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McCoy MJ, Fire AZ. Parallel gene size and isoform expansion of ancient neuronal genes. Curr Biol 2024; 34:1635-1645.e3. [PMID: 38460513 PMCID: PMC11043017 DOI: 10.1016/j.cub.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/16/2023] [Accepted: 02/11/2024] [Indexed: 03/11/2024]
Abstract
How nervous systems evolved is a central question in biology. A diversity of synaptic proteins is thought to play a central role in the formation of specific synapses leading to nervous system complexity. The largest animal genes, often spanning hundreds of thousands of base pairs, are known to be enriched for expression in neurons at synapses and are frequently mutated or misregulated in neurological disorders and diseases. Although many of these genes have been studied independently in the context of nervous system evolution and disease, general principles underlying their parallel evolution remain unknown. To investigate this, we directly compared orthologous gene sizes across eukaryotes. By comparing relative gene sizes within organisms, we identified a distinct class of large genes with origins predating the diversification of animals and, in many cases, the emergence of neurons as dedicated cell types. We traced this class of ancient large genes through evolution and found orthologs of the large synaptic genes potentially driving the immense complexity of metazoan nervous systems, including in humans and cephalopods. Moreover, we found that while these genes are evolving under strong purifying selection, as demonstrated by low dN/dS ratios, they have simultaneously grown larger and gained the most isoforms in animals. This work provides a new lens through which to view this distinctive class of large and multi-isoform genes and demonstrates how intrinsic genomic properties, such as gene length, can provide flexibility in molecular evolution and allow groups of genes and their host organisms to evolve toward complexity.
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Affiliation(s)
- Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.
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Hildyard JCW, Piercy RJ. When Size Really Matters: The Eccentricities of Dystrophin Transcription and the Hazards of Quantifying mRNA from Very Long Genes. Biomedicines 2023; 11:2082. [PMID: 37509720 PMCID: PMC10377302 DOI: 10.3390/biomedicines11072082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
At 2.3 megabases in length, the dystrophin gene is enormous: transcription of a single mRNA requires approximately 16 h. Principally expressed in skeletal muscle, the dystrophin protein product protects the muscle sarcolemma against contraction-induced injury, and dystrophin deficiency results in the fatal muscle-wasting disease, Duchenne muscular dystrophy. This gene is thus of key clinical interest, and therapeutic strategies aimed at eliciting dystrophin restoration require quantitative analysis of its expression. Approaches for quantifying dystrophin at the protein level are well-established, however study at the mRNA level warrants closer scrutiny: measured expression values differ in a sequence-dependent fashion, with significant consequences for data interpretation. In this manuscript, we discuss these nuances of expression and present evidence to support a transcriptional model whereby the long transcription time is coupled to a short mature mRNA half-life, with dystrophin transcripts being predominantly nascent as a consequence. We explore the effects of such a model on cellular transcriptional dynamics and then discuss key implications for the study of dystrophin gene expression, focusing on both conventional (qPCR) and next-gen (RNAseq) approaches.
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Affiliation(s)
- John C. W. Hildyard
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London NW1 0TU, UK;
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3
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Eisen B, Binah O. Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Int J Mol Sci 2023; 24:ijms24108657. [PMID: 37240001 DOI: 10.3390/ijms24108657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.
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Affiliation(s)
- Binyamin Eisen
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ofer Binah
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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Wilton-Clark H, Yokota T. Biological and genetic therapies for the treatment of Duchenne muscular dystrophy. Expert Opin Biol Ther 2023; 23:49-59. [PMID: 36409820 DOI: 10.1080/14712598.2022.2150543] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Duchenne muscular dystrophy is a lethal genetic disease which currently has no cure, and poor standard treatment options largely focused on symptom relief. The development of multiple biological and genetic therapies is underway across various stages of clinical progress which could markedly affect how DMD patients are treated in the future. AREAS COVERED The purpose of this review is to provide an introduction to the different therapeutic modalities currently being studied, as well as a brief description of their progress to date and relative advantages and disadvantages for the treatment of DMD. This review discusses exon skipping therapy, microdystrophin therapy, stop codon readthrough therapy, CRISPR-based gene editing, cell-based therapy, and utrophin upregulation. Secondary therapies addressing nonspecific symptoms of DMD were excluded. EXPERT OPINION Despite the vast potential held by gene replacement therapy options such as microdystrophin production and utrophin upregulation, safety risks inherent to the adeno-associated virus delivery vector might hamper the clinical viability of these approaches until further improvements can be made. Of the mutation-specific therapies, exon skipping therapy remains the most extensively validated and explored option, and the cell-based CAP-1002 therapy may prove to be a suitable adjunct therapy filling the urgent need for cardiac-specific therapies.
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Affiliation(s)
- Harry Wilton-Clark
- Faculty of Medicine and Dentistry, Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Toshifumi Yokota
- Faculty of Medicine and Dentistry, Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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6
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Kaplan KM, Morgan KG. The importance of dystrophin and the dystrophin associated proteins in vascular smooth muscle. Front Physiol 2022; 13:1059021. [PMID: 36505053 PMCID: PMC9732661 DOI: 10.3389/fphys.2022.1059021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
This review details the role of dystrophin and the dystrophin associated proteins (DAPs) in the vascular smooth muscle. Dystrophin is most comprehensively studied in the skeletal muscle due to serious symptoms found related to the skeletal muscle of patients with muscular dystrophy. Mutations in the dystrophin gene, or DAPs genes, result in a wide range of muscular dystrophies. In skeletal muscle, dystrophin is known to act to as a cytoskeletal stabilization protein and protects cells against contraction-induced damage. In skeletal muscle, dystrophin stabilizes the plasma membrane by transmitting forces generated by sarcomeric contraction to the extracellular matrix (ECM). Dystrophin is a scaffold that binds the dystroglycan complex (DGC) and has many associated proteins (DAPs). These DAPs include sarcoglycans, syntrophins, dystroglycans, dystrobrevin, neuronal nitric oxide synthase, and caveolins. The DAPs provide biomechanical support to the skeletal or cardiac plasma membrane during contraction, and loss of one or several of these DAPs leads to plasma membrane fragility. Dystrophin is expressed near the plasma membrane of all muscles, including cardiac and vascular smooth muscle, and some neurons. Dystrophic mice have noted biomechanical irregularities in the carotid arteries and spontaneous motor activity in portal vein altered when compared to wild type mice. Additionally, some studies suggest the vasculature of patients and animal models with muscular dystrophy is abnormal. Although the function of dystrophin and the DAPs in vascular smooth muscle is not thoroughly established in the field, this review makes the point that these proteins are expressed, and important and further study is warranted.
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Gosselin MRF, Mournetas V, Borczyk M, Verma S, Occhipinti A, Róg J, Bozycki L, Korostynski M, Robson SC, Angione C, Pinset C, Gorecki DC. Loss of full-length dystrophin expression results in major cell-autonomous abnormalities in proliferating myoblasts. eLife 2022; 11:75521. [PMID: 36164827 PMCID: PMC9514850 DOI: 10.7554/elife.75521] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/02/2022] [Indexed: 12/05/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) affects myofibers and muscle stem cells, causing progressive muscle degeneration and repair defects. It was unknown whether dystrophic myoblasts—the effector cells of muscle growth and regeneration—are affected. Using transcriptomic, genome-scale metabolic modelling and functional analyses, we demonstrate, for the first time, convergent abnormalities in primary mouse and human dystrophic myoblasts. In Dmdmdx myoblasts lacking full-length dystrophin, the expression of 170 genes was significantly altered. Myod1 and key genes controlled by MyoD (Myog, Mymk, Mymx, epigenetic regulators, ECM interactors, calcium signalling and fibrosis genes) were significantly downregulated. Gene ontology analysis indicated enrichment in genes involved in muscle development and function. Functionally, we found increased myoblast proliferation, reduced chemotaxis and accelerated differentiation, which are all essential for myoregeneration. The defects were caused by the loss of expression of full-length dystrophin, as similar and not exacerbated alterations were observed in dystrophin-null Dmdmdx-βgeo myoblasts. Corresponding abnormalities were identified in human DMD primary myoblasts and a dystrophic mouse muscle cell line, confirming the cross-species and cell-autonomous nature of these defects. The genome-scale metabolic analysis in human DMD myoblasts showed alterations in the rate of glycolysis/gluconeogenesis, leukotriene metabolism, and mitochondrial beta-oxidation of various fatty acids. These results reveal the disease continuum: DMD defects in satellite cells, the myoblast dysfunction affecting muscle regeneration, which is insufficient to counteract muscle loss due to myofiber instability. Contrary to the established belief, our data demonstrate that DMD abnormalities occur in myoblasts, making these cells a novel therapeutic target for the treatment of this lethal disease.
