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Shang Z, Zhao J, Yang M, Xiao Y, Chu W, Xu S, Zhang X, Yi X, Lin M, Xia F. Precise control of transmembrane current via regulating bionic lipid membrane composition. SCIENCE ADVANCES 2024; 10:eadq0118. [PMID: 39213352 PMCID: PMC11364097 DOI: 10.1126/sciadv.adq0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The transport of ions through biological ion channels is regulated not only by their structural characteristics but also by the composition of the phospholipid membrane, which serves as a carrier for nanochannels. Inspired by the modulation of ion currents by lipid membrane composition, exemplified by the activation of the K+ channel of Streptomyces A by anionic lipids, we present a biomimetic nanochannel system based on combining DNA nanotechnology with two-dimensional graphene oxide (GO) nanosheets. By designing multibranched DNA nanowires, we assemble programmable DNA scaffold networks (DSNs) on the GO surface to precisely control membrane composition. Modulating the DSN layers from one to five enhances DNA composition, yielding a maximum 12-fold enhancement in ion current, primarily due to charge effects. Incorporating DNAzymes facilitates reversible modulation of membrane composition, enabling cyclic conversion of ion current. This approach offers a pathway for creating devices with highly efficient, tunable ion transport, applicable in diverse fields like mass transport, environmental protection, biomimetic channels, and biosensors.
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Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jing Zhao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yuling Xiao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wenjing Chu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shijun Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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2
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Shorrock HK, Lennon CD, Aliyeva A, Davey EE, DeMeo CC, Pritchard CE, Planco L, Velez JM, Mascorro-Huamancaja A, Shin DS, Cleary JD, Berglund JA. Widespread alternative splicing dysregulation occurs presymptomatically in CAG expansion spinocerebellar ataxias. Brain 2024; 147:486-504. [PMID: 37776516 PMCID: PMC10834251 DOI: 10.1093/brain/awad329] [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: 05/31/2023] [Revised: 07/31/2023] [Accepted: 09/03/2023] [Indexed: 10/02/2023] Open
Abstract
The spinocerebellar ataxias (SCAs) are a group of dominantly inherited neurodegenerative diseases, several of which are caused by CAG expansion mutations (SCAs 1, 2, 3, 6, 7 and 12) and more broadly belong to the large family of over 40 microsatellite expansion diseases. While dysregulation of alternative splicing is a well defined driver of disease pathogenesis across several microsatellite diseases, the contribution of alternative splicing in CAG expansion SCAs is poorly understood. Furthermore, despite extensive studies on differential gene expression, there remains a gap in our understanding of presymptomatic transcriptomic drivers of disease. We sought to address these knowledge gaps through a comprehensive study of 29 publicly available RNA-sequencing datasets. We identified that dysregulation of alternative splicing is widespread across CAG expansion mouse models of SCAs 1, 3 and 7. These changes were detected presymptomatically, persisted throughout disease progression, were repeat length-dependent, and were present in brain regions implicated in SCA pathogenesis including the cerebellum, pons and medulla. Across disease progression, changes in alternative splicing occurred in genes that function in pathways and processes known to be impaired in SCAs, such as ion channels, synaptic signalling, transcriptional regulation and the cytoskeleton. We validated several key alternative splicing events with known functional consequences, including Trpc3 exon 9 and Kcnma1 exon 23b, in the Atxn1154Q/2Q mouse model. Finally, we demonstrated that alternative splicing dysregulation is responsive to therapeutic intervention in CAG expansion SCAs with Atxn1 targeting antisense oligonucleotide rescuing key splicing events. Taken together, these data demonstrate that widespread presymptomatic dysregulation of alternative splicing in CAG expansion SCAs may contribute to disease onset, early neuronal dysfunction and may represent novel biomarkers across this devastating group of neurodegenerative disorders.
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Affiliation(s)
| | - Claudia D Lennon
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
| | - Asmer Aliyeva
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
- Department of Biology, University at Albany—SUNY, Albany, NY 12222, USA
| | - Emily E Davey
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
| | - Cristina C DeMeo
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
| | | | - Lori Planco
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
| | - Jose M Velez
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
- Department of Biology, University at Albany—SUNY, Albany, NY 12222, USA
| | | | - Damian S Shin
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA
| | - John D Cleary
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
| | - J Andrew Berglund
- The RNA Institute, University at Albany—SUNY, Albany, NY 12222, USA
- Department of Biology, University at Albany—SUNY, Albany, NY 12222, USA
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3
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Dwivedi OP, Barreiro K, Käräjämäki A, Valo E, Giri AK, Prasad RB, Roy RD, Thorn LM, Rannikko A, Holthöfer H, Gooding KM, Sourbron S, Delic D, Gomez MF, Groop PH, Tuomi T, Forsblom C, Groop L, Puhka M. Genome-wide mRNA profiling in urinary extracellular vesicles reveals stress gene signature for diabetic kidney disease. iScience 2023; 26:106686. [PMID: 37216114 PMCID: PMC10193229 DOI: 10.1016/j.isci.2023.106686] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/19/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Urinary extracellular vesicles (uEV) are a largely unexplored source of kidney-derived mRNAs with potential to serve as a liquid kidney biopsy. We assessed ∼200 uEV mRNA samples from clinical studies by genome-wide sequencing to discover mechanisms and candidate biomarkers of diabetic kidney disease (DKD) in Type 1 diabetes (T1D) with replication in Type 1 and 2 diabetes. Sequencing reproducibly showed >10,000 mRNAs with similarity to kidney transcriptome. T1D DKD groups showed 13 upregulated genes prevalently expressed in proximal tubules, correlated with hyperglycemia and involved in cellular/oxidative stress homeostasis. We used six of them (GPX3, NOX4, MSRB, MSRA, HRSP12, and CRYAB) to construct a transcriptional "stress score" that reflected long-term decline of kidney function and could even identify normoalbuminuric individuals showing early decline. We thus provide workflow and web resource for studying uEV transcriptomes in clinical urine samples and stress-linked DKD markers as potential early non-invasive biomarkers or drug targets.
