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Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.
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Affiliation(s)
- Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lourdes Ruiz Desviat
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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2
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Kordala AJ, Stoodley J, Ahlskog N, Hanifi M, Garcia Guerra A, Bhomra A, Lim WF, Murray LM, Talbot K, Hammond SM, Wood MJA, Rinaldi C. PRMT inhibitor promotes SMN2 exon 7 inclusion and synergizes with nusinersen to rescue SMA mice. EMBO Mol Med 2023; 15:e17683. [PMID: 37724723 PMCID: PMC10630883 DOI: 10.15252/emmm.202317683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of infant mortality. The advent of approved treatments for this devastating condition has significantly changed SMA patients' life expectancy and quality of life. Nevertheless, these are not without limitations, and research efforts are underway to develop new approaches for improved and long-lasting benefits for patients. Protein arginine methyltransferases (PRMTs) are emerging as druggable epigenetic targets, with several small-molecule PRMT inhibitors already in clinical trials. From a screen of epigenetic molecules, we have identified MS023, a potent and selective type I PRMT inhibitor able to promote SMN2 exon 7 inclusion in preclinical SMA models. Treatment of SMA mice with MS023 results in amelioration of the disease phenotype, with strong synergistic amplification of the positive effect when delivered in combination with the antisense oligonucleotide nusinersen. Moreover, transcriptomic analysis revealed that MS023 treatment has minimal off-target effects, and the added benefit is mainly due to targeting neuroinflammation. Our study warrants further clinical investigation of PRMT inhibition both as a stand-alone and add-on therapy for SMA.
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Affiliation(s)
- Anna J Kordala
- Department of Physiology Anatomy and GeneticsUniversity of OxfordOxfordUK
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Jessica Stoodley
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Nina Ahlskog
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | | | - Antonio Garcia Guerra
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Amarjit Bhomra
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Wooi Fang Lim
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Lyndsay M Murray
- Centre for Discovery Brain Sciences, College of Medicine and Veterinary MedicineUniversity of EdinburghEdinburghUK
- Euan McDonald Centre for Motor Neuron Disease ResearchUniversity of EdinburghEdinburghUK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, John Radcliffe HospitalUniversity of OxfordOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | | | - Matthew JA Wood
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
- MDUK Oxford Neuromuscular CentreOxfordUK
| | - Carlo Rinaldi
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
- MDUK Oxford Neuromuscular CentreOxfordUK
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Jiang T, Qu R, Liu X, Hou Y, Wang L, Hua Y. HnRNPR strongly represses splicing of a critical exon associated with spinal muscular atrophy through binding to an exonic AU-rich element. J Med Genet 2023; 60:1105-1115. [PMID: 37225410 DOI: 10.1136/jmg-2023-109186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/08/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a motor neuron disease caused by mutations of survival of motor neuron 1 (SMN1) gene, which encodes the SMN protein. SMN2, a nearly identical copy of SMN1, with several single-nucleotide substitutions leading to predominant skipping of its exon 7, is insufficient to compensate for loss of SMN1. Heterogeneous nuclear ribonucleoprotein R (hnRNPR) has been previously shown to interact with SMN in the 7SK complex in motoneuron axons and is implicated in the pathogenesis of SMA. Here, we show that hnRNPR also interacts with SMN1/2 pre-mRNAs and potently inhibits exon 7 inclusion. METHODS In this study, to examine the mechanism that hnRNPR regulates SMN1/2 splicing, deletion analysis in an SMN2 minigene system, RNA-affinity chromatography, co-overexpression analysis and tethering assay were performed. We screened antisense oligonucleotides (ASOs) in a minigene system and identified a few that markedly promoted SMN2 exon 7 splicing. RESULTS We pinpointed an AU-rich element located towards the 3' end of the exon that mediates splicing repression by hnRNPR. We uncovered that both hnRNPR and Sam68 bind to the element in a competitive manner, and the inhibitory effect of hnRNPR is much stronger than Sam68. Moreover, we found that, among the four hnRNPR splicing isoforms, the exon 5-skipped one has the minimal inhibitory effect, and ASOs inducing hnRNPR exon 5 skipping also promote SMN2 exon 7 inclusion. CONCLUSION We identified a novel mechanism that contributes to mis-splicing of SMN2 exon 7.
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Affiliation(s)
- Tao Jiang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Ruobing Qu
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
- College of Chemistry Chemical Engineering and Materials Science, Soochow University, Suzhou, Jiangsu, China
| | - Xuan Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu, China
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu, China
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Joudaki A, Takeda JI, Masuda A, Ode R, Fujiwara K, Ohno K. FexSplice: A LightGBM-Based Model for Predicting the Splicing Effect of a Single Nucleotide Variant Affecting the First Nucleotide G of an Exon. Genes (Basel) 2023; 14:1765. [PMID: 37761905 PMCID: PMC10531444 DOI: 10.3390/genes14091765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported that Fex-SNVs affect splicing when the length of the polypyrimidine tract is short or degenerate. However, we cannot readily predict the splicing effects of Fex-SNVs. We here scrutinized the available literature and identified 106 splicing-affecting Fex-SNVs based on experimental evidence. We similarly identified 106 neutral Fex-SNVs in the dbSNP database with a global minor allele frequency (MAF) of more than 0.01 and less than 0.50. We extracted 115 features representing the strength of splicing cis-elements and developed machine-learning models with support vector machine, random forest, and gradient boosting to discriminate splicing-affecting and neutral Fex-SNVs. Gradient boosting-based LightGBM outperformed the other two models, and the length and nucleotide compositions of the polypyrimidine tract played critical roles in the discrimination. Recursive feature elimination showed that the LightGBM model using 15 features achieved the best performance with an accuracy of 0.80 ± 0.12 (mean and SD), a Matthews Correlation Coefficient (MCC) of 0.57 ± 0.15, an area under the curve of the receiver operating characteristics curve (AUROC) of 0.86 ± 0.08, and an area under the curve of the precision-recall curve (AUPRC) of 0.87 ± 0.09 using a 10-fold cross-validation. We developed a web service program, named FexSplice that accepts a genomic coordinate either on GRCh37/hg19 or GRCh38/hg38 and returns a predicted probability of aberrant splicing of A, C, and T variants.