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Affiliation(s)
- Maxime R F Gosselin
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | | | - Malgorzata Borczyk
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology PAS, Krakow, Poland
| | - Suraj Verma
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, United Kingdom
| | - Annalisa Occhipinti
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, United Kingdom
| | - Justyna Róg
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.,Laboratory of Cellular Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Lukasz Bozycki
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.,Laboratory of Cellular Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Michal Korostynski
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology PAS, Krakow, Poland
| | - Samuel C Robson
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.,Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, United Kingdom
| | | | - Dariusz C Gorecki
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
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8
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Mazille M, Buczak K, Scheiffele P, Mauger O. Stimulus-specific remodeling of the neuronal transcriptome through nuclear intron-retaining transcripts. EMBO J 2022; 41:e110192. [PMID: 36149731 DOI: 10.15252/embj.2021110192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
The nuclear envelope has long been considered primarily a physical barrier separating nuclear and cytosolic contents. More recently, nuclear compartmentalization has been shown to have additional regulatory functions in controlling gene expression. A sizeable proportion of protein-coding mRNAs is more prevalent in the nucleus than in the cytosol, suggesting regulated mRNA trafficking to the cytosol, but the mechanisms underlying controlled nuclear mRNA retention remain unclear. Here, we provide a comprehensive map of the subcellular localization of mRNAs in mature mouse cortical neurons, and reveal that transcripts retained in the nucleus comprise the majority of stable intron-retaining mRNAs. Systematically probing the fate of nuclear transcripts upon neuronal stimulation, we found opposite effects on sub-populations of transcripts: while some are targeted for degradation, others complete splicing to generate fully mature mRNAs that are exported to the cytosol and mediate rapid increases in protein levels. Finally, different forms of stimulation mobilize distinct groups of intron-retaining transcripts, with this selectivity arising from the activation of specific signaling pathways. Overall, our findings uncover a cue-specific control of intron retention as a major regulator of acute remodeling of the neuronal transcriptome.
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Affiliation(s)
- Maxime Mazille
- Biozentrum of the University of Basel, Basel, Switzerland
| | | | | | - Oriane Mauger
- Biozentrum of the University of Basel, Basel, Switzerland
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9
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Hildyard JC, Riddell DO, Harron RC, Rawson F, Foster EM, Massey C, Taylor-Brown F, Wells DJ, Piercy RJ. The skeletal muscle phenotype of the DE50-MD dog model of Duchenne muscular dystrophy. Wellcome Open Res 2022; 7:238. [PMID: 36865375 PMCID: PMC9971692 DOI: 10.12688/wellcomeopenres.18251.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Animal models of Duchenne muscular dystrophy (DMD) are essential to study disease progression and assess efficacy of therapeutic intervention, however dystrophic mice fail to display a clinically relevant phenotype, limiting translational utility. Dystrophin-deficient dogs exhibit disease similar to humans, making them increasingly important for late-stage preclinical evaluation of candidate therapeutics. The DE50-MD canine model of DMD carries a mutation within a human 'hotspot' region of the dystrophin gene, amenable to exon-skipping and gene editing strategies. As part of a large natural history study of disease progression, we have characterised the DE50-MD skeletal muscle phenotype to identify parameters that could serve as efficacy biomarkers in future preclinical trials. Methods: Vastus lateralis muscles were biopsied from a large cohort of DE50-MD dogs and healthy male littermates at 3-monthly intervals (3-18 months) for longitudinal analysis, with multiple muscles collected post-mortem to evaluate body-wide changes. Pathology was characterised quantitatively using histology and measurement of gene expression to determine statistical power and sample sizes appropriate for future work. Results: DE50-MD skeletal muscle exhibits widespread degeneration/regeneration, fibrosis, atrophy and inflammation. Degenerative/inflammatory changes peak during the first year of life, while fibrotic remodelling appears more gradual. Pathology is similar in most skeletal muscles, but in the diaphragm, fibrosis is more prominent, associated with fibre splitting and pathological hypertrophy. Picrosirius red and acid phosphatase staining represent useful quantitative histological biomarkers for fibrosis and inflammation respectively, while qPCR can be used to measure regeneration ( MYH3, MYH8), fibrosis ( COL1A1), inflammation ( SPP1), and stability of DE50-MD dp427 transcripts. Conclusion: The DE50-MD dog is a valuable model of DMD, with pathological features similar to young, ambulant human patients. Sample size and power calculations show that our panel of muscle biomarkers are of strong pre-clinical value, able to detect therapeutic improvements of even 25%, using trials with only six animals per group.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,
| | - Dominique O. Riddell
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Rachel C.M. Harron
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Faye Rawson
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,Langford Veterinary Services, University of Bristol, Langford, UK
| | - Emma M.A. Foster
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Claire Massey
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Frances Taylor-Brown
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,Cave Veterinary Specialists, George's Farm, West Buckland, UK
| | - Dominic J. Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, London, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,
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10
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Muskovic W, Slavich E, Maslen B, Kaczorowski DC, Cursons J, Crampin E, Kavallaris M. High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes. Genome Res 2022; 32:1463-1473. [PMID: 35760562 PMCID: PMC9435739 DOI: 10.1101/gr.276818.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/24/2022] [Indexed: 11/24/2022]
Abstract
The advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Despite the diversity of reported lncRNA regulatory mechanisms, where causal cis-regulatory relationships exist, lncRNA transcription is expected to precede changes in target gene expression. Using a high temporal resolution RNA-seq time course, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal that lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.
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Affiliation(s)
- Walter Muskovic
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales 2052, Australia
| | - Eve Slavich
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ben Maslen
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | | | - Joseph Cursons
- The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Edmund Crampin
- Systems Biology Laboratory, School of Mathematics and Statistics and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales 2052, Australia
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11
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Fingerhut JM, Yamashita YM. The regulation and potential functions of intronic satellite DNA. Semin Cell Dev Biol 2022; 128:69-77. [PMID: 35469677 DOI: 10.1016/j.semcdb.2022.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have started to elucidate the function of satellite DNA, yet little is known about the peculiar case where satellite DNA is found within the introns of protein coding genes, resulting in incredibly large introns, a phenomenon termed intron gigantism. Studies in Drosophila demonstrated that satellite DNA-containing introns are transcribed with the gene and require specialized mechanisms to overcome the burdens imposed by the extremely long stretches of repetitive DNA. Whether intron gigantism confers any benefit or serves any functional purpose for cells and/or organisms remains elusive. Here we review our current understanding of intron gigantism: where it is found, the challenges it imposes, how it is regulated and what purpose it may serve.
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Affiliation(s)
- Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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12
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Manini A, Abati E, Nuredini A, Corti S, Comi GP. Adeno-Associated Virus (AAV)-Mediated Gene Therapy for Duchenne Muscular Dystrophy: The Issue of Transgene Persistence. Front Neurol 2022; 12:814174. [PMID: 35095747 PMCID: PMC8797140 DOI: 10.3389/fneur.2021.814174] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive, infancy-onset neuromuscular disorder characterized by progressive muscle weakness and atrophy, leading to delay of motor milestones, loss of autonomous ambulation, respiratory failure, cardiomyopathy, and premature death. DMD originates from mutations in the DMD gene that result in a complete absence of dystrophin. Dystrophin is a cytoskeletal protein which belongs to the dystrophin-associated protein complex, involved in cellular signaling and myofiber membrane stabilization. To date, the few available therapeutic options are aimed at lessening disease progression, but persistent loss of muscle tissue and function and premature death are unavoidable. In this scenario, one of the most promising therapeutic strategies for DMD is represented by adeno-associated virus (AAV)-mediated gene therapy. DMD gene therapy relies on the administration of exogenous micro-dystrophin, a miniature version of the dystrophin gene lacking unnecessary domains and encoding a truncated, but functional, dystrophin protein. Limited transgene persistence represents one of the most significant issues that jeopardize the translatability of DMD gene replacement strategies from the bench to the bedside. Here, we critically review preclinical and clinical studies of AAV-mediated gene therapy in DMD, focusing on long-term transgene persistence in transduced tissues, which can deeply affect effectiveness and sustainability of gene replacement in DMD. We also discuss the role played by the overactivation of the immune host system in limiting long-term expression of genetic material. In this perspective, further studies aimed at better elucidating the need for immune suppression in AAV-treated subjects are warranted in order to allow for life-long therapy in DMD patients.