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Affiliation(s)
- Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Karina Barreiro
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPrep Core, University of Helsinki, Helsinki, Finland
| | - Annemari Käräjämäki
- Department of Primary Health Care, Vaasa Central Hospital, Hietalahdenkatu 2-4, 65130 Vaasa, Finland
- Diabetes Center, Vaasa Health Care Center, Sepänkyläntie 14-16, 65100 Vaasa, Finland
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anil K. Giri
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute (FCI), Tukholmankatu 8, 00290 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Rashmi B. Prasad
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, SE 214 28 Malmö, Sweden
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lena M. Thorn
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
- Department of Urology, 00014 University of Helsinki, and Helsinki University Hospital, 00100 Helsinki, Finland
| | - Harry Holthöfer
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Kim M. Gooding
- Diabetes and Vascular Research Centre, National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Steven Sourbron
- Department of Imaging, Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- Fifth Department of Medicine, Nephrology/Endocrinology/Rheumatology/Pneumology, University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Maria F. Gomez
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, SE 214 28 Malmö, Sweden
| | | | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School Monash University, Melbourne, VIC, Australia
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, SE 214 28 Malmö, Sweden
- Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
| | - Carol Forsblom
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, SE 214 28 Malmö, Sweden
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPrep Core, University of Helsinki, Helsinki, Finland
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Hu N, Kim E, Antoury L, Wheeler TM. Correction of Clcn1 alternative splicing reverses muscle fiber type transition in mice with myotonic dystrophy. Nat Commun 2023; 14:1956. [PMID: 37029100 PMCID: PMC10082032 DOI: 10.1038/s41467-023-37619-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
In myotonic dystrophy type 1 (DM1), deregulated alternative splicing of the muscle chloride channel Clcn1 causes myotonia, a delayed relaxation of muscles due to repetitive action potentials. The degree of weakness in adult DM1 is associated with increased frequency of oxidative muscle fibers. However, the mechanism for glycolytic-to-oxidative fiber type transition in DM1 and its relationship to myotonia are uncertain. Here we cross two mouse models of DM1 to create a double homozygous model that features progressive functional impairment, severe myotonia, and near absence of type 2B glycolytic fibers. Intramuscular injection of an antisense oligonucleotide for targeted skipping of Clcn1 exon 7a corrects Clcn1 alternative splicing, increases glycolytic 2B levels to ≥ 40% frequency, reduces muscle injury, and improves fiber hypertrophy relative to treatment with a control oligo. Our results demonstrate that fiber type transitions in DM1 result from myotonia and are reversible, and support the development of Clcn1-targeting therapies for DM1.
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Affiliation(s)
- Ningyan Hu
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eunjoo Kim
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Layal Antoury
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thurman M Wheeler
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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5
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Kunitake K, Sathyaprakash C, Motohashi N, Aoki Y. Quantitative Evaluation of Exon Skipping in Urine-Derived Cells for Duchenne Muscular Dystrophy. Methods Mol Biol 2023; 2587:153-164. [PMID: 36401029 DOI: 10.1007/978-1-0716-2772-3_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antisense oligonucleotide (ASO)-based exon skipping therapy is thought to be promising for Duchenne muscular dystrophy (DMD). For the screening or assessing patient eligibility before administering ASO to patients, in vitro testing using myoblasts derived from each DMD patient is considered crucial. We previously reported state-of-the-art technology to obtain patient primary myoblasts from MYOD1-induced urine-derived cells (UDCs) as a model of DMD. We hypothesize that the myoblasts may potentially reflect specific pathological phenotypes, leading to a path for precision medicine in DMD patients. Here, we describe a detailed protocol for both acquiring MYOD1-induced myoblasts from UDCs and evaluating the correction of DMD mRNA and protein levels after exon-skipping in the cells.
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Affiliation(s)
- Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Chaitra Sathyaprakash
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Norio Motohashi
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.
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6
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Nabariya DK, Heinz A, Derksen S, Krauß S. Intracellular and intercellular transport of RNA organelles in CXG repeat disorders: The strength of weak ties. Front Mol Biosci 2022; 9:1000932. [PMID: 36589236 PMCID: PMC9800848 DOI: 10.3389/fmolb.2022.1000932] [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: 07/22/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
RNA is a vital biomolecule, the function of which is tightly spatiotemporally regulated. RNA organelles are biological structures that either membrane-less or surrounded by membrane. They are produced by the all the cells and indulge in vital cellular mechanisms. They include the intracellular RNA granules and the extracellular exosomes. RNA granules play an essential role in intracellular regulation of RNA localization, stability and translation. Aberrant regulation of RNA is connected to disease development. For example, in microsatellite diseases such as CXG repeat expansion disorders, the mutant CXG repeat RNA's localization and function are affected. RNA is not only transported intracellularly but can also be transported between cells via exosomes. The loading of the exosomes is regulated by RNA-protein complexes, and recent studies show that cytosolic RNA granules and exosomes share common content. Intracellular RNA granules and exosome loading may therefore be related. Exosomes can also transfer pathogenic molecules of CXG diseases from cell to cell, thereby driving disease progression. Both intracellular RNA granules and extracellular RNA vesicles may serve as a source for diagnostic and treatment strategies. In therapeutic approaches, pharmaceutical agents may be loaded into exosomes which then transport them to the desired cells/tissues. This is a promising target specific treatment strategy with few side effects. With respect to diagnostics, disease-specific content of exosomes, e.g., RNA-signatures, can serve as attractive biomarker of central nervous system diseases detecting early physiological disturbances, even before symptoms of neurodegeneration appear and irreparable damage to the nervous system occurs. In this review, we summarize the known function of cytoplasmic RNA granules and extracellular vesicles, as well as their role and dysfunction in CXG repeat expansion disorders. We also provide a summary of established protocols for the isolation and characterization of both cytoplasmic and extracellular RNA organelles.
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Affiliation(s)
| | | | | | - Sybille Krauß
- Human Biology/Neurobiology, Institute of Biology, Faculty IV, School of Science and Technology, University of Siegen, Siegen, Germany
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7
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
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Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
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9
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Nieuwenhuis S, Widomska J, Blom P, ‘t Hoen PBAC, van Engelen BGM, Glennon JC. Blood Transcriptome Profiling Links Immunity to Disease Severity in Myotonic Dystrophy Type 1 (DM1). Int J Mol Sci 2022; 23:3081. [PMID: 35328504 PMCID: PMC8954763 DOI: 10.3390/ijms23063081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
The blood transcriptome was examined in relation to disease severity in type I myotonic dystrophy (DM1) patients who participated in the Observational Prolonged Trial In DM1 to Improve QoL- Standards (OPTIMISTIC) study. This sought to (a) ascertain if transcriptome changes were associated with increasing disease severity, as measured by the muscle impairment rating scale (MIRS), and (b) establish if these changes in mRNA expression and associated biological pathways were also observed in the Dystrophia Myotonica Biomarker Discovery Initiative (DMBDI) microarray dataset in blood (with equivalent MIRS/DMPK repeat length). The changes in gene expression were compared using a number of complementary pathways, gene ontology and upstream regulator analyses, which suggested that symptom severity in DM1 was linked to transcriptomic alterations in innate and adaptive immunity associated with muscle-wasting. Future studies should explore the role of immunity in DM1 in more detail to assess its relevance to DM1.
