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Tuttolomondo A, Simonetta I, Duro G, Pecoraro R, Miceli S, Colomba P, Zizzo C, Nucera A, Daidone M, Di Chiara T, Scaglione R, Della Corte V, Corpora F, Vogiatzis D, Pinto A. Inter-familial and intra-familial phenotypic variability in three Sicilian families with Anderson-Fabry disease. Oncotarget 2017; 8:61415-61424. [PMID: 28977874 PMCID: PMC5617434 DOI: 10.18632/oncotarget.18250] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/11/2017] [Indexed: 12/27/2022] Open
Abstract
Background Anderson-Fabry disease (AFD) is an inborn lysosomal enzymopathy resulting from the deficient or absent activity of the lysosomal exogalactohydrolase, α-galactosidase A. This deficiency, results in the altered metabolism of glycosphingolipids which leads to their accumulation in lysosomes, thus to cellular and vascular dysfunction. To date, numerous mutations (according to recent data more than 1000 mutations) have been reported in the GLA intronic and exonic mutations. Traditionally, clinical manifestations are more severe in affected hemizygous males than in females. Nevertheless, recent studies have described severe organ dysfunction in women. The aim of the study This study reports clinical, biochemical, and molecular findings of the members of three Sicilian families. The clinical history of these patients highlights a remarkable interfamilial and intrafamilial phenotypic variability which characterizes Fabry disease relative to target organs and severity of clinical manifestations. Discussion Our findings, in agreement with previous data, report a little genotype-phenotype correlation for the disease, suggesting that the wide phenotypic variability of Anderson-Fabry disease is not completely ascribable to different gene mutations but other factors and mechanisms seem to be involved in the pathogenesis and clinical expression of the disease. Moreover, this study emphasies the importance of pedigree analysis in the family of each proband for identifying other possibly affected relatives.
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Affiliation(s)
- Antonino Tuttolomondo
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Irene Simonetta
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Giovanni Duro
- CNR-IBIM: Institute of Biomedicine and Molecular Immunology "A. Monroy" Palermo, Palermo, Italy
| | - Rosaria Pecoraro
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Salvatore Miceli
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Paolo Colomba
- CNR-IBIM: Institute of Biomedicine and Molecular Immunology "A. Monroy" Palermo, Palermo, Italy
| | - Carmela Zizzo
- CNR-IBIM: Institute of Biomedicine and Molecular Immunology "A. Monroy" Palermo, Palermo, Italy
| | - Antonia Nucera
- Stroke Unit, Neurology, Saint Andrea Hospital, La Spezia, Italy.,Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada
| | - Mario Daidone
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Tiziana Di Chiara
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Rosario Scaglione
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Vittoriano Della Corte
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Francesca Corpora
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Danai Vogiatzis
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
| | - Antonio Pinto
- U.O.C di Medicina Interna con Stroke Care, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), University of Palermo, Palermo, Italy
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152
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Vaidyanathan V, Naidu V, Karunasinghe N, Jabed A, Pallati R, Marlow G, R. Ferguson L. SNP-SNP interactions as risk factors for aggressive prostate cancer. F1000Res 2017; 6:621. [PMID: 28580135 PMCID: PMC5437948 DOI: 10.12688/f1000research.11027.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2017] [Indexed: 12/23/2022] Open
Abstract
Prostate cancer (PCa) is one of the most significant male health concerns worldwide. Single nucleotide polymorphisms (SNPs) are becoming increasingly strong candidate biomarkers for identifying susceptibility to PCa. We identified a number of SNPs reported in genome-wide association analyses (GWAS) as risk factors for aggressive PCa in various European populations, and then defined SNP-SNP interactions, using PLINK software, with nucleic acid samples from a New Zealand cohort. We used this approach to find a gene x environment marker for aggressive PCa, as although statistically gene x environment interactions can be adjusted for, it is highly impossible in practicality, and thus must be incorporated in the search for a reliable biomarker for PCa. We found two intronic SNPs statistically significantly interacting with each other as a risk for aggressive prostate cancer on being compared to healthy controls in a New Zealand population.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, Auckland, New Zealand
| | - Vijay Naidu
- School of Engineering,Computer and Mathematical Sciences, Auckland University of Technology, Auckland, New Zealand
| | | | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland, New Zealand
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland, New Zealand
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, UK
| | - Lynnette R. Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, Auckland, New Zealand
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153
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Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017; 136:1113-1127. [PMID: 28429085 DOI: 10.1007/s00439-017-1803-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Abstract
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene. In recent years, a growing body of evidence suggests that unbalanced AS, the formation of certain pro-tumorigenic isoforms and the reduction of anti-tumorigenic isoforms, is implicated in a variety of cancers. It is becoming increasingly clear that cancer-associated AS contributes to increased growth and proliferation, partially due to effects on metabolic reprogramming. Here, we summarize the known roles of AS in regulating cancer metabolism. We present evidence supporting the idea that AS, in many types of cancer, acts as a molecular switch that alters metabolism to drive tumorigenesis. We propose that the elucidation of misregulated AS and its downstream effects on cancer metabolism emphasizes the need for new therapeutic approaches aiming to modulate the splicing machinery to selectively target cancer cells.
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Affiliation(s)
- Itamar Kozlovski
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel.
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154
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Ding L, Rath E, Bai Y. Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data. Curr Genomics 2017; 18:268-277. [PMID: 28659722 PMCID: PMC5476949 DOI: 10.2174/1389202918666170215125048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is a posttranscriptional process that produces differ-ent transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been de-fined. Multiple bioinformatics tools have been developed to detect AS from experimental data. OBJECTIVES The goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools. METHOD We selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted. RESULT We reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks. CONCLUSION Through comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.
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Affiliation(s)
| | | | - Yongsheng Bai
- Department of Biology.,The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN, USA
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155
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Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O'Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med 2017; 9:eaal5209. [PMID: 28424332 PMCID: PMC5548421 DOI: 10.1126/scitranslmed.aal5209] [Citation(s) in RCA: 451] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/29/2017] [Indexed: 12/21/2022]
Abstract
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.
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Affiliation(s)
- Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Jamie L Marshall
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leigh B Waddell
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sarah A Sandaradura
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Gina L O'Grady
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Elicia Estrella
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hemakumar M Reddy
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Fengmei Zhao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ben Weisburd
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel Birnbaum
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, University College London Institute of Child Health, London WC1N 1EH, U.K
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hernan Gonorazky
- Division of Neurology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Kristl Claeys
- Department of Neurology, University Hospitals Leuven and University of Leuven (Katholieke Universiteit Leuven), Leuven 3000, Belgium
| | - Himanshu Joshi
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Adam Bournazos
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Emily C Oates
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Roula Ghaoui
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia 6009, Australia
| | - Nigel G Laing
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia 6009, Australia
- Harry Perkins Institute of Medical Research, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, MRC (Medical Research Council) Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, U.K
| | - Peter B Kang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn N North
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Melbourne, Victoria 3052, Australia
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC (Medical Research Council) Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, U.K
| | - James J Dowling
- Division of Neurology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London Institute of Child Health, London WC1N 1EH, U.K
| | - Nigel F Clarke
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sandra T Cooper
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
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156
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The elusive MAESTRO gene: Its human reproductive tissue-specific expression pattern. PLoS One 2017; 12:e0174873. [PMID: 28406912 PMCID: PMC5391009 DOI: 10.1371/journal.pone.0174873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 03/16/2017] [Indexed: 12/16/2022] Open
Abstract
The encoded transcript of the Maestro—Male-specific Transcription in the developing Reproductive Organs (MRO) gene exhibits sexual dimorphic expression during murine gonadal development. The gene has no homology to any known gene and its expression pattern, protein function or structure are still unknown. Previously, studying gene expression in human ovarian cumulus cells, we found increased expression of MRO in lean-type Polycystic Ovarian Syndrome (PCOS) subjects, as compared to controls. In this study, we examined the MRO splice variants and protein expression pattern in various human tissues and cells. We found a differential expression pattern of the MRO 5’-UTR region in luteinized granulosa-cumulus cells and in testicular tissues as compared to non-gonadal tissues. Our study also shows a punctate nuclear expression pattern and disperse cytoplasmic expression pattern of the MRO protein in human granulosa-cumulus cells and in testicular germ cells, which was later validated by western blotting. The tentative and unique features of the protein hampered our efforts to gain more insight about this elusive protein. A better understanding of the tissue-specific MRO isoforms expression patterns and the unique structure of the protein may provide important insights into the function of this gene and possibly to the pathophysiology of PCOS.