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Affiliation(s)
- Arianna Manini
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Elena Abati
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Andi Nuredini
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.,Neurology Unit, Neuroscience Section, Dino Ferrari Center, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Maggiore Policlinico, Milan, Italy
| | - Giacomo Pietro Comi
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.,Neurology Unit, Neuroscience Section, Dino Ferrari Center, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Maggiore Policlinico, Milan, Italy
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13
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Antisense and Gene Therapy Options for Duchenne Muscular Dystrophy Arising from Mutations in the N-Terminal Hotspot. Genes (Basel) 2022; 13:genes13020257. [PMID: 35205302 PMCID: PMC8872079 DOI: 10.3390/genes13020257] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal genetic disease affecting children that is caused by a mutation in the gene encoding for dystrophin. In the absence of functional dystrophin, patients experience progressive muscle deterioration, leaving them wheelchair-bound by age 12 and with few patients surviving beyond their third decade of life as the disease advances and causes cardiac and respiratory difficulties. In recent years, an increasing number of antisense and gene therapies have been studied for the treatment of muscular dystrophy; however, few of these therapies focus on treating mutations arising in the N-terminal encoding region of the dystrophin gene. This review summarizes the current state of development of N-terminal antisense and gene therapies for DMD, mainly focusing on exon-skipping therapy for duplications and deletions, as well as microdystrophin therapy.
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14
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Crawford AH, Hildyard JCW, Rushing SAM, Wells DJ, Diez-Leon M, Piercy RJ. Validation of DE50-MD dogs as a model for the brain phenotype of Duchenne muscular dystrophy. Dis Model Mech 2022; 15:273974. [PMID: 35019137 PMCID: PMC8906169 DOI: 10.1242/dmm.049291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), a fatal musculoskeletal disease, is associated with neurodevelopmental disorders and cognitive impairment caused by brain dystrophin deficiency. Dog models of DMD represent key translational tools to study dystrophin biology and to develop novel therapeutics. However, characterisation of dystrophin expression and function in the canine brain is lacking. We studied the DE50-MD canine model of DMD that has a missense mutation in the donor splice site of exon 50. Using a battery of cognitive tests, we detected a neurocognitive phenotype in DE50-MD dogs, including reduced attention, problem solving and exploration of novel objects. Through a combination of capillary immunoelectrophoresis, immunolabelling, quantitative PCR and RNAScope in situ hybridisation, we show that regional dystrophin expression in the adult canine brain reflects that of humans, and that the DE50-MD dog lacks full-length dystrophin (Dp427) protein expression but retains expression of the two shorter brain-expressed isoforms, Dp140 and Dp71. Thus, the DE50-MD dog is a translationally relevant pre-clinical model to study the consequences of Dp427 deficiency in the brain and to develop therapeutic strategies for the neurological sequelae of DMD. Summary: The DE50-MD canine model of Duchenne muscular dystrophy (DMD) shows cognitive and brain biochemical changes secondary to dystrophin deficiency in the brain, and is a relevant pre-clinical model to develop therapies for DMD.
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Affiliation(s)
- Abbe H Crawford
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - John C W Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Sophie A M Rushing
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Dominic J Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Maria Diez-Leon
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Richard J Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
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15
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Fixed and Distributed Gene Expression Time Delays in Reaction-Diffusion Systems. Bull Math Biol 2022; 84:98. [PMID: 35934760 PMCID: PMC9357602 DOI: 10.1007/s11538-022-01052-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/30/2022] [Indexed: 12/17/2022]
Abstract
Time delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction-diffusion systems. In particular, past work has shown that such time delays can shrink the Turing space, thereby inhibiting patterns from forming across large ranges of parameters. Such delays can also increase the time taken for pattern formation even when Turing instabilities occur. Here, we consider reaction-diffusion models incorporating fixed or distributed time delays, modelling the underlying stochastic nature of gene expression dynamics, and analyse these through a systematic linear instability analysis and numerical simulations for several sets of different reaction kinetics. We find that even complicated distribution kernels (skewed Gaussian probability density functions) have little impact on the reaction-diffusion dynamics compared to fixed delays with the same mean delay. We show that the location of the delay terms in the model can lead to changes in the size of the Turing space (increasing or decreasing) as the mean time delay, [Formula: see text], is increased. We show that the time to pattern formation from a perturbation of the homogeneous steady state scales linearly with [Formula: see text], and conjecture that this is a general impact of time delay on reaction-diffusion dynamics, independent of the form of the kinetics or location of the delayed terms. Finally, we show that while initial and boundary conditions can influence these dynamics, particularly the time-to-pattern, the effects of delay appear robust under variations of initial and boundary data. Overall, our results help clarify the role of gene expression time delays in reaction-diffusion patterning, and suggest clear directions for further work in studying more realistic models of pattern formation.
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16
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Zabłocka B, Górecki DC, Zabłocki K. Disrupted Calcium Homeostasis in Duchenne Muscular Dystrophy: A Common Mechanism behind Diverse Consequences. Int J Mol Sci 2021; 22:11040. [PMID: 34681707 PMCID: PMC8537421 DOI: 10.3390/ijms222011040] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 09/30/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) leads to disability and death in young men. This disease is caused by mutations in the DMD gene encoding diverse isoforms of dystrophin. Loss of full-length dystrophins is both necessary and sufficient for causing degeneration and wasting of striated muscles, neuropsychological impairment, and bone deformities. Among this spectrum of defects, abnormalities of calcium homeostasis are the common dystrophic feature. Given the fundamental role of Ca2+ in all cells, this biochemical alteration might be underlying all the DMD abnormalities. However, its mechanism is not completely understood. While abnormally elevated resting cytosolic Ca2+ concentration is found in all dystrophic cells, the aberrant mechanisms leading to that outcome have cell-specific components. We probe the diverse aspects of calcium response in various affected tissues. In skeletal muscles, cardiomyocytes, and neurons, dystrophin appears to serve as a scaffold for proteins engaged in calcium homeostasis, while its interactions with actin cytoskeleton influence endoplasmic reticulum organisation and motility. However, in myoblasts, lymphocytes, endotheliocytes, and mesenchymal and myogenic cells, calcium abnormalities cannot be clearly attributed to the loss of interaction between dystrophin and the calcium toolbox proteins. Nevertheless, DMD gene mutations in these cells lead to significant defects and the calcium anomalies are a symptom of the early developmental phase of this pathology. As the impaired calcium homeostasis appears to underpin multiple DMD abnormalities, understanding this alteration may lead to the development of new therapies. In fact, it appears possible to mitigate the impact of the abnormal calcium homeostasis and the dystrophic phenotype in the total absence of dystrophin. This opens new treatment avenues for this incurable disease.
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Affiliation(s)
- Barbara Zabłocka
- Molecular Biology Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Dariusz C. Górecki
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael’s Building, White Swan Road, Portsmouth PO1 2DT, UK
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
| | - Krzysztof Zabłocki
- Laboratory of Cellular Metabolism, Nencki Institute of Experimental Biology Polish Academy of Sciences, 02-093 Warsaw, Poland
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17
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Brüning JG, Marians KJ. Bypass of complex co-directional replication-transcription collisions by replisome skipping. Nucleic Acids Res 2021; 49:9870-9885. [PMID: 34469567 PMCID: PMC8464059 DOI: 10.1093/nar/gkab760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/27/2022] Open
Abstract
Collisions between the replisome and RNA polymerases [RNAP(s)] are the main obstacle to DNA replication. These collisions can occur either head-on or co-directionally with respect to the direction of translocation of both complexes. Whereas head-on collisions require additional factors to be resolved, co-directional collisions are thought to be overcome by the replisome itself using the mRNA transcript as a primer. We show that mRNA takeover is utilized primarily after collisions with single RNAP complexes with short transcripts. Bypass of more complex transcription complexes requires the synthesis of a new primer downstream of the RNAP for the replisome to resume leading-strand synthesis. In both cases, bypass proceeds with displacement of the RNAP. Rep, Mfd, UvrD and RNase H can process the RNAP block and facilitate replisome bypass by promoting the formation of continuous leading strands. Bypass of co-directional RNAP(s) and/or R-loops is determined largely by the length of the obstacle that the replisome needs to traverse: R-loops are about equally as potent obstacles as RNAP arrays if they occupy the same length of the DNA template.
