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Bernou C, Mouthon MA, Daynac M, Kortulewski T, Demaille B, Barroca V, Couillard-Despres S, Dechamps N, Ménard V, Bellenger L, Antoniewski C, Chicheportiche AD, Boussin FD. Switching of RNA splicing regulators in immature neuroblasts during adult neurogenesis. eLife 2024; 12:RP87083. [PMID: 39576691 PMCID: PMC11584179 DOI: 10.7554/elife.87083] [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] [Indexed: 11/24/2024] Open
Abstract
The lateral wall of the mouse subventricular zone harbors neural stem cells (NSC, B cells) which generate proliferating transient-amplifying progenitors (TAP, C cells) that ultimately give rise to neuroblasts (NB, A cells). Molecular profiling at the single-cell level struggles to distinguish these different cell types. Here, we combined transcriptome analyses of FACS-sorted cells and single-cell RNAseq to demonstrate the existence of an abundant, clonogenic and multipotent population of immature neuroblasts (iNB cells) at the transition between TAP and migrating NB (mNB). iNB are reversibly engaged in neuronal differentiation. Indeed, they keep molecular features of both undifferentiated progenitors, plasticity and unexpected regenerative properties. Strikingly, they undergo important progressive molecular switches, including changes in the expression of splicing regulators leading to their differentiation in mNB subdividing them into two subtypes, iNB1 and iNB2. Due to their plastic properties, iNB could represent a new target for regenerative therapy of brain damage.
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Affiliation(s)
- Corentin Bernou
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Marc-André Mouthon
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Mathieu Daynac
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Thierry Kortulewski
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Benjamin Demaille
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Vilma Barroca
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Sebastien Couillard-Despres
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Institute of Experimental Neuroregeneration, Paracelsus Medical University, Salzburg, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Nathalie Dechamps
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Véronique Ménard
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - Léa Bellenger
- Inserm, ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Alexandra Déborah Chicheportiche
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
| | - François Dominique Boussin
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRP/iRCM, Fontenay-aux-Roses, France
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2
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Zeng X, Wu C, Zhang L, Lan L, Fu W, Wang S. Molecular Mechanism of Resistance to Alternaria alternata Apple Pathotype in Apple by Alternative Splicing of Transcription Factor MdMYB6-like. Int J Mol Sci 2024; 25:4353. [PMID: 38673937 PMCID: PMC11050356 DOI: 10.3390/ijms25084353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
As a fruit tree with great economic value, apple is widely cultivated in China. However, apple leaf spot disease causes significant damage to apple quality and economic value. In our study, we found that MdMYB6-like is a transcription factor without auto-activation activity and with three alternative spliced variants. Among them, MdMYB6-like-β responded positively to the pathogen infection. Overexpression of MdMYB6-like-β increased the lignin content of leaves and improved the pathogenic resistance of apple flesh callus. In addition, all three alternative spliced variants of MdMYB6-like could bind to the promoter of MdBGLU H. Therefore, we believe that MdMYB6-like plays an important role in the infection process of the pathogen and lays a solid foundation for breeding disease-resistant cultivars of apple in the future.
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Affiliation(s)
| | | | | | | | | | - Sanhong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.Z.); (C.W.); (L.Z.); (L.L.); (W.F.)
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3
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Li X, He G, Jiang S, Yang C, Yang B, Ming F. Function of two splicing variants of RcCPR5 in the resistance of Rosa chinensis to powdery mildew. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111678. [PMID: 37385384 DOI: 10.1016/j.plantsci.2023.111678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 07/01/2023]
Abstract
Rosa chinensis is an important economic and ornamental crop, but powdery mildew greatly reduces its ornamental and economic value. The RcCPR5 gene, encoding a constitutive expressor of pathogenesis-related genes, has two splicing variants in R. chinensis. Compared with RcCPR5-1, RcCPR5-2 has a large C-terminal deletion. During disease development, RcCPR5-2 responded quickly and coordinated with RcCPR5-1 to resist the invasion of the powdery mildew pathogen. In virus-induced gene silencing experiments, down-regulation of RcCPR5 improved the resistance of R. chinensis to powdery mildew. This was confirmed to be broad-spectrum resistance. In the absence of pathogen infection, RcCPR5-1 and RcCPR5-2 formed homodimers and heterodimers to regulate plant growth; but when infected by the powdery mildew pathogen, the RcCPR5-1 and RcCPR5-2 complexes disassociated and released RcSIM/RcSMR to induce effector-triggered immunity, thereby inducing resistance to pathogen infection.