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Affiliation(s)
- Atefeh Joudaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Rikumo Ode
- Department of Materials Science and Engineering, Nagoya University Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.O.); (K.F.)
| | - Koichi Fujiwara
- Department of Materials Science and Engineering, Nagoya University Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.O.); (K.F.)
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
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Wang L, Ji Y, Chen Y, Bai J, Gao P, Feng P. A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy. Hum Mol Genet 2023; 32:971-983. [PMID: 36255739 DOI: 10.1093/hmg/ddac260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a fatal neuromuscular disease caused by homozygous deletions or mutations of the SMN1 gene. SMN2 is a paralogous gene of SMN1 and a modifying gene of SMA. A better understanding of how SMN2 exon 7 splicing is regulated helps discover new therapeutic targets for SMA therapy. Based on an antisense walk method to map exonic and intronic splicing silencers (ESSs and ISSs) in SMN2 exon 7 and the proximal regions of its flanking introns, we identified one ISS (ISS6-KH) at upstream of the branch point site in intron 6. By using mutagenesis-coupled RT-PCR with SMN1/2 minigenes, immunochromatography, overexpression and siRNA-knockdown, we found this ISS consists of a bipartite hnRNP A1 binding cis-element and a poly-U sequence located between the proximal hnRNP A1 binding site (UAGCUA) and the branch site. Both HuR and hnRNP C1 proteins promote exon 7 skipping through the poly-U stretch. Mutations or deletions of these motifs lead to efficient SMN2 exon 7 inclusion comparable to SMN1 gene. Furthermore, we identified an optimal antisense oligonucleotide that binds the intron six ISS and causes striking exon 7 inclusion in the SMN2 gene in patient fibroblasts and SMA mouse model. Our findings demonstrate that this novel ISS plays an important role in SMN2 exon 7 skipping and highlight a new therapeutic target for SMA therapy.
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Affiliation(s)
- Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yinfeng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuqing Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pengchao Feng
- Nanjing Antisense Biopharmaceutical Co., Ltd, Nanjing 210046, China
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6
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Qiu J, Qu R, Lin M, Xu J, Zhu Q, Zhang Z, Sun J. Position-dependent effects of hnRNP A1/A2 in SMN1/2 exon7 splicing. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194875. [DOI: 10.1016/j.bbagrm.2022.194875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/08/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
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7
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Kanda S, Moulton E, Butchbach MER. Effects of inhibitors of SLC9A-type sodium-protein exchangers on Survival Motor Neuron 2 ( SMN2) mRNA splicing and expression. Mol Pharmacol 2022; 102:92-105. [PMID: 35667685 PMCID: PMC9341265 DOI: 10.1124/molpharm.122.000529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive, pediatric-onset disorder caused by the loss of spinal motor neurons thereby leading to muscle atrophy. SMA is caused by the loss of or mutations in the survival motor neuron 1 (SMN1) gene. SMN1 is duplicated in humans to give rise to the paralogous SMN2 gene. This paralog is nearly identical except for a cytosine to thymine (C-to-T) transition within an exonic splicing enhancer (ESE) element within exon 7. As a result, the majority of SMN2 transcripts lack exon 7 (SMNΔ7) which produces a truncated and unstable SMN protein. Since SMN2 copy number is inversely related to disease severity, it is a well-established target for SMA therapeutics development. 5-(N-ethyl-N-isopropyl)amiloride (EIPA), an inhibitor of sodium/proton exchangers (NHEs), has previously been shown to increase exon 7 inclusion and SMN protein levels in SMA cells. In this study, NHE inhibitors were evaluated for their ability to modulate SMN2 expression. EIPA as well as 5-(N,N-hexamethylene)amiloride (HMA) increase exon 7 inclusion in SMN2 splicing reporter lines as well as in SMA fibroblasts. The EIPA-induced exon 7 inclusion occurs via a unique mechanism that does not involve previously identified splicing factors. Transcriptome analysis identified novel targets, including TIA1 and FABP3, for further characterization. EIPA and HMA are more selective at inhibiting the NHE5 isoform, which is expressed in fibroblasts as well as in neuronal cells. These results show that NHE5 inhibition increases SMN2 expression and may be a novel target for therapeutics development. Significance Statement This study demonstrates a molecular mechanism by which inhibitors of the sodium-protein exchanger increase the alternative splicing of SMN2 in spinal muscular atrophy cells. NHE5 selective inhibitors increase the inclusion of full-length SMN2 mRNAs by targeting TIA1 and FABP3 expression, which is distinct from other small molecule regulators of SMN2 alternative splicing. This study provides a novel means to increase full-length SMN2 expression and a novel target for therapeutics development.