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Affiliation(s)
- Jan-Gert Brüning
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Kenneth J Marians
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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18
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Ohlendieck K, Swandulla D. Complexity of skeletal muscle degeneration: multi-systems pathophysiology and organ crosstalk in dystrophinopathy. Pflugers Arch 2021; 473:1813-1839. [PMID: 34553265 PMCID: PMC8599371 DOI: 10.1007/s00424-021-02623-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Duchenne muscular dystrophy is a highly progressive muscle wasting disorder due to primary abnormalities in one of the largest genes in the human genome, the DMD gene, which encodes various tissue-specific isoforms of the protein dystrophin. Although dystrophinopathies are classified as primary neuromuscular disorders, the body-wide abnormalities that are associated with this disorder and the occurrence of organ crosstalk suggest that a multi-systems pathophysiological view should be taken for a better overall understanding of the complex aetiology of X-linked muscular dystrophy. This article reviews the molecular and cellular effects of deficiency in dystrophin isoforms in relation to voluntary striated muscles, the cardio-respiratory system, the kidney, the liver, the gastrointestinal tract, the nervous system and the immune system. Based on the establishment of comprehensive biomarker signatures of X-linked muscular dystrophy using large-scale screening of both patient specimens and genetic animal models, this article also discusses the potential usefulness of novel disease markers for more inclusive approaches to differential diagnosis, prognosis and therapy monitoring that also take into account multi-systems aspects of dystrophinopathy. Current therapeutic approaches to combat muscular dystrophy are summarised.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Co. Kildare, Maynooth, W23F2H6, Ireland.
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Co. Kildare, Maynooth, W23F2H6, Ireland.
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, 53115, Bonn, Germany.
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19
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Nagae F, Brandani GB, Takada S, Terakawa T. The lane-switch mechanism for nucleosome repositioning by DNA translocase. Nucleic Acids Res 2021; 49:9066-9076. [PMID: 34365508 PMCID: PMC8450081 DOI: 10.1093/nar/gkab664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Translocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone octamers and forms nucleosomes, translocases inevitably encounter nucleosomes. A previous study has shown that a nucleosome repositions downstream when a translocase collides with the nucleosome. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identified the lane-switch mechanism for downstream repositioning with molecular dynamics simulations and validated it with restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding lane to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have broad implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.
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Affiliation(s)
- Fritz Nagae
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan
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20
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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21
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Abou Chakra M, Isserlin R, Tran TN, Bader GD. Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering. eLife 2021; 10:64951. [PMID: 34212855 PMCID: PMC8279763 DOI: 10.7554/elife.64951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
Cell cycle duration changes dramatically during development, starting out fast to generate cells quickly and slowing down over time as the organism matures. The cell cycle can also act as a transcriptional filter to control the expression of long gene transcripts, which are partially transcribed in short cycles. Using mathematical simulations of cell proliferation, we identify an emergent property that this filter can act as a tuning knob to control gene transcript expression, cell diversity, and the number and proportion of different cell types in a tissue. Our predictions are supported by comparison to single-cell RNA-seq data captured over embryonic development. Additionally, evolutionary genome analysis shows that fast-developing organisms have a narrow genomic distribution of gene lengths while slower developers have an expanded number of long genes. Our results support the idea that cell cycle dynamics may be important across multicellular animals for controlling gene transcript expression and cell fate.
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Affiliation(s)
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Thinh N Tran
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada
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22
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Ban Q, Yang P, Chou SJ, Qiao L, Xia H, Xue J, Wang F, Xu X, Sun N, Zhang RY, Zhang C, Lee A, Liu W, Lin TY, Ko YL, Antovski P, Zhang X, Chiou SH, Lee CF, Hui W, Liu D, Jonas SJ, Weiss PS, Tseng HR. Supramolecular Nanosubstrate-Mediated Delivery for CRISPR/Cas9 Gene Disruption and Deletion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100546. [PMID: 34105245 PMCID: PMC8282741 DOI: 10.1002/smll.202100546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/30/2021] [Indexed: 06/12/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) is an efficient and precise gene-editing technology that offers a versatile solution for establishing treatments directed at genetic diseases. Currently, CRISPR/Cas9 delivery into cells relies primarily on viral vectors, which suffer from limitations in packaging capacity and safety concerns. These issues with a nonviral delivery strategy are addressed, where Cas9•sgRNA ribonucleoprotein (RNP) complexes can be encapsulated into supramolecular nanoparticles (SMNP) to form RNP⊂SMNPs, which can then be delivered into targeted cells via supramolecular nanosubstrate-mediated delivery. Utilizing the U87 glioblastoma cell line as a model system, a variety of parameters for cellular-uptake of the RNP-laden nanoparticles are examined. Dose- and time-dependent CRISPR/Cas9-mediated gene disruption is further examined in a green fluorescent protein (GFP)-expressing U87 cell line (GFP-U87). The utility of an optimized SMNP formulation in co-delivering Cas9 protein and two sgRNAs that target deletion of exons 45-55 (708 kb) of the dystrophin gene is demonstrated. Mutations in this region lead to Duchenne muscular dystrophy, a severe genetic muscle wasting disease. Efficient delivery of these gene deletion cargoes is observed in a human cardiomyocyte cell line (AC16), induced pluripotent stem cells, and mesenchymal stem cells.
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Affiliation(s)
- Qian Ban
- School of Life Sciences, Center for Stem Cell and Translational Medicine, Anhui University, Hefei, 230601, China
| | - Peng Yang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Shih-Jie Chou
- Department of Medical Research, and Stem Cell Center, Division of Basic Research, Taipei Veterans General Hospital, Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street 112, Taipei, Taiwan
| | - Li Qiao
- School of Life Sciences, Center for Stem Cell and Translational Medicine, Anhui University, Hefei, 230601, China
| | - Haidong Xia
- School of Life Sciences, Center for Stem Cell and Translational Medicine, Anhui University, Hefei, 230601, China
| | - Jingjing Xue
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fang Wang
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Xiaobin Xu
- Department of Chemistry and Biochemistry, Department of Bioengineering, Department of Materials Science and Engineering, California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
- School of Materials Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Na Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ryan Y Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ceng Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Athena Lee
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Wenfei Liu
- Department of Chemistry and Biochemistry, Department of Bioengineering, Department of Materials Science and Engineering, California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ting-Yi Lin
- Department of Medical Research, and Stem Cell Center, Division of Basic Research, Taipei Veterans General Hospital, Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street 112, Taipei, Taiwan
| | - Yu-Ling Ko
- Department of Medical Research, and Stem Cell Center, Division of Basic Research, Taipei Veterans General Hospital, Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street 112, Taipei, Taiwan
| | - Petar Antovski
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xinyue Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Shih-Hwa Chiou
- Department of Medical Research, and Stem Cell Center, Division of Basic Research, Taipei Veterans General Hospital, Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street 112, Taipei, Taiwan
| | - Chin-Fa Lee
- Department of Chemistry, i-Center for Advanced Science and Technology (iCAST), Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University (NCHU), 145 Xingda Road, South Dist., Taichung, 402, Taiwan
| | - Wenqiao Hui
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Sciences, Hefei, 230031, China
| | - Dahai Liu
- School of Stomatology and Medicine, Foshan University, Foshan, 528000, China
| | - Steven J Jonas
- Department of Pediatrics, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Children's Discovery and Innovation Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Paul S Weiss
- Department of Chemistry and Biochemistry, Department of Bioengineering, Department of Materials Science and Engineering, California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California NanoSystems Institute (CNSI), Crump Institute for Molecular Imaging (CIMI), University of California, Los Angeles, Los Angeles, CA, 90095, USA
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23
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Hanson B, Wood MJA, Roberts TC. Molecular correction of Duchenne muscular dystrophy by splice modulation and gene editing. RNA Biol 2021; 18:1048-1062. [PMID: 33472516 DOI: 10.1080/15476286.2021.1874161] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a currently incurable X-linked neuromuscular disorder, characterized by progressive muscle wasting and premature death, typically as a consequence of cardiac failure. DMD-causing mutations in the dystrophin gene are highly diverse, meaning that the development of a universally-applicable therapy to treat all patients is very challenging. The leading therapeutic strategy for DMD is antisense oligonucleotide-mediated splice modulation, whereby one or more specific exons are excluded from the mature dystrophin mRNA in order to correct the translation reading frame. Indeed, three exon skipping oligonucleotides have received FDA approval for use in DMD patients. Second-generation exon skipping drugs (i.e. peptide-antisense oligonucleotide conjugates) exhibit enhanced potency, and also induce dystrophin restoration in the heart. Similarly, multiple additional antisense oligonucleotide drugs targeting various exons are in clinical development in order to treat a greater proportion of DMD patient mutations. Relatively recent advances in the field of genome engineering (specifically, the development of the CRISPR/Cas system) have provided multiple promising therapeutic approaches for the RNA-directed genetic correction of DMD, including exon excision, exon reframing via the introduction of insertion/deletion mutations, disruption of splice signals to promote exon skipping, and the templated correction of point mutations by seamless homology directed repair or base editing technology. Potential limitations to the clinical translation of the splice modulation and gene editing approaches are discussed, including drug delivery, the importance of uniform dystrophin expression in corrected myofibres, safety issues (e.g. renal toxicity, viral vector immunogenicity, and off-target gene editing), and the high cost of therapy.