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157
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Wang Q, Shi CJ, Lv SH. Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways. ACTA ACUST UNITED AC 2017; 50:e5981. [PMID: 28380197 PMCID: PMC5423740 DOI: 10.1590/1414-431x20175981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/13/2017] [Indexed: 12/22/2022]
Abstract
Different pathways act synergistically to participate in many biological processes. Thus, the purpose of our study was to extract dysregulated pathways to investigate the pathogenesis of colorectal cancer (CRC) based on the functional dependency among pathways. Protein-protein interaction (PPI) information and pathway data were retrieved from STRING and Reactome databases, respectively. After genes were aligned to the pathways, each pathway activity was calculated using the principal component analysis (PCA) method, and the seed pathway was discovered. Subsequently, we constructed the pathway interaction network (PIN), where each node represented a biological pathway based on gene expression profile, PPI data, as well as pathways. Dysregulated pathways were then selected from the PIN according to classification performance and seed pathway. A PIN including 11,960 interactions was constructed to identify dysregulated pathways. Interestingly, the interaction of mRNA splicing and mRNA splicing-major pathway had the highest score of 719.8167. Maximum change of the activity score between CRC and normal samples appeared in the pathway of DNA replication, which was selected as the seed pathway. Starting with this seed pathway, a pathway set containing 30 dysregulated pathways was obtained with an area under the curve score of 0.8598. The pathway of mRNA splicing, mRNA splicing-major pathway, and RNA polymerase I had the maximum genes of 107. Moreover, we found that these 30 pathways had crosstalks with each other. The results suggest that these dysregulated pathways might be used as biomarkers to diagnose CRC.
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Affiliation(s)
- Q Wang
- Department of General Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi Province, China
| | - C-J Shi
- Department of Endocrinology, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, China
| | - S-H Lv
- Department of Gastroenterology, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, China
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158
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Mthembu NN, Mbita Z, Hull R, Dlamini Z. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:77-93. [PMID: 28694706 PMCID: PMC5490432 DOI: 10.2147/hiv.s124911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies.
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Affiliation(s)
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa
| | - Rodney Hull
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
| | - Zodwa Dlamini
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
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159
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Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ. Improved definition of the mouse transcriptome via targeted RNA sequencing. Genome Res 2017; 26:705-16. [PMID: 27197243 PMCID: PMC4864457 DOI: 10.1101/gr.199760.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.
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Affiliation(s)
- Giovanni Bussotti
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
| | - Tommaso Leonardi
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lorenzo Malquori
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cedric Notredame
- Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Anton J Enright
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
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Transcriptome analysis of bronchoalveolar lavage fluid from children with severe Mycoplasma pneumoniae pneumonia reveals novel gene expression and immunodeficiency. Hum Genomics 2017; 11:4. [PMID: 28302172 PMCID: PMC5356355 DOI: 10.1186/s40246-017-0101-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/10/2017] [Indexed: 12/27/2022] Open
Abstract
Background A growing number of severe Mycoplasma pneumoniae pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to identify gene expression and alternative splicing profiles to provide insights into the pathogenesis of severe MPP. Methods RNAs of bronchoalveolar lavage fluid (BALF) samples from three severe MPP children and three mild MPP children were analyzed respectively by deep sequencing followed by computational annotation and quantification. Results The gene expression analysis revealed 14 up-regulated and 34 down-regulated genes in severe MPP children comparing to mild MPP children. The top 10 most up-regulated genes were IGHV1-69, CH17-472G23.1, ATP1B2, FCER2, MUC21, IL13, FCRLB, CLEC5A, FAM124A, and INHBA. The top 10 most down-regulated genes were OSTN-AS1, IL22RA2, COL3A1, C1orf141, IGKV2-29, RP11-731F5.2, IGHV4-4, KIRREL, DNASE1L3, and COL6A2. Clustering analysis revealed similar expression pattern of CLEC5A, IL13, FCER2, and FLT1. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed changes related to primary immunodeficiency in severe MPP children comparing to mild MPP children; the pathway involves CD19, TNFRSF13C, CD79A, and AICDA genes. Among the differentially expressed genes, significant alternative splicing events were found in FCER2 and FCRLA. Conclusions The current study on RNA sequencing provides novel insights into the pathogenesis of severe MPP in terms of gene expression and alternative splicing. The up-regulation of IL13, FCER2, FLT1, and CLEC5A and the down-regulation of CD79A, AICDA, CD19, and TNFRSF13C may contribute to the pathogenesis of severe MPP. The differential expressions of FCER2 and FCRLA could be due to their alternative splicing. Electronic supplementary material The online version of this article (doi:10.1186/s40246-017-0101-y) contains supplementary material, which is available to authorized users.
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The impact of RABL2B gene (rs144944885) on human male infertility in patients with oligoasthenoteratozoospermia and immotile short tail sperm defects. J Assist Reprod Genet 2017; 34:505-510. [PMID: 28138870 DOI: 10.1007/s10815-016-0863-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Male infertility is a multifactorial disorder with impressively genetic basis; besides, sperm abnormalities are the cause of numerous cases of male infertility. In this study, we evaluated the genetic variants in exons 4 and 5 and their intron-exon boundaries in RABL2B gene in infertile men with oligoasthenoteratozoospermia (OAT) and immotile short tail sperm (ISTS) defects to define if there is any association between these variants and human male infertility. METHODS To this purpose, DNA was extracted from peripheral blood and after PCR reaction and sequencing, the results of sequenced segments were analyzed. In the present study, 30 infertile men with ISTS defect and 30 oligoasthenoteratozoospermic infertile men were recruited. All men were of Iranian origin and it took 3 years to collect patient's samples with ISTS defect. RESULTS As a result, the 50776482 delC intronic variant (rs144944885) was identified in five patients with oligoasthenoteratozoospermia defect and one patient with ISTS defect in heterozygote form. This variant was not identified in controls. The allelic frequency of the 50776482 delC variant was significantly statistically higher in oligoasthenoteratozoospermic infertile men (p < 0.05). Bioinformatics studies suggested that the 50776482 delC allele would modify the splicing of RABL2B pre-mRNA. In addition, we identified a new genetic variant in RABL2B gene. CONCLUSIONS According to the present study, 50776482 delC allele in the RABL2B gene could be a risk factor in Iranian infertile men with oligoasthenoteratozoospermia defect, but more genetic studies are required to understand the accurate role of this variant in pathogenesis of human male infertility.
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LOX-1 and Its Splice Variants: A New Challenge for Atherosclerosis and Cancer-Targeted Therapies. Int J Mol Sci 2017; 18:ijms18020290. [PMID: 28146073 PMCID: PMC5343826 DOI: 10.3390/ijms18020290] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/15/2017] [Accepted: 01/23/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a process in which precursor messenger RNA (pre-mRNA) splicing sites are differentially selected to diversify the protein isoform population. Changes in AS patterns have an essential role in normal development, differentiation and response to physiological stimuli. It is documented that AS can generate both “risk” and “protective” splice variants that can contribute to the pathogenesis of several diseases including atherosclerosis. The main endothelial receptor for oxidized low-density lipoprotein (ox-LDLs) is LOX-1 receptor protein encoded by the OLR1 gene. When OLR1 undergoes AS events, it generates three variants: OLR1, OLR1D4 and LOXIN. The latter lacks exon 5 and two-thirds of the functional domain. Literature data demonstrate a protective role of LOXIN in pathologies correlated with LOX-1 overexpression such as atherosclerosis and tumors. In this review, we summarize recent developments in understanding of OLR1 AS while also highlighting data warranting further investigation of this process as a novel therapeutic target.
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163
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Wang X, Cui X, Zhang Y, Hao H, Ju Z, Liu D, Jiang Q, Yang C, Sun Y, Wang C, Huang J, Zhu H. Splicing-related single nucleotide polymorphism of RAB, member of RAS oncogene family like 2B (RABL2B) jeopardises semen quality in Chinese Holstein bulls. Reprod Fertil Dev 2017; 29:2411-2418. [DOI: 10.1071/rd17111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/18/2017] [Indexed: 11/23/2022] Open
Abstract
RAB, member of RAS oncogene family like 2B (RABL2B) is a member of a poorly characterised clade of the RAS GTPase superfamily, which plays an essential role in male fertility, sperm intraflagellar transport and tail assembly. In the present study, we identified a novel RABL2B splice variant in bovine testis and spermatozoa. This splice variant, designated RABL2B-TV, is characterised by exon 2 skipping. Moreover, a single nucleotide polymorphism (SNP), namely c.125G>A, was found within the exonic splicing enhancer (ESE) motif, indicating that the SNP caused the production of the RABL2B-TV aberrant splice variant. This was demonstrated by constructing a pSPL3 exon capturing vector with different genotypes and transfecting these vectors into murine Leydig tumour cell line (MLTC-1) cells. Expression of the RABL2B-TV transcript was lower in semen from high- versus low-performance bulls. Association analysis showed that sperm deformity rate was significantly lower in Chinese Holstein bulls with the GG or GA genotype than in bulls with the AA genotype (P < 0.05). In addition, initial sperm motility was significantly higher in individuals with the GG or GA genotype than in individuals with the AA genotype (P < 0.05). The findings of the present study suggest that the difference in semen quality in bulls with different RABL2B genotypes is generated via an alternative splicing mechanism caused by a functional SNP within the ESE motif.