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Affiliation(s)
- Sambee Kanda
- Biological Sciences, University of Delaware, United States
| | - Emily Moulton
- Biomedical Research, Nemours Children's Hospital Delaware, United States
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8
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Holm LL, Doktor TK, Hansen MB, Petersen USS, Andresen BS. Vulnerable exons, like ACADM exon 5, are highly dependent on maintaining a correct balance between splicing enhancers and silencers. Hum Mutat 2021; 43:253-265. [PMID: 34923709 DOI: 10.1002/humu.24321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022]
Abstract
It is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affecting cis-acting splicing regulatory elements, but there is a misconception that all exons have an equal dependency on splicing regulatory elements and thus a similar susceptibility to aberrant splicing. We investigated exonic mutations in ACADM exon 5 to experimentally examine their effect on splicing and found that 7 out of 11 tested mutations affected exon inclusion, demonstrating that this constitutive exon is particularly vulnerable to exonic splicing mutations. Employing ACADM exon 5 and 6 as models, we demonstrate that the balance between splicing enhancers and silencers, flanking intron length, and flanking splice site strength are important factors that determine exon definition and splicing efficiency of the exon in question. Our study shows that two constitutive exons in ACADM have different inherent vulnerabilities to exonic splicing mutations. This suggests that in silico prediction of potential pathogenic effects on splicing from exonic mutations may be improved by also considering the inherent vulnerability of the exon. Moreover, we show that single nucleotide polymorphism that affect either of two different exonic splicing silencers, located far apart in exon 5, all protect against both immediately flanking and more distant exonic splicing mutations.
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Affiliation(s)
- Lise L Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Michael B Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
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Hujová P, Souček P, Radová L, Kramárek M, Kováčová T, Freiberger T. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. Cell Mol Life Sci 2021; 78:6979-6993. [PMID: 34596691 PMCID: PMC11072513 DOI: 10.1007/s00018-021-03943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022]
Abstract
Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.
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Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic.
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic.
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
| | - Tatiana Kováčová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
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10
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Thibault PA, Ganesan A, Kalyaanamoorthy S, Clarke JPWE, Salapa HE, Levin MC. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease. BIOLOGY 2021; 10:biology10080712. [PMID: 34439945 PMCID: PMC8389229 DOI: 10.3390/biology10080712] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022]
Abstract
The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not been clearly differentiated. Herein, we provide a comprehensive assembly of the literature on these proteins. We find that there are critical gaps in our grasp of A/B proteins' alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and propose that future mechanistic research integrating multiple A/B proteins will significantly improve our understanding of how this essential protein family contributes to cell homeostasis and disease.
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Affiliation(s)
- Patricia A. Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Aravindhan Ganesan
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Joseph-Patrick W. E. Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Hannah E. Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Michael C. Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Correspondence:
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11
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Ryu HG, Jung Y, Lee N, Seo JY, Kim SW, Lee KH, Kim DY, Kim KT. HNRNP A1 Promotes Lung Cancer Cell Proliferation by Modulating VRK1 Translation. Int J Mol Sci 2021; 22:ijms22115506. [PMID: 34071140 PMCID: PMC8197126 DOI: 10.3390/ijms22115506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 01/12/2023] Open
Abstract
THeterogeneous nuclear ribonucleoprotein (HNRNP) A1 is the most abundant and ubiquitously expressed member of the HNRNP protein family. In recent years, it has become more evident that HNRNP A1 contributes to the development of neurodegenerative diseases. However, little is known about the underlying role of HNRNP A1 in cancer development. Here, we report that HNRNP A1 expression is significantly increased in lung cancer tissues and is negatively correlated with the overall survival of patients with lung cancer. Additionally, HNRNP A1 positively regulates vaccinia-related kinase 1 (VRK1) translation via binding directly to the 3′ untranslated region (UTR) of VRK1 mRNA, thus increasing cyclin D1 (CCND1) expression by VRK1-mediated phosphorylation of the cAMP response element–binding protein (CREB). Furthermore, HNRNP A1 binding to the cis-acting region of the 3′UTR of VRK1 mRNA contributes to increased lung cancer cell proliferation. Thus, our study unveils a novel role of HNRNP A1 in lung carcinogenesis via post-transcriptional regulation of VRK1 expression and suggests its potential as a therapeutic target for patients with lung cancer.
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Affiliation(s)
- Hye Guk Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea;
| | - Youngseob Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (Y.J.); (J.-Y.S.); (S.W.K.)
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01065, USA;
| | - Ji-Young Seo
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (Y.J.); (J.-Y.S.); (S.W.K.)
| | - Sung Wook Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (Y.J.); (J.-Y.S.); (S.W.K.)
| | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Gyeongsan 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea;
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea;
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (Y.J.); (J.-Y.S.); (S.W.K.)
- Correspondence: ; Tel.: +82-54-279-2297
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12
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McCormack NM, Abera MB, Arnold ES, Gibbs RM, Martin SE, Buehler E, Chen YC, Chen L, Fischbeck KH, Burnett BG. A high-throughput genome-wide RNAi screen identifies modifiers of survival motor neuron protein. Cell Rep 2021; 35:109125. [PMID: 33979606 PMCID: PMC8679797 DOI: 10.1016/j.celrep.2021.109125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/17/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a debilitating neurological disorder marked by degeneration of spinal motor neurons and muscle atrophy. SMA results from mutations in survival motor neuron 1 (SMN1), leading to deficiency of survival motor neuron (SMN) protein. Current therapies increase SMN protein and improve patient survival but have variable improvements in motor function, making it necessary to identify complementary strategies to further improve disease outcomes. Here, we perform a genome-wide RNAi screen using a luciferase-based activity reporter and identify genes involved in regulating SMN gene expression, RNA processing, and protein stability. We show that reduced expression of Transcription Export complex components increases SMN levels through the regulation of nuclear/cytoplasmic RNA transport. We also show that the E3 ligase, Neurl2, works cooperatively with Mib1 to ubiquitinate and promote SMN degradation. Together, our screen uncovers pathways through which SMN expression is regulated, potentially revealing additional strategies to treat SMA. Treatments for spinal muscular atrophy aim to increase survival motor neuron (SMN) protein. Using a genome-wide RNAi screen, McCormack et al. identify modifiers of SMN expression, including genes that are involved in transcription regulation, RNA processing, and protein stability.