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Affiliation(s)
- Britt Hanson
- Department of Paediatrics, University of Oxford, Oxford, UK.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
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24
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Brolin C, Lim EWK, Nielsen PE. In Vivo Administration of Splice Switching PNAs Using the mdx Mouse as a Model System. Methods Mol Biol 2021; 2105:241-250. [PMID: 32088875 DOI: 10.1007/978-1-0716-0243-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Duchenne muscular dystrophy (DMD) is the most common and severe form of muscular dystrophy and is caused by gene mutations that abolish production of functional dystrophin muscle protein. A promising new treatment exploits specifically targeted RNA-acting drugs that are able to partially restore the dystrophin protein. The mdx mouse model (animal model of DMD) serves as a good in vivo model for testing these antisense drugs. The simplest in vivo test, which circumvents the systemic circulation, is intramuscular administration of the compound. After 7 days it is possible to detect exon skipping by reverse transcriptase PCR, and newly synthesized dystrophin-positive fibers by immunohistochemistry and western blotting. All muscles, including the heart, are affected by the disease and must be treated. Therefore the use of antisense therapy for treatment of DMD requires systemic administration, and the model is also useful for systemic administration.
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Affiliation(s)
- Camilla Brolin
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Ernest Wee Kiat Lim
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Goyal M, Gupta A, Agarwal K, Kapoor S, Kumar S. Duchenne muscular dystrophy: Genetic and clinical profile in the population of Rajasthan, India. Ann Indian Acad Neurol 2021; 24:873-878. [PMID: 35359537 PMCID: PMC8965960 DOI: 10.4103/aian.aian_126_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 11/04/2022] Open
Abstract
Background: Materials and Methods: Results: Conclusions:
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26
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Chen BR, You CX, Shu CC. The common misuse of noise decomposition as applied to genetic systems. Biosystems 2020; 198:104269. [PMID: 33038463 DOI: 10.1016/j.biosystems.2020.104269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/22/2020] [Accepted: 10/02/2020] [Indexed: 10/23/2022]
Abstract
The noise-decomposition technique is applied in several fields, including genetic systems, optical images, recording, and navigation. In genetic systems, noise decomposition is usually achieved by using two reporters [Elowitz M.B., Levine A.J., Siggia E.D., Swain P·S., 2002. Stochastic gene expression in a single cell. Science 297, 1183-6.]. A reporter is a protein with fluorescence, an RNA hybridized with a fluorescent probe, or any other detectable intracellular component. If a reporter is constructed in addition to the original reporter, the system's stochasticity may change. Such phenomena became severe for genes in plasmids with a high copy number. By SSA (stochastic simulation algorithm), we observed an approximately 50% increment in the coefficient of variation while introducing additional reporters. Besides, if two reporters respond to the upstream element at a different time, the trunk noise (or extrinsic noise) cannot be accurately determined. This is because the "calculative trunk noise" changes along with the delay, though the real trunk noise does not. For RNA reporters, a 5-min transcriptional delay caused a calculative trunk noise that was 90% less than the real trunk noise. Fortunately, this problem is negligible when the degradation rate constant is low, and it is usually true in the case of the protein reporters. One can check the lifespan of the reporter before applying the noise-decomposition technique.
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Affiliation(s)
- Bo-Ren Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taiwan
| | - Chao-Xuan You
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taiwan
| | - Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taiwan.
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Ham KA, Aung-Htut MT, Fletcher S, Wilton SD. Nonsequential Splicing Events Alter Antisense-Mediated Exon Skipping Outcome in COL7A1. Int J Mol Sci 2020; 21:ijms21207705. [PMID: 33081018 PMCID: PMC7590164 DOI: 10.3390/ijms21207705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
The COL7A1 gene encodes homotrimer fibrils essential for anchoring dermal and epidermal layers, and pathogenic mutations in COL7A1 can cause recessive or dominant dystrophic epidermolysis bullosa. As a monogenic disease gene, COL7A1 constitutes a potential target for antisense oligomer-mediated exon skipping, a therapy applicable to a growing number of other genetic disorders. However, certain characteristics of COL7A1: many exons, low average intron size, and repetitive and guanine-cytosine rich coding sequence, present challenges to the design of specific and effective antisense oligomers. While targeting COL7A1 exons 10 and 73 for excision from the mature mRNA, we discovered that antisense oligomers comprised of 2′-O-methyl modified bases on a phosphorothioate backbone and phosphorodiamidate morpholino oligomers produced similar, but distinctive, splicing patterns including excision of adjacent nontargeted exons and/or retention of nearby introns in some transcripts. We found that the nonsequential splicing of certain introns may alter pre-mRNA processing during antisense oligomer-mediated exon skipping and, therefore, additional studies are required to determine if the order of intron removal influences multiexon skipping and/or intron retention in processing of the COL7A1 pre-mRNA.
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Affiliation(s)
- Kristin A. Ham
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
- Correspondence:
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Ovics P, Regev D, Baskin P, Davidor M, Shemer Y, Neeman S, Ben-Haim Y, Binah O. Drug Development and the Use of Induced Pluripotent Stem Cell-Derived Cardiomyocytes for Disease Modeling and Drug Toxicity Screening. Int J Mol Sci 2020; 21:E7320. [PMID: 33023024 PMCID: PMC7582587 DOI: 10.3390/ijms21197320] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 12/19/2022] Open
Abstract
: Over the years, numerous groups have employed human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) as a superb human-compatible model for investigating the function and dysfunction of cardiomyocytes, drug screening and toxicity, disease modeling and for the development of novel drugs for heart diseases. In this review, we discuss the broad use of iPSC-CMs for drug development and disease modeling, in two related themes. In the first theme-drug development, adverse drug reactions, mechanisms of cardiotoxicity and the need for efficient drug screening protocols-we discuss the critical need to screen old and new drugs, the process of drug development, marketing and Adverse Drug reactions (ADRs), drug-induced cardiotoxicity, safety screening during drug development, drug development and patient-specific effect and different mechanisms of ADRs. In the second theme-using iPSC-CMs for disease modeling and developing novel drugs for heart diseases-we discuss the rationale for using iPSC-CMs and modeling acquired and inherited heart diseases with iPSC-CMs.
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Affiliation(s)
- Paz Ovics
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Danielle Regev
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Polina Baskin
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Mor Davidor
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Yuval Shemer
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Shunit Neeman
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Yael Ben-Haim
- Institute of Molecular and Clinical Sciences, St. George’s University of London, London SW17 0RE, UK;
- Cardiology Clinical Academic Group, St. George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Ofer Binah
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
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Hildyard JCW, Rawson F, Wells DJ, Piercy RJ. Multiplex in situ hybridization within a single transcript: RNAscope reveals dystrophin mRNA dynamics. PLoS One 2020; 15:e0239467. [PMID: 32970731 PMCID: PMC7514052 DOI: 10.1371/journal.pone.0239467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/08/2020] [Indexed: 01/22/2023] Open
Abstract
Dystrophin plays a vital role in maintaining muscle health, yet low mRNA expression, lengthy transcription time and the limitations of traditional in-situ hybridization (ISH) methodologies mean that the dynamics of dystrophin transcription remain poorly understood. RNAscope is highly sensitive ISH method that can be multiplexed, allowing detection of individual transcript molecules at sub-cellular resolution, with different target mRNAs assigned to distinct fluorophores. We instead multiplex within a single transcript, using probes targeted to the 5' and 3' regions of muscle dystrophin mRNA. Our approach shows this method can reveal transcriptional dynamics in health and disease, resolving both nascent myonuclear transcripts and exported mature mRNAs in quantitative fashion (with the latter absent in dystrophic muscle, yet restored following therapeutic intervention). We show that even in healthy muscle, immature dystrophin mRNA predominates (60-80% of total), with the surprising implication that the half-life of a mature transcript is markedly shorter than the time invested in transcription: at the transcript level, supply may exceed demand. Our findings provide unique spatiotemporal insight into the behaviour of this long transcript (with implications for therapeutic approaches), and further suggest this modified multiplex ISH approach is well-suited to long genes, offering a highly tractable means to reveal complex transcriptional dynamics.