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164
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Jahantigh D, Hosseinzadeh Colagar A. XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies. Int J Endocrinol 2017; 2017:4795076. [PMID: 28421111 PMCID: PMC5379132 DOI: 10.1155/2017/4795076] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/26/2016] [Accepted: 01/04/2017] [Indexed: 11/17/2022] Open
Abstract
We evaluate the association between genetic polymorphisms of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T with male infertility susceptibility. A total of 392 men including 178 infertile males (102 idiopathic azoospermia and 76 severe oligozoospermia) and 214 healthy controls were recruited. XRCC6 -61C>G and XRCC7 6721G>T genotyping was performed by PCR-RFLP whereas XRCC5 VNTR was performed by PCR. The 2R allele and 2R allele carriers of XRCC5 VNTR polymorphism significantly decreased risk of male infertility. The mutant GG genotypes and carriers of the CG and GG genotypes of XRCC6 -61C>G showed increased risk for the male infertility. Furthermore, the G allele of the XRCC6 -61C>G was correlated with increased susceptibility to male infertility. Likewise, the T allele of the XRCC7 6721G>T polymorphism was associated with increased susceptibility to male infertility in azoospermia. In silico analysis predicted that the presence of tandem repeats in XRCC5 gene prompter can be sequence to bind to more nuclear factors. Also, rs2267437 (C>G) variant was located in a well-conserved region in XRCC6 promoter and this variation might lead to differential allelic expression. The XRCC7 6721G>T gene polymorphism occurred in an acceptor-splicing site, but this polymorphism has no severe modification on XRCC7 mRNA splicing. Our results indicate the association of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T gene polymorphisms with male infertility in Iranian men.
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Affiliation(s)
- Danial Jahantigh
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
- *Abasalt Hosseinzadeh Colagar:
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166
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Tang Q, Rodriguez-Santiago S, Wang J, Pu J, Yuste A, Gupta V, Moldón A, Xu YZ, Query CC. SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing. Genes Dev 2016; 30:2710-2723. [PMID: 28087715 PMCID: PMC5238730 DOI: 10.1101/gad.291872.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022]
Abstract
Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations. Furthermore, we show that mutations in these motifs from both human disease and yeast genetic screens alter the physical interaction with Prp5p, alter branch region specification, and phenocopy mutations in Prp5p. These and other data demonstrate that mutations in Hsh155p and Prp5p alter splicing because they change the direct physical interaction between Hsh155p and Prp5p. This altered physical interaction results in altered loading (i.e., "fidelity") of the BS-U2 duplex into the SF3B complex during prespliceosome formation. These results provide a mechanistic framework to explain the consequences of intron recognition and splicing of SF3B1 mutations found in disease.
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Affiliation(s)
- Qing Tang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | | | - Jing Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Jia Pu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Andrea Yuste
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Alberto Moldón
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Yong-Zhen Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
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167
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Santo J, Lopez-Herrera C, Apolit C, Bareche Y, Lapasset L, Chavey C, Capozi S, Mahuteau-Betzer F, Najman R, Fornarelli P, Lopez-Mejía IC, Béranger G, Casas F, Amri EZ, Pau B, Scherrer D, Tazi J. Pharmacological modulation of LMNA SRSF1-dependent splicing abrogates diet-induced obesity in mice. Int J Obes (Lond) 2016; 41:390-401. [PMID: 27916986 DOI: 10.1038/ijo.2016.220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/26/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022]
Abstract
Bakground/Objectives:Intense drug discovery efforts in the metabolic field highlight the need for novel strategies for the treatment of obesity. Alternative splicing (AS) and/or polyadenylation enable the LMNA gene to express distinct protein isoforms that exert opposing effects on energy metabolism and lifespan. Here we aimed to use the splicing factor SRSF1 that contribute to the production of these different isoforms as a target to uncover new anti-obesity drug. SUBJECTS/METHODS Small molecules modulating SR protein activity and splicing were tested for their abilities to interact with SRSF1 and to modulate LMNA (AS). Using an LMNA luciferase reporter we selected molecules that were tested in diet-induced obese (DIO) mice. Transcriptomic analyses were performed in the white adipose tissues from untreated and treated DIO mice and mice fed a chow diet. RESULTS We identified a small molecule that specifically interacted with the RS domain of SRSF1. ABX300 abolished DIO in mice, leading to restoration of adipose tissue homeostasis. In contrast, ABX300 had no effect on mice fed a standard chow diet. A global transcriptomic analysis revealed similar profiles of white adipose tissue from DIO mice treated with ABX300 and from untreated mice fed a chow diet. Mice treated with ABX300 exhibited an increase in O2 consumption and a switch in fuel preference toward lipids. CONCLUSIONS Targeting SRSF1 with ABX300 compensates for changes in RNA biogenesis induced by fat accumulation and consequently represents a novel unexplored approach for the treatment of obesity.
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Affiliation(s)
- J Santo
- ABIVAX, Montpellier Cedex 5, France
| | | | - C Apolit
- ABIVAX, Montpellier Cedex 5, France
| | - Y Bareche
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, University of Montpellier, Montpellier Cedex 5, France
| | | | - C Chavey
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, University of Montpellier, Montpellier Cedex 5, France
| | - S Capozi
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, University of Montpellier, Montpellier Cedex 5, France
| | - F Mahuteau-Betzer
- Institut Curie, PSL Research University, CNRS, INSERM, Orsay, France
| | - R Najman
- ABIVAX, Montpellier Cedex 5, France.,Institut Curie, PSL Research University, CNRS, INSERM, Orsay, France
| | - P Fornarelli
- ABIVAX, Montpellier Cedex 5, France.,Institut Curie, PSL Research University, CNRS, INSERM, Orsay, France
| | - I C Lopez-Mejía
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, University of Montpellier, Montpellier Cedex 5, France
| | - G Béranger
- Institut de Biologie de Valrose, UMR CNRS 7277-UMR INSERM 1091, Université de Nice Sophia Antipolis, Faculté de Médecine, Nice Cedex 2, France
| | - F Casas
- UMR Dynamique Musculaire et Métabolisme, INRA-CAMPUS SUPAGRO 2 place Viala, Montpellier Cedex 2, France
| | - E-Z Amri
- Institut de Biologie de Valrose, UMR CNRS 7277-UMR INSERM 1091, Université de Nice Sophia Antipolis, Faculté de Médecine, Nice Cedex 2, France
| | - B Pau
- Université de Montpellier, UFR Pharmacie, Montpellier, France
| | | | - J Tazi
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, University of Montpellier, Montpellier Cedex 5, France
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168
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Grañé-Boladeras N, Spring CM, Hanna WJB, Pastor-Anglada M, Coe IR. Novel nuclear hENT2 isoforms regulate cell cycle progression via controlling nucleoside transport and nuclear reservoir. Cell Mol Life Sci 2016; 73:4559-4575. [PMID: 27271752 PMCID: PMC11108336 DOI: 10.1007/s00018-016-2288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 10/25/2022]
Abstract
Nucleosides participate in many cellular processes and are the fundamental building blocks of nucleic acids. Nucleoside transporters translocate nucleosides across plasma membranes although the mechanism by which nucleos(t)ides are translocated into the nucleus during DNA replication is unknown. Here, we identify two novel functional splice variants of equilibrative nucleoside transporter 2 (ENT2), which are present at the nuclear envelope. Under proliferative conditions, these splice variants are up-regulated and recruit wild-type ENT2 to the nuclear envelope to translocate nucleosides into the nucleus for incorporation into DNA during replication. Reduced presence of hENT2 splice variants resulted in a dramatic decrease in cell proliferation and dysregulation of cell cycle due to a lower incorporation of nucleotides into DNA. Our findings support a novel model of nucleoside compartmentalisation at the nuclear envelope and translocation into the nucleus through hENT2 and its variants, which are essential for effective DNA synthesis and cell proliferation.
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Affiliation(s)
- Natalia Grañé-Boladeras
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain.