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Affiliation(s)
- Nikki M McCormack
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Mahlet B Abera
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Eveline S Arnold
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Rebecca M Gibbs
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Scott E Martin
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Eugen Buehler
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Yu-Chi Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Lu Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Barrington G Burnett
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA.
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13
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Clarke JP, Thibault PA, Salapa HE, Levin MC. A Comprehensive Analysis of the Role of hnRNP A1 Function and Dysfunction in the Pathogenesis of Neurodegenerative Disease. Front Mol Biosci 2021; 8:659610. [PMID: 33912591 PMCID: PMC8072284 DOI: 10.3389/fmolb.2021.659610] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a member of the hnRNP family of conserved proteins that is involved in RNA transcription, pre-mRNA splicing, mRNA transport, protein translation, microRNA processing, telomere maintenance and the regulation of transcription factor activity. HnRNP A1 is ubiquitously, yet differentially, expressed in many cell types, and due to post-translational modifications, can vary in its molecular function. While a plethora of knowledge is known about the function and dysfunction of hnRNP A1 in diseases other than neurodegenerative disease (e.g., cancer), numerous studies in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, multiple sclerosis, spinal muscular atrophy, Alzheimer’s disease, and Huntington’s disease have found that the dysregulation of hnRNP A1 may contribute to disease pathogenesis. How hnRNP A1 mechanistically contributes to these diseases, and whether mutations and/or altered post-translational modifications contribute to pathogenesis, however, is currently under investigation. The aim of this comprehensive review is to first describe the background of hnRNP A1, including its structure, biological functions in RNA metabolism and the post-translational modifications known to modify its function. With this knowledge, the review then describes the influence of hnRNP A1 in neurodegenerative disease, and how its dysfunction may contribute the pathogenesis.
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Affiliation(s)
- Joseph P Clarke
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael C Levin
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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14
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Frederiksen SB, Holm LL, Larsen MR, Doktor TK, Andersen HS, Hastings ML, Hua Y, Krainer AR, Andresen BS. Identification of SRSF10 as a regulator of SMN2 ISS-N1. Hum Mutat 2020; 42:246-260. [PMID: 33300159 DOI: 10.1002/humu.24149] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/22/2020] [Accepted: 12/06/2020] [Indexed: 01/02/2023]
Abstract
Understanding the splicing code can be challenging as several splicing factors bind to many splicing-regulatory elements. The SMN1 and SMN2 silencer element ISS-N1 is the target of the antisense oligonucleotide drug, Spinraza, which is the treatment against spinal muscular atrophy. However, limited knowledge about the nature of the splicing factors that bind to ISS-N1 and inhibit splicing exists. It is likely that the effect of Spinraza comes from blocking binding of these factors, but so far, an unbiased characterization has not been performed and only members of the hnRNP A1/A2 family have been identified by Western blot analysis and nuclear magnetic resonance to bind to this silencer. Employing an MS/MS-based approach and surface plasmon resonance imaging, we show for the first time that splicing factor SRSF10 binds to ISS-N1. Furthermore, using splice-switching oligonucleotides we modulated the splicing of the SRSF10 isoforms generating either the long or the short protein isoform of SRSF10 to regulate endogenous SMN2 exon 7 inclusion. We demonstrate that the isoforms of SRSF10 regulate SMN1 and SMN2 splicing with different strength correlating with the length of their RS domain. Our results suggest that the ratio between the SRSF10 isoforms is important for splicing regulation.
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Affiliation(s)
- Sabrina B Frederiksen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Lise L Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Henriette S Andersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Center for Genetic Diseases, Chicago Medical School and School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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15
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Auslander N, Ramos DM, Zelaya I, Karathia H, Crawford TO, Schäffer AA, Sumner CJ, Ruppin E. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases. Mol Syst Biol 2020; 16:e9701. [PMID: 33438800 PMCID: PMC7754056 DOI: 10.15252/msb.20209701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre-mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient-derived cells leads to increased full-length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.
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Affiliation(s)
- Noam Auslander
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of HealthBethesdaMDUSA
| | - Daniel M Ramos
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivette Zelaya
- Interdepartmental Program in BioinformaticsUniversity of California Los AngelesLos AngelesCAUSA
| | - Hiren Karathia
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer InstituteNational Institutes of HealthMDUSA
| | - Thomas O. Crawford
- Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Charlotte J Sumner
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
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16
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Low YH, Asi Y, Foti SC, Lashley T. Heterogeneous Nuclear Ribonucleoproteins: Implications in Neurological Diseases. Mol Neurobiol 2020; 58:631-646. [PMID: 33000450 PMCID: PMC7843550 DOI: 10.1007/s12035-020-02137-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are a complex and functionally diverse family of RNA binding proteins with multifarious roles. They are involved, directly or indirectly, in alternative splicing, transcriptional and translational regulation, stress granule formation, cell cycle regulation, and axonal transport. It is unsurprising, given their heavy involvement in maintaining functional integrity of the cell, that their dysfunction has neurological implications. However, compared to their more established roles in cancer, the evidence of hnRNP implication in neurological diseases is still in its infancy. This review aims to consolidate the evidences for hnRNP involvement in neurological diseases, with a focus on spinal muscular atrophy (SMA), Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), multiple sclerosis (MS), congenital myasthenic syndrome (CMS), and fragile X-associated tremor/ataxia syndrome (FXTAS). Understanding more about hnRNP involvement in neurological diseases can further elucidate the pathomechanisms involved in these diseases and perhaps guide future therapeutic advances.