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Affiliation(s)
- John C. W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Faye Rawson
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Dominic J. Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
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30
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"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
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31
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Hildyard JCW, Crawford AH, Rawson F, Riddell DO, Harron RCM, Piercy RJ. Single-transcript multiplex in situ hybridisation reveals unique patterns of dystrophin isoform expression in the developing mammalian embryo. Wellcome Open Res 2020; 5:76. [PMID: 32724863 PMCID: PMC7372313 DOI: 10.12688/wellcomeopenres.15762.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background: The dystrophin gene has multiple isoforms: full-length dystrophin (dp427) is principally known for its expression in skeletal and cardiac muscle, but is also expressed in the brain, and several internal promoters give rise to shorter, N-terminally truncated isoforms with wider tissue expression patterns (dp260 in the retina, dp140 in the brain and dp71 in many tissues). These isoforms are believed to play unique cellular roles both during embryogenesis and in adulthood, but their shared sequence identity at both mRNA and protein levels makes study of distinct isoforms challenging by conventional methods. Methods: RNAscope is a novel in-situ hybridisation technique that offers single-transcript resolution and the ability to multiplex, with different target sequences assigned to distinct fluorophores. Using probes designed to different regions of the dystrophin transcript (targeting 5', central and 3' sequences of the long dp427 mRNA), we can simultaneously detect and distinguish multiple dystrophin mRNA isoforms at sub-cellular histological levels. We have used these probes in healthy and dystrophic canine embryos to gain unique insights into isoform expression and distribution in the developing mammal. Results: Dp427 is found in developing muscle as expected, apparently enriched at nascent myotendinous junctions. Endothelial and epithelial surfaces express dp71 only. Within the brain and spinal cord, all three isoforms are expressed in spatially distinct regions: dp71 predominates within proliferating germinal layer cells, dp140 within maturing, migrating cells and dp427 appears within more established cell populations. Dystrophin is also found within developing bones and teeth, something previously unreported, and our data suggests orchestrated involvement of multiple isoforms in formation of these tissues. Conclusions: Overall, shorter isoforms appear associated with proliferation and migration, and longer isoforms with terminal lineage commitment: we discuss the distinct structural contributions and transcriptional demands suggested by these findings.
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Affiliation(s)
- John C. W. Hildyard
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Abbe H. Crawford
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Faye Rawson
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Dominique O. Riddell
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Rachel C. M. Harron
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Richard J. Piercy
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
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32
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Choi IY, Kwon EC, Kim NS. The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy. Genes Genomics 2020; 42:699-714. [DOI: 10.1007/s13258-020-00941-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
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33
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Zamani G, Hosseini Bereshneh A, Azizi Malamiri R, Bagheri S, Moradi K, Ashrafi MR, Tavasoli AR, Mohammadi M, Badv RS, Ghahvechi Akbari M, Heidari M. The First Comprehensive Cohort of the Duchenne Muscular Dystrophy in Iranian Population: Mutation Spectrum of 314 Patients and Identifying Two Novel Nonsense Mutations. J Mol Neurosci 2020; 70:1565-1573. [DOI: 10.1007/s12031-020-01594-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/14/2020] [Indexed: 12/17/2022]
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34
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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35
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Abdullah M, Hassan A, Rashid S, Naeem M. Tyrosine phosphorylation as a regulator of dystrophin and beta-dystroglycan interaction: A molecular insight. J Mol Graph Model 2020; 99:107623. [PMID: 32348939 DOI: 10.1016/j.jmgm.2020.107623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/25/2022]
Abstract
Dystrophin-β-dystroglycan interaction has gained a special attention during current years due to its association with the pathogenesis of muscular dystrophies. Dystrophin is an important component of dystrophin associated protein complex that functions in the normal physiology and cell signaling in addition to membrane stabilization and provides integrity to skeletal muscle fibers. WW, EF-hand and ZZ domains of dystrophin are known to bind with extreme C-terminal region of beta-dystroglycan (β-DG) containing PPxY motif and this interaction is experimentally proven to be coordinated and regulated by two tyrosine (Tyr886 and Tyr892) residues in the C-terminus of beta-dystroglycan. These tyrosine residues are phosphorylated in adhesion dependent manner that disrupts dystrophin-β-DG interaction. The failure of dystrophin to interact with β-DG causes muscular dystrophies. In this study, we have performed molecular docking analysis of dystrophin with phosphorylated and mutated variants of β-DG to pinpoint the actual nature of this interaction at molecular level. We have discovered significant structural and conformational changes in β-DG molecule caused by mutations and tyrosine phosphorylation that alter the nature and site of its interaction with dystrophin. Our results not only support the previous findings but also bring to attention previously unreported discoveries about the nature of this interaction and behavior of different β-DG variants with dystrophin WW, EF-hand and ZZ domains.
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Affiliation(s)
- Muhammad Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Adeena Hassan
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Naeem
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan.
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36
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Hildyard JCW, Crawford AH, Rawson F, Riddell DO, Harron RCM, Piercy RJ. Single-transcript multiplex in situ hybridisation reveals unique patterns of dystrophin isoform expression in the developing mammalian embryo. Wellcome Open Res 2020; 5:76. [PMID: 32724863 PMCID: PMC7372313 DOI: 10.12688/wellcomeopenres.15762.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 07/30/2023] Open
Abstract
Background: The dystrophin gene has multiple isoforms: full-length dystrophin (dp427) is principally known for its expression in skeletal and cardiac muscle, but is also expressed in the brain, and several internal promoters give rise to shorter, N-terminally truncated isoforms with wider tissue expression patterns (dp260 in the retina, dp140 in the brain and dp71 in many tissues). These isoforms are believed to play unique cellular roles both during embryogenesis and in adulthood, but their shared sequence identity at both mRNA and protein levels makes study of distinct isoforms challenging by conventional methods. Methods: RNAscope is a novel in-situ hybridisation technique that offers single-transcript resolution and the ability to multiplex, with different target sequences assigned to distinct fluorophores. Using probes designed to different regions of the dystrophin transcript (targeting 5', central and 3' sequences of the long dp427 mRNA), we can simultaneously detect and distinguish multiple dystrophin mRNA isoforms at sub-cellular histological levels. We have used these probes in healthy and dystrophic canine embryos to gain unique insights into isoform expression and distribution in the developing mammal. Results: Dp427 is found in developing muscle as expected, apparently enriched at nascent myotendinous junctions. Endothelial and epithelial surfaces express dp71 only. Within the brain and spinal cord, all three isoforms are expressed in spatially distinct regions: dp71 predominates within proliferating germinal layer cells, dp140 within maturing, migrating cells and dp427 appears within more established cell populations. Dystrophin is also found within developing bones and teeth, something previously unreported, and our data suggests orchestrated involvement of multiple isoforms in formation of these tissues. Conclusions: Overall, shorter isoforms appear associated with proliferation and migration, and longer isoforms with terminal lineage commitment: we discuss the distinct structural contributions and transcriptional demands suggested by these findings.
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Affiliation(s)
- John C. W. Hildyard
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Abbe H. Crawford
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Faye Rawson
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Dominique O. Riddell
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Rachel C. M. Harron
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
| | - Richard J. Piercy
- Department of Clinical Science and Services, Royal Veterinary College, London, Camden, London, NW1 0TU, UK
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37
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Douglas J, Kingston R, Drummond AJ. Bayesian inference and comparison of stochastic transcription elongation models. PLoS Comput Biol 2020; 16:e1006717. [PMID: 32059006 PMCID: PMC7046298 DOI: 10.1371/journal.pcbi.1006717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/27/2020] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Transcription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations. We have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes of E. coli, S. cerevisiae and Bacteriophage T7. Our analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared to E. coli RNAP and S. cerevisiae pol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets. Transcription is a critical biological process which occurs in all living organisms. It involves copying the organism’s genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques. Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.