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada.
| | - Christopher M Spring
- Research Core Facilities, Keenan Research Centre, Li Ka Shing Knowledge Institute, Saint Michael's Hospital, Toronto, ON, M5B 1T8, Canada
| | - W J Brad Hanna
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Marçal Pastor-Anglada
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Imogen R Coe
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada
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Pirmoradian M, Aarsland D, Zubarev RA. Isoelectric point region pI≈7.4 as a treasure island of abnormal proteoforms in blood. Discoveries (Craiova) 2016; 4:e67. [PMID: 32309586 PMCID: PMC7159840 DOI: 10.15190/d.2016.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Theoretical distribution of isoelectric points (pI values) of human blood proteins exhibits multi-modality with a deep minimum in the range between pI 7.30 and 7.50. Considering that the pH of human blood is 7.4±0.1, normal forms of human proteins tend to eschew this specific pI region, thus avoiding charge neutrality that can result in enhanced precipitation. However, abnormal protein isoforms (proteoforms), which are the hallmarks and potential biomarkers of certain diseases, are likely to be found everywhere in the pI distribution, including this “forbidden” region. Therefore, we hypothesized that damaging proteoforms characteristic for neurodegenerative diseases are best detected around pI≈7.4. Blood serum samples from 14 Alzheimer's disease patients were isolated by capillary isoelectric focusing and analyzed by liquid chromatography hyphenated with tandem mass spectrometry. Consistent with the pI≈7.4 hypothesis, the 8 patients with fast memory decline had a significantly (p<0.003) higher concentration of proteoforms in the pI=7.4±0.1 region than the 6 patients with a slow memory decline. Moreover, protein compositions differed more from each other than for any other investigated pI region, providing absolute separation of the fast and slow decliner samples. The discovery of the “treasure island” of abnormal proteoforms in form of the pI≈7.4 region promises to boost biomarker development for a range of diseases.
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Affiliation(s)
- Mohammad Pirmoradian
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Biomotif AB, Stockholm, Sweden
| | - Dag Aarsland
- Alzheimer's Disease Research Centre, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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170
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Jiao H, Dong P, Yan L, Yang Z, Lv X, Li Q, Zong X, Fan J, Fu X, Liu X, Xiao R. TGF-β1 Induces Polypyrimidine Tract-Binding Protein to Alter Fibroblasts Proliferation and Fibronectin Deposition in Keloid. Sci Rep 2016; 6:38033. [PMID: 27897224 PMCID: PMC5126665 DOI: 10.1038/srep38033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 11/03/2016] [Indexed: 02/04/2023] Open
Abstract
Human dermal fibrotic disease keloid has been a clinical challenge because of its tumour-like growth and the lack of effective therapy. Dysregulated alternative splicing events have been demonstrated in tumours and fibrosis. In the current study, for the first time, it was demonstrated that the splicing regulator polypyrimidine tract-binding protein (PTB), which plays a pivotal role in tumour proliferation, invasion and metastasis, is overexpressed in keloid tissues and fibroblasts. Additionally, TGF-β1 upregulated the expressions of PTB and its upstream regulator, C-MYC, in keloid fibroblasts. Furthermore, we suppressed PTB using siRNA in keloid fibroblasts and in a keloid xenograft nude mouse model. PTB knockdown significantly slowed the proliferation of keloid fibroblasts and accelerated the regression of transplanted keloid tissues, which was accompanied by a shift in the alternative splicing of USP5 and RTN4. Moreover, when PTB was suppressed, there was a reduction in excessive deposition of FN1 and COL3A1 in transplanted keloid tissues. However, only FN1 was downregulated in keloid fibroblasts that were cultured in media supplemented with TGF-β1. Our study provides evidence for the role of PTB in keloid pathophysiology and offers a novel therapeutic target for keloids. Most importantly, the role TGF-β1 regulation of PTB may provide new insights into the mechanisms underlying inflammatory cytokine-induced fibrosis.
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Affiliation(s)
- Hu Jiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Ping Dong
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Li Yan
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Zhigang Yang
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Xiaoyan Lv
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Qiuchen Li
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Xianlei Zong
- Scar Plastic Department of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Jincai Fan
- Scar Plastic Department of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Xin Fu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Xia Liu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
| | - Ran Xiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, P.R. China
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Chen S, Le BT, Rahimizadeh K, Shaikh K, Mohal N, Veedu RN. Synthesis of a Morpholino Nucleic Acid (MNA)-Uridine Phosphoramidite, and Exon Skipping Using MNA/2'-O-Methyl Mixmer Antisense Oligonucleotide. Molecules 2016; 21:molecules21111582. [PMID: 27879669 PMCID: PMC6274534 DOI: 10.3390/molecules21111582] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 01/14/2023] Open
Abstract
In this study, we synthesised a morpholino nucleoside-uridine (MNA-U) phosphoramidite and evaluated the potential of a MNA-modified antisense oligonucleotide (AO) sequences to induce exon 23 skipping in mdx mouse myotubes in vitro towards extending the applicability of morpholino chemistry with other nucleotide monomers. We designed, synthesised, and compared exon skipping efficiencies of 20 mer MNA-modified 2'-O-methyl RNA mixmer AO on a phosphorothioate backbone (MNA/2'-OMePS) to the corresponding fully modified 2'-O-methyl RNA AO (2'-OMePS) as a control. Our results showed that the MNA/2'-OMePS efficiently induced exon 23 skipping. As expected, the 2'-OMePS AO control yielded efficient exon 23 skipping. Under the applied conditions, both the AOs showed minor products corresponding to exon 22/23 dual exon skipping in low yield. As these are very preliminary data, more detailed studies are necessary; however, based on the preliminary results, MNA nucleotides might be useful in constructing antisense oligonucleotides.
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Affiliation(s)
- Suxiang Chen
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Bao T Le
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Kamal Rahimizadeh
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
| | - Khalil Shaikh
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Narinder Mohal
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
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Wang K, Jiao Z, Xu M, Wang Y, Li R, Cui X, Gu L, Zhang S. Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis. HORTICULTURAL PLANT JOURNAL 2016; 2:338-350. [PMID: 0 DOI: 10.1016/j.hpj.2017.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Pfau T, Pacheco MP, Sauter T. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief Bioinform 2016; 17:1060-1069. [PMID: 26615025 PMCID: PMC5142010 DOI: 10.1093/bib/bbv100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Genome-scale metabolic network reconstructions provide a basis for the investigation of the metabolic properties of an organism. There are reconstructions available for multiple organisms, from prokaryotes to higher organisms and methods for the analysis of a reconstruction. One example is the use of flux balance analysis to improve the yields of a target chemical, which has been applied successfully. However, comparison of results between existing reconstructions and models presents a challenge because of the heterogeneity of the available reconstructions, for example, of standards for presenting gene-protein-reaction associations, nomenclature of metabolites and reactions or selection of protonation states. The lack of comparability for gene identifiers or model-specific reactions without annotated evidence often leads to the creation of a new model from scratch, as data cannot be properly matched otherwise. In this contribution, we propose to improve the predictive power of metabolic models by switching from gene-protein-reaction associations to transcript-isoform-reaction associations, thus taking advantage of the improvement of precision in gene expression measurements. To achieve this precision, we discuss available databases that can be used to retrieve this type of information and point at issues that can arise from their neglect. Further, we stress issues that arise from non-standardized building pipelines, like inconsistencies in protonation states. In addition, problems arising from the use of non-specific cofactors, e.g. artificial futile cycles, are discussed, and finally efforts of the metabolic modelling community to unify model reconstructions are highlighted.
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Exploring Splicing-Switching Molecules For Seckel Syndrome Therapy. Biochim Biophys Acta Mol Basis Dis 2016; 1863:15-20. [PMID: 27639833 DOI: 10.1016/j.bbadis.2016.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022]
Abstract
The c.2101A>G synonymous change (p.G674G) in the gene for ATR, a key player in the DNA-damage response, has been the first identified genetic cause of Seckel Syndrome (SS), an orphan disease characterized by growth and mental retardation. This mutation mainly causes exon 9 skipping, through an ill-defined mechanism. Through ATR minigene expression studies, we demonstrated that the detrimental effect of this mutation (6±1% of correct transcripts only) depends on the poor exon 9 definition (47±4% in the ATRwt context), because the change was ineffective when the weak 5' or the 3' splice sites (ss) were strengthened (scores from 0.54 to 1) by mutagenesis. Interestingly, the exonic c.2101A nucleotide is conserved across species, and the SS-causing mutation is predicted to concurrently strengthen a Splicing Silencer (ESS) and weaken a Splicing Enhancer (ESE). Consistently, the artificial c.2101A>C change, predicted to weaken the ESE only, moderately impaired exon inclusion (28±7% of correct transcripts). The observation that an antisense oligonucleotide (AONATR) targeting the c.2101A position recovers exon inclusion in the mutated context supports a major role of the underlying ESS. A U1snRNA variant (U1ATR) designed to perfectly base-pair the weak 5'ss, rescued exon inclusion (63±3%) in the ATRSS-allele. Most importantly, upon lentivirus-mediated delivery, the U1ATR partially rescued ATR mRNA splicing (from ~19% to ~54%) and protein (from negligible to ~6%) in embryonic fibroblasts derived from humanized ATRSS mice. Altogether these data elucidate the molecular mechanisms of the ATR c.2101A>G mutation and identify two potential complementary RNA-based therapies for Seckel syndrome.