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Affiliation(s)
- Yi-Hua Low
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Duke-NUS Medical School, Singapore, Singapore
| | - Yasmine Asi
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sandrine C Foti
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK. .,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
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17
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Kováčová T, Souček P, Hujová P, Freiberger T, Grodecká L. Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition. Int J Mol Sci 2020; 21:ijms21186553. [PMID: 32911621 PMCID: PMC7554774 DOI: 10.3390/ijms21186553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023] Open
Abstract
Acceptor splice site recognition (3′ splice site: 3′ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3′ss, of which U2AF35 has a dual function: (i) It binds to the intron–exon border of some 3′ss and (ii) mediates enhancer-binding splicing activators’ interactions with the spliceosome. Alternative mechanisms for 3′ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3′ss recognition where the intron–exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3′ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3′ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons’ inclusion. Most probably, both factors stochastically bind the 3′ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3′ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants’ effects on splicing.
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Affiliation(s)
- Tatiana Kováčová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Přemysl Souček
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Pavla Hujová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Correspondence:
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18
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Bruun GH, Bang JMV, Christensen LL, Brøner S, Petersen USS, Guerra B, Grønning AGB, Doktor TK, Andresen BS. Blocking of an intronic splicing silencer completely rescues IKBKAP exon 20 splicing in familial dysautonomia patient cells. Nucleic Acids Res 2019; 46:7938-7952. [PMID: 29762696 PMCID: PMC6125618 DOI: 10.1093/nar/gky395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 04/30/2018] [Indexed: 12/22/2022] Open
Abstract
Familial dysautonomia (FD) is a severe genetic disorder causing sensory and autonomic dysfunction. It is predominantly caused by a c.2204+6T>C mutation in the IKBKAP gene. This mutation decreases the 5′ splice site strength of IKBKAP exon 20 leading to exon 20 skipping and decreased amounts of full-length IKAP protein. We identified a binding site for the splicing regulatory protein hnRNP A1 downstream of the IKBKAP exon 20 5′-splice site. We show that hnRNP A1 binds to this splicing regulatory element (SRE) and that two previously described inhibitory SREs inside IKBKAP exon 20 are also bound by hnRNP A1. Knockdown of hnRNP A1 in FD patient fibroblasts increases IKBKAP exon 20 inclusion demonstrating that hnRNP A1 is a negative regulator of IKBKAP exon 20 splicing. Furthermore, by mutating the SREs in an IKBKAP minigene we show that all three SREs cause hnRNP A1-mediated exon repression. We designed splice switching oligonucleotides (SSO) that blocks the intronic hnRNP A1 binding site, and demonstrate that this completely rescues splicing of IKBKAP exon 20 in FD patient fibroblasts and increases the amounts of IKAP protein. We propose that this may be developed into a potential new specific treatment of FD.
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Affiliation(s)
- Gitte H Bruun
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jeanne M V Bang
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Lise L Christensen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Sabrina Brøner
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Barbara Guerra
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Alexander G B Grønning
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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19
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Singh RN, Singh NN. Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes. ADVANCES IN NEUROBIOLOGY 2018; 20:31-61. [PMID: 29916015 DOI: 10.1007/978-3-319-89689-2_2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% cases of SMA result from deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. However, correction of SMN2 exon 7 splicing has proven to confer therapeutic benefits in SMA patients. The only approved drug for SMA is an antisense oligonucleotide (Spinraza™/Nusinersen), which corrects SMN2 exon 7 splicing by blocking intronic splicing silencer N1 (ISS-N1) located immediately downstream of exon 7. ISS-N1 is a complex regulatory element encompassing overlapping negative motifs and sequestering a cryptic splice site. More than 40 protein factors have been implicated in the regulation of SMN exon 7 splicing. There is evidence to support that multiple exons of SMN are alternatively spliced during oxidative stress, which is associated with a growing number of pathological conditions. Here, we provide the most up to date account of the mechanism of splicing regulation of the SMN genes.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
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20
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Beusch I, Barraud P, Moursy A, Cléry A, Allain FHT. Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7. eLife 2017. [PMID: 28650318 PMCID: PMC5503513 DOI: 10.7554/elife.25736] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic. DOI:http://dx.doi.org/10.7554/eLife.25736.001
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Affiliation(s)
- Irene Beusch
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire d'expression génétique microbienne, UMR 8261, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de biologie physico-chimique, Paris, France
| | - Ahmed Moursy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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21
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Hillebrand F, Peter JO, Brillen AL, Otte M, Schaal H, Erkelenz S. Differential hnRNP D isoform incorporation may confer plasticity to the ESSV-mediated repressive state across HIV-1 exon 3. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:205-217. [PMID: 27919832 DOI: 10.1016/j.bbagrm.2016.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/22/2016] [Accepted: 12/01/2016] [Indexed: 11/27/2022]
Abstract
Even though splicing repression by hnRNP complexes bound to exonic sequences is well-documented, the responsible effector domains of hnRNP proteins have been described for only a select number of hnRNP constituents. Thus, there is only limited information available for possible varying silencer activities amongst different hnRNP proteins and composition changes within possible hnRNP complex assemblies. In this study, we identified the glycine-rich domain (GRD) of hnRNP proteins as a unifying feature in splice site repression. We also show that all four hnRNP D isoforms can act as genuine splicing repressors when bound to exonic positions. The presence of an extended GRD, however, seemed to potentiate the hnRNP D silencer activity of isoforms p42 and p45. Moreover, we demonstrate that hnRNP D proteins associate with the HIV-1 ESSV silencer complex, probably through direct recognition of "UUAG" sequences overlapping with the previously described "UAGG" motifs bound by hnRNP A1. Consequently, this spatial proximity seems to cause mutual interference between hnRNP A1 and hnRNP D. This interplay between hnRNP A1 and D facilitates a dynamic regulation of the repressive state of HIV-1 exon 3 which manifests as fluctuating relative levels of spliced vpr- and unspliced gag/pol-mRNAs.