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Affiliation(s)
- Jordan Douglas
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Richard Kingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Alexei J. Drummond
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
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38
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Krause AL, Klika V, Woolley TE, Gaffney EA. From one pattern into another: analysis of Turing patterns in heterogeneous domains via WKBJ. J R Soc Interface 2020; 17:20190621. [PMID: 31937231 PMCID: PMC7014807 DOI: 10.1098/rsif.2019.0621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023] Open
Abstract
Pattern formation from homogeneity is well studied, but less is known concerning symmetry-breaking instabilities in heterogeneous media. It is non-trivial to separate observed spatial patterning due to inherent spatial heterogeneity from emergent patterning due to nonlinear instability. We employ WKBJ asymptotics to investigate Turing instabilities for a spatially heterogeneous reaction-diffusion system, and derive conditions for instability which are local versions of the classical Turing conditions. We find that the structure of unstable modes differs substantially from the typical trigonometric functions seen in the spatially homogeneous setting. Modes of different growth rates are localized to different spatial regions. This localization helps explain common amplitude modulations observed in simulations of Turing systems in heterogeneous settings. We numerically demonstrate this theory, giving an illustrative example of the emergent instabilities and the striking complexity arising from spatially heterogeneous reaction-diffusion systems. Our results give insight both into systems driven by exogenous heterogeneity, as well as successive pattern forming processes, noting that most scenarios in biology do not involve symmetry breaking from homogeneity, but instead consist of sequential evolutions of heterogeneous states. The instability mechanism reported here precisely captures such evolution, and extends Turing's original thesis to a far wider and more realistic class of systems.
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Affiliation(s)
- Andrew L. Krause
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova 13, 120 00 Prague, Czech Republic
| | - Thomas E. Woolley
- Cardiff School of Mathematics, Cardiff University, Senghennydd Road, Cardiff CF24 4AG, UK
| | - Eamonn A. Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
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Rahhal R, Seto E. Emerging roles of histone modifications and HDACs in RNA splicing. Nucleic Acids Res 2019; 47:4911-4926. [PMID: 31162605 PMCID: PMC6547430 DOI: 10.1093/nar/gkz292] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Histone modifications and RNA splicing, two seemingly unrelated gene regulatory processes, greatly increase proteome diversity and profoundly influence normal as well as pathological eukaryotic cellular functions. Like many histone modifying enzymes, histone deacetylases (HDACs) play critical roles in governing cellular behaviors and are indispensable in numerous biological processes. While the association between RNA splicing and histone modifications is beginning to be recognized, a lack of knowledge exists regarding the role of HDACs in splicing. Recent studies however, reveal that HDACs interact with spliceosomal and ribonucleoprotein complexes, actively control the acetylation states of splicing-associated histone marks and splicing factors, and thereby unexpectedly could modulate splicing. Here, we review the role of histone/protein modifications and HDACs in RNA splicing and discuss the convergence of two parallel fields, which supports the argument that HDACs, and perhaps most histone modifying enzymes, are much more versatile and far more complicated than their initially proposed functions. Analogously, an HDAC-RNA splicing connection suggests that splicing is regulated by additional upstream factors and pathways yet to be defined or not fully characterized. Some human diseases share common underlying causes of aberrant HDACs and dysregulated RNA splicing and, thus, further support the potential link between HDACs and RNA splicing.
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Affiliation(s)
- Raneen Rahhal
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Edward Seto
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
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40
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Campa CC, Weisbach NR, Santinha AJ, Incarnato D, Platt RJ. Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods 2019; 16:887-893. [PMID: 31406383 DOI: 10.1038/s41592-019-0508-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022]
Abstract
The ability to modify multiple genetic elements simultaneously would help to elucidate and control the gene interactions and networks underlying complex cellular functions. However, current genome engineering technologies are limited in both the number and the type of perturbations that can be performed simultaneously. Here, we demonstrate that both Cas12a and a clustered regularly interspaced short palindromic repeat (CRISPR) array can be encoded in a single transcript by adding a stabilizer tertiary RNA structure. By leveraging this system, we illustrate constitutive, conditional, inducible, orthogonal and multiplexed genome engineering of endogenous targets using up to 25 individual CRISPR RNAs delivered on a single plasmid. Our method provides a powerful platform to investigate and orchestrate the sophisticated genetic programs underlying complex cell behaviors.
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Affiliation(s)
- Carlo C Campa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Niels R Weisbach
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - António J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Department of Chemistry, University of Basel, Basel, Switzerland.
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Polavarapu K, Preethish-Kumar V, Sekar D, Vengalil S, Nashi S, Mahajan NP, Thomas PT, Sadasivan A, Warrier M, Gupta A, Arunachal G, Debnath M, Keerthipriya MS, Pradeep-Chandra-Reddy C, Puttegowda A, John AP, Tavvala A, Gunasekaran S, Sathyaprabha TN, Chandra SR, Kramer B, Delhaas T, Nalini A. Mutation pattern in 606 Duchenne muscular dystrophy children with a comparison between familial and non-familial forms: a study in an Indian large single-center cohort. J Neurol 2019; 266:2177-2185. [PMID: 31139960 DOI: 10.1007/s00415-019-09380-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
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Grelet S, Howe PH. hnRNP E1 at the crossroads of translational regulation of epithelial-mesenchymal transition. ACTA ACUST UNITED AC 2019; 5. [PMID: 31681852 PMCID: PMC6824538 DOI: 10.20517/2394-4722.2018.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The epithelial-mesenchymal transition (EMT), in which cells undergo a switch from a polarized, epithelial phenotype to a highly motile fibroblastic or mesenchymal phenotype is fundamental during embryonic development and can be reactivated in a variety of diseases including cancer. Spatio-temporally-regulated mechanisms are constantly orchestrated to allow cells to adapt to their constantly changing environments when disseminating to distant organs. Although numerous transcriptional regulatory factors are currently well-characterized, the post-transcriptional control of EMT requires continued investigation. The hnRNP E1 protein displays a major role in the control of tumor cell plasticity by regulating the translatome through multiple non-redundant mechanisms, and this role is exemplified when E1 is absent. hnRNP E1 binding to RNA molecules leads to direct or indirect translational regulation of specific sets of proteins: (1) hnRNP E1 binding to specific targets has a direct role in translation by preventing elongation of translation; (2) hnRNP E1-dependent alternative splicing can prevent the generation of a competing long non-coding RNA that acts as a decoy for microRNAs (miRNAs) involved in translational inhibition of EMT master regulators; (3) hnRNP E1 binding to the 3’ untranslated region of transcripts can also positively regulate the stability of certain mRNAs to improve their translation. Globally, hnRNP E1 appears to control proteome reprogramming during cell plasticity, either by direct or indirect regulation of protein translation.
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Affiliation(s)
- Simon Grelet
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA.,Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Philip H Howe
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA.,Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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43
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Rogers SO. Integrated evolution of ribosomal RNAs, introns, and intron nurseries. Genetica 2018; 147:103-119. [PMID: 30578455 DOI: 10.1007/s10709-018-0050-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
The initial components of ribosomes first appeared more than 3.8 billion years ago during a time when many types of RNAs were evolving. While modern ribosomes are complex molecular machines consisting of rRNAs and proteins, they were assembled during early evolution by the association and joining of small functional RNA units. Introns may have provided the means to ligate many of these pieces together. All four classes of introns (group I, group II, spliceosomal, and archaeal) are present in many rRNA gene loci over a broad phylogenetic range. A survey of rRNA intron sequences across the three major life domains suggests that some of the classes of introns may have diverged from one another within rRNA gene loci. Analyses of rRNA sequences revealed self-splicing group I and group II introns are present in ancestral regions of the SSU (small subunit) and LSU (large subunit), whereas spliceosomal and archaeal introns appeared in sections of the rRNA that evolved later. Most classes of introns increased in number for approximately 1 billion years. However, their frequencies are low in the most recently evolved regions added to the SSU and LSU rRNAs. Furthermore, many of the introns appear to have been in the same locations for billions of years, suggesting an ancient origin for these sequences. In this Perspectives paper, I reviewed and analyzed rRNA intron sequences, locations, structural characteristics, and splicing mechanisms; and suggest that rRNA gene loci may have served as evolutionary nurseries for intron formation and diversification.