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Affiliation(s)
- Sylvia Nieuwenhuis
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands; (S.N.); (P.-B.A.C.‘t.H.)
- Department of Cognitive Neuroscience, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, 6525 EN Nijmegen, The Netherlands;
| | - Joanna Widomska
- Department of Cognitive Neuroscience, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, 6525 EN Nijmegen, The Netherlands;
| | - Paul Blom
- VDL Enabling Technologies Group B.V., 5651 GH Eindhoven, The Netherlands;
| | - Peter-Bram A. C. ‘t Hoen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands; (S.N.); (P.-B.A.C.‘t.H.)
| | - Baziel G. M. van Engelen
- Department of Neurology, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands;
| | - Jeffrey C. Glennon
- Department of Cognitive Neuroscience, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, 6525 EN Nijmegen, The Netherlands;
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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10
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Lin T, Xu Y, Zhao A, He W, Xiao F. Flexible electrochemical sensors integrated with nanomaterials for in situ determination of small molecules in biological samples: A review. Anal Chim Acta 2022; 1207:339461. [DOI: 10.1016/j.aca.2022.339461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
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11
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Canonico F, Chirivi M, Maiullari F, Milan M, Rizzi R, Arcudi A, Galli M, Pane M, Gowran A, Pompilio G, Mercuri E, Crea F, Bearzi C, D'Amario D. Focus on the road to modelling cardiomyopathy in muscular dystrophy. Cardiovasc Res 2021; 118:1872-1884. [PMID: 34254111 DOI: 10.1093/cvr/cvab232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/07/2021] [Indexed: 11/13/2022] Open
Abstract
Alterations in the DMD gene, which codes for the protein dystrophin, cause forms of dystrophinopathies such as Duchenne muscular dystrophy, an X-linked disease. Cardiomyopathy linked to DMD mutations is becoming the leading cause of death in patients with dystrophinopathy. Since phenotypic pathophysiological mechanisms are not fully understood, the improvement and development of new disease models, considering their relative advantages and disadvantages, is essential. The application of genetic engineering approaches on induced pluripotent stem cells, such as gene editing technology, enables the development of physiologically relevant human cell models for in vitro dystrophinopathy studies. The combination of induced pluripotent stem cells-derived cardiovascular cell types and 3 D bioprinting technologies hold great promise for the study of dystrophin-linked cardiomyopathy. This combined approach enables the assessment of responses to physical or chemical stimuli, and the influence of pharmaceutical approaches. The critical objective of in vitro microphysiological systems is to more accurately reproduce the microenvironment observed in vivo. Ground-breaking methodology involving the connection of multiple microphysiological systems comprised of different tissues would represent a move toward precision body-on-chip disease modelling could lead to a critical expansion in what is known about inter-organ responses to disease and novel therapies that have the potential to replace animal models. In this review, we will focus on the generation, development, and application of current cellular, animal and potential for bio-printed models, in the study of the pathophysiological mechanisms underlying dystrophin-linked cardiomyopathy in the direction of personalized medicine.
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Affiliation(s)
- Francesco Canonico
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Cardiovascular Sciences, Rome, Italy
| | - Maila Chirivi
- Institute of Biochemistry and Cell Biology, National Research Council of Italy (IBBC-CNR), Monterotondo, Rome, Italy.,Istituto Nazionale Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Fabio Maiullari
- Istituto Nazionale Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Marika Milan
- Institute of Biochemistry and Cell Biology, National Research Council of Italy (IBBC-CNR), Monterotondo, Rome, Italy.,Istituto Nazionale Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Roberto Rizzi
- Istituto Nazionale Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy.,Institute of Biomedical Technologies, National Research Council of Italy (ITB-CNR), Segrate, Milan, Italy
| | - Alessandra Arcudi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Cardiovascular Sciences, Rome, Italy
| | - Mattia Galli
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Cardiovascular Sciences, Rome, Italy
| | - Marika Pane
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Women, Children and Public Health Sciences, Rome, Italy
| | - Aoife Gowran
- Centro Cardiologico Monzino IRCCS, Unit of Vascular Biology and Regenerative Medicine, Milan, Italy
| | - Giulio Pompilio
- Centro Cardiologico Monzino IRCCS, Unit of Vascular Biology and Regenerative Medicine, Milan, Italy.,Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Eugenio Mercuri
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Women, Children and Public Health Sciences, Rome, Italy
| | - Filippo Crea
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Cardiovascular Sciences, Rome, Italy
| | - Claudia Bearzi
- Istituto Nazionale Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Milan, Italy
| | - Domenico D'Amario
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Department of Cardiovascular Sciences, Rome, Italy
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12
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Hao Z, Luo Y, Huang C, Wang Z, Song G, Pan Y, Zhao X, Liu S. An Intelligent Graphene-Based Biosensing Device for Cytokine Storm Syndrome Biomarkers Detection in Human Biofluids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101508. [PMID: 34110682 DOI: 10.1002/smll.202101508] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Abnormal elevated levels of cytokines such as interferon (IFN), interleukin (IL), and tumor necrosis factor (TNF), are considered as one of the prognosis biomarkers for indicating the progression to severe or critical COVID-19. Hence, it is of great significance to develop devices for monitoring their levels in COVID-19 patients, and thus enabling detecting COVID-19 patients that are worsening and to treat them before they become critically ill. Here, an intelligent aptameric dual channel graphene-TWEEN 80 field effect transistor (DGTFET) biosensing device for on-site detection of IFN-γ, TNF-α, and IL-6 within 7 min with limits of detection (LODs) of 476 × 10-15 , 608 × 10-15 , or 611 × 10-15 m respectively in biofluids is presented. Using the customized Android App together with this intelligent device, asymptomatic or mild COVID-19 patients can have a preliminary self-detection of cytokines and get a warning reminder while the condition starts to deteriorate. Also, the device can be fabricated on flexible substrates toward wearable applications for moderate or even critical COVID-19 cases for consistently monitoring cytokines under different deformations. Hence, the intelligent aptameric DGTFET biosensing device is promising to be used for point-of-care applications for monitoring conditions of COVID-19 patients who are in different situations.