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Han B, Gu J, Zhao L, Guo H, Xie Y, Zhao S, Song X, Han L, Liu L. Factors Affecting the Radiosensitivity of Hexaploid Wheat to γ-Irradiation: Radiosensitivity of Hexaploid Wheat (Triticum aestivum L.) [Corrected]. PLoS One 2016; 11:e0161700. [PMID: 27551965 PMCID: PMC4995049 DOI: 10.1371/journal.pone.0161700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/10/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding the radiosensitivity of plants, an important factor in crop mutation breeding programs, requires a thorough investigation of the factors that contribute to this trait. In this study, we used the highly radiosensitive wheat (Triticum aestivum L.) variety HY1 and J411, a γ-irradiation-insensitive control, which were screened from a natural population, to examine the factors affecting radiosensitivity, including free radical content and total antioxidant capacity, as well as the expression of TaKu70 and TaKu80 (DNA repair-related genes) as measured by real-time PCR. We also investigated the alternative splicing of this gene in the wild-type wheat ecotype by sequence analysis. Free radical contents and total antioxidant capacity significantly increased upon exposure of HY1 wheat to γ-irradiation in a dose-dependent manner. By contrast, in J411, the free radical contents exhibited a similar trend, but the total antioxidant capacity exhibited a downward trend upon increasing γ-irradiation. Additionally, we detected dose-dependent increases in TaKu70 and TaKu80 expression levels in γ-irradiated HY1, while in J411, TaKu70 expression levels increased, followed by a decline. We also detected alternative splicing of TaKu70 mRNA, namely, intron retention, in HY1 but not in J411. Our findings indicate that γ-irradiation induces oxidative stress and DNA damage in hexaploid wheat, resulting in growth retardation of seedlings, and they suggest that TaKu70 may play a causal role in radiosensitivity in HY1. Further studies are required to exploit these factors to improve radiosensitivity in other wheat varieties.
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Affiliation(s)
- Bing Han
- Academy of Life Science, Qingdao Agricultural University, Qingdao, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Xiyun Song
- Academy of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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Kim YG, Kim M, Kang JH, Kim HJ, Park JW, Lee JM, Suh JY, Kim JY, Lee JH, Lee Y. Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns. Hum Genomics 2016; 10:28. [PMID: 27531006 PMCID: PMC4988046 DOI: 10.1186/s40246-016-0084-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/04/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing. METHODS The pooled RNAs of 10 gingival tissues from both healthy and periodontitis patients were analyzed by deep sequencing followed by computational annotation and quantification of mRNA structures. RESULTS The differential expression analysis designated 400 up-regulated genes in periodontitis tissues especially in the pathways of defense/immunity protein, receptor, protease, and signaling molecules. The top 10 most up-regulated genes were CSF3, MAFA, CR2, GLDC, SAA1, LBP, MME, MMP3, MME-AS1, and SAA4. The 62 down-regulated genes in periodontitis were mainly cytoskeletal and structural proteins. The top 10 most down-regulated genes were SERPINA12, MT4, H19, KRT2, DSC1, PSORS1C2, KRT27, LCE3C, AQ5, and LCE6A. The differential alternative splicing analysis revealed unique transcription variants in periodontitis tissues. The EDB exon was predominantly included in FN1, while exon 2 was mostly skipped in BCL2A1. CONCLUSIONS These findings using RNA sequencing provide novel insights into the pathogenesis mechanism of periodontitis in terms of gene expression and alternative splicing.
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Affiliation(s)
- Yong-Gun Kim
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.,Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea
| | - Minjung Kim
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea
| | - Ji Hyun Kang
- Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Hyo Jeong Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Jin-Woo Park
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jae-Mok Lee
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jo-Young Suh
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jae-Young Kim
- Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea.,Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea. .,Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul, 02447, Korea.
| | - Youngkyun Lee
- Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea. .,Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea.
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Peffers MJ, Goljanek-Whysall K, Collins J, Fang Y, Rushton M, Loughlin J, Proctor C, Clegg PD. Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq. PLoS One 2016; 11:e0160517. [PMID: 27533049 PMCID: PMC4988628 DOI: 10.1371/journal.pone.0160517] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/20/2016] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based regenerative medicine and tissue engineering. Epigenetic mechanisms, like DNA methylation, contribute to the changes in gene expression in ageing. However there was a lack of sufficient knowledge of the role that differential methylation plays during chondrogenic, osteogenic and tenogenic differentiation from ageing MSCs. This study undertook genome level determination of the effects of DNA methylation on expression in engineered tissues from chronologically aged MSCs. We compiled unique DNA methylation signatures from chondrogenic, osteogenic, and tenogenic engineered tissues derived from young; n = 4 (21.8 years ± 2.4 SD) and old; n = 4 (65.5 years±8.3SD) human MSCs donors using the Illumina HumanMethylation 450 Beadchip arrays and compared these to gene expression by RNA sequencing. Unique and common signatures of global DNA methylation were identified. There were 201, 67 and 32 chondrogenic, osteogenic and tenogenic age-related DE protein-coding genes respectively. Findings inferred the nature of the transcript networks was predominantly for 'cell death and survival', 'cell morphology', and 'cell growth and proliferation'. Further studies are required to validate if this gene expression effect translates to cell events. Alternative splicing (AS) was dysregulated in ageing with 119, 21 and 9 differential splicing events identified in chondrogenic, osteogenic and tenogenic respectively, and enrichment in genes associated principally with metabolic processes. Gene ontology analysis of differentially methylated loci indicated age-related enrichment for all engineered tissue types in 'skeletal system morphogenesis', 'regulation of cell proliferation' and 'regulation of transcription' suggesting that dynamic epigenetic modifications may occur in genes associated with shared and distinct pathways dependent upon engineered tissue type. An altered phenotype in engineered tissues was observed with ageing at numerous levels. These changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients. In addition we have identified a number of tissue-dependant pathways, which warrant further studies.
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Affiliation(s)
- Mandy Jayne Peffers
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - Katarzyna Goljanek-Whysall
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - John Collins
- Thurston Arthritis Research Centre, School Of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA, 27599
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, UK, L69 7ZB
| | - Michael Rushton
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - Carole Proctor
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
- Newcastle University Institute for Ageing, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK, NE4 5PL
| | - Peter David Clegg
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
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Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3681094. [PMID: 27610372 PMCID: PMC5004037 DOI: 10.1155/2016/3681094] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/27/2016] [Accepted: 07/03/2016] [Indexed: 02/06/2023]
Abstract
In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics.
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180
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Göttgens EL, Span PN, Zegers MM. Roles and Regulation of Epithelial Splicing Regulatory Proteins 1 and 2 in Epithelial-Mesenchymal Transition. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 327:163-194. [PMID: 27692175 DOI: 10.1016/bs.ircmb.2016.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The transformation of polarized epithelial cells into cells with mesenchymal characteristics by the morphogenetic process of epithelial-mesenchymal transition (EMT) is a well-characterized process essential for embryonic development and associated with cancer progression. EMT is a program driven by changes in gene expression induced by several EMT-specific transcription factors, which inhibit the expression of cell-cell adhesion proteins and other epithelial markers, causing a characteristic loss of cell-cell adhesion, a switch to mesenchymal cell morphology, and increased migratory capabilities. Recently, it has become apparent that in addition to these transcriptionally regulated changes, EMT may also be regulated posttranscriptionally, that is, by alternative splicing. Specifically, the epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) have been described as epithelial-specific splicing master regulators specifically involved in EMT-associated alternative splicing. Here, we discuss the regulation of ESRP activity, as well as the evidence supporting a causal role of ESRPs in EMT.
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Affiliation(s)
- E-L Göttgens
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - P N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M M Zegers
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Nowicka M, Robinson MD. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Res 2016; 5:1356. [PMID: 28105305 PMCID: PMC5200948 DOI: 10.12688/f1000research.8900.2] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2016] [Indexed: 02/03/2023] Open
Abstract
There are many instances in genomics data analyses where measurements are made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There are situations where differences (e.g. between normal and disease state) in the relative ratio of expressed isoforms may have significant phenotypic consequences or lead to prognostic capabilities. Similarly, knowledge of single nucleotide polymorphisms (SNPs) that affect splicing, so-called splicing quantitative trait loci (sQTL) will help to characterize the effects of genetic variation on gene expression. RNA sequencing (RNA-seq) has provided an attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods for transcript quantification have become available. We propose a statistical framework based on the Dirichlet-multinomial distribution that can discover changes in isoform usage between conditions and SNPs that affect relative expression of transcripts using these quantifications. The Dirichlet-multinomial model naturally accounts for the differential gene expression without losing information about overall gene abundance and by joint modeling of isoform expression, it has the capability to account for their correlated nature. The main challenge in this approach is to get robust estimates of model parameters with limited numbers of replicates. We approach this by sharing information and show that our method improves on existing approaches in terms of standard statistical performance metrics. The framework is applicable to other multivariate scenarios, such as Poly-A-seq or where beta-binomial models have been applied (e.g., differential DNA methylation). Our method is available as a Bioconductor R package called DRIMSeq.
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Affiliation(s)
- Malgorzata Nowicka
- Institute for Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D Robinson
- Institute for Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
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182
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Nowicka M, Robinson MD. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Res 2016; 5:1356. [PMID: 28105305 PMCID: PMC5200948 DOI: 10.12688/f1000research.8900.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2016] [Indexed: 08/31/2023] Open
Abstract
There are many instances in genomics data analyses where measurements are made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There are situations where differences (e.g. between normal and disease state) in the relative ratio of expressed isoforms may have significant phenotypic consequences or lead to prognostic capabilities. Similarly, knowledge of single nucleotide polymorphisms (SNPs) that affect splicing, so-called splicing quantitative trait loci (sQTL) will help to characterize the effects of genetic variation on gene expression. RNA sequencing (RNA-seq) has provided an attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods for transcript quantification have become available. We propose a statistical framework based on the Dirichlet-multinomial distribution that can discover changes in isoform usage between conditions and SNPs that affect relative expression of transcripts using these quantifications. The Dirichlet-multinomial model naturally accounts for the differential gene expression without losing information about overall gene abundance and by joint modeling of isoform expression, it has the capability to account for their correlated nature. The main challenge in this approach is to get robust estimates of model parameters with limited numbers of replicates. We approach this by sharing information and show that our method improves on existing approaches in terms of standard statistical performance metrics. The framework is applicable to other multivariate scenarios, such as Poly-A-seq or where beta-binomial models have been applied (e.g., differential DNA methylation). Our method is available as a Bioconductor R package called DRIMSeq.
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Affiliation(s)
- Malgorzata Nowicka
- Institute for Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute for Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
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183
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Meyer F. Viral interactions with components of the splicing machinery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 142:241-68. [PMID: 27571697 DOI: 10.1016/bs.pmbts.2016.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Eukaryotic genes are often interrupted by stretches of sequence with no protein coding potential or obvious function. After transcription, these interrupting sequences must be removed to give rise to the mature messenger RNA. This fundamental process is called RNA splicing and is achieved by complicated machinery made of protein and RNA that assembles around the RNA to be edited. Viruses also use RNA splicing to maximize their coding potential and economize on genetic space, and use clever strategies to manipulate the splicing machinery to their advantage. This article gives an overview of the splicing process and provides examples of viral strategies that make use of various components of the splicing system to promote their replicative cycle. Representative virus families have been selected to illustrate the interaction with various regulatory proteins and ribonucleoproteins. The unifying theme is fine regulation through protein-protein and protein-RNA interactions with the spliceosome components and associated factors to promote or prevent spliceosome assembly on given splice sites, in addition to a strong influence from cis-regulatory sequences on viral transcripts. Because there is an intimate coupling of splicing with the processes that direct mRNA biogenesis, a description of how these viruses couple the regulation of splicing with the retention or stability of mRNAs is also included. It seems that a unique balance of suppression and activation of splicing and nuclear export works optimally for each family of viruses.
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Affiliation(s)
- F Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, USA.
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184
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Pié J, Puisac B, Hernández-Marcos M, Teresa-Rodrigo ME, Gil-Rodríguez M, Baquero-Montoya C, Ramos-Cáceres M, Bernal M, Ayerza-Casas A, Bueno I, Gómez-Puertas P, Ramos FJ. Special cases in Cornelia de Lange syndrome: The Spanish experience. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:198-205. [PMID: 27164022 DOI: 10.1002/ajmg.c.31501] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cornelia de Lange Syndrome (CdLS) is an autosomal dominant (NIPBL, SMC3, and RAD21) or X-linked (SMC1A and HDAC8) disorder, characterized by distinctive craniofacial appearance, growth retardation, intellectual disability, and limb anomalies. In 2005, the Spanish CdLS Reference Center was started and now we have more than 270 cases in our database. In this special issue, we describe some of the unique or atypical patients studied by our group, whose clinical features have contributed to the expansion of the CdLS classical phenotype, helping clinicians to diagnose it. We include the case of a male with unilateral tibial hypoplasia and peroneal agenesis who had a mutation in NIPBL; we also describe one patient with a mutation in NIPBL and somatic mosaicism identified by new generation sequencing techniques; we also include one patient with CdLS and Turner syndrome; and last, an interesting patient with a duplication of the SMC1A gene. Finally, we make a short review of the splicing mutations we have found in NIPBL regarding the new knowledge on the physiological variants of the gene. © 2016 Wiley Periodicals, Inc.
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185
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Kawaguchi R, Kiryu H. Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinformatics 2016; 17:203. [PMID: 27153986 PMCID: PMC4858847 DOI: 10.1186/s12859-016-1067-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/29/2016] [Indexed: 02/08/2023] Open
Abstract
Background RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Results Our novel software, “ParasoR”, is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. Conclusions We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1067-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Risa Kawaguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
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186
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Seo J, Singh NN, Ottesen EW, Sivanesan S, Shishimorova M, Singh RN. Oxidative Stress Triggers Body-Wide Skipping of Multiple Exons of the Spinal Muscular Atrophy Gene. PLoS One 2016; 11:e0154390. [PMID: 27111068 PMCID: PMC4844106 DOI: 10.1371/journal.pone.0154390] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/12/2016] [Indexed: 12/18/2022] Open
Abstract
Humans carry two nearly identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Loss of SMN1 leads to spinal muscular atrophy (SMA), the most frequent genetic cause of infant mortality. While SMN2 cannot compensate for the loss of SMN1 due to predominant skipping of exon 7, correction of SMN2 exon 7 splicing holds the promise of a cure for SMA. Previously, we used cell-based models coupled with a multi-exon-skipping detection assay (MESDA) to demonstrate the vulnerability of SMN2 exons to aberrant splicing under the conditions of oxidative stress (OS). Here we employ a transgenic mouse model and MESDA to examine the OS-induced splicing regulation of SMN2 exons. We induced OS using paraquat that is known to trigger production of reactive oxygen species and cause mitochondrial dysfunction. We show an overwhelming co-skipping of SMN2 exon 5 and exon 7 under OS in all tissues except testis. We also show that OS increases skipping of SMN2 exon 3 in all tissues except testis. We uncover several new SMN2 splice isoforms expressed at elevated levels under the conditions of OS. We analyze cis-elements and transacting factors to demonstrate the diversity of mechanisms for splicing misregulation under OS. Our results of proteome analysis reveal downregulation of hnRNP H as one of the potential consequences of OS in brain. Our findings suggest SMN2 as a sensor of OS with implications to SMA and other diseases impacted by low levels of SMN protein.
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Affiliation(s)
- Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
| | - Natalia N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
| | - Eric W. Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
| | - Senthilkumar Sivanesan
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
| | - Maria Shishimorova
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
| | - Ravindra N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, United States of America
- * E-mail:
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187
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Vichas A, Laurie MT, Zallen JA. The Ski2-family helicase Obelus regulates Crumbs alternative splicing and cell polarity. J Cell Biol 2016; 211:1011-24. [PMID: 26644515 PMCID: PMC4674277 DOI: 10.1083/jcb.201504083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The conserved Ski2-family helicase Obelus regulates alternative splicing of the Crumbs polarity protein to control epithelial polarity and junctional organization in Drosophila. Alternative splicing can have profound consequences for protein activity, but the functions of most alternative splicing regulators are not known. We show that Obelus, a conserved Ski2-family helicase, is required for cell polarity and adherens junction organization in the Drosophila melanogaster embryo. In obelus mutants, epithelial cells display an expanded apical domain, aggregation of adherens junctions at the cell membrane, and microtubule-dependent defects in centrosome positioning. Through whole-genome transcriptome analysis, we found that Obelus is required for the alternative splicing of a small number of transcripts in the early embryo, including the pre-mRNA that encodes the apical polarity protein Crumbs. In obelus mutants, inclusion of an alternative exon results in increased expression of a Crumbs isoform that contains an additional epidermal growth factor–like repeat in the extracellular domain. Overexpression of this alternative Crumbs isoform recapitulates the junctional aggregation and centrosome positioning defects of obelus mutants. These results indicate that regulation of Crumbs alternative splicing by the Obelus helicase modulates epithelial polarity during development.
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Affiliation(s)
- Athea Vichas
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Matthew T Laurie
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jennifer A Zallen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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188
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Wang J, Ye Z, Huang THM, Shi H, Jin V. A survey of computational methods in transcriptome-wide alternative splicing analysis. Biomol Concepts 2016; 6:59-66. [PMID: 25719337 DOI: 10.1515/bmc-2014-0040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/13/2015] [Indexed: 11/15/2022] Open
Abstract
Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.
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189
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Lee SR, Adams PJ, Yue DT. Large Ca²⁺-dependent facilitation of Ca(V)2.1 channels revealed by Ca²⁺ photo-uncaging. J Physiol 2016; 593:2753-78. [PMID: 25809476 DOI: 10.1113/jp270091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/18/2015] [Indexed: 01/30/2023] Open
Abstract
KEY POINTS CaV 2.1 channels constitute a dominant Ca(2+) entry pathway into brain neurons, triggering downstream Ca(2+) -dependent processes such as neurotransmitter release. CaV 2.1 is itself modulated by Ca(2+) , resulting in activity-dependent enhancement of channel opening termed Ca(2+) -dependent facilitation (CDF). Real-time Ca(2+) imaging and Ca(2+) uncaging here reveal that CDF turns out to be strikingly faster, more Ca(2+) sensitive, and larger than anticipated on previous grounds. Robust resolution of the quantitative profile of CDF enables deduction of a realistic biophysical model for this process. These results suggest that CaV 2.1 CDF would figure most prominently in short-term synaptic plasticity and cerebellar Purkinje cell rhythmicity. ABSTRACT CaV 2.1 (P-type) voltage-gated Ca(2+) channels constitute a major source of neuronal Ca(2+) current, strongly influencing rhythmicity and triggering neurotransmitter release throughout the central nervous system. Fitting with such stature among Ca(2+) entry pathways, CaV 2.1 is itself feedback regulated by intracellular Ca(2+) , acting through calmodulin to facilitate channel opening. The precise neurophysiological role of this calcium-dependent facilitation (CDF) remains uncertain, however, in large measure because the very magnitude, Ca(2+) dependence and kinetics of CDF have resisted quantification by conventional means. Here, we utilize the photo-uncaging of Ca(2+) with CaV 2.1 channels fluxing Li(+) currents, so that voltage-dependent activation of channel gating is no longer conflated with Ca(2+) entry, and CDF is then driven solely by light-induced increases in Ca(2+) . By using this strategy, we now find that CDF can be unexpectedly large, enhancing currents by as much as twofold at physiological voltages. CDF is steeply Ca(2+) dependent, with a Hill coefficient of approximately two, a half-maximal effect reached by nearly 500 nm Ca(2+) , and Ca(2+) on/off kinetics in the order of milliseconds to tens of milliseconds. These properties were established for both native P-type currents in cerebellar Purkinje neurons, as well as their recombinant channel counterparts under heterologous expression. Such features suggest that CDF of CaV 2.1 channels may substantially enhance the regularity of rhythmic firing in cerebellar Purkinje neurons, where regularity is believed crucial for motor coordination. In addition, this degree of extensive CDF would be poised to exert large order-of-magnitude effects on short-term synaptic plasticity via rapid modulation of presynaptic Ca(2+) entry.
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Affiliation(s)
- Shin-Rong Lee
- Calcium Signals Laboratory, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Departments of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Paul J Adams
- Department of Biology, Kwantlen Polytechnic University, Surrey, BC, Canada, V3W 2M8
| | - David T Yue
- Calcium Signals Laboratory, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Departments of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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190
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Sutherland JM, Siddall NA, Hime GR, McLaughlin EA. RNA binding proteins in spermatogenesis: an in depth focus on the Musashi family. Asian J Androl 2016; 17:529-36. [PMID: 25851660 PMCID: PMC4492041 DOI: 10.4103/1008-682x.151397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Controlled gene regulation during gamete development is vital for maintaining reproductive potential. During the complex process of mammalian spermatogenesis, male germ cells experience extended periods of the inactive transcription despite heavy translational requirements for continued growth and differentiation. Hence, spermatogenesis is highly reliant on mechanisms of posttranscriptional regulation of gene expression, facilitated by RNA binding proteins (RBPs), which remain abundantly expressed throughout this process. One such group of proteins is the Musashi family, previously identified as critical regulators of testis germ cell development and meiosis in Drosophila, and also shown to be vital to sperm development and reproductive potential in the mouse. This review describes the role and function of RBPs within the scope of male germ cell development, focusing on our recent knowledge of the Musashi proteins in spermatogenesis. The functional mechanisms utilized by RBPs within the cell are outlined in depth, and the significance of sub-cellular localization and stage-specific expression in relation to the mode and impact of posttranscriptional regulation is also highlighted. We emphasize the historical role of the Musashi family of RBPs in stem cell function and cell fate determination, as originally characterized in Drosophila and Xenopus, and conclude with our current understanding of the differential roles and functions of the mammalian Musashi proteins, Musashi-1 and Musashi-2, with a primary focus on our findings in spermatogenesis. This review highlights both the essential contribution of RBPs to posttranscriptional regulation and the importance of the Musashi family as master regulators of male gamete development.
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Affiliation(s)
| | | | | | - Eileen A McLaughlin
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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191
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Song L, Sabunciyan S, Florea L. CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Res 2016; 44:e98. [PMID: 26975657 PMCID: PMC4889935 DOI: 10.1093/nar/gkw158] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2016] [Indexed: 11/29/2022] Open
Abstract
Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to accurately capture splicing variation has proven difficult. Current programs can find major isoforms of a gene but miss lower abundance variants, or are sensitive but imprecise. CLASS2 is a novel open source tool for accurate genome-guided transcriptome assembly from RNA-seq reads based on the model of splice graph. An extension of our program CLASS, CLASS2 jointly optimizes read patterns and the number of supporting reads to score and prioritize transcripts, implemented in a novel, scalable and efficient dynamic programming algorithm. When compared against reference programs, CLASS2 had the best overall accuracy and could detect up to twice as many splicing events with precision similar to the best reference program. Notably, it was the only tool to produce consistently reliable transcript models for a wide range of applications and sequencing strategies, including ribosomal RNA-depleted samples. Lightweight and multi-threaded, CLASS2 requires <3GB RAM and can analyze a 350 million read set within hours, and can be widely applied to transcriptomics studies ranging from clinical RNA sequencing, to alternative splicing analyses, and to the annotation of new genomes.
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Affiliation(s)
- Li Song
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Liliana Florea
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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192
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Moreno PMD, Santos JC, Gomes CP, Varela-Moreira A, Costa A, Leiro V, Mansur H, Pêgo AP. Delivery of Splice Switching Oligonucleotides by Amphiphilic Chitosan-Based Nanoparticles. Mol Pharm 2016; 13:344-56. [PMID: 26702499 DOI: 10.1021/acs.molpharmaceut.5b00538] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Splice switching oligonucleotides (SSOs) are a class of single-stranded antisense oligonucleotides (ssONs) being used as gene therapeutics and demonstrating great therapeutic potential. The availability of biodegradable and biocompatible delivery vectors that could improve delivery efficiencies, reduce dosage, and, in parallel, reduce toxicity concerns could be advantageous for clinical translation. In this work we explored the use of quaternized amphiphilic chitosan-based vectors in nanocomplex formation and delivery of splice switching oligonucleotides (SSO) into cells, while providing insights regarding cellular uptake of such complexes. Results show that the chitosan amphiphilic character is important when dealing with SSOs, greatly improving colloidal stability under serum conditions, as analyzed by dynamic light scattering, and enhancing cellular association. Nanocomplexes were found to follow an endolysosomal route with a long lysosome residence time. Conjugation of a hydrophobic moiety, stearic acid, to quaternized chitosan was a necessary condition to achieve transfection, as an unmodified quaternary chitosan was completely ineffective. We thus demonstrate that amphiphilic quaternized chitosan is a biomaterial that holds promise and warrants further development as a platform for SSO delivery strategies.
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Affiliation(s)
- Pedro M D Moreno
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal
| | - Joyce C Santos
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal.,CeNano2I, Department of Metallurgical and Materials Engineering, UFMG, 31270-901 Belo Horizonte, Brazil
| | - Carla P Gomes
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal.,Faculdade de Engenharia da UPorto (FEUP), 4200-319 Porto, Portugal
| | - Aida Varela-Moreira
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal.,Faculdade de Medicina da UPorto (FMUP), 4200-319 Porto, Portugal
| | - Artur Costa
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal
| | - Victoria Leiro
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal
| | - Herman Mansur
- CeNano2I, Department of Metallurgical and Materials Engineering, UFMG, 31270-901 Belo Horizonte, Brazil
| | - Ana P Pêgo
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto (UPorto) , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde , UPorto, 4200-135 Porto, Portugal.,Faculdade de Engenharia da UPorto (FEUP), 4200-319 Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS) , UPorto, 4050-313 Porto, Portugal
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193
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Muir R, Diot A, Poulton J. Mitochondrial content is central to nuclear gene expression: Profound implications for human health. Bioessays 2016; 38:150-6. [PMID: 26725055 PMCID: PMC4819685 DOI: 10.1002/bies.201500105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects on gene expression affecting the risk of degenerative diseases, cancer and ageing. In 2015 the UK parliament approved a change in the regulation of IVF techniques, allowing "Mitochondrial replacement therapy" to become a reproductive choice for women at risk of transmitting mitochondrial disease to their children. This is the first time that this technique will be available. Therefore understanding the interaction between mitochondria and the nucleus has never been more important.