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Affiliation(s)
- Scott O Rogers
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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44
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Akpulat U, Wang H, Becker K, Contreras A, Partridge TA, Novak JS, Cirak S. Shorter Phosphorodiamidate Morpholino Splice-Switching Oligonucleotides May Increase Exon-Skipping Efficacy in DMD. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:534-542. [PMID: 30396145 PMCID: PMC6222172 DOI: 10.1016/j.omtn.2018.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022]
Abstract
Duchenne muscular dystrophy is a fatal muscle disease, caused by mutations in DMD, leading to loss of dystrophin expression. Phosphorodiamidate morpholino splice-switching oligonucleotides (PMO-SSOs) have been used to elicit the restoration of a partially functional truncated dystrophin by excluding disruptive exons from the DMD messenger. The 30-mer PMO eteplirsen (EXONDYS51) developed for exon 51 skipping is the first dystrophin-restoring, conditionally FDA-approved drug in history. Clinical trials had shown a dose-dependent variable and patchy dystrophin restoration. The main obstacle for efficient dystrophin restoration is the inadequate uptake of PMOs into skeletal muscle fibers at low doses. The excessive cost of longer PMOs has limited the utilization of higher dosing. We designed shorter 25-mer PMOs directed to the same eteplirsen-targeted region of exon 51 and compared their efficacies in vitro and in vivo in the mdx52 murine model. Our results showed that skipped-dystrophin induction was comparable between the 30-mer PMO sequence of eteplirsen and one of the shorter PMOs, while the other 25-mer PMOs showed lower exon-skipping efficacies. Shorter PMOs would make higher doses economically feasible, and high dosing would result in better drug uptake into muscle, induce higher levels of dystrophin restoration in DMD muscle, and, ultimately, increase the clinical efficacy.
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Affiliation(s)
- Ugur Akpulat
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany; Department of Pediatrics, University Hospital Cologne, Cologne 50937, Germany; Department of Medical Biology, Faculty of Medicine, Kastamonu University, Kastamonu 37100, Turkey
| | - Haicui Wang
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany; Department of Pediatrics, University Hospital Cologne, Cologne 50937, Germany
| | - Kerstin Becker
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany; Department of Pediatrics, University Hospital Cologne, Cologne 50937, Germany
| | - Adriana Contreras
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany; Department of Pediatrics, University Hospital Cologne, Cologne 50937, Germany
| | - Terence A Partridge
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
| | - James S Novak
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
| | - Sebahattin Cirak
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany.
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45
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Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Res 2018; 46:6996-7005. [PMID: 29986098 PMCID: PMC6101502 DOI: 10.1093/nar/gky556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
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46
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Crispi V, Matsakas A. Duchenne muscular dystrophy: genome editing gives new hope for treatment. Postgrad Med J 2018; 94:296-304. [DOI: 10.1136/postgradmedj-2017-135377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/03/2018] [Accepted: 01/13/2018] [Indexed: 12/20/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive wasting disease of skeletal and cardiac muscles, representing one of the most common recessive fatal inherited genetic diseases with 1:3500–1:5000 in yearly incidence. It is caused by mutations in the DMD gene that encodes the membrane-associated dystrophin protein. Over the years, many have been the approaches to management of DMD, but despite all efforts, no effective treatment has yet been discovered. Hope for the development of potential therapeutics has followed the recent advances in genome editing and gene therapy. This review gives an overview to DMD and summarises current lines of evidence with regard to treatment and disease management alongside the appropriate considerations.
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47
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Gherardi S, Bovolenta M, Passarelli C, Falzarano MS, Pigini P, Scotton C, Neri M, Armaroli A, Osman H, Selvatici R, Gualandi F, Recchia A, Mora M, Bernasconi P, Maggi L, Morandi L, Ferlini A, Perini G. Transcriptional and epigenetic analyses of the DMD locus reveal novel cis‑acting DNA elements that govern muscle dystrophin expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1138-1147. [PMID: 28867298 DOI: 10.1016/j.bbagrm.2017.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/02/2017] [Accepted: 08/28/2017] [Indexed: 11/25/2022]
Abstract
The dystrophin gene (DMD) is the largest gene in the human genome, mapping on the Xp21 chromosome locus. It spans 2.2Mb and accounts for approximately 0,1% of the entire human genome. Mutations in this gene cause Duchenne and Becker Muscular Dystrophy, X-linked Dilated Cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16h, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques. Our results unveil a surprisingly powerful processivity of the RNA polymerase II along the entire 2.2Mb of the DMD locus with just one site of pausing around intron 52. We also discovered epigenetic marks highlighting the existence of four novel cis‑DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA. Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.
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Affiliation(s)
- Samuele Gherardi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; CIRI Health Sciences & Technologies (HST), Bologna, Italy
| | - Matteo Bovolenta
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Chiara Passarelli
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy; Paediatric Hospital Bambino Gesù, Laboratory of Medical Genetics, Rome, Italy
| | - Maria Sofia Falzarano
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Paolo Pigini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Chiara Scotton
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Marcella Neri
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Annarita Armaroli
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Hana Osman
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy
| | - Alessandra Recchia
- Department of Life Sciences, University of Modena & Reggio Emilia, Modena, Italy
| | - Marina Mora
- Neuromuscular Disease and Immunology Unit, Fondazione IRCCS Istituto Neurologico "C. Besta", Milan, Italy
| | - Pia Bernasconi
- Neuromuscular Disease and Immunology Unit, Fondazione IRCCS Istituto Neurologico "C. Besta", Milan, Italy
| | - Lorenzo Maggi
- Neuromuscular Disease and Immunology Unit, Fondazione IRCCS Istituto Neurologico "C. Besta", Milan, Italy
| | - Lucia Morandi
- Neuromuscular Disease and Immunology Unit, Fondazione IRCCS Istituto Neurologico "C. Besta", Milan, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Italy; Neuromuscular Unit, Great Ormond Street Hospital, University College London, UK.
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; CIRI Health Sciences & Technologies (HST), Bologna, Italy.
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Grelet S, Link LA, Howley B, Obellianne C, Palanisamy V, Gangaraju VK, Diehl JA, Howe PH. A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression. Nat Cell Biol 2017; 19:1105-1115. [PMID: 28825698 PMCID: PMC5578890 DOI: 10.1038/ncb3595] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/19/2017] [Indexed: 12/12/2022]
Abstract
The contribution of lncRNAs to tumour progression and the regulatory mechanisms driving their expression are areas of intense investigation. Here, we characterize the binding of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) to a nucleic acid structural element located in exon 12 of PNUTS (also known as PPP1R10) pre-RNA that regulates its alternative splicing. HnRNP E1 release from this structural element, following its silencing, nucleocytoplasmic translocation or in response to TGFβ, allows alternative splicing and generates a non-coding isoform of PNUTS. Functionally the lncRNA-PNUTS serves as a competitive sponge for miR-205 during epithelial-mesenchymal transition (EMT). In mesenchymal breast tumour cells and in breast tumour samples, the expression of lncRNA-PNUTS is elevated and correlates with levels of ZEB mRNAs. Thus, PNUTS is a bifunctional RNA encoding both PNUTS mRNA and lncRNA-PNUTS, each eliciting distinct biological functions. While PNUTS mRNA is ubiquitously expressed, lncRNA-PNUTS appears to be tightly regulated dependent on the status of hnRNP E1 and tumour context.
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Affiliation(s)
- Simon Grelet
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Laura A Link
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Breege Howley
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Clémence Obellianne
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Viswanathan Palanisamy
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Vamsi K Gangaraju
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - J Alan Diehl
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Philip H Howe
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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49
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Mauger O, Lemoine F, Scheiffele P. Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity. Neuron 2017; 92:1266-1278. [PMID: 28009274 DOI: 10.1016/j.neuron.2016.11.032] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/14/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023]
Abstract
Activity-dependent transcription has emerged as a major source of gene products that regulate neuronal excitability, connectivity, and synaptic properties. However, the elongation rate of RNA polymerases imposes a significant temporal constraint for transcript synthesis, in particular for long genes where new synthesis requires hours. Here we reveal a novel, transcription-independent mechanism that releases transcripts within minutes of neuronal stimulation. We found that, in the mouse neocortex, polyadenylated transcripts retain select introns and are stably accumulated in the cell nucleus. A subset of these intron retention transcripts undergoes activity-dependent splicing, cytoplasmic export, and ribosome loading, thus acutely releasing mRNAs in response to stimulation. This process requires NMDA receptor- and calmodulin-dependent kinase pathways, and it is particularly prevalent for long transcripts. We conclude that regulated intron retention in fully transcribed RNAs represents a mechanism to rapidly mobilize a pool of mRNAs in response to neuronal activity.
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Affiliation(s)
- Oriane Mauger
- Biozentrum of the University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Frédéric Lemoine
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Peter Scheiffele
- Biozentrum of the University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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50
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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