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Affiliation(s)
- Zhuang Hao
- State Key Laboratory of Robotics and Systems, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, 150001, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
| | - Yang Luo
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110169, China
| | - Cong Huang
- State Key Laboratory of Robotics and Systems, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
| | - Ziran Wang
- State Key Laboratory of Robotics and Systems, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
| | - Guoli Song
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110169, China
| | - Yunlu Pan
- State Key Laboratory of Robotics and Systems, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
| | - Xuezeng Zhao
- State Key Laboratory of Robotics and Systems, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
| | - Shaoqin Liu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Micro-systems and Micro-structures Manufacturing, Ministry of Education, Harbin Institute of Technology, Harbin, 150080, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150080, China
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13
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van der Plas E, Gutmann L, Thedens D, Shields RK, Langbehn K, Guo Z, Sonka M, Nopoulos P. Quantitative muscle MRI as a sensitive marker of early muscle pathology in myotonic dystrophy type 1. Muscle Nerve 2021; 63:553-562. [PMID: 33462896 PMCID: PMC8442354 DOI: 10.1002/mus.27174] [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: 07/28/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Quantitative muscle MRI as a sensitive marker of early muscle pathology and disease progression in adult-onset myotonic dystrophy type 1. The utility of muscle MRI as a marker of muscle pathology and disease progression in adult-onset myotonic dystrophy type 1 (DM1) was evaluated. METHODS This prospective, longitudinal study included 67 observations from 36 DM1 patients (50% female), and 92 observations from 49 healthy adults (49% female). Lower-leg 3T magnetic resonance imaging (MRI) scans were acquired. Volume and fat fraction (FF) were estimated using a three-point Dixon method, and T2-relaxometry was determined using a multi-echo spin-echo sequence. Muscles were segmented automatically. Mixed linear models were conducted to determine group differences across muscles and image modality, accounting for age, sex, and repeated observations. Differences in rate of change in volume, T2-relaxometry, and FF were also determined with mixed linear regression that included a group by elapsed time interaction. RESULTS Compared with healthy adults, DM1 patients exhibited reduced volume of the tibialis anterior, soleus, and gastrocnemius (GAS) (all, P < .05). T2-relaxometry and FF were increased across all calf muscles in DM1 compared to controls. (all, P < .01). Signs of muscle pathology, including reduced volume, and increased T2-relaxometry and FF were already noted in DM1 patients who did not exhibit clinical motor symptoms of DM1. As a group, DM1 patients exhibited a more rapid change than did controls in tibialis posterior volume (P = .05) and GAS T2-relaxometry (P = .03) and FF (P = .06). CONCLUSIONS Muscle MRI renders sensitive, early markers of muscle pathology and disease progression in DM1. T2 relaxometry may be particularly sensitive to early muscle changes related to DM1.
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Affiliation(s)
- Ellen van der Plas
- Department of Psychiatry, University of Iowa Hospital & Clinics, Iowa City, IA, USA
| | - Laurie Gutmann
- Department of Neurology, University of Iowa Hospital & Clinics, Iowa City, IA, USA
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dan Thedens
- Department of Radiology, University of Iowa Hospital & Clinics, Iowa City, IA, USA
| | - Richard K. Shields
- Department of Physical Therapy and Rehabilitation Science, University of Iowa Hospital & Clinics, Iowa City, IA, USA
| | - Kathleen Langbehn
- Department of Psychiatry, University of Iowa Hospital & Clinics, Iowa City, IA, USA
| | - Zhihui Guo
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, USA
| | - Milan Sonka
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, USA
| | - Peggy Nopoulos
- Department of Psychiatry, University of Iowa Hospital & Clinics, Iowa City, IA, USA
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14
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Otero BA, Poukalov K, Hildebrandt RP, Thornton CA, Jinnai K, Fujimura H, Kimura T, Hagerman KA, Sampson JB, Day JW, Wang ET. Transcriptome alterations in myotonic dystrophy frontal cortex. Cell Rep 2021; 34:108634. [PMID: 33472074 PMCID: PMC9272850 DOI: 10.1016/j.celrep.2020.108634] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Myotonic dystrophy (DM) is caused by expanded CTG/CCTG repeats, causing symptoms in skeletal muscle, heart, and central nervous system (CNS). CNS issues are debilitating and include hypersomnolence, executive dysfunction, white matter atrophy, and neurofibrillary tangles. Here, we generate RNA-seq transcriptomes from DM and unaffected frontal cortex and identify 130 high-confidence splicing changes, most occurring only in cortex, not skeletal muscle or heart. Mis-spliced exons occur in neurotransmitter receptors, ion channels, and synaptic scaffolds, and GRIP1 mis-splicing modulates kinesin association. Optical mapping of expanded CTG repeats reveals extreme mosaicism, with some alleles showing >1,000 CTGs. Mis-splicing severity correlates with CTG repeat length across individuals. Upregulated genes tend to be microglial and endothelial, suggesting neuroinflammation, and downregulated genes tend to be neuronal. Many gene expression changes strongly correlate with mis-splicing, suggesting candidate biomarkers of disease. These findings provide a framework for mechanistic and therapeutic studies of the DM CNS.
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Affiliation(s)
- Brittney A Otero
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kiril Poukalov
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ryan P Hildebrandt
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Kenji Jinnai
- Department of Neurology, National Hospital Organization Hyogo-Chuo Hospital, Sanda, Japan
| | - Harutoshi Fujimura
- Department of Neurology, National Hospital Organization Toneyama Hospital, Osaka, Japan
| | - Takashi Kimura
- Department of Neurology, Hyogo College of Medicine, Nichinomiya, Japan
| | | | | | - John W Day
- Department of Neurology, Stanford University, Palo Alto, CA, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
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15
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Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, Cai P, Xing S, Bao P, Jin Y, Zhao W, Chen Y, Zhao H, Jia X, Lu S, Lu Y, Chen L, Yin J, Lu ZJ. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 2021; 11:181-193. [PMID: 33391469 PMCID: PMC7681086 DOI: 10.7150/thno.48206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. Methods: We investigated different variations (i.e. differential expression, alternative splicing, alternative polyadenylation, and differential editing) in diverse long exRNA species (e.g. long noncoding RNAs and circular RNAs) using 79 plasma exosomal RNA-seq (exoRNA-seq) datasets of multiple cancer types. We then integrated 53 exoRNA-seq datasets and 65 self-profiled cell-free RNA-seq (cfRNA-seq) datasets to identify recurrent variations in liver cancer patients. We further combined TCGA tissue RNA-seq datasets and validated biomarker candidates by RT-qPCR in an individual cohort of more than 100 plasma samples. Finally, we used machine learning models to identify a signature of 3 noncoding RNAs for the detection of liver cancer. Results: We found that different types of RNA variations identified from exoRNA-seq data were enriched in pathways related to tumorigenesis and metastasis, immune, and metabolism, suggesting that cancer signals can be detected from long exRNAs. Subsequently, we identified more than 100 recurrent variations in plasma from liver cancer patients by integrating exoRNA-seq and cfRNA-seq datasets. From these datasets, 5 significantly up-regulated long exRNAs were confirmed by TCGA data and validated by RT-qPCR in an independent cohort. When using machine learning models to combine two of these validated circular and structured RNAs (SNORD3B-1, circ-0080695) with a miRNA (miR-122) as a panel to classify liver cancer patients from healthy donors, the average AUROC of the cross-validation was 89.4%. The selected 3-RNA panel successfully detected 79.2% AFP-negative samples and 77.1% early-stage liver cancer samples in the testing and validation sets. Conclusions: Our study revealed that different types of RNA variations related to cancer can be detected in plasma and identified a 3-RNA detection panel for liver cancer, especially for AFP-negative and early-stage patients.
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Affiliation(s)
- Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weina Tang
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghui Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Shanshan Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Yinying Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 201805, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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16
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Tosar JP, Segovia M, Castellano M, Gámbaro F, Akiyama Y, Fagúndez P, Olivera Á, Costa B, Possi T, Hill M, Ivanov P, Cayota A. Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome. Nucleic Acids Res 2020; 48:12874-12888. [PMID: 32785615 PMCID: PMC7736827 DOI: 10.1093/nar/gkaa674] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/19/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
A major proportion of extracellular RNAs (exRNAs) do not copurify with extracellular vesicles (EVs) and remain in ultracentrifugation supernatants of cell-conditioned medium or mammalian blood serum. However, little is known about exRNAs beyond EVs. We have previously shown that the composition of the nonvesicular exRNA fraction is highly biased toward specific tRNA-derived fragments capable of forming RNase-protecting dimers. To solve the problem of stability in exRNA analysis, we developed a method based on sequencing the size exclusion chromatography (SEC) fractions of nonvesicular extracellular samples treated with RNase inhibitors (RI). This method revealed dramatic compositional changes in exRNA population when enzymatic RNA degradation was inhibited. We demonstrated the presence of ribosomes and full-length tRNAs in cell-conditioned medium of a variety of mammalian cell lines. Their fragmentation generates some small RNAs that are highly resistant to degradation. The extracellular biogenesis of some of the most abundant exRNAs demonstrates that extracellular abundance is not a reliable input to estimate RNA secretion rates. Finally, we showed that chromatographic fractions containing extracellular ribosomes are probably not silent from an immunological perspective and could possibly be decoded as damage-associated molecular patterns.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mercedes Segovia
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Mauricio Castellano
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Molecular Virology Laboratory, Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
| | - Yasutoshi Akiyama
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pablo Fagúndez
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Álvaro Olivera
- Centro Universitario Regional Este, Universidad de la República, Uruguay
| | - Bruno Costa
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Tania Possi
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Marcelo Hill
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Uruguay
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17
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Zhong GX, Ye CL, Wei HX, Yang LY, Wei QX, Liu ZJ, Fu LX, Lin XH, Chen JY. Ultrasensitive Detection of RNA with Single-Base Resolution by Coupling Electrochemical Sensing Strategy with Chimeric DNA Probe-Aided Ligase Chain Reaction. Anal Chem 2020; 93:911-919. [PMID: 33284015 DOI: 10.1021/acs.analchem.0c03563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate and sensitive detection of single-base mutations in RNAs is of great value in basic studies of life science and medical diagnostics. However, the current available RNA detection methods are challenged by heterogeneous clinical samples in which trace RNA mutants usually existed in a large pool of normal wild sequences. Thus, there is still great need for developing the highly sensitive and highly specific methods in detecting single-base mutations of RNAs in heterogeneous clinical samples. In the present study, a new chimeric DNA probe-aided ligase chain reaction-based electrochemical method (cmDNA-eLCR) was developed for RNA mutation detection through the BSA-based carrier platform and the horseradish peroxidase-hydrogen peroxide-tetramethylbenzidine (HRP-H2O2-TMB) system. The denaturing polyacrylamide gel electrophoresis and a fluorophore-labeled probe was ingeniously designed to demonstrate the advantage of cmDNA in ligation to normal DNA templated by RNA with the catalysis of T4 RNA ligase 2 as well as its higher selectivity than DNA ligase system. Finally, the proposed cmDNA-eLCR, compared with the traditional eLCR, showed excellent performance in discriminating single base-mismatched sequences, where the signal response for mismatched targets at a high concentration could overlap completely with that for the blank control. Besides, this cmDNA-eLCR assay had a wide linear range crossing six orders of magnitude from 1.0 × 10-15 to1.0 × 10-10 M with a limit of detection as low as 0.6 fM. Furthermore, this assay was applied to detect RNA in real sample with a satisfactory result, thereby demonstrating its great potential in diagnosis of RNA-related diseases.
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Affiliation(s)
- Guang-Xian Zhong
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China
| | - Hong-Xiang Wei
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Leng-Xi Fu
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
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18
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Antisense oligonucleotide and adjuvant exercise therapy reverse fatigue in old mice with myotonic dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:393-405. [PMID: 33473325 PMCID: PMC7787993 DOI: 10.1016/j.omtn.2020.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
Patients with myotonic dystrophy type 1 (DM1) identify chronic fatigue as the most debilitating symptom, which manifests in part as prolonged recovery after exercise. Clinical features of DM1 result from pathogenic gain-of-function activity of transcripts containing an expanded microsatellite CUG repeat (CUGexp). In DM1 mice, therapies targeting the CUGexp transcripts correct the molecular phenotype, reverse myotonia, and improve muscle pathology. However, the effect of targeted molecular therapies on fatigue in DM1 is unknown. Here, we use two mouse models of DM1, age-matched wild-type controls, an exercise-activity assay, electrical impedance myography, and therapeutic antisense oligonucleotides (ASOs) to show that exaggerated exercise-induced fatigue progresses with age, is unrelated to muscle fiber size, and persists despite correction of the molecular phenotype for 3 months. In old DM1 mice, ASO treatment combined with an exercise training regimen consisting of treadmill walking 30 min per day 6 days per week for 3 months reverse all measures of fatigue. Exercise training without ASO therapy improves some measures of fatigue without correction of the molecular pathology. Our results highlight a key limitation of ASO monotherapy for this clinically important feature and support the development of moderate-intensity exercise as an adjuvant for targeted molecular therapies of DM1.
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19
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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20
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Seol W, Kim H, Son I. Urinary Biomarkers for Neurodegenerative Diseases. Exp Neurobiol 2020; 29:325-333. [PMID: 33154195 PMCID: PMC7649089 DOI: 10.5607/en20042] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Global incidence of neurodegenerative diseases (NDDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD) is rapidly increasing, but the diagnosis of these diseases at their early stage is challenging. Therefore, the availability of reproducible and reliable biomarkers to diagnose such diseases is more critical than ever. In addition, biomarkers could be used not only to diagnose diseases but also to monitor the development of disease therapeutics. Urine is an excellent biofluid that can be utilized as a source of biomarker to diagnose not only several renal diseases but also other diseases because of its abundance in invasive sampling. However, urine was conventionally regarded as inappropriate as a source of biomarker for neurodegenerative diseases because it is anatomically distant from the central nervous system (CNS), a major pathologic site of NDD, in comparison to other biofluids such as cerebrospinal fluid (CSF) and plasma. However, recent studies have suggested that urine could be utilized as a source of NDD biomarker if an appropriate marker is predetermined by metabolomic and proteomic approaches in urine and other samples. In this review, we summarize such studies related to NDD.
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Affiliation(s)
- Wongi Seol
- InAm Neuroscience Research Center, Gunpo 15865, Korea
| | - Hyejung Kim
- InAm Neuroscience Research Center, Gunpo 15865, Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Gunpo 15865, Korea
- Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
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21
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O'Brien K, Breyne K, Ughetto S, Laurent LC, Breakefield XO. RNA delivery by extracellular vesicles in mammalian cells and its applications. Nat Rev Mol Cell Biol 2020; 21:585-606. [PMID: 32457507 PMCID: PMC7249041 DOI: 10.1038/s41580-020-0251-y] [Citation(s) in RCA: 962] [Impact Index Per Article: 240.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
The term 'extracellular vesicles' refers to a heterogeneous population of vesicular bodies of cellular origin that derive either from the endosomal compartment (exosomes) or as a result of shedding from the plasma membrane (microvesicles, oncosomes and apoptotic bodies). Extracellular vesicles carry a variety of cargo, including RNAs, proteins, lipids and DNA, which can be taken up by other cells, both in the direct vicinity of the source cell and at distant sites in the body via biofluids, and elicit a variety of phenotypic responses. Owing to their unique biology and roles in cell-cell communication, extracellular vesicles have attracted strong interest, which is further enhanced by their potential clinical utility. Because extracellular vesicles derive their cargo from the contents of the cells that produce them, they are attractive sources of biomarkers for a variety of diseases. Furthermore, studies demonstrating phenotypic effects of specific extracellular vesicle-associated cargo on target cells have stoked interest in extracellular vesicles as therapeutic vehicles. There is particularly strong evidence that the RNA cargo of extracellular vesicles can alter recipient cell gene expression and function. During the past decade, extracellular vesicles and their RNA cargo have become better defined, but many aspects of extracellular vesicle biology remain to be elucidated. These include selective cargo loading resulting in substantial differences between the composition of extracellular vesicles and source cells; heterogeneity in extracellular vesicle size and composition; and undefined mechanisms for the uptake of extracellular vesicles into recipient cells and the fates of their cargo. Further progress in unravelling the basic mechanisms of extracellular vesicle biogenesis, transport, and cargo delivery and function is needed for successful clinical implementation. This Review focuses on the current state of knowledge pertaining to packaging, transport and function of RNAs in extracellular vesicles and outlines the progress made thus far towards their clinical applications.
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Affiliation(s)
- Killian O'Brien
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefano Ughetto
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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22
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Al Ali J, Vaine CA, Shah S, Campion L, Hakoum A, Supnet ML, Acuña P, Aldykiewicz G, Multhaupt-Buell T, Ganza NGM, Lagarde JBB, De Guzman JK, Go C, Currall B, Trombetta B, Webb PK, Talkowski M, Arnold SE, Cheah PS, Ito N, Sharma N, Bragg DC, Ozelius L, Breakefield XO. TAF1 Transcripts and Neurofilament Light Chain as Biomarkers for X-linked Dystonia-Parkinsonism. Mov Disord 2020; 36:206-215. [PMID: 32975318 PMCID: PMC7891430 DOI: 10.1002/mds.28305] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background X‐linked dystonia‐parkinsonism is a rare neurological disease endemic to the Philippines. Dystonic symptoms appear in males at the mean age of 40 years and progress to parkinsonism with degenerative pathology in the striatum. A retrotransposon inserted in intron 32 of the TAF1 gene leads to alternative splicing in the region and a reduction of the full‐length mRNA transcript. Objectives The objective of this study was to discover cell‐based and biofluid‐based biomarkers for X‐linked dystonia‐parkinsonism. Methods RNA from patient‐derived neural progenitor cells and their secreted extracellular vesicles were used to screen for dysregulation of TAF1 expression. Droplet‐digital polymerase chain reaction was used to quantify the expression of TAF1 mRNA fragments 5′ and 3′ to the retrotransposon insertion and the disease‐specific splice variant TAF1‐32i in whole‐blood RNA. Plasma levels of neurofilament light chain were measured using single‐molecule array. Results In neural progenitor cells and their extracellular vesicles, we confirmed that the TAF1‐3′/5′ ratio was lower in patient samples, whereas TAF1‐32i expression is higher relative to controls. In whole‐blood RNA, both TAF1‐3′/5′ ratio and TAF1‐32i expression can differentiate patient (n = 44) from control samples (n = 18) with high accuracy. Neurofilament light chain plasma levels were significantly elevated in patients (n = 43) compared with both carriers (n = 16) and controls (n = 21), with area under the curve of 0.79. Conclusions TAF1 dysregulation in blood serves as a disease‐specific biomarker that could be used as a readout for monitoring therapies targeting TAF1 splicing. Neurofilament light chain could be used in monitoring neurodegeneration and disease progression in patients. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jamal Al Ali
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Christine A Vaine
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Shivangi Shah
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Lindsey Campion
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Ahmad Hakoum
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Melanie L Supnet
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Patrick Acuña
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Sunshine Care Foundation, Roxas City, Philippines
| | - Gabrielle Aldykiewicz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Trisha Multhaupt-Buell
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | | | | | - Jan K De Guzman
- Sunshine Care Foundation, Roxas City, Philippines.,Department of Neurology, Jose R. Reyes Memorial Medical Center, Metro Manila, Philippines
| | - Criscely Go
- Department of Neurology, Jose R. Reyes Memorial Medical Center, Metro Manila, Philippines
| | - Benjamin Currall
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Center for Genomic Medicine, Mass General Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bianca Trombetta
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Pia K Webb
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Michael Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Genomic Medicine, Mass General Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Pike S Cheah
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Naoto Ito
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Laurie Ozelius
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
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23
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Wu D, Ji C, Chen Z, Wang K. Novel NEXMIF gene pathogenic variant in a female patient with refractory epilepsy and intellectual disability. Am J Med Genet A 2020; 182:2765-2772. [PMID: 32924309 DOI: 10.1002/ajmg.a.61848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022]
Abstract
We identified a novel nonsense de novo pathogenic variant of the NEXMIF gene in a 29 year-old female patient with refractory epilepsy and mild intellectual disability. The patient presented with episodic atypical absence status (AS), the longest duration of her seizures was approximately 36 hr. She also had occasional eyelid myoclonia during absence seizure. EEG highlighted a photosensitivity phenomenon and generalized epileptiform discharges that were induced by eye closure. Whole exome sequencing revealed a novel nonsense pathogenic variant c.1063delC (p.L355*) in exon 3 of the NEXMIF gene. The mRNA expression of NEXMIF in this female patient was below -2 SD from the mean of control group. In addition to adding a novel pathogenic variant type to the NEXMIF variant database and conducting mRNA studies, this report also describes a unique phenotype in a patient with atypical AS associated with a NEXMIF variant. We discuss implications for medication management in similar patients.
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Affiliation(s)
- Dengchang Wu
- Department of Neurology, First Affiliated Hospital, School of Medicine, Epilepsy Center, Zhejiang University, Hangzhou, China
| | - Caihong Ji
- Department of Neurology, First Affiliated Hospital, School of Medicine, Epilepsy Center, Zhejiang University, Hangzhou, China
| | - Zhongqin Chen
- Department of Neurology, First Affiliated Hospital, School of Medicine, Epilepsy Center, Zhejiang University, Hangzhou, China
| | - Kang Wang
- Department of Neurology, First Affiliated Hospital, School of Medicine, Epilepsy Center, Zhejiang University, Hangzhou, China
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24
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EMQN best practice guidelines for genetic testing in dystrophinopathies. Eur J Hum Genet 2020; 28:1141-1159. [PMID: 32424326 PMCID: PMC7608854 DOI: 10.1038/s41431-020-0643-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
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25
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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell 2020; 177:446-462.e16. [PMID: 30951671 DOI: 10.1016/j.cell.2019.03.024] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/29/2018] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.
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26
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Shields RK, Lee J, Buelow A, Petrie M, Dudley-Javoroski S, Cross S, Gutmann L, Nopoulos PC. Myotonic dystrophy type 1 alters muscle twitch properties, spinal reflexes, and perturbation-induced trans-cortical reflexes. Muscle Nerve 2019; 61:205-212. [PMID: 31773755 DOI: 10.1002/mus.26767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Neurophysiologic biomarkers are needed for clinical trials of therapies for myotonic dystrophy (DM1). We characterized muscle properties, spinal reflexes (H-reflexes), and trans-cortical long-latency reflexes (LLRs) in a cohort with mild/moderate DM1. METHODS Twenty-four people with DM1 and 25 matched controls underwent assessment of tibial nerve H-reflexes and soleus muscle twitch properties. Quadriceps LLRs were elicited by delivering an unexpected perturbation during a single-limb squat (SLS) visuomotor tracking task. RESULTS DM1 was associated with decreased H-reflex depression. The efficacy of doublet stimulation was enhanced, yielding an elevated double-single twitch ratio. DM1 participants demonstrated greater error during the SLS task. DM1 individuals with the least-robust LLR responses showed the greatest loss of spinal H-reflex depression. CONCLUSIONS DM1 is associated with abnormalities of muscle twitch properties. Co-occurring alterations of spinal and trans-cortical reflex properties underscore the central nervous system manifestations of this disorder and may assist in gauging efficacy during clinical trials.
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Affiliation(s)
- Richard K Shields
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jinhyun Lee
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Aaron Buelow
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Michael Petrie
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Shauna Dudley-Javoroski
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Stephen Cross
- Department of Psychiatry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Laurie Gutmann
- Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Peggy C Nopoulos
- Department of Psychiatry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
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27
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Thangarajh M, Zhang A, Gill K, Ressom HW, Li Z, Varghese RS, Hoffman EP, Nagaraju K, Hathout Y, Boca SM. Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne. PLoS One 2019; 14:e0219507. [PMID: 31310630 PMCID: PMC6634414 DOI: 10.1371/journal.pone.0219507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
Urine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we considered the mdx mice-a murine model of DMD-to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, a corticosteroid commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle control via liquid chromatography tandem mass spectrometry. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a metabolite with m/z = 357 and creatine, which were also reported in a previous human study looking at serum. Novel observations in this study included peaks identified as biliverdin and hypusine. These four metabolites were significantly higher at baseline in the urine of mdx mice compared to wild-type, and significantly changed their levels over time after baseline. Creatine and biliverdin levels were also different between treated and control groups, but for creatine this may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD or prednisolone treatment.
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Affiliation(s)
- Mathula Thangarajh
- Department of Neurology, George Washington University School of Medicine and Children’s National Health Systems, Washington, D.C., United States of America
| | - Aiping Zhang
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Children’s National Health Systems, Washington, D.C., United States of America
| | - Kirandeep Gill
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Habtom W. Ressom
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Zhenzhi Li
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Rency S. Varghese
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Eric P. Hoffman
- School of Pharmacy & Pharmaceutical Sciences, Binghamton University, Binghamton, N.Y., United States of America
| | - Kanneboyina Nagaraju
- School of Pharmacy & Pharmaceutical Sciences, Binghamton University, Binghamton, N.Y., United States of America
| | - Yetrib Hathout
- School of Pharmacy & Pharmaceutical Sciences, Binghamton University, Binghamton, N.Y., United States of America
| | - Simina M. Boca
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, D.C., United States of America
- Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, Washington, D.C., United States of America
- * E-mail:
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28
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Antoury L, Hu N, Darras B, Wheeler TM. Urine mRNA to identify a novel pseudoexon causing dystrophinopathy. Ann Clin Transl Neurol 2019; 6:1106-1112. [PMID: 31211175 PMCID: PMC6562067 DOI: 10.1002/acn3.777] [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: 03/08/2019] [Accepted: 03/20/2019] [Indexed: 11/16/2022] Open
Abstract
In muscular dystrophies, identification of pathogenic pseudoexons involves sequencing of the target gene cDNA derived from muscle mRNA. Here we use a urine “liquid biopsy,” droplet digital PCR, and sequencing of PCR products to identify a novel cryptic splice site in DMD intron 67 that causes dystrophinopathy. Pseudoexon inclusion is 35% in urine cells, 34% in urine extracellular RNA (exRNA), and 54% in muscle biopsy tissue, but absent in serum exRNA. Our results suggest that cryptic splice site use varies depending on the RNA source, and that urine RNA has the potential to substitute for muscle biopsies to identify DMD pseudoexons.