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Affiliation(s)
- Rebecca Muir
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alan Diot
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Joanna Poulton
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
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194
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Reyes Román JF, Pastor Ó, Casamayor JC, Valverde F. Applying Conceptual Modeling to Better Understand the Human Genome. CONCEPTUAL MODELING 2016. [DOI: 10.1007/978-3-319-46397-1_31] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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195
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Hestand MS, Zeng Z, Coleman SJ, Liu J, MacLeod JN. Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression. PLoS One 2015; 10:e0144302. [PMID: 26713731 PMCID: PMC4695084 DOI: 10.1371/journal.pone.0144302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/16/2015] [Indexed: 12/29/2022] Open
Abstract
Cellular mechanisms that achieve protein diversity in eukaryotes are multifaceted, including transcriptional components such as RNA splicing. Through alternative splicing, a single protein-coding gene can generate multiple mRNA transcripts and protein isoforms, some of which are tissue-specific. We have conducted qualitative and quantitative analyses of the Bodymap 2.0 messenger RNA-sequencing data from 16 human tissue samples and identified 209,363 splice junctions. Of these, 22,231 (10.6%) were not previously annotated and 21,650 (10.3%) were expressed in a tissue-restricted pattern. Tissue-restricted alternative splicing was found to be widespread, with approximately 65% of expressed multi-exon genes containing at least one tissue-specific splice junction. Interestingly, we observed many tissue-specific splice junctions not only in genes expressed in one or a few tissues, but also from gene loci with a broad pattern of expression.
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Affiliation(s)
- Matthew S. Hestand
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - Zheng Zeng
- Department of Computer Science, University of Kentucky, Lexington, KY, United States of America
| | - Stephen J. Coleman
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, KY, United States of America
| | - James N. MacLeod
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
- * E-mail:
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196
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Faigenbloom L, Rubinstein ND, Kloog Y, Mayrose I, Pupko T, Stein R. Regulation of alternative splicing at the single-cell level. Mol Syst Biol 2015; 11:845. [PMID: 26712315 PMCID: PMC4704489 DOI: 10.15252/msb.20156278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a key cellular mechanism for generating distinct isoforms, whose relative abundances regulate critical cellular processes. It is therefore essential that inclusion levels of alternative exons be tightly regulated. However, how the precision of inclusion levels among individual cells is governed is poorly understood. Using single-cell gene expression, we show that the precision of inclusion levels of alternative exons is determined by the degree of evolutionary conservation at their flanking intronic regions. Moreover, the inclusion levels of alternative exons, as well as the expression levels of the transcripts harboring them, also contribute to this precision. We further show that alternative exons whose inclusion levels are considerably changed during stem cell differentiation are also subject to this regulation. Our results imply that alternative splicing is coordinately regulated to achieve accuracy in relative isoform abundances and that such accuracy may be important in determining cell fate.
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Affiliation(s)
- Lior Faigenbloom
- The Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nimrod D Rubinstein
- The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yoel Kloog
- The Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itay Mayrose
- The Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Reuven Stein
- The Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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197
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Zizzo C, Monte I, Pisani A, Fatuzzo P, Riccio E, Rodolico MS, Colomba P, Uva M, Cammarata G, Alessandro R, Iemolo F, Duro G. Molecular and clinical studies in five index cases with novel mutations in the GLA gene. Gene 2015; 578:100-4. [PMID: 26691501 DOI: 10.1016/j.gene.2015.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
Fabry disease is a metabolic and lysosomal storage disorder caused by the functional defect of the α-galactosidase A enzyme; this defect is due to mutations in the GLA gene, that is composed of seven exons and is located on the long arm of the X-chromosome (Xq21-22). The enzymatic deficit is responsible for the accumulation of glycosphingolipids in lysosomes of different cellular types, mainly in those ones of vascular endothelium. It consequently causes a cellular and microvascular dysfunction. In this paper, we described five novel mutations in the GLA gene, related to absent enzymatic activity and typical manifestations of Fabry disease. We identified three mutations (c.846_847delTC, p.E341X and p.C382X) that lead to the introduction of a stop codon in positions 297, 341 and 382. Moreover we found a missense mutation (p.R227P) in the exon 5 of the GLA gene and a single point mutation (c.639+5 G>T) occurring five base pairs beyond the end of the exon 4. These mutations have never been found in our group of healthy control subjects >2300. The studied patients presented some clinical manifestations, such as cornea verticillata, hypo-anhidrosis, left ventricular hypertrophy, cerebrovascular disorders and renal failure, that, considering the null enzymatic activity, suggest that the new mutations reported here are related to the classic form of Fabry disease. The identification of novel mutations in patients with symptomatology referable to FD increases the molecular knowledge of the GLA gene and it gives clinicians an important support for the proper diagnosis of the disease.
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Affiliation(s)
- Carmela Zizzo
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy.
| | - Ines Monte
- Clinical Echocardiography, Research and Training European CVI Laboratory, Cardio-Thorax-Vascular Transplant Department, Policlinic "G. Rodolico" of University, Catania, Italy
| | - Antonio Pisani
- Department of Public Health, Section of Nephrology, Federico II University of Naples, Italy
| | - Pasquale Fatuzzo
- Internal Medicine, Nephrology and Dialysis Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Eleonora Riccio
- Department of Public Health, Section of Nephrology, Federico II University of Naples, Italy
| | | | - Paolo Colomba
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
| | - Maurizio Uva
- Operative Unit of Ophthalmology, University of Catania, Italy
| | - Giuseppe Cammarata
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
| | - Riccardo Alessandro
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy; Department of Biopathology and Medical Biotechnology, University of Palermo, Italy
| | - Francesco Iemolo
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
| | - Giovanni Duro
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
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198
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Huertas CS, Carrascosa LG, Bonnal S, Valcárcel J, Lechuga LM. Quantitative evaluation of alternatively spliced mRNA isoforms by label-free real-time plasmonic sensing. Biosens Bioelectron 2015; 78:118-125. [PMID: 26599481 DOI: 10.1016/j.bios.2015.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/16/2015] [Accepted: 11/09/2015] [Indexed: 12/12/2022]
Abstract
Alternative splicing of mRNA precursors enables cells to generate different protein outputs from the same gene depending on their developmental or homeostatic status. Its deregulation is strongly linked to disease onset and progression. Current methodologies for monitoring alternative splicing demand elaborate procedures and often present difficulties in discerning between closely related isoforms, e.g. due to cross-hybridization during their detection. Herein, we report a general methodology using a Surface Plasmon Resonance (SPR) biosensor for label-free monitoring of alternative splicing events in real-time, without any cDNA synthesis or PCR amplification requirements. We applied this methodology to RNA isolated from HeLa cells for the quantification of alternatively spliced isoforms of the Fas gene, involved in cancer progression through regulation of programmed cell death. We demonstrate that our methodology is isoform-specific, with virtually no cross-hybridization, achieving limits of detection (LODs) in the picoMolar (pM) range. Similar results were obtained for the detection of the BCL-X gene mRNA isoforms. The results were independently validated by RT-qPCR, with excellent concordance in the determination of isoform ratios. The simplicity and robustness of this biosensor technology can greatly facilitate the exploration of alternative splicing biomarkers in disease diagnosis and therapy.
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Affiliation(s)
- César S Huertas
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - L G Carrascosa
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - S Bonnal
- Centre de Regulació Genòmica and The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - J Valcárcel
- Centre de Regulació Genòmica and The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Spain
| | - L M Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
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199
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Tang Y, Wang H, Wei B, Guo Y, Gu L, Yang Z, Zhang Q, Wu Y, Yuan Q, Zhao G, Ji G. CUG-BP1 regulates RyR1 ASI alternative splicing in skeletal muscle atrophy. Sci Rep 2015; 5:16083. [PMID: 26531141 PMCID: PMC4632035 DOI: 10.1038/srep16083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
RNA binding protein is identified as an important mediator of aberrant alternative splicing in muscle atrophy. The altered splicing of calcium channels, such as ryanodine receptors (RyRs), plays an important role in impaired excitation-contraction (E-C) coupling in muscle atrophy; however, the regulatory mechanisms of ryanodine receptor 1 (RyR1) alternative splicing leading to skeletal muscle atrophy remains to be investigated. In this study we demonstrated that CUG binding protein 1 (CUG-BP1) was up-regulated and the alternative splicing of RyR1 ASI (exon70) was aberrant during the process of neurogenic muscle atrophy both in human patients and mouse models. The gain and loss of function experiments in vivo demonstrated that altered splicing pattern of RyR1 ASI was directly mediated by an up-regulated CUG-BP1 function. Furthermore, we found that CUG-BP1 affected the calcium release activity in single myofibers and the extent of atrophy was significantly reduced upon gene silencing of CUG-BP1 in atrophic muscle. These findings improve our understanding of calcium signaling related biological function of CUG-BP1 in muscle atrophy. Thus, we provide an intriguing perspective of involvement of mis-regulated RyR1 splicing in muscular disease.
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Affiliation(s)
- Yinglong Tang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huiwen Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Bin Wei
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Yuting Guo
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Gu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguang Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Zhang
- Department of Anesthesiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Yanyun Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Qi Yuan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, Forth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Guangju Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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200
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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