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Affiliation(s)
- Xiaorui Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Guoren He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shenghang Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chun Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Binan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
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4
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Chikhale R, Sinha SK, Wanjari M, Gurav NS, Ayyanar M, Prasad S, Khanal P, Dey YN, Patil RB, Gurav SS. Computational assessment of saikosaponins as adjuvant treatment for COVID-19: molecular docking, dynamics, and network pharmacology analysis. Mol Divers 2021; 25:1889-1904. [PMID: 33492566 PMCID: PMC7829483 DOI: 10.1007/s11030-021-10183-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/06/2021] [Indexed: 12/29/2022]
Abstract
Saikosaponins are major biologically active triterpenoids, usually as glucosides, isolated from Traditional Chinese Medicines (TCM) such as Bupleurum spp., Heteromorpha spp., and Scrophularia scorodonia with their antiviral and immunomodulatory potential. This investigation presents molecular docking, molecular dynamics simulation, and free energy calculation studies of saikosaponins as adjuvant therapy in the treatment for COVID19. Molecular docking studies for 23 saikosaponins on the crystal structures of the extracellular domains of human lnterleukin-6 receptor (IL6), human Janus Kinase-3 (JAK3), and dehydrogenase domain of Cylindrospermum stagnale NADPH-oxidase 5 (NOX5) were performed, and selected protein-ligand complexes were subjected to 100 ns molecular dynamics simulations. The molecular dynamics trajectories were subjected to free energy calculation by the MM-GBSA method. Molecular docking and molecular dynamics simulation studies revealed that IL6 in complex with Saikosaponin_U and Saikosaponin_V, JAK3 in complex with Saikosaponin_B4 and Saikosaponin_I, and NOX5 in complex with Saikosaponin_BK1 and Saikosaponin_C have good docking and molecular dynamics profiles. However, the Janus Kinase-3 is the best interacting partner for the saikosaponin compounds. The network pharmacology analysis suggests saikosaponins interact with the proteins CAT Gene CAT (Catalase) and Checkpoint kinase 1 (CHEK1); both of these enzymes play a major role in cell homeostasis and DNA damage during infection, suggesting a possible improvement in immune response toward COVID-19.
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Affiliation(s)
- Rupesh Chikhale
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Saurabh K Sinha
- Department of Pharmaceutical Sciences, Mohanlal Shukhadia University, Udaipur, Rajasthan, 313 001, India
| | - Manish Wanjari
- Regional Ayurveda Research Institute for Drug Development, Gwalior, Madhya Pradesh, 474009, India
| | - Nilambari S Gurav
- PES's Rajaram and Tarabai Bandekar College of Pharmacy, Goa University, Ponda, Goa, 403401, India
| | - Muniappan Ayyanar
- Department of Botany, A. Veeriya Vandayar Memorial Sri Pushpam College (Autonomous), Affiliated To Bharathidasan University, Poondi, Thanjavur, 613 503, India
| | - Satyendra Prasad
- Department of Pharmaceutical Sciences, R.T.M. University, Nagpur, Maharashtra, 440033, India
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
| | - Yadu Nandan Dey
- School of Pharmaceutical Technology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Rajesh B Patil
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy, Pune, Maharashtra, India.
| | - Shailendra S Gurav
- Department of Pharmacognosy and Phytochemistry, Goa College of Pharmacy, Goa University, Panaji, Goa, 403 001, India.
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5
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Ali A, Thorgaard GH, Salem M. PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes. Front Genet 2021; 12:683408. [PMID: 34335690 PMCID: PMC8321248 DOI: 10.3389/fgene.2021.683408] [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: 03/20/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Gary H. Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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6
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Wang Y, Xu C, Ma L, Mou Y, Zhang B, Zhou S, Tian Y, Trinh J, Zhang X, Li XJ. Drug screening with human SMN2 reporter identifies SMN protein stabilizers to correct SMA pathology. Life Sci Alliance 2019; 2:2/2/e201800268. [PMID: 30910806 PMCID: PMC6435041 DOI: 10.26508/lsa.201800268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 01/14/2023] Open
Abstract
Spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, is caused by reduced levels of functional survival motor neuron (SMN) protein. To identify therapeutic agents for SMA, we established a versatile SMN2-GFP reporter line by targeting the human SMN2 gene. We then screened a compound library and identified Z-FA-FMK as a potent candidate. Z-FA-FMK, a cysteine protease inhibitor, increased functional SMN through inhibiting the protease-mediated degradation of both full-length and exon 7-deleted forms of SMN. Further studies reveal that CAPN1, CAPN7, CTSB, and CTSL mediate the degradation of SMN proteins, providing novel targets for SMA. Notably, Z-FA-FMK mitigated mitochondriopathy and neuropathy in SMA patient-derived motor neurons and showed protective effects in SMA animal model after intracerebroventricular injection. E64d, another cysteine protease inhibitor which can pass through the blood-brain barrier, showed even more potent therapeutic effects after subcutaneous delivery to SMA mice. Taken together, we have successfully established a human SMN2 reporter for future drug discovery and identified the potential therapeutic value of cysteine protease inhibitors in treating SMA via stabilizing SMN proteins.
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Affiliation(s)
- Yiran Wang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chongchong Xu
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Lin Ma
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai, China.,Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University, School of Medicine, Shanghai, China
| | - Yongchao Mou
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Bowen Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shanshan Zhou
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yue Tian
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jessica Trinh
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA
| | - Xiaoqing Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China .,Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai, China.,Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University, School of Medicine, Shanghai, China.,Tsingtao Advanced Research Institute, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China.,Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue-Jun Li
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA .,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
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7
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Cheung AK, Hurley B, Kerrigan R, Shu L, Chin DN, Shen Y, O'Brien G, Sung MJ, Hou Y, Axford J, Cody E, Sun R, Fazal A, Fridrich C, Sanchez CC, Tomlinson RC, Jain M, Deng L, Hoffmaster K, Song C, Van Hoosear M, Shin Y, Servais R, Towler C, Hild M, Curtis D, Dietrich WF, Hamann LG, Briner K, Chen KS, Kobayashi D, Sivasankaran R, Dales NA. Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA). J Med Chem 2018; 61:11021-11036. [PMID: 30407821 DOI: 10.1021/acs.jmedchem.8b01291] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinal muscular atrophy (SMA), a rare neuromuscular disorder, is the leading genetic cause of death in infants and toddlers. SMA is caused by the deletion or a loss of function mutation of the survival motor neuron 1 (SMN1) gene. In humans, a second closely related gene SMN2 exists; however it codes for a less stable SMN protein. In recent years, significant progress has been made toward disease modifying treatments for SMA by modulating SMN2 pre-mRNA splicing. Herein, we describe the discovery of LMI070/branaplam, a small molecule that stabilizes the interaction between the spliceosome and SMN2 pre-mRNA. Branaplam (1) originated from a high-throughput phenotypic screening hit, pyridazine 2, and evolved via multiparameter lead optimization. In a severe mouse SMA model, branaplam treatment increased full-length SMN RNA and protein levels, and extended survival. Currently, branaplam is in clinical studies for SMA.
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Affiliation(s)
- Atwood K Cheung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Brian Hurley
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ryan Kerrigan
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lei Shu
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Donovan N Chin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yiping Shen
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Gary O'Brien
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Moo Je Sung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ying Hou
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jake Axford
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Emma Cody
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Robert Sun
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cary Fridrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Carina C Sanchez
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ronald C Tomlinson
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Monish Jain
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lin Deng
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Keith Hoffmaster
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cheng Song
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Mailin Van Hoosear
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Youngah Shin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Rebecca Servais
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Christopher Towler
- Novartis Pharmaceuticals , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Marc Hild
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Daniel Curtis
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - William F Dietrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lawrence G Hamann
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karen S Chen
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Dione Kobayashi
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Natalie A Dales
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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8
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Zhao X, Feng Z, Ling KKY, Mollin A, Sheedy J, Yeh S, Petruska J, Narasimhan J, Dakka A, Welch EM, Karp G, Chen KS, Metzger F, Ratni H, Lotti F, Tisdale S, Naryshkin NA, Pellizzoni L, Paushkin S, Ko CP, Weetall M. Pharmacokinetics, pharmacodynamics, and efficacy of a small-molecule SMN2 splicing modifier in mouse models of spinal muscular atrophy. Hum Mol Genet 2016; 25:1885-1899. [PMID: 26931466 PMCID: PMC5062580 DOI: 10.1093/hmg/ddw062] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/22/2016] [Indexed: 12/26/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by the loss or mutation of both copies of the survival motor neuron 1 (SMN1) gene. The related SMN2 gene is retained, but due to alternative splicing of exon 7, produces insufficient levels of the SMN protein. Here, we systematically characterize the pharmacokinetic and pharmacodynamics properties of the SMN splicing modifier SMN-C1. SMN-C1 is a low-molecular weight compound that promotes the inclusion of exon 7 and increases production of SMN protein in human cells and in two transgenic mouse models of SMA. Furthermore, increases in SMN protein levels in peripheral blood mononuclear cells and skin correlate with those in the central nervous system (CNS), indicating that a change of these levels in blood or skin can be used as a non-invasive surrogate to monitor increases of SMN protein levels in the CNS. Consistent with restored SMN function, SMN-C1 treatment increases the levels of spliceosomal and U7 small-nuclear RNAs and corrects RNA processing defects induced by SMN deficiency in the spinal cord of SMNΔ7 SMA mice. A 100% or greater increase in SMN protein in the CNS of SMNΔ7 SMA mice robustly improves the phenotype. Importantly, a ∼50% increase in SMN leads to long-term survival, but the SMA phenotype is only partially corrected, indicating that certain SMA disease manifestations may respond to treatment at lower doses. Overall, we provide important insights for the translation of pre-clinical data to the clinic and further therapeutic development of this series of molecules for SMA treatment.
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Affiliation(s)
- Xin Zhao
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Zhihua Feng
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Karen K Y Ling
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna Mollin
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | | | - Shirley Yeh
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | | | | | - Amal Dakka
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Ellen M Welch
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Gary Karp
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Karen S Chen
- SMA Foundation, 888 Seventh Avenue, Suite 400, New York, NY 10019, USA
| | - Friedrich Metzger
- F. Hoffmann-La Roche, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Hasane Ratni
- F. Hoffmann-La Roche, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Francesco Lotti
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA and
| | - Sarah Tisdale
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA and
| | | | - Livio Pellizzoni
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA and
| | - Sergey Paushkin
- SMA Foundation, 888 Seventh Avenue, Suite 400, New York, NY 10019, USA
| | - Chien-Ping Ko
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA,
| | - Marla Weetall
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA,
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9
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2015; 11:511-7. [PMID: 26030728 DOI: 10.1038/nchembio.1837] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/06/2015] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric mortality. A duplicate copy (SMN2) is inefficiently spliced, producing a truncated and unstable protein. We describe herein a potent, orally active, small-molecule enhancer of SMN2 splicing that elevates full-length SMN protein and extends survival in a severe SMA mouse model. We demonstrate that the molecular mechanism of action is via stabilization of the transient double-strand RNA structure formed by the SMN2 pre-mRNA and U1 small nuclear ribonucleic protein (snRNP) complex. The binding affinity of U1 snRNP to the 5' splice site is increased in a sequence-selective manner, discrete from constitutive recognition. This new mechanism demonstrates the feasibility of small molecule-mediated, sequence-selective splice modulation and the potential for leveraging this strategy in other splicing diseases.
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Affiliation(s)
- James Palacino
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Susanne E Swalley
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Cheng Song
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Atwood K Cheung
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lei Shu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaolu Zhang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mailin Van Hoosear
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Youngah Shin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Donovan N Chin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Martin Beibel
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Nicole A Renaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Thomas M Smith
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael Salcius
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaoying Shi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Rebecca Servais
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Monish Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lin Deng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Caroline Bullock
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael McLellan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Leo Murphy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Cecile Blaustein
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Frada Berenshteyn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Arnaud Lacoste
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jason R Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Gregory A Michaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Brian S Tseng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jeffery A Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - John A Tallarico
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lawrence G Hamann
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Daniel Curtis
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mark C Fishman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - William F Dietrich
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Natalie A Dales
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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10
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Järver P, Zaghloul EM, Arzumanov AA, Saleh AF, McClorey G, Hammond SM, Hällbrink M, Langel Ü, Smith CIE, Wood MJA, Gait MJ, El Andaloussi S. Peptide nanoparticle delivery of charge-neutral splice-switching morpholino oligonucleotides. Nucleic Acid Ther 2015; 25:65-77. [PMID: 25594433 PMCID: PMC4376484 DOI: 10.1089/nat.2014.0511] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oligonucleotide analogs have provided novel therapeutics targeting various disorders. However, their poor cellular uptake remains a major obstacle for their clinical development. Negatively charged oligonucleotides, such as 2′-O-Methyl RNA and locked nucleic acids have in recent years been delivered successfully into cells through complex formation with cationic polymers, peptides, liposomes, or similar nanoparticle delivery systems. However, due to the lack of electrostatic interactions, this promising delivery method has been unsuccessful to date using charge-neutral oligonucleotide analogs. We show here that lipid-functionalized cell-penetrating peptides can be efficiently exploited for cellular transfection of the charge-neutral oligonucleotide analog phosphorodiamidate morpholino. The lipopeptides form complexes with splice-switching phosphorodiamidate morpholino oligonucleotide and can be delivered into clinically relevant cell lines that are otherwise difficult to transfect while retaining biological activity. To our knowledge, this is the first study to show delivery through complex formation of biologically active charge-neutral oligonucleotides by cationic peptides.
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Affiliation(s)
- Peter Järver
- 1 Medical Research Council , Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
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11
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Abstract
Rice is a monocot gramineous crop, and one of the most important staple foods. Rice is considered a model species for most gramineous crops. Extensive research on rice has provided critical guidance for other crops, such as maize and wheat. In recent years, climate change and exacerbated soil degradation have resulted in a variety of abiotic stresses, such as greenhouse effects, lower temperatures, drought, floods, soil salinization and heavy metal pollution. As such, there is an extremely high demand for additional research, in order to address these negative factors. Studies have shown that the alternative splicing of many genes in rice is affected by stress conditions, suggesting that manipulation of the alternative splicing of specific genes may be an effective approach for rice to adapt to abiotic stress. With the advancement of microarrays, and more recently, next generation sequencing technology, several studies have shown that more than half of the genes in the rice genome undergo alternative splicing. This mini-review summarizes the latest progress in the research of splicing and alternative splicing in rice, compared to splicing in humans. Furthermore, we discuss how additional studies may change the landscape of investigation of rice functional genomics and genetically improved rice. [BMB Reports 2013; 46(9): 439-447]
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Affiliation(s)
- Zhiguo E
- Nantong University, Nantong 226001, P.R. China ;
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12
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Cho S, Moon H, Loh TJ, Oh HK, Williams DR, Liao DJ, Zhou J, Green MR, Zheng X, Shen H. PSF contacts exon 7 of SMN2 pre-mRNA to promote exon 7 inclusion. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:517-25. [PMID: 24632473 DOI: 10.1016/j.bbagrm.2014.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 12/23/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease and a leading cause of infant mortality. Deletions or mutations of SMN1 cause SMA, a gene that encodes a SMN protein. SMN is important for the assembly of Sm proteins onto UsnRNA to UsnRNP. SMN has also been suggested to direct axonal transport of β-actin mRNA in neurons. Humans contain a second SMN gene called SMN2 thus SMA patients produce some SMN but not with sufficient levels. The majority of SMN2 mRNA does not include exon 7. Here we show that increased expression of PSF promotes inclusion of exon 7 in the SMN2 whereas reduced expression of PSF promotes exon 7 skipping. In addition, we present evidence showing that PSF interacts with the GAAGGA enhancer in exon 7. We also demonstrate that a mutation in this enhancer abolishes the effects of PSF on exon 7 splicing. Furthermore we show that the RNA target sequences of PSF and tra2β in exon 7 are partially overlapped. These results lead us to conclude that PSF interacts with an enhancer in exon 7 to promote exon 7 splicing of SMN2 pre-mRNA.
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Affiliation(s)
- Sunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Heegyum Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyun Kyung Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Darren Reese Williams
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - D Joshua Liao
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | | | - Michael R Green
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
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13
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Cho S, Moon H, Loh TJ, Oh HK, Cho S, Choy HE, Song WK, Chun JS, Zheng X, Shen H. hnRNP M facilitates exon 7 inclusion of SMN2 pre-mRNA in spinal muscular atrophy by targeting an enhancer on exon 7. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:306-15. [PMID: 24533984 DOI: 10.1016/j.bbagrm.2014.02.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 12/24/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease, which causes death of motor neurons in the anterior horn of the spinal cord. Genetic cause of SMA is the deletion or mutation of SMN1 gene, which encodes the SMN protein. Although SMA patients include SMN2 gene, a duplicate of SMN1 gene, predominant production of exon 7 skipped isoform from SMN2 pre-mRNA, fails to rescue SMA patients. Here we show that hnRNP M, a member of hnRNP protein family, when knocked down, promotes exon 7 skipping of both SMN2 and SMN1 pre-mRNA. By contrast, overexpression of hnRNP M promotes exon 7 inclusion of both SMN2 and SMN1 pre-mRNA. Significantly, hnRNP M promotes exon 7 inclusion in SMA patient cells. Thus, we conclude that hnRNP M promotes exon 7 inclusion of both SMN1 and SMN2 pre-mRNA. We also demonstrate that hnRNP M contacts an enhancer on exon 7, which was previously shown to provide binding site for tra2β. We present evidence that hnRNP M and tra2β contact overlapped sequence on exon 7 but with slightly different RNA sequence requirements. In addition, hnRNP M promotes U2AF65 recruitment on the flanking intron of exon 7. We conclude that hnRNP M promotes exon 7 inclusion of SMN1 and SMN2 pre-mRNA through targeting an enhancer on exon 7 through recruiting U2AF65. Our results provide a clue that hnRNP M is a potential therapeutic target for SMA.
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Affiliation(s)
- Sunghee Cho
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Heegyum Moon
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tiing Jen Loh
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Huyn Kyung Oh
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Sungchan Cho
- Bio-Therapeutics Research Institute, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do 363-883, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Dong-gu, Gwangju, Republic of Korea
| | - Woo Keun Song
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jang-Soo Chun
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Xuexiu Zheng
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Haihong Shen
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
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14
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Kim T, Kim JO, Oh JG, Hong SE, Kim DH. Pressure-overload cardiac hypertrophy is associated with distinct alternative splicing due to altered expression of splicing factors. Mol Cells 2014; 37:81-7. [PMID: 24552714 PMCID: PMC3907004 DOI: 10.14348/molcells.2014.2337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/18/2013] [Indexed: 01/05/2023] Open
Abstract
Chronic pressure-overload cardiac hypertrophy is associated with an increased risk of morbidity/mortality, largely due to maladaptive remodeling and dilatation that progresses to dilated cardiomyopathy. Alternative splicing is an important biological mechanism that generates proteomic complexity and diversity. The recent development of next-generation RNA sequencing has improved our understanding of the qualitative signatures associated with alternative splicing in various biological conditions. However, the role of alternative splicing in cardiac hypertrophy is yet unknown. The present study employed RNA-Seq and a bioinformatic approach to detect the RNA splicing regulatory elements involved in alternative splicing during pressure-overload cardiac hypertrophy. We found GC-rich exonic motifs that regulate intron retention in 5' UTRs and AT-rich exonic motifs that are involved in exclusion of the AT-rich elements that cause mRNA instability in 3' UTRs. We also identified motifs in the intronic regions involved in exon exclusion and inclusion, which predicted splicing factors that bind to these motifs. We found, through Western blotting, that the expression levels of three splicing factors, ESRP1, PTB and SF2/ASF, were significantly altered during cardiac hypertrophy. Collectively, the present results suggest that chronic pressure-overload hypertrophy is closely associated with distinct alternative splicing due to altered expression of splicing factors.
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Affiliation(s)
- Taeyong Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Jin Ock Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | | | - Seong-Eui Hong
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Do Han Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
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15
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Goldsmith T, Fuchs-Telem D, Israeli S, Sarig O, Padalon-Brauch G, Bergman R, Indelman M, Sprecher E, Nousbeck J. The sound of silence: autosomal recessive congenital ichthyosis caused by a synonymous mutation in ABCA12. Exp Dermatol 2013; 22:251-4. [PMID: 23528209 DOI: 10.1111/exd.12110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2013] [Indexed: 12/19/2022]
Abstract
Autosomal recessive congenital ichthyosis refers to a heterogeneous group of cornification disorders of major impact on patients' life. The disease has been linked so far to mutations in 8 distinct genes. We report a consanguineous family of Arab Muslim origin with several members displaying a severe form of congenital ichthyosiform erythroderma. Using a panel of polymorphic microsatellite markers, we identified a region of homozygosity shared by all patients on 2q34, in a region harbouring the ABCA12 gene. Direct sequencing of genomic DNA derived from a patient failed to reveal any obviously pathogenic change in the coding sequence of this gene. In contrast, cDNA sequence analysis revealed the existence of a 163-bp-long deletion in exon 24, thus pointing to a splicing defect. Careful reanalysis of the genomic DNA sequence revealed apart from several known single-nucleotide polymorphisms, a hitherto unreported homozygous synonymous mutation in exon 24 (c.3456G>A; p.S1152S), which was found to lead to the formation of a novel splicing acceptor site. Synonymous mutations have been shown to uncommonly cause inherited disorders in humans. Here, we present the first example of a congenital form of ichthyosis resulting from such a genetic defect.
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Affiliation(s)
- Tomer Goldsmith
- Department of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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16
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Saha A, Robertson ES. Impact of EBV essential nuclear protein EBNA-3C on B-cell proliferation and apoptosis. Future Microbiol 2013; 8:323-52. [PMID: 23464371 DOI: 10.2217/fmb.12.147] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For over 40 years, EBV infection has been implicated in the etiology of a variety of lymphoid malignancies with the exceptional ability to drive resting B cells to continuously proliferate by successfully overriding cellular apoptotic stimuli. EBV utilizes the normal physiology of B-cell differentiation to persist within the memory B-cell pool of the immunocompetent host and subsequently establishes a life-long latent infection. During latency, out of a subset of viral genes expressed, EBNA-3C is one of the essential antigens required for in vitro primary B-cell transformation. EBNA-3C acts as a transcriptional coregulator by interacting with various cellular and viral factors. For the last 10 years, we have been actively engaged in discerning the biological significance of these interactions and revealed that EBNA-3C primarily targets two important cellular pathways - cell cycle and apoptosis. This review aims to summarize our current knowledge on EBNA-3C-mediated functions and describe how EBNA-3C seizes these cellular pathways that eventually promote B-cell lymphomagenesis. A scrupulous understanding of the critical relationship between EBNA-3C and these cellular machineries will not only aid in elucidating EBV pathogenesis, but also largely facilitate the development of novel diagnostic, as well as therapeutic, strategies against a vast range of EBV-associated B-cell lymphomas.
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Affiliation(s)
- Abhik Saha
- Presidency University, Department of Biotechnology, 86/1, College Street, Kolkata-700073, West Bengal, India
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17
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Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013; 14:543. [PMID: 23937650 PMCID: PMC3751371 DOI: 10.1186/1471-2164-14-543] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/07/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV. RESULTS Novel EBV RNAs and RNA structures were identified by computational modeling and RNA-Seq analyses of EBV. Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the closely related Macacine herpesvirus 4 using the RNAz program discovered 265 regions with high probability of forming conserved RNA structures. Secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. The analysis of RNA-Seq data uncovered the first observation of a stable intronic sequence RNA (sisRNA) in EBV. The abundance of this sisRNA rivals that of the well-known and highly expressed EBV-encoded non-coding RNAs (EBERs). CONCLUSION This work identifies regions of the EBV genome likely to generate functional RNAs and RNA structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. Enhanced understanding of the EBV transcriptome will guide future experimental analyses of the discovered RNAs and RNA structures.
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Affiliation(s)
- Walter N Moss
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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18
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Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW. Alternative splicing for diseases, cancers, drugs, and databases. ScientificWorldJournal 2013; 2013:703568. [PMID: 23766705 PMCID: PMC3674688 DOI: 10.1155/2013/703568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023] Open
Abstract
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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19
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Verhaart IEC, Aartsma-Rus A. The effect of 6-thioguanine on alternative splicing and antisense-mediated exon skipping treatment for duchenne muscular dystrophy. PLOS CURRENTS 2012; 4. [PMID: 23259153 PMCID: PMC3523663 DOI: 10.1371/currents.md.597d700f92eaa70de261ea0d91821377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The severe muscle wasting disorder Duchenne muscular dystrophy (DMD) is caused by genetic defects in the DMD gene, leading to a complete absence of dystrophin protein. Of the therapeutic approaches addressing the underlying genetic defect, exon skipping through antisense oligonucleotides (AONs) is the closest to clinical application. Several strategies to improve the efficiency of this approach are currently being investigated, such as the use of small chemical compounds that improve AONmediated exon skipping levels. Recently, enhanced exon skipping in combination with a guanine analogue, 6-thioguanine (6TG) was reported for phosphorodiamidate morpholino oligomers (PMO). Here the effect of 6TG on the exon skipping efficacy of 2’-O-methyl phosphorothioate RNA (2OMePS) and PMO AONs in vitro and in vivo was further evaluated, as well as the effect of 6TG by itself. Results confirm an increase of exon skipping levels in vitro, however, in contrast to the previous report, no effect was observed in vivo. Importantly, 6TG treatment in vitro resulted in numerous additional DMD exon skipping events. This, in combination with the known cytotoxic effects of 6TG after incorporation in DNA, warrants reconsidering of the use of 6TG as enhancer of AON efficiency in DMD, were chronic treatment will be required.
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Affiliation(s)
- Ingrid E C Verhaart
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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20
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Gimba ER, Tilli TM. Human osteopontin splicing isoforms: known roles, potential clinical applications and activated signaling pathways. Cancer Lett 2012; 331:11-7. [PMID: 23246372 DOI: 10.1016/j.canlet.2012.12.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 12/18/2022]
Abstract
Human osteopontin is subject to alternative splicing, which generates three isoforms, termed OPNa, OPNb and OPNc. These variants show specific expression and roles in different cell contexts. We present an overview of current knowledge of the expression profile of human OPN splicing isoforms (OPN-SIs), their tissue-specific roles, and the pathways mediating their functional properties in different pathophysiological conditions. We also describe their putative application as biomarkers, and their potential use as therapeutic targets by using antibodies, oligonucleotides or siRNA molecules. This synthesis provides new clues for a better understanding of human OPN splice variants, their roles in normal and pathological conditions, and their possible clinical applications.
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Affiliation(s)
- E R Gimba
- Universidade Federal Fluminense/Polo Universitário de Rio das Ostras, Rua Recife s/n, CEP: 28890-000, Rio das Ostras, RJ, Brazil.
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Southwell AL, Skotte NH, Bennett CF, Hayden MR. Antisense oligonucleotide therapeutics for inherited neurodegenerative diseases. Trends Mol Med 2012; 18:634-43. [PMID: 23026741 DOI: 10.1016/j.molmed.2012.09.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/25/2012] [Accepted: 09/07/2012] [Indexed: 12/12/2022]
Abstract
The rising median age of our population and the age-dependent risk of neurodegeneration translate to exponentially increasing numbers of afflicted individuals in the coming years. Although symptomatic treatments are available for some neurodegenerative diseases, most are only moderately efficacious and are often associated with significant side effects. The development of small molecule, disease-modifying drugs has been hindered by complex pathogenesis and a failure to clearly define the rate-limiting steps in disease progression. An alternative approach is to directly target the mutant gene product or a defined causative protein. Antisense oligonucleotides (ASOs) - with their diverse functionality, high target specificity, and relative ease of central nervous system (CNS) delivery - are uniquely positioned as potential therapies for neurological diseases. Here we review the development of ASOs for the treatment of inherited neurodegenerative diseases.
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Affiliation(s)
- Amber L Southwell
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, V5Z 4H4, Canada.
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