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Affiliation(s)
- Layal Antoury
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
| | - Ningyan Hu
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
| | - Basil Darras
- Harvard Medical School Boston Massachusetts.,Department of Neurology Boston Children's Hospital Boston Massachusetts
| | - Thurman M Wheeler
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
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29
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Voellenkle C, Perfetti A, Carrara M, Fuschi P, Renna LV, Longo M, Sain SB, Cardani R, Valaperta R, Silvestri G, Legnini I, Bozzoni I, Furling D, Gaetano C, Falcone G, Meola G, Martelli F. Dysregulation of Circular RNAs in Myotonic Dystrophy Type 1. Int J Mol Sci 2019; 20:ijms20081938. [PMID: 31010208 PMCID: PMC6515344 DOI: 10.3390/ijms20081938] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Circular RNAs (circRNAs) constitute a recently re-discovered class of non-coding RNAs functioning as sponges for miRNAs and proteins, affecting RNA splicing and regulating transcription. CircRNAs are generated by “back-splicing”, which is the linking covalently of 3′- and 5′-ends of exons. Thus, circRNA levels might be deregulated in conditions associated with altered RNA-splicing. Significantly, growing evidence indicates their role in human diseases. Specifically, myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by expanded CTG repeats in the DMPK gene which results in abnormal mRNA-splicing. In this investigation, circRNAs expressed in DM1 skeletal muscles were identified by analyzing RNA-sequencing data-sets followed by qPCR validation. In muscle biopsies, out of nine tested, four transcripts showed an increased circular fraction: CDYL, HIPK3, RTN4_03, and ZNF609. Their circular fraction values correlated with skeletal muscle strength and with splicing biomarkers of disease severity, and displayed higher values in more severely affected patients. Moreover, Receiver-Operating-Characteristics curves of these four circRNAs discriminated DM1 patients from controls. The identified circRNAs were also detectable in peripheral-blood-mononuclear-cells (PBMCs) and the plasma of DM1 patients, but they were not regulated significantly. Finally, increased circular fractions of RTN4_03 and ZNF609 were also observed in differentiated myogenic cell lines derived from DM1 patients. In conclusion, this pilot study identified circRNA dysregulation in DM1 patients.
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Affiliation(s)
- Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Laura Valentina Renna
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Marialucia Longo
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Simona Baghai Sain
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Rosanna Cardani
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Rea Valaperta
- Research Laboratories, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Gabriella Silvestri
- Department of Geriatrics, Orthopaedic and Neuroscience, Institute of Neurology, Catholic University of Sacred Heart, Fondazione Policlinico Gemelli, 00168 Rome, Italy.
| | - Ivano Legnini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Irene Bozzoni
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Denis Furling
- Sorbonne Université, INSERM, Association Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France.
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri, 27100 Pavia, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Giovanni Meola
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
- Department of Neurology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
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Takizawa H, Hara Y, Mizobe Y, Ohno T, Suzuki S, Inoue K, Takeshita E, Shimizu-Motohashi Y, Ishiyama A, Hoshino M, Komaki H, Takeda S, Aoki Y. Modelling Duchenne muscular dystrophy in MYOD1-converted urine-derived cells treated with 3-deazaneplanocin A hydrochloride. Sci Rep 2019; 9:3807. [PMID: 30846748 PMCID: PMC6405839 DOI: 10.1038/s41598-019-40421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe muscle disorder characterised by mutations in the DMD gene. Recently, we have completed a phase I study in Japan based on systemic administration of the morpholino antisense that is amenable to exon-53 skipping, successfully. However, to achieve the effective treatment of DMD, in vitro assays on patient muscle cells to screen drugs and patient eligibility before clinical trials are indispensable. Here, we report a novel MYOD1-converted, urine-derived cells (UDCs) as a novel DMD muscle cell model. We discovered that 3-deazaneplanocin A hydrochloride, a histone methyltransferase inhibitor, could significantly promote MYOGENIN expression and myotube differentiation. We also demonstrated that our system, based on UDCs from DMD patients, could be used successfully to evaluate exon-skipping drugs targeting DMD exons including 44, 50, 51, and 55. This new autologous UDC-based disease modelling could lead to the application of precision medicine for various muscle diseases.
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Affiliation(s)
- Hotake Takizawa
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuko Hara
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yoshitaka Mizobe
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Taisuke Ohno
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Sadafumi Suzuki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yuko Shimizu-Motohashi
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Mikio Hoshino
- Department of Biochemistry & Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan. .,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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31
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Non-invasive monitoring of alternative splicing outcomes to identify candidate therapies for myotonic dystrophy type 1. Nat Commun 2018; 9:5227. [PMID: 30531949 PMCID: PMC6286378 DOI: 10.1038/s41467-018-07517-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/07/2018] [Indexed: 01/16/2023] Open
Abstract
During drug development, tissue samples serve as indicators of disease activity and pharmacodynamic responses. Reliable non-invasive measures of drug target engagement will facilitate identification of promising new treatments. Here we develop and validate a novel bi-transgenic mouse model of myotonic dystrophy type 1 (DM1) in which expression of either DsRed or GFP is determined by alternative splicing of an upstream minigene that is mis-regulated in DM1. Using a novel in vivo fluorescence spectroscopy system, we show that quantitation of the DsRed/GFP ratio provides an accurate estimation of splicing outcomes in muscle tissue of live mice that nearly doubles throughput over conventional fluorescence imaging techniques. Serial in vivo spectroscopy measurements in mice treated with a C16 fatty acid ligand conjugated antisense (LICA) oligonucleotide reveal a dose-dependent therapeutic response within seven days, confirm a several-week duration of action, and demonstrate a two-fold greater target engagement as compared to the unconjugated parent oligonucleotide.
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