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Affiliation(s)
- Frank Hillebrand
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jan Otto Peter
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marianne Otte
- Institute of Evolutionary Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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22
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Palhais B, Dembic M, Sabaratnam R, Nielsen KS, Doktor TK, Bruun GH, Andresen BS. The prevalent deep intronic c. 639+919 G>A GLA mutation causes pseudoexon activation and Fabry disease by abolishing the binding of hnRNPA1 and hnRNP A2/B1 to a splicing silencer. Mol Genet Metab 2016; 119:258-269. [PMID: 27595546 DOI: 10.1016/j.ymgme.2016.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 11/21/2022]
Abstract
Fabry disease is an X-linked recessive inborn disorder of the glycosphingolipid metabolism, caused by total or partial deficiency of the lysosomal α-galactosidase A enzyme due to mutations in the GLA gene. The prevalent c.639+919 G>A mutation in GLA leads to pathogenic insertion of a 57bp pseudoexon sequence from intron 4, which is responsible for the cardiac variant phenotype. In this study we investigate the splicing regulatory mechanism leading to GLA pseudoexon activation. Splicing analysis of GLA minigenes revealed that pseudoexon activation is influenced by cell-type. We demonstrate that the wild-type sequence harbors an hnRNP A1 and hnRNP A2/B1-binding exonic splicing silencer (ESS) overlapping the 5'splice site (5'ss) that prevents pseudoexon inclusion. The c.639+919 G>A mutation disrupts this ESS allowing U1 snRNP recognition of the 5'ss. We show that the wild-type GLA 5'ss motif with the ESS is also able to inhibit inclusion of an unrelated pseudoexon in the FGB gene, and that also in the FGB context inactivation of the ESS by the c.639+919 G>A mutation causes pseudoexon activation, underscoring the universal nature of the ESS. Finally, we demonstrate that splice switching oligonucleotide (SSO) mediated blocking of the pseudoexon 3'ss and 5'ss effectively restores normal GLA splicing. This indicates that SSO based splicing correction may be a therapeutic alternative in the treatment of Fabry disease.
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Affiliation(s)
- Bruno Palhais
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Rugivan Sabaratnam
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Kira S Nielsen
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
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23
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Doktor TK, Hua Y, Andersen HS, Brøner S, Liu YH, Wieckowska A, Dembic M, Bruun GH, Krainer AR, Andresen BS. RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns. Nucleic Acids Res 2016; 45:395-416. [PMID: 27557711 PMCID: PMC5224493 DOI: 10.1093/nar/gkw731] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 11/21/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity is correlated with decreased snRNP assembly activity. In particular, the minor spliceosomal snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in patient cells and animal models. SMA is characterized by loss of motor neurons, but the underlying mechanism is largely unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show elevated U12-intron retention in all examined tissues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN in HeLa cells. Furthermore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and that many transcriptional changes are reversed. Finally, we report on missplicing of several Ca2+ channel genes that may explain disrupted Ca2+ homeostasis in SMA and activation of Cdk5.
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Affiliation(s)
- Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Henriette Skovgaard Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Sabrina Brøner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Anna Wieckowska
- Department of Gamete and Embryo Biology, Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-243 Olsztyn, Poland
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark .,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
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24
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Bruun GH, Doktor TK, Borch-Jensen J, Masuda A, Krainer AR, Ohno K, Andresen BS. Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol 2016; 14:54. [PMID: 27380775 PMCID: PMC4932749 DOI: 10.1186/s12915-016-0279-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/23/2016] [Indexed: 01/14/2023] Open
Abstract
Background Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. Results Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5’ splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5′ splice site can be blocked by SSOs to activate the exon. Conclusions The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0279-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gitte H Bruun
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Jonas Borch-Jensen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY, 11724, USA
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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25
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Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J. Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency. Proteomics 2016; 16:1166-76. [PMID: 26867521 DOI: 10.1002/pmic.201500336] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/22/2016] [Accepted: 02/08/2016] [Indexed: 11/11/2022]
Abstract
Deficiency of mitochondrial sulfur dioxygenase (ETHE1) causes the severe metabolic disorder ethylmalonic encephalopathy, which is characterized by early-onset encephalopathy and defective cytochrome C oxidase because of hydrogen sulfide accumulation. Although the severe systemic consequences of the disorder are becoming clear, the molecular effects are not well defined. Therefore, for further elucidating the effects of ETHE1-deficiency, we performed a large scale quantitative proteomics study on liver tissue from ETHE1-deficient mice. Our results demonstrated a clear link between ETHE1-deficiency and redox active proteins, as reflected by downregulation of several proteins related to oxidation-reduction, such as different dehydrogenases and cytochrome P450 (CYP450) members. Furthermore, the protein data indicated impact of the ETHE1-deficiency on metabolic reprogramming through upregulation of glycolytic enzymes and by altering several heterogeneous ribonucleoproteins, indicating novel link between ETHE1 and gene expression regulation. We also found increase in total protein acetylation level, pointing out the link between ETHE1 and acetylation, which is likely controlled by both redox state and cellular metabolites. These findings are relevant for understanding the complexity of the disease and may shed light on important functions influenced by ETHE1 deficiency and by the concomitant increase in the gaseous mediator hydrogen sulfide. All MS data have been deposited in the ProteomeXchange with the dataset identifiers PXD002741 (http://proteomecentral.proteomexchange.org/dataset/PXD002741) and PXD002742 (http://proteomecentral.proteomexchange.org/dataset/PXD002741).
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Affiliation(s)
- Navid Sahebekhtiari
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Michelle M Thomsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Jens J Sloth
- Research Group for NanoBio Science, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Vibeke Stenbroen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Wellcome Trust/MRC Building, Cambridge, UK
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Carlo Viscomi
- Mitochondrial Biology Unit, Medical Research Council, Wellcome Trust/MRC Building, Cambridge, UK.,IRCCS Foundation Neurological Institute "C. Besta,", Milano, Italy
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
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26
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Wee CD, Havens MA, Jodelka FM, Hastings ML. Targeting SR proteins improves SMN expression in spinal muscular atrophy cells. PLoS One 2014; 9:e115205. [PMID: 25506695 PMCID: PMC4266657 DOI: 10.1371/journal.pone.0115205] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/19/2014] [Indexed: 12/19/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common inherited causes of pediatric mortality. SMA is caused by deletions or mutations in the survival of motor neuron 1 (SMN1) gene, which results in SMN protein deficiency. Humans have a centromeric copy of the survival of motor neuron gene, SMN2, which is nearly identical to SMN1. However, SMN2 cannot compensate for the loss of SMN1 because SMN2 has a single-nucleotide difference in exon 7, which negatively affects splicing of the exon. As a result, most mRNA produced from SMN2 lacks exon 7. SMN2 mRNA lacking exon 7 encodes a truncated protein with reduced functionality. Improving SMN2 exon 7 inclusion is a goal of many SMA therapeutic strategies. The identification of regulators of exon 7 inclusion may provide additional therapeutic targets or improve the design of existing strategies. Although a number of regulators of exon 7 inclusion have been identified, the function of most splicing proteins in exon 7 inclusion is unknown. Here, we test the role of SR proteins and hnRNP proteins in SMN2 exon 7 inclusion. Knockdown and overexpression studies reveal that SRSF1, SRSF2, SRSF3, SRSF4, SRSF5, SRSF6, SRSF7, SRSF11, hnRNPA1/B1 and hnRNP U can inhibit exon 7 inclusion. Depletion of two of the most potent inhibitors of exon 7 inclusion, SRSF2 or SRSF3, in cell lines derived from SMA patients, increased SMN2 exon 7 inclusion and SMN protein. Our results identify novel regulators of SMN2 exon 7 inclusion, revealing potential targets for SMA therapeutics.
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Affiliation(s)
- Claribel D. Wee
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Mallory A. Havens
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Francine M. Jodelka
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
- * E-mail:
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27
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Absence of an intron splicing silencer in porcine Smn1 intron 7 confers immunity to the exon skipping mutation in human SMN2. PLoS One 2014; 9:e98841. [PMID: 24892836 PMCID: PMC4043917 DOI: 10.1371/journal.pone.0098841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/08/2014] [Indexed: 11/19/2022] Open
Abstract
Spinal Muscular Atrophy is caused by homozygous loss of SMN1. All patients retain at least one copy of SMN2 which produces an identical protein but at lower levels due to a silent mutation in exon 7 which results in predominant exclusion of the exon. Therapies targeting the splicing of SMN2 exon 7 have been in development for several years, and their efficacy has been measured using either in vitro cellular assays or in vivo small animal models such as mice. In this study we evaluated the potential for constructing a mini-pig animal model by introducing minimal changes in the endogenous porcine Smn1 gene to maintain the native genomic structure and regulation. We found that while a Smn2-like mutation can be introduced in the porcine Smn1 gene and can diminish the function of the ESE, it would not recapitulate the splicing pattern seen in human SMN2 due to absence of a functional ISS immediately downstream of exon 7. We investigated the ISS region and show here that the porcine ISS is inactive due to disruption of a proximal hnRNP A1 binding site, while a distal hnRNP A1 binding site remains functional but is unable to maintain the functionality of the ISS as a whole.
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28
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Vezain M, Gérard B, Drunat S, Funalot B, Fehrenbach S, N'Guyen-Viet V, Vallat JM, Frébourg T, Tosi M, Martins A, Saugier-Veber P. A leaky splicing mutation affecting SMN1 exon 7 inclusion explains an unexpected mild case of spinal muscular atrophy. Hum Mutat 2014; 32:989-94. [PMID: 21542063 DOI: 10.1002/humu.21528] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/19/2011] [Indexed: 11/10/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting, in most cases, from homozygous deletions of the SMN1 gene or, in rare cases, from SMN1 intragenic mutations. Here we describe the identification and characterization of c.835-3C>T, a novel SMA-causing mutation detected in the intron 6 of the single SMN1 allele of a type IV SMA patient. We demonstrate both ex vivo and in vivo that c.835-3C>T is a deleterious splicing mutation that induces a modest but unequivocal exclusion of exon 7 from the SMN1 transcripts, its "leakiness" explaining the exceptionally mild phenotype of this patient. This mutation creates a putative high-affinity binding site for the splicing repressor protein hnRNP A1 overlapping the splice acceptor site of exon 7 (UAG|GGU). Our findings support the current therapeutic strategies aiming at correcting exon 7 splicing in SMA patients, and bring clues about the level of exon 7 inclusion required to achieve a therapeutic effect.
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Affiliation(s)
- Myriam Vezain
- Inserm U614, IFRMP, Institute for Biomedical Research, Rouen University Medical School, Rouen, France
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29
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Grodecká L, Lockerová P, Ravčuková B, Buratti E, Baralle FE, Dušek L, Freiberger T. Exon first nucleotide mutations in splicing: evaluation of in silico prediction tools. PLoS One 2014; 9:e89570. [PMID: 24586880 PMCID: PMC3931810 DOI: 10.1371/journal.pone.0089570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/21/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 3′ splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 3′ splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.
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Affiliation(s)
- Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavla Lockerová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Barbora Ravčuková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Ladislav Dušek
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Clinical Immunology and Allergology, St. Anne’s University Hospital and Masaryk University, Brno, Czech Republic
- * E-mail:
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30
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Olsen RKJ, Brøner S, Sabaratnam R, Doktor TK, Andersen HS, Bruun GH, Gahrn B, Stenbroen V, Olpin SE, Dobbie A, Gregersen N, Andresen BS. TheETFDHc.158A>G Variation Disrupts the Balanced Interplay of ESE- and ESS-Binding Proteins thereby Causing Missplicing and Multiple Acyl-CoA Dehydrogenation Deficiency. Hum Mutat 2013; 35:86-95. [DOI: 10.1002/humu.22455] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 09/25/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Rikke K. J. Olsen
- Research Unit for Molecular Medicine; Aarhus University Hospital and Department of Clinical Medicine, Aarhus University; Aarhus Denmark
| | - Sabrina Brøner
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
| | - Rugivan Sabaratnam
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
| | - Thomas K. Doktor
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
| | - Henriette S. Andersen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
| | - Gitte H. Bruun
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
| | - Birthe Gahrn
- Research Unit for Molecular Medicine; Aarhus University Hospital and Department of Clinical Medicine, Aarhus University; Aarhus Denmark
| | - Vibeke Stenbroen
- Research Unit for Molecular Medicine; Aarhus University Hospital and Department of Clinical Medicine, Aarhus University; Aarhus Denmark
| | - Simon E. Olpin
- Department of Clinical Chemistry; The Children's Hospital; Sheffield United Kingdom
| | - Angus Dobbie
- Department of Clinical Genetics; St James's University Hospital; Leeds United Kingdom
| | - Niels Gregersen
- Research Unit for Molecular Medicine; Aarhus University Hospital and Department of Clinical Medicine, Aarhus University; Aarhus Denmark
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
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31
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Risom L, Christoffersen L, Daugaard-Jensen J, Hove HD, Andersen HS, Andresen BS, Kreiborg S, Duno M. Identification of six novel PTH1R mutations in families with a history of primary failure of tooth eruption. PLoS One 2013; 8:e74601. [PMID: 24058597 PMCID: PMC3776825 DOI: 10.1371/journal.pone.0074601] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/05/2013] [Indexed: 11/23/2022] Open
Abstract
Primary Failure of tooth Eruption (PFE) is a non-syndromic disorder which can be caused by mutations in the parathyroid hormone receptor 1 gene (PTH1R). Traditionally, the disorder has been identified clinically based on post-emergent failure of eruption of permanent molars. However, patients with PTH1R mutations will not benefit from surgical and/or orthodontic treatment and it is therefore clinically important to establish whether a given failure of tooth eruption is caused by a PTH1R defect or not. We analyzed the PTH1R gene in six patients clinically diagnosed with PFE, all of which had undergone surgical and/or orthodontic interventions, and identified novel PTH1R mutations in all. Four of the six mutations were predicted to abolish correct mRNA maturation either through introduction of premature stop codons (c.947C>A and c.1082G>A), or by altering correct mRNA splicing (c.544-26_544-23del and c.989G>T). The latter was validated by transfection of minigenes. The six novel mutations expand the mutation spectrum for PFE from eight to 14 pathogenic mutations. Loss-of-function mutations in PTH1R are also associated with recessively inherited Blomstrand chondrodysplasia. We compiled all published PTH1R mutations and identified a mutational overlap between Blomstrand chondrodysplasia and PFE. The results suggest that a genetic approach to preclinical diagnosis will have important implication for surgical and orthodontic treatment of patients with failure of tooth eruption.
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Affiliation(s)
- Lotte Risom
- Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Line Christoffersen
- Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | | | - Hanne Dahlgaard Hove
- Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | | | | | - Sven Kreiborg
- Department of Paediatric Dentistry and Clinical Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Morten Duno
- Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
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Di Giacomo D, Gaildrat P, Abuli A, Abdat J, Frébourg T, Tosi M, Martins A. Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements. Hum Mutat 2013; 34:1547-57. [PMID: 23983145 DOI: 10.1002/humu.22428] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/14/2013] [Indexed: 11/06/2022]
Abstract
Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing.
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Affiliation(s)
- Daniela Di Giacomo
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
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Jean-Philippe J, Paz S, Caputi M. hnRNP A1: the Swiss army knife of gene expression. Int J Mol Sci 2013; 14:18999-9024. [PMID: 24065100 PMCID: PMC3794818 DOI: 10.3390/ijms140918999] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic cells express a large variety of RNA binding proteins (RBPs), with diverse affinities and specificities towards target RNAs. These proteins play a crucial role in almost every aspect of RNA biogenesis, expression and function. The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a complex and diverse family of RNA binding proteins. hnRNPs display multiple functions in the processing of heterogeneous nuclear RNAs into mature messenger RNAs. hnRNP A1 is one of the most abundant and ubiquitously expressed members of this protein family. hnRNP A1 plays multiple roles in gene expression by regulating major steps in the processing of nascent RNA transcripts. The transcription, splicing, stability, export through nuclear pores and translation of cellular and viral transcripts are all mechanisms modulated by this protein. The diverse functions played by hnRNP A1 are not limited to mRNA biogenesis, but extend to the processing of microRNAs, telomere maintenance and the regulation of transcription factor activity. Genomic approaches have recently uncovered the extent of hnRNP A1 roles in the development and differentiation of living organisms. The aim of this review is to highlight recent developments in the study of this protein and to describe its functions in cellular and viral gene expression and its role in human pathologies.
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Affiliation(s)
- Jacques Jean-Philippe
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA.
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Bruun GH, Doktor TK, Andresen BS. A synonymous polymorