities. We focused on a subgroup of 29 patients for whom genetic diagnosis was pending because at least one of their identified variants in or around exon 10 of OCA2 is of uncertain significance (VUS). By minigene assay, we investigated the effect of these VUS on exon 10 skipping and showed that not only intronic but also some synonymous variants can result in enhanced exon skipping. We further found that excessive skipping of exon 10 could be detected directly on blood samples of patients and of their one parent with the causal variant, avoiding invasive skin biopsies. Moreover, we show that variants, which result in lack of detectable OCA2 mRNA can be identified from blood samples as well, as shown for the most common OCA2 pathogenic missense variant c.1327G>A/p.(Val443Ile). In conclusion, blood cell RNA analysis allows testing the potential effect of any OCA2 VUS on transcription products. This should help to elucidate yet unsolved OCA2 patients and improve genetic counseling.
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Affiliation(s)
- Vincent Michaud
- Rare Diseases Genetics and Metabolism, INSERM U1211, SBM Department, University of Bordeaux, Bordeaux, France
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Angèle Sequeira
- Rare Diseases Genetics and Metabolism, INSERM U1211, SBM Department, University of Bordeaux, Bordeaux, France
| | - Elina Mercier
- Rare Diseases Genetics and Metabolism, INSERM U1211, SBM Department, University of Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Claudio Plaisant
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Smail Hadj-Rabia
- Department of Dermatology, Reference Center for Genodermatoses and Rare Skin Diseases (MAGEC), INSERM U1163, University of Paris, Imagine Institute, AP-HP5, Necker-Enfants Malades Hospital, Paris, France
| | - Sandra Whalen
- Clinical Genetics, Centre de Référence Maladies Rares Anomalies du développement et syndromes malformatifs, APHP, Sorbonne University, Hospital Armand Trousseau, Paris, France
| | | | - Anne Dieux-Coeslier
- Clinical Genetics Department, Reference Center for Developmental Anomalies, CHU Lille, Lille, France
| | - Fanny Morice-Picard
- Pediatric Dermatology Unit, National Center for Rare Skin Disorders, University Hospital of Bordeaux, Bordeaux, France
| | - Juliette Coursimault
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, Rouen, France
| | - Benoît Arveiler
- Rare Diseases Genetics and Metabolism, INSERM U1211, SBM Department, University of Bordeaux, Bordeaux, France
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Sophie Javerzat
- Rare Diseases Genetics and Metabolism, INSERM U1211, SBM Department, University of Bordeaux, Bordeaux, France
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23
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McCormack NM, Calabrese KA, Sun CM, Tully CB, Heier CR, Fiorillo AA. Deletion of miR-146a enhances therapeutic protein restoration in model of dystrophin exon skipping. bioRxiv 2023:2023.05.09.540042. [PMID: 37214870 PMCID: PMC10197665 DOI: 10.1101/2023.05.09.540042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive muscle disease caused by the absence of dystrophin protein. One current DMD therapeutic strategy, exon skipping, produces a truncated dystrophin isoform using phosphorodiamidate morpholino oligomers (PMOs). However, the potential of exon skipping therapeutics has not been fully realized as increases in dystrophin protein have been minimal in clinical trials. Here, we investigate how miR-146a-5p, which is highly elevated in dystrophic muscle, impacts dystrophin protein levels. We find inflammation strongly induces miR-146a in dystrophic, but not wild-type myotubes. Bioinformatics analysis reveals that the dystrophin 3'UTR harbors a miR-146a binding site, and subsequent luciferase assays demonstrate miR-146a binding inhibits dystrophin translation. In dystrophin-null mdx52 mice, co-injection of miR-146a reduces dystrophin restoration by an exon 51 skipping PMO. To directly investigate how miR-146a impacts therapeutic dystrophin rescue, we generated mdx52 with body-wide miR-146a deletion (146aX). Administration of an exon skipping PMO via intramuscular or intravenous injection markedly increases dystrophin protein levels in 146aX versus mdx52 muscles; skipped dystrophin transcript levels are unchanged, suggesting a post-transcriptional mechanism-of-action. Together, these data show that miR-146a expression opposes therapeutic dystrophin restoration, suggesting miR-146a inhibition warrants further research as a potential DMD exon skipping co-therapy.
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Affiliation(s)
- Nikki M. McCormack
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
| | - Kelsey A. Calabrese
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
| | - Christina M. Sun
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
| | - Christopher B. Tully
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
| | - Christopher R. Heier
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Alyson A. Fiorillo
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
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24
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Stirm M, Shashikadze B, Blutke A, Kemter E, Lange A, Stöckl JB, Jaudas F, Laane L, Kurome M, Keßler B, Zakhartchenko V, Bähr A, Klymiuk N, Nagashima H, Walter MC, Wurst W, Kupatt C, Fröhlich T, Wolf E. Systemic deletion of DMD exon 51 rescues clinically severe Duchenne muscular dystrophy in a pig model lacking DMD exon 52. Proc Natl Acad Sci U S A 2023; 120:e2301250120. [PMID: 37428903 PMCID: PMC10629550 DOI: 10.1073/pnas.2301250120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 06/10/2023] [Indexed: 07/12/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked disease caused by mutations in the DMD gene, leading to complete absence of dystrophin and progressive degeneration of skeletal musculature and myocardium. In DMD patients and in a corresponding pig model with a deletion of DMD exon 52 (DMDΔ52), expression of an internally shortened dystrophin can be achieved by skipping of DMD exon 51 to reframe the transcript. To predict the best possible outcome of this strategy, we generated DMDΔ51-52 pigs, additionally representing a model for Becker muscular dystrophy (BMD). DMDΔ51-52 skeletal muscle and myocardium samples stained positive for dystrophin and did not show the characteristic dystrophic alterations observed in DMDΔ52 pigs. Western blot analysis confirmed the presence of dystrophin in the skeletal muscle and myocardium of DMDΔ51-52 pigs and its absence in DMDΔ52 pigs. The proteome profile of skeletal muscle, which showed a large number of abundance alterations in DMDΔ52 vs. wild-type (WT) samples, was normalized in DMDΔ51-52 samples. Cardiac function at age 3.5 mo was significantly reduced in DMDΔ52 pigs (mean left ventricular ejection fraction 58.8% vs. 70.3% in WT) but completely rescued in DMDΔ51-52 pigs (72.3%), in line with normalization of the myocardial proteome profile. Our findings indicate that ubiquitous deletion of DMD exon 51 in DMDΔ52 pigs largely rescues the rapidly progressing, severe muscular dystrophy and the reduced cardiac function of this model. Long-term follow-up studies of DMDΔ51-52 pigs will show if they develop symptoms of the milder BMD.
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Affiliation(s)
- Michael Stirm
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Andreas Blutke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Munich80539, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Andreas Lange
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Jan B. Stöckl
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Florian Jaudas
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Laeticia Laane
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Mayuko Kurome
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Barbara Keßler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Andrea Bähr
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
| | - Nikolai Klymiuk
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
| | - Hiroshi Nagashima
- Meiji University International Institute for Bio-Resource Research, Kawasaki214-8571, Japan
| | - Maggie C. Walter
- Department of Neurology, Friedrich Baur Institute, LMU Munich, Munich80336, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg85674, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising85354, Germany
| | - Christian Kupatt
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich81675, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer, LMU Munich, Munich81377, Germany
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Shah MNA, Yokota T. Cardiac therapies for Duchenne muscular dystrophy. Ther Adv Neurol Disord 2023; 16:17562864231182934. [PMID: 37425427 PMCID: PMC10328182 DOI: 10.1177/17562864231182934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/11/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating disease that results in life-limiting complications such as loss of skeletal muscle function as well as respiratory and cardiac complications. Advanced therapeutics in pulmonary care have significantly reduced respiratory complication-related mortality, making cardiomyopathy the main determinant factor of survival. While there are multiple therapies such as the use of anti-inflammatory drugs, physical therapy, and ventilatory assistance targeted toward delaying the disease progression in DMD, a cure remains elusive. In the last decade, several therapeutic approaches have been developed to improve patient survival. These include small molecule-based therapy, micro-dystrophin gene delivery, CRISPR-mediated gene editing, nonsense readthrough, exon skipping, and cardiosphere-derived cell therapy. Associated with the specific benefits of each of these approaches are their individual risks and limitations. The variability in the genetic aberrations leading to DMD also limits the widespread use of these therapies. While numerous approaches have been explored to treat DMD pathophysiology, only a handful have successfully advanced through the preclinical stages. In this review, we summarize the currently approved as well as the most promising therapeutics undergoing clinical trials aimed toward treating DMD with a focus on its cardiac manifestations.
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Affiliation(s)
- Md Nur Ahad Shah
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Czifrus E, Berlau DJ. Viltolarsen: a treatment option for Duchenne muscular dystrophy patients who are amenable to exon 53 skipping therapy. Expert Rev Neurother 2023; 23:853-858. [PMID: 37572081 DOI: 10.1080/14737175.2023.2246658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is a progressive genetic disease leading to muscular weakness. DMD is caused by mutations of the dystrophin gene on the X chromosome that is responsible for production of dystrophin protein. Dystrophin contributes to structural support in muscle cells and mutations result in dystrophin protein deficiency which causes muscle damage and the associated clinical presentation. Exon skipping medications, including the exon 53 targeting viltolarsen, are the first agents with the ability to partially restore dystrophin protein. AREAS COVERED Herein, the authors profile viltolarsen for the DMD patients who are amenable to exon 53 skipping therapy and provide their expert perspectives on this subject. EXPERT OPINION Current findings suggest that viltolarsen could play a role in the current and possible future treatment of DMD. Viltolarsen seems to be safe and restores dystrophin protein to around 6% of the normal level. Due to orphan drug status, after the completion of the phase 2 clinical trial, viltolarsen was granted accelerated approval in Japan and in the US. A phase 3 trial is currently in progress and needs to earn full approval. Although a multidisciplinary approach continues to be critical, the addition of exon skipping agents like viltolarsen may improve the quality of patients' lives. However, data on the long-term safety and efficacy of this medication are not yet available due to its recent accelerated approval.
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Affiliation(s)
- Eszter Czifrus
- Semmelweis University Faculty of Medicine, Budapest, Hungary
| | - Daniel J Berlau
- Department of Pharmaceutical Sciences, Regis University School of Pharmacy, Denver, CO, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chai AC, Chemello F, Li H, Nishiyama T, Chen K, Zhang Y, Sánchez-Ortiz E, Alomar A, Xu L, Liu N, Bassel-Duby R, Olson EN. Single-swap editing for the correction of common Duchenne muscular dystrophy mutations. Mol Ther Nucleic Acids 2023; 32:522-535. [PMID: 37215149 PMCID: PMC10192335 DOI: 10.1016/j.omtn.2023.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disease of progressive muscle weakness and wasting caused by the absence of dystrophin protein. Current gene therapy approaches using antisense oligonucleotides require lifelong dosing and have limited efficacy in restoring dystrophin production. A gene editing approach could permanently correct the genome and restore dystrophin protein expression. Here, we describe single-swap editing, in which an adenine base editor edits a single base pair at a splice donor site or splice acceptor site to enable exon skipping or reframing. In human induced pluripotent stem cell-derived cardiomyocytes, we demonstrate that single-swap editing can enable beneficial exon skipping or reframing for the three most therapeutically relevant exons-DMD exons 45, 51, and 53-which could be beneficial for 30% of all DMD patients. Furthermore, an adeno-associated virus delivery method for base editing components can efficiently restore dystrophin production locally and systemically in skeletal and cardiac muscles of a DMD mouse model containing a deletion of Dmd exon 44. Our studies demonstrate single-swap editing as a potential gene editing therapy for common DMD mutations.
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Affiliation(s)
- Andreas C. Chai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takahiko Nishiyama
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Efraín Sánchez-Ortiz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeeb Alomar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Torella A, Budillon A, Zanobio M, Del Vecchio Blanco F, Picillo E, Politano L, Nigro V, Piluso G. Alu-Mediated Insertions in the DMD Gene: A Difficult Puzzle to Interpret Clinically. Int J Mol Sci 2023; 24:ijms24119241. [PMID: 37298193 DOI: 10.3390/ijms24119241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Disrupting variants in the DMD gene are associated with Duchenne or Becker muscular dystrophy (DMD/BMD) or with hyperCKemia, all of which present very different degrees of clinical severity. The clinical phenotypes of these disorders could not be distinguished in infancy or early childhood. Accurate phenotype prediction based on DNA variants may therefore be required in addition to invasive tests, such as muscle biopsy. Transposon insertion is one of the rarest mutation types. Depending on their position and characteristics, transposon insertions may affect the quality and/or quantity of dystrophin mRNA, leading to unpredictable alterations in gene products. Here, we report the case of a three-year-old boy showing initial skeletal muscle involvement in whom we characterized a transposon insertion (Alu sequence) in exon 15 of the DMD gene. In similar cases, the generation of a null allele is predicted, resulting in a DMD phenotype. However, mRNA analysis of muscle biopsy tissue revealed skipping of exon 15, which restored the reading frame, thus predicting a milder phenotype. This case is similar to very few others already described in the literature. This case further enriches our knowledge of the mechanisms perturbing splicing and causing exon skipping in DMD, helping to properly guide clinical diagnosis.
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Affiliation(s)
- Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Alberto Budillon
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Zanobio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Francesca Del Vecchio Blanco
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Esther Picillo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Luisa Politano
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
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Happi Mbakam C, Roustant J, Rousseau J, Yameogo P, Lu Y, Bigot A, Mamchaoui K, Mouly V, Lamothe G, Tremblay JP. Prime editing strategies to mediate exon skipping in DMD gene. Front Med (Lausanne) 2023; 10:1128557. [PMID: 37305116 PMCID: PMC10248452 DOI: 10.3389/fmed.2023.1128557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/20/2023] [Indexed: 06/13/2023] Open
Abstract
Duchenne muscular dystrophy is a rare and lethal hereditary disease responsible for progressive muscle wasting due to mutations in the DMD gene. We used the CRISPR-Cas9 Prime editing technology to develop different strategies to correct frameshift mutations in DMD gene carrying the deletion of exon 52 or exons 45 to 52. With optimized epegRNAs, we were able to induce the specific substitution of the GT nucleotides of the splice donor site of exon 53 in up to 32% of HEK293T cells and 28% of patient myoblasts. We also achieved up to 44% and 29% deletion of the G nucleotide of the GT splice site of exon 53, as well as inserted 17% and 5.5% GGG between the GT splice donor site of exon 51 in HEK293T cells and human myoblasts, respectively. The modification of the splice donor site for exon 51 and exon 53 provoke their skipping and allowed exon 50 to connect to exon 53 and allowed exon 44 to connect to exon 54, respectively. These corrections restored the expression of dystrophin as demonstrated by western blot. Thus, Prime editing was used to induce specific substitutions, insertions and deletions in the splice donor sites for exons 51 and 53 to correct the frameshift mutations in DMD gene carrying deletions of exon 52 and exons 45 to 52, respectively.
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Affiliation(s)
- Cedric Happi Mbakam
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
| | | | - Joel Rousseau
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Pouire Yameogo
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Yaoyao Lu
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Anne Bigot
- Institute of Myology, Myology Research Center, Paris, France
| | - Kamel Mamchaoui
- Institute of Myology, Myology Research Center, Paris, France
| | - Vincent Mouly
- Institute of Myology, Myology Research Center, Paris, France
| | - Gabriel Lamothe
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Jacques P. Tremblay
- CHU de Québec Research Centre, Laval University, Québec, QC, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, QC, Canada
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Bai R, Chen D, Xiong H, Song H, Wang T, Yang X, Tang J, Feng Y, Li J, Li F. SPAG6 c.900 T>C affects boar semen quality and blood-testis barrier function by creating a new splice acceptor site. Anim Genet 2023. [PMID: 37211688 DOI: 10.1111/age.13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/16/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Sperm associated antigen 6 (SPAG6) acts as a scaffolding protein in the center of the flagellar axoneme and has an impact on the maturation of the motility of mammalian sperm flagella and the maintenance of sperm structure. In our previous research, SPAG6 c.900 T>C in exon 7 and exon 7 skipped transcript was identified by analyzing RNA-seq data of testicular tissues from 60 day (sexually immature) and 180 day (sexually mature) Large White boars. Herein, we found porcine SPAG6 c.900 T>C to be associated with semen quality traits in Duroc, Large White and Landrace pigs. SPAG6 c.900 C can generate a new splice acceptor site, inhibit the occurrence of SPAG6 exon 7 skipping to a certain extent, thereby promote the growth of Sertoli cells and maintain the normal blood-testis barrier function. This study provides new insights into the molecular regulation of spermatogenesis and a new genetic marker for the improvement of semen quality in pigs.
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Affiliation(s)
- Rong Bai
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Dake Chen
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hao Xiong
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Huibin Song
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Tiansu Wang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xinpeng Yang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jinhua Tang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yue Feng
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jialian Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Fenge Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Yan L, Sun Y, Guo J, Jia R. PD-L1 Exon 3 Is a Hidden Switch of Its Expression and Function in Oral Cancer Cells. Int J Mol Sci 2023; 24:ijms24098193. [PMID: 37175900 PMCID: PMC10178889 DOI: 10.3390/ijms24098193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The interaction between programmed cell death 1 ligand 1 (PD-L1) and programmed cell death protein 1 (PD-1) protects tumor cells from immune surveillance. PD-L1 exon 3 is a potential alternative exon and encodes an Ig variable (IgV) domain. Here, we found that a lack of exon 3 leads to the significant loss of cellular membrane locations and the dramatically reduced protein expression of PD-L1, indicating that PD-L1 exon 3 is essential for its protein expression and translocation to the cell membrane. Notably, oral cancer cells show almost no exon 3 skipping to ensure the expression of the full-length, functional PD-L1 protein. We discovered two key exonic splicing enhancers (ESEs) for exon 3 inclusion. Two efficient antisense oligonucleotides (ASOs) were identified to block these two ESEs, which can significantly trigger exon 3 skipping and decrease the production of full-length, functional PD-L1 on the surface of cancer cells. Treatment of oral cancer cells with these ASOs significantly enhanced immune cells' suppression of cancer cell proliferation. Surprisingly, these two ASOs also significantly inhibited cell growth and induced cell pyroptosis in oral cancer cells. Altogether, the results of our study demonstrate the pivotal roles of exon 3 in PD-L1 expression and provide a novel anti-PD-L1 method.
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Affiliation(s)
- Lingyan Yan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Yanan Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
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Abstract
Duchenne muscular dystrophy (DMD) was named more than 150 years ago. About four decades ago, the DMD gene was discovered, and the reading frame shift was determined as the genetic underpinning. These pivotal findings significantly changed the landscape of DMD therapy development. Restoration of dystrophin expression with gene therapy became a primary focus. Investment in gene therapy has led to the approval of exon skipping by regulatory agencies, multiple clinical trials of systemic microdystrophin therapy using adeno-associated virus vectors, and revolutionary genome editing therapy using the CRISPR technology. However, many important issues surfaced during the clinical translation of DMD gene therapy (such as low efficiency of exon skipping, immune toxicity-induced serious adverse events, and patient death). In this issue of Human Gene Therapy, several research articles highlighted some of the latest developments in DMD gene therapy. Importantly, a collection of articles from experts in the field reviewed the progress, major challenges, and future directions of DMD gene therapy. These insightful discussions have significant implications for gene therapy of other neuromuscular diseases.
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Affiliation(s)
- Dongsheng Duan
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA
- Department of Neurology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Department of Chemical and Biomedical Engineering, College of Engineering, University of Missouri, Columbia, Missouri, USA
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Brogna C, Pane M, Coratti G, D'Amico A, Pegoraro E, Bello L, Sansone VAM, Albamonte E, Messina S, Pini A, D'Angelo MG, Bruno C, Mongini T, Ricci FS, Berardinelli A, Battini R, Masson R, Bertini ES, Politano L, Mercuri E. Upper Limb Changes in DMD Patients Amenable to Skipping Exons 44, 45, 51 and 53: A 24-Month Study. Children (Basel) 2023; 10:children10040746. [PMID: 37189996 DOI: 10.3390/children10040746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
INTRODUCTION The Performance of Upper Limb version 2.0 (PUL 2.0) is increasingly used in Duchenne Muscular Dystrophy (DMD) to study longitudinal functional changes of motor upper limb function in ambulant and non-ambulant patients. The aim of this study was to evaluate changes in upper limb functions in patients carrying mutations amenable to skipping exons 44, 45, 51 and 53. METHODS All DMD patients were assessed using the PUL 2.0 for at least 2 years, focusing on 24-month paired visits in those with mutations eligible for skipping exons 44, 45, 51 and 53. RESULTS 285 paired assessments were available. The mean total PUL 2.0 12-month change was -0.67 (2.80), -1.15 (3.98), -1.46 (3.37) and -1.95 (4.04) in patients carrying mutations amenable to skipping exon 44, 45, 51 and 53, respectively. The mean total PUL 2.0 24-month change was -1.47 (3.73), -2.78 (5.86), -2.95 (4.56) and -4.53 (6.13) in patients amenable to skipping exon 44, 45, 51 and 53, respectively. The difference in PUL 2.0 mean changes among the type of exon skip class for the total score was not significant at 12 months but was significant at 24 months for the total score (p < 0.001), the shoulder (p = 0.01) and the elbow domain (p < 0.001), with patients amenable to skipping exon 44 having smaller changes compared to those amenable to skipping exon 53. There was no difference within ambulant or non-ambulant cohorts when subdivided by exon skip class for the total and subdomains score (p > 0.05). CONCLUSIONS Our results expand the information on upper limb function changes detected by the PUL 2.0 in a relatively large group of DMD patients with distinct exon-skipping classes. This information can be of help when designing clinical trials or in the interpretation of the real world data including non-ambulant patients.
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Affiliation(s)
- Claudia Brogna
- Pediatric Neurology, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Marika Pane
- Pediatric Neurology, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Giorgia Coratti
- Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, 35128 Padua, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, 35128 Padua, Italy
| | - Valeria Ada Maria Sansone
- The NEMO Center in Milan, Neurorehabilitation Unit, University of Milan, ASST Niguarda Hospital, 20162 Milan, Italy
| | - Emilio Albamonte
- The NEMO Center in Milan, Neurorehabilitation Unit, University of Milan, ASST Niguarda Hospital, 20162 Milan, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy
| | - Antonella Pini
- Neuromuscular Pediatric Unit, IRRCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
| | | | - Claudio Bruno
- Center of Translational and Experimental Myology and Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, IRCCS Istituto Giannina Gaslini and University of Genoa, 16132 Genoa, Italy
| | - Tiziana Mongini
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Torino, 10100 Turin, Italy
| | - Federica Silvia Ricci
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Torino, 10100 Turin, Italy
| | - Angela Berardinelli
- National Neurological Institute C. Mondino Foundation, IRCCS, 27100 Pavia, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris, 56018 Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Riccardo Masson
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Enrico Silvio Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Luisa Politano
- Cardiomiology and Medical Genetics, Department of Experimental Medicine, Università della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Eugenio Mercuri
- Pediatric Neurology, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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van Deutekom J, Beekman C, Bijl S, Bosgra S, van den Eijnde R, Franken D, Groenendaal B, Harquouli B, Janson A, Koevoets P, Mulder M, Muilwijk D, Peterburgska G, Querido B, Testerink J, Verheul R, de Visser P, Weij R, Aartsma-Rus A, Puoliväli J, Bragge T, O'Neill C, Datson NA. Next Generation Exon 51 Skipping Antisense Oligonucleotides for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2023. [PMID: 37036788 DOI: 10.1089/nat.2022.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
In the last two decades, antisense oligonucleotides (AONs) that induce corrective exon skipping have matured as promising therapies aimed at tackling the dystrophin deficiency that underlies the severe and progressive muscle fiber degeneration in Duchenne muscular dystrophy (DMD) patients. Pioneering first generation exon 51 skipping AONs like drisapersen and eteplirsen have more recently been followed up by AONs for exons 53 and 45, with, to date, a total of four exon skipping AON drugs having reached (conditional) regulatory US Food and Drug Administration (FDA) approval for DMD. Nonetheless, considering the limited efficacy of these drugs, there is room for improvement. The aim of this study was to develop more efficient [2'-O-methyl-modified phosphorothioate (2'OMePS) RNA] AONs for DMD exon 51 skipping by implementing precision chemistry as well as identifying a more potent target binding site. More than a hundred AONs were screened in muscle cell cultures, followed by a selective comparison in the hDMD and hDMDdel52/mdx mouse models. Incorporation of 5-methylcytosine and position-specific locked nucleic acids in AONs targeting the drisapersen/eteplirsen binding site resulted in 15-fold higher exon 51 skipping levels compared to drisapersen in hDMDdel52/mdx mice. However, with similarly modified AONs targeting an alternative site in exon 51, 65-fold higher skipping levels were obtained, restoring dystrophin up to 30% of healthy control. Targeting both sites in exon 51 with a single AON further increased exon skipping (100-fold over drisapersen) and dystrophin (up to 40%) levels. These dystrophin levels allowed for normalization of creatine kinase (CK) and lactate dehydrogenase (LDH) levels, and improved motor function in hDMDdel52/mdx mice. As no major safety observation was obtained, the improved therapeutic index of these next generation AONs is encouraging for further (pre)clinical development.
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Affiliation(s)
- Judith van Deutekom
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Chantal Beekman
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Suzanne Bijl
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Sieto Bosgra
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Rani van den Eijnde
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Dennis Franken
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Bas Groenendaal
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Bouchra Harquouli
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Anneke Janson
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Paul Koevoets
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Melissa Mulder
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Daan Muilwijk
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Galyna Peterburgska
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Bianca Querido
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Janwillem Testerink
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Ruurd Verheul
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Peter de Visser
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Rudie Weij
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Timo Bragge
- Charles River Discovery Services, Kuopio, Finland
| | | | - Nicole A Datson
- VICO Therapeutics B.V., formerly BioMarin Nederland B.V., Leiden, The Netherlands
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Heier CR, McCormack NM, Tully CB, Novak JS, Newell‐Stamper BL, Russell AJ, Fiorillo AA. The X-linked Becker muscular dystrophy (bmx) mouse models Becker muscular dystrophy via deletion of murine dystrophin exons 45-47. J Cachexia Sarcopenia Muscle 2023; 14:940-954. [PMID: 36628607 PMCID: PMC10067474 DOI: 10.1002/jcsm.13171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Becker muscular dystrophy (BMD) is a genetic neuromuscular disease of growing importance caused by in-frame, partial loss-of-function mutations in the dystrophin (DMD) gene. BMD presents with reduced severity compared with Duchenne muscular dystrophy (DMD), the allelic disorder of complete dystrophin deficiency. Significant therapeutic advancements have been made in DMD, including four FDA-approved drugs. BMD, however, is understudied and underserved-there are no drugs and few clinical trials. Discordance in therapeutic efforts is due in part to lack of a BMD mouse model which would enable greater understanding of disease and de-risk potential therapeutics before first-in-human trials. Importantly, a BMD mouse model is becoming increasingly critical as emerging DMD dystrophin restoration therapies aim to convert a DMD genotype into a BMD phenotype. METHODS We use CRISPR/Cas9 technology to generate bmx (Becker muscular dystrophy, X-linked) mice, which express an in-frame ~40 000 bp deletion of exons 45-47 in the murine Dmd gene, reproducing the most common BMD patient mutation. Here, we characterize muscle pathogenesis using molecular and histological techniques and then test skeletal muscle and cardiac function using muscle function assays and echocardiography. RESULTS Overall, bmx mice present with significant muscle weakness and heart dysfunction versus wild-type (WT) mice, despite a substantial improvement in pathology over dystrophin-null mdx52 mice. bmx mice show impaired motor function in grip strength (-39%, P < 0.0001), wire hang (P = 0.0025), and in vivo as well as ex vivo force assays. In aged bmx, echocardiography reveals decreased heart function through reduced fractional shortening (-25%, P = 0.0036). Additionally, muscle-specific serum CK is increased >60-fold (P < 0.0001), indicating increased muscle damage. Histologically, bmx muscles display increased myofibre size variability (minimal Feret's diameter: P = 0.0017) and centrally located nuclei indicating degeneration/regeneration (P < 0.0001). bmx muscles also display dystrophic pathology; however, levels of the following parameters are moderate in comparison with mdx52: inflammatory/necrotic foci (P < 0.0001), collagen deposition (+1.4-fold, P = 0.0217), and sarcolemmal damage measured by intracellular IgM (P = 0.0878). Like BMD patients, bmx muscles show reduced dystrophin protein levels (~20-50% of WT), whereas Dmd transcript levels are unchanged. At the molecular level, bmx muscles express increased levels of inflammatory genes, inflammatory miRNAs and fibrosis genes. CONCLUSIONS The bmx mouse recapitulates BMD disease phenotypes with histological, molecular and functional deficits. Importantly, it can inform both BMD pathology and DMD dystrophin restoration therapies. This novel model will enable further characterization of BMD disease progression, identification of biomarkers, identification of therapeutic targets and new preclinical drug studies aimed at developing therapies for BMD patients.
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Affiliation(s)
- Christopher R. Heier
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
- Department of Genomics and Precision MedicineGeorge Washington University School of Medicine and Health SciencesWashingtonDCUSA
| | - Nikki M. McCormack
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
| | | | - James S. Novak
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
- Department of Genomics and Precision MedicineGeorge Washington University School of Medicine and Health SciencesWashingtonDCUSA
| | | | - Alan J. Russell
- Edgewise Therapeutics, BioFrontiers InstituteUniversity of ColoradoBoulderCO80303USA
| | - Alyson A. Fiorillo
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
- Department of Genomics and Precision MedicineGeorge Washington University School of Medicine and Health SciencesWashingtonDCUSA
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Mou H, Eskiocak O, Özler KA, Gorman M, Yue J, Jin Y, Wang Z, Gao Y, Janowitz T, Meyer HV, Yu T, Wilkinson JE, Kucukural A, Ozata DM, Beyaz S. CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer. J Pathol 2023; 259:415-427. [PMID: 36641763 PMCID: PMC10273193 DOI: 10.1002/path.6054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/01/2022] [Accepted: 01/12/2023] [Indexed: 01/16/2023]
Abstract
CRISPR/Cas9-driven cancer modeling studies are based on the disruption of tumor suppressor genes by small insertions or deletions (indels) that lead to frame-shift mutations. In addition, CRISPR/Cas9 is widely used to define the significance of cancer oncogenes and genetic dependencies in loss-of-function studies. However, how CRISPR/Cas9 influences gain-of-function oncogenic mutations is elusive. Here, we demonstrate that single guide RNA targeting exon 3 of Ctnnb1 (encoding β-catenin) results in exon skipping and generates gain-of-function isoforms in vivo. CRISPR/Cas9-mediated exon skipping of Ctnnb1 induces liver tumor formation in synergy with YAPS127A in mice. We define two distinct exon skipping-induced tumor subtypes with different histological and transcriptional features. Notably, ectopic expression of two exon-skipped β-catenin transcript isoforms together with YAPS127A phenocopies the two distinct subtypes of liver cancer. Moreover, we identify similar CTNNB1 exon-skipping events in patients with hepatocellular carcinoma. Collectively, our findings advance our understanding of β-catenin-related tumorigenesis and reveal that CRISPR/Cas9 can be repurposed, in vivo, to study gain-of-function mutations of oncogenes in cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Haiwei Mou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kadir A. Özler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Megan Gorman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Junjiayu Yue
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ying Jin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Zhikai Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ya Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John E Wilkinson
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Alper Kucukural
- Bioinformatics Core, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, USA
| | - Deniz M. Ozata
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Li H, Wang C, Che R, Zheng B, Zhou W, Huang S, Jia Z, Zhang A, Zhao F, Ding G. A Potential Therapy Using Antisense Oligonucleotides to Treat Autosomal Recessive Polycystic Kidney Disease. J Clin Med 2023; 12. [PMID: 36835961 DOI: 10.3390/jcm12041428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
(1) Background: Autosomal recessive polycystic kidney disease (ARPKD) is a rare ciliopathy characterized by progressively enlarged kidneys with fusiform dilatation of the collecting ducts. Loss-of-function mutations in the PKHD1 gene, which encodes fibrocystin/polyductin, cause ARPKD; however, an efficient treatment method and drug for ARPKD have yet to be found. Antisense oligonucleotides (ASOs) are short special oligonucleotides which function to regulate gene expression and alter mRNA splicing. Several ASOs have been approved by the FDA for the treatment of genetic disorders, and many are progressing at present. We designed ASOs to verify whether ASOs mediate the correction of splicing further to treat ARPKD arising from splicing defects and explored them as a potential treatment option. (2) Methods: We screened 38 children with polycystic kidney disease for gene detection using whole-exome sequencing (WES) and targeted next-generation sequencing. Their clinical information was investigated and followed up. The PKHD1 variants were summarized and analyzed, and association analysis was carried out to analyze the relationship between genotype and phenotype. Various bioinformatics tools were used to predict pathogenicity. Hybrid minigene analysis was performed as part of the functional splicing analysis. Moreover, the de novo protein synthesis inhibitor cycloheximide was selected to verify the degraded pathway of abnormal pre-mRNAs. ASOs were designed to rescue aberrant splicing, and this was verified. (3) Results: Of the 11 patients with PKHD1 variants, all of them exhibited variable levels of complications of the liver and kidneys. We found that patients with truncating variants and variants in certain regions had a more severe phenotype. Two splicing variants of the PKHD1 genotypes were studied via the hybrid minigene assay: variants c.2141-3T>C and c.11174+5G>A. These cause aberrant splicing, and their strong pathogenicity was confirmed. We demonstrated that the abnormal pre-mRNAs produced from the variants escaped from the NMD pathway with the use of the de novo protein synthesis inhibitor cycloheximide. Moreover, we found that the splicing defects were rescued by using ASOs, which efficiently induced the exclusion of pseudoexons. (4) Conclusion: Patients with truncating variants and variants in certain regions had a more severe phenotype. ASOs are a potential drug for treating ARPKD patients harboring splicing mutations of the PKHD1 gene by correcting the splicing defects and increasing the expression of the normal PKHD1 gene.
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Filonova G, Aartsma-Rus A. Next steps for the optimization of exon therapy for Duchenne muscular dystrophy. Expert Opin Biol Ther 2023; 23:133-143. [PMID: 36655939 DOI: 10.1080/14712598.2023.2169070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION It is established that the exon-skipping approach can restore dystrophin in Duchenne muscular dystrophy (DMD) patients. However, dystrophin restoration levels are low, and the field is evolving to provide solutions for improved exon skipping. DMD is a neuromuscular disorder associated with chronic muscle tissue loss attributed to the lack of dystrophin, which causes muscle inflammation, fibrosis formation, and impaired regeneration. Currently, four antisense oligonucleotides (AONs) based on phosphorodiamidate morpholino oligomer (PMO) chemistry are approved by US Food and Drug Administration for exon skipping therapy of eligible DMD patients. AREAS COVERED This review describes a preclinical and clinical experience with approved and newly developed AONs for DMD, outlines efforts that have been done to enhance AON efficiency, reviews challenges of clinical trials, and summarizes the current state of the exon skipping approach in the DMD field. EXPERT OPINION The exon skipping approach for DMD is under development, and several chemical modifications with improved properties are under (pre)-clinical investigation. Despite existing advantages of these modifications, their safety and effectiveness have to be examined in clinical trials, which are planned or ongoing. Furthermore, we propose clinical settings using natural history controls to facilitate studying the functional effect of the therapy.
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Affiliation(s)
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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40
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Hedgespeth BA, Snider DB, Bitting KJ, Cruse G. The exon-skipping oligonucleotide, KitStop, depletes tissue-resident mast cells in vivo to ameliorate anaphylaxis. Front Immunol 2023; 14:1006741. [PMID: 36798116 PMCID: PMC9927222 DOI: 10.3389/fimmu.2023.1006741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Anaphylaxis represents the most extreme and life-threatening form of allergic disease and is considered a medical emergency requiring immediate intervention. Additionally, some people with mastocytosis experience recurrent episodes of anaphylaxis during normal daily activities without exposure to known triggers. While acute therapy consists primarily of epinephrine and supportive care, chronic therapy relies mostly on desensitization and immunotherapy against the offending allergen, which is a time-consuming and sometimes unsuccessful process. These treatments also necessitate identification of the triggering allergen which is not always possible, and thus highlighting a need for alternative treatments for mast cell-mediated diseases. Methods The exon-skipping oligonucleotide KitStop was administered to mice intradermally, intraperitoneally, or systemically at a dose of 12.5 mg/kg. Local mast cell numbers were enumerated via peritoneal lavage or skin histology, and passive systemic anaphylaxis was induced to evaluate KitStop's global systemic effect. A complete blood count and biochemistry panel were performed to assess the risk of acute toxicity following KitStop administration. Results Here, we report the use of an exon-skipping oligonucleotide, which we have previously termed KitStop, to safely reduce the severity and duration of the anaphylactic response via mast cell depopulation in tissues. KitStop administration results in the integration of a premature stop codon within the mRNA transcript of the KIT receptor-a receptor tyrosine kinase found primarily on mast cells and whose gain-of-function mutation can lead to systemic mastocytosis. Following either local or systemic KitStop treatment, mice had significantly reduced mast cell numbers in the skin and peritoneum. In addition, KitStop-treated mice experienced a significantly diminished anaphylactic response using a model of passive systemic anaphylaxis when compared with control mice. Discussion KitStop treatment results in a significant reduction in systemic mast cell responses, thus offering the potential to serve as a powerful additional treatment modality for patients that suffer from anaphylaxis.
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Affiliation(s)
- Barry A Hedgespeth
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States.,Comparative Medicine and Translational Research Training Program, North Carolina State University, Raleigh, NC, United States
| | - Douglas B Snider
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States.,Comparative Medicine and Translational Research Training Program, North Carolina State University, Raleigh, NC, United States
| | - Katie J Bitting
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States
| | - Glenn Cruse
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
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41
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Yeter Doğan B, Günay N, Ada Y, Doğan ME. A novel MTX2 gene splice site variant resulting in exon skipping, causing the recently described mandibuloacral dysplasia progeroid syndrome. Am J Med Genet A 2023; 191:173-182. [PMID: 36269149 DOI: 10.1002/ajmg.a.63010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/09/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022]
Abstract
Until recently, mandibuloacral dysplasia (MAD) with type A and type B lipodystrophy was the first to come to mind in the association of mandibular hypoplasia, lipodystrophy, and acro-osteolysis. However, it has recently been added to the differential diagnosis of MAD, a newly defined syndrome, called MDPS. MDPS is a skeletal dysplasia characterized by postnatal growth retardation, hypotonia, generalized lipodystrophy, skin changes, progeroid traits, and dysmorphic facial features, including prominent eyes, long pinched nose, mandibular hypoplasia, and a small mouth. Biallelic null variants of the MTX2 gene are responsible for this syndrome. We performed whole-exome sequencing (WES) in a 6-year-old patient with skeletal dysplasia. WES revealed a novel homozygous c.543+1G>T splice site variant in the MTX2 gene. We also extracted total RNA from peripheral blood and used reverse transcription-polymerase chain reaction to generate cDNA. Sanger sequencing from cDNA showed that exon 8 of MTX2 was skipped. This study adds to the genetics and phenotype of MDPS and underlines the importance of comprehensive clinical and molecular research.
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Affiliation(s)
- Burcu Yeter Doğan
- Division of Pediatric Genetics, Department of Pediatrics, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Neslihan Günay
- Division of Pediatric Nephrology, Department of Pediatrics, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Yasin Ada
- Department of Medical Genetics, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Muhammet Ensar Doğan
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
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Aartsma-Rus A, Garanto A, van Roon-Mom W, McConnell EM, Suslovitch V, Yan WX, Watts JK, Yu TW. Consensus Guidelines for the Design and In Vitro Preclinical Efficacy Testing N-of-1 Exon Skipping Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:17-25. [PMID: 36516128 PMCID: PMC9940807 DOI: 10.1089/nat.2022.0060] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) can modulate pre-mRNA splicing. This offers therapeutic opportunities for numerous genetic diseases, often in a mutation-specific and sometimes even individual-specific manner. Developing therapeutic ASOs for as few as even a single patient has been shown feasible with the development of Milasen for an individual with Batten disease. Efforts to develop individualized ASOs for patients with different genetic diseases are ongoing globally. The N = 1 Collaborative (N1C) is an umbrella organization dedicated to supporting the nascent field of individualized medicine. N1C recently organized a workshop to discuss and advance standards for the rigorous design and testing of splice-switching ASOs. In this study, we present guidelines resulting from that meeting and the key recommendations: (1) dissemination of standardized experimental designs, (2) use of standardized reference ASOs, and (3) a commitment to data sharing and exchange.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,N = 1 Collaborative
| | - Alejandro Garanto
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Pediatrics and Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Victoria Suslovitch
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Jonathan K Watts
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Timothy W Yu
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Division of Genetics and Genomics, Boston, Massachusetts, USA
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O’Grady TM, Baddoo M, Flemington SA, Ishaq EY, Ungerleider NA, Flemington EK. Reversal of splicing infidelity is a pre-activation step in B cell differentiation. Front Immunol 2022; 13:1060114. [PMID: 36601126 PMCID: PMC9806119 DOI: 10.3389/fimmu.2022.1060114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. Methods We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in an in vitro laboratory model of B cell activation and differentiation (Epstein Barr virus infection). Results Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Discussion Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using the in vitro model suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.
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Affiliation(s)
- Tina M. O’Grady
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States,*Correspondence: Tina M. O’Grady, ; Erik K. Flemington,
| | - Melody Baddoo
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Samuel A. Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Eman Y. Ishaq
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Nathan A. Ungerleider
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Erik K. Flemington
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States,*Correspondence: Tina M. O’Grady, ; Erik K. Flemington,
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Alfen F, Putscher E, Hecker M, Zettl UK, Hermann A, Lukas J. Abnormal Pre-mRNA Splicing in Exonic Fabry Disease-Causing GLA Mutations. Int J Mol Sci 2022; 23:ijms232315261. [PMID: 36499585 PMCID: PMC9737616 DOI: 10.3390/ijms232315261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Fabry disease (FD) is a rare X-linked disease due to a multiverse of disrupting mutations within the GLA gene encoding lysosomal α-galactosidase A (AGAL). Absent AGAL activity causes the accumulation of complex glycosphingolipids inside of lysosomes in a variety of cell types and results in a progressive multisystem disease. Known disease-associated point mutations in protein-coding gene regions usually cause translational perturbations and result in premature chain termination, punctual amino acid sequence alterations or overall altered sequence alterations downstream of the mutation site. However, nucleotide exchanges at the border between introns and exons can affect splicing behavior and lead to abnormal pre-mRNA processing. Prediction with the Human Splicing Finder (HSF) revealed an indication of a significant change in splicing-relevant information for some known FD-associated GLA mutations. To experimentally determine the extent of the change, we made use of a minigene reporter assay and verified alternative splicing events for the exonic mutations c.194G>T and c.358C>G, which led to the usage of alternative donor splice sites at exon 1 and exon 2, respectively. In addition, the mutations c.548G>T and c.638A>T led to significant exon 4 skipping. We conclude that splicing phenotype analysis should be employed in the in vitro analysis of exonic GLA gene mutations, since abnormal splicing may result in a reduction of enzyme activity and alter the amenability for treatment with pharmacological chaperone (PC).
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Affiliation(s)
- Franziska Alfen
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, 18147 Rostock, Germany
| | - Elena Putscher
- Neuroimmunology Section, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Michael Hecker
- Neuroimmunology Section, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Uwe Klaus Zettl
- Neuroimmunology Section, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Deutsches Zentrum für Neurodegenerative (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
| | - Jan Lukas
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Correspondence:
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Wang P, Li H, Zhu M, Han RY, Guo S, Han R. Correction of DMD in human iPSC-derived cardiomyocytes by base-editing-induced exon skipping. Mol Ther Methods Clin Dev 2022; 28:40-50. [PMID: 36588820 PMCID: PMC9792405 DOI: 10.1016/j.omtm.2022.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene. Previously, we showed that adenine base editing (ABE) can efficiently correct a nonsense point mutation in a DMD mouse model. Here, we explored the feasibility of base-editing-mediated exon skipping as a therapeutic strategy for DMD using cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs). We first generated a DMD hiPSC line with a large deletion spanning exon 48 through 54 (ΔE48-54) using CRISPR-Cas9 gene editing. Dystrophin expression was disrupted in DMD hiPSC-derived cardiomyocytes (iCMs) as examined by RT-PCR, western blot, and immunofluorescence staining. Transfection of ABE and a guide RNA (gRNA) targeting the splice acceptor led to efficient conversion of AG to GG (35.9% ± 5.7%) and enabled exon 55 skipping. Complete AG to GG conversion in a single clone restored dystrophin expression (42.5% ± 11% of wild type [WT]) in DMD iCMs. Moreover, we designed gRNAs to target the splice sites of exons 6, 7, 8, 43, 44, 46, and 53 in the mutational hotspots and demonstrated their efficiency to induce exon skipping in iCMs. These results highlight the great promise of ABE-mediated exon skipping as a promising therapeutic approach for DMD.
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Affiliation(s)
- Peipei Wang
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Haiwen Li
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Mandi Zhu
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Rena Y. Han
- Olentangy Liberty High School, Powell, OH 43065, USA
| | - Shuliang Guo
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Renzhi Han
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA,Corresponding author Renzhi Han, PhD, Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
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Douben HCW, Nellist M, van Unen L, Elfferich P, Kasteleijn E, Hoogeveen-Westerveld M, Louwen J, van Veghel-Plandsoen M, de Valk W, Saris JJ, Hendriks F, Korpershoek E, Hoefsloot LH, van Vliet M, van Bever Y, van de Laar I, Aten E, Lachmeijer AMA, Taal W, van den Bersselaar L, Schuurmans J, Oostenbrink R, van Minkelen R, van Ierland Y, van Ham TJ. High-yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing. Hum Mutat 2022; 43:2130-2140. [PMID: 36251260 PMCID: PMC10099955 DOI: 10.1002/humu.24487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused by inactivating mutations in NF1. Due to the size, complexity, and high mutation rate at the NF1 locus, the identification of causative variants can be challenging. To obtain a molecular diagnosis in 15 individuals meeting diagnostic criteria for NF1, we performed transcriptome analysis (RNA-seq) on RNA obtained from cultured skin fibroblasts. In each case, routine molecular DNA diagnostics had failed to identify a disease-causing variant in NF1. A pathogenic variant or abnormal mRNA splicing was identified in 13 cases: 6 deep intronic variants and 2 transposon insertions causing noncanonical splicing, 3 postzygotic changes, 1 branch point mutation and, in 1 case, abnormal splicing for which the responsible DNA change remains to be identified. These findings helped resolve the molecular findings for an additional 17 individuals in multiple families with NF1, demonstrating the utility of skin-fibroblast-based transcriptome analysis for molecular diagnostics. RNA-seq improves mutation detection in NF1 and provides a powerful complementary approach to DNA-based methods. Importantly, our approach is applicable to other genetic disorders, particularly those caused by a wide variety of variants in a limited number of genes and specifically for individuals in whom routine molecular DNA diagnostics did not identify the causative variant.
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Affiliation(s)
- Hannie C W Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esmee Kasteleijn
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jesse Louwen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Walter de Valk
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Femke Hendriks
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esther Korpershoek
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Margreethe van Vliet
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Walter Taal
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisa van den Bersselaar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juliette Schuurmans
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rianne Oostenbrink
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of General Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Bizot F, Goossens R, Tensorer T, Dmitriev S, Garcia L, Aartsma-rus A, Spitali P, Goyenvalle A. Histone deacetylase inhibitors improve antisense-mediated exon-skipping efficacy in mdx mice. Molecular Therapy - Nucleic Acids 2022; 30:606-620. [PMID: 36514350 PMCID: PMC9722397 DOI: 10.1016/j.omtn.2022.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Antisense-mediated exon skipping is one of the most promising therapeutic strategies for Duchenne muscular dystrophy (DMD), and some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA despite their low efficacy. The potential of this therapy is still limited by several challenges, including the reduced expression of the dystrophin transcript and the strong 5'-3' imbalance in mutated transcripts. We therefore hypothesize that increasing histone acetylation using histone deacetylase inhibitors (HDACi) could correct the transcript imbalance, offering more available pre-mRNA target and ultimately increasing dystrophin rescue. Here, we evaluated the impact of such a combined therapy on the Dmd transcript imbalance phenomenon and on dystrophin restoration levels in mdx mice. Analysis of the Dmd transcript levels at different exon-exon junctions revealed a tendency to correct the 5'-3' imbalance phenomenon following treatment with HDACi. Significantly higher levels of dystrophin restoration (up to 74% increase) were obtained with givinostat and valproic acid compared with mice treated with ASO alone. Additionally, we demonstrate an increase in H3K9 acetylation in human myocytes after treatment with valproic acid. These findings indicate that HDACi can improve the therapeutic potential of exon-skipping approaches, offering promising perspectives for the treatment of DMD.
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Xu T, Zhang J, Liu Y, Zhang Q, Li W, Zhang Y, Wu M, Chen T, Ding D, Wang W, Zhang Z. Exon skipping in IspE Gene is associated with abnormal chloroplast development in rice albino leaf 4 mutant. Front Plant Sci 2022; 13:986678. [PMID: 36426160 PMCID: PMC9678938 DOI: 10.3389/fpls.2022.986678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The formation of leaf color largely depends on the components of pigment accumulation in plastids, which are involved in chloroplast development and division. Here, we isolated and characterized the rice albino leaf 4 (al4) mutant, which exhibited an albino phenotype and eventually died at the three-leaf stage. The chloroplasts in al4 mutant were severely damaged and unable to form intact thylakoid structure. Further analysis revealed that the candidate gene encodes 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE), which participates in the methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis. We further demonstrated that the mutation at the exon-intron junction site cause alternative splicing factors fail to distinguish the origin of the GT-AG intron, leading to exon skipping and producing a truncated OsIspE in the al4 mutant. Notably, disruption of OsIspE led to the reduced expression of chloroplast-associated genes, including chloroplast biosynthetic and translation related genes and photosynthetic associated nuclear genes (PhANGs). In summary, these findings reveal that OsIspE plays a crucial role in chloroplast biogenesis and provides novel insights into the function of CMK during chloroplast development in rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wenyi Wang
- *Correspondence: Zemin Zhang, ; Wenyi Wang,
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Fisher G, Mackels L, Markati T, Sarkozy A, Ochala J, Jungbluth H, Ramdas S, Servais L. Early clinical and pre-clinical therapy development in Nemaline myopathy. Expert Opin Ther Targets 2022; 26:853-867. [PMID: 36524401 DOI: 10.1080/14728222.2022.2157258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Nemaline myopathies (NM) represent a group of clinically and genetically heterogeneous congenital muscle disorders with the common denominator of nemaline rods on muscle biopsy. NEB and ACTA1 are the most common causative genes. Currently, available treatments are supportive. AREAS COVERED We explored experimental treatments for NM, identifying at least eleven mainly pre-clinical approaches utilizing murine and/or human muscle cells. These approaches target either i) the causative gene or associated genes implicated in the same pathway; ii) pathophysiologically relevant biochemical mechanisms such as calcium/myosin regulation of muscle contraction; iii) myogenesis; iv) other therapies that improve or optimize muscle function more generally; v) and/or combinations of the above. The scope and efficiency of these attempts is diverse, ranging from gene-specific effects to those widely applicable to all NM-associated genes. EXPERT OPINION The wide range of experimental therapies currently under consideration for NM is promising. Potential translation into clinical use requires consideration of additional factors such as the potential muscle type specificity as well as the possibility of gene expression remodeling. Challenges in clinical translation include the rarity and heterogeneity of genotypes, phenotypes, and disease trajectories, as well as the lack of longitudinal natural history data and validated outcomes and biomarkers.
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Affiliation(s)
- Gemma Fisher
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Laurane Mackels
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Neuromuscular Reference Center, University and University Hospital of Liège, Liège, Belgium
| | - Theodora Markati
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Hospital, Institute of Child Health, London, UK
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heinz Jungbluth
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK.,Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and Medicine (FoLSM), King's College London, London, UK
| | - Sithara Ramdas
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Department of Paediatric Neurology, John Radcliffe Hospital, Oxford, UK
| | - Laurent Servais
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Neuromuscular Reference Center, University and University Hospital of Liège, Liège, Belgium
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Das R, Jakubowski MA, Spildener J, Cheng YW. Identification of Novel MET Exon 14 Skipping Variants in Non-Small Cell Lung Cancer Patients: A Prototype Workflow Involving in Silico Prediction and RT-PCR. Cancers (Basel) 2022; 14:cancers14194814. [PMID: 36230737 PMCID: PMC9563401 DOI: 10.3390/cancers14194814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background and aims: The MET exon 14 skipping (METex14) is an oncogenic driver mutation that provides a therapeutic opportunity in non-small cell lung cancer (NSCLCs) patients. This event often results from sequence changes at the MET canonical splicing sites. We characterize two novel non-canonical splicing site variants of MET that produce METex14. Materials and Methods: Two variants were identified in three advanced-stage NSCLC patients in a next-generation sequencing panel. The potential impact on splicing was predicted using in silico tools. METex14 mutation was confirmed using reverse transcription (RT)-PCR and a Sanger sequencing analysis on RNA extracted from stained cytology smears. Results: The interrogated MET (RefSeq ID NM_000245.3) variants include a single nucleotide substitution, c.3028+3A>T, in intron 14 and a deletion mutation, c.3012_3028del, in exon 14. The in silico prediction analysis exhibited reduced splicing strength in both variants compared with the MET normal transcript. The RT-PCR and subsequent Sanger sequencing analyses confirmed METex14 skipping in all three patients carrying these variants. Conclusion: This study reveals two non-canonical MET splice variants that cause exon 14 skipping, concurrently also proposes a clinical workflow for the classification of such non-canonical splicing site variants detected by routine DNA-based NGS test. It shows the usefulness of in silico prediction to identify potential METex14 driver mutation and exemplifies the opportunity of routine cytology slides for RNA-based testing.
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Affiliation(s)
| | | | | | - Yu-Wei Cheng
- Correspondence: ; Tel.: +1-216-445-0757; Fax: +1-216-445-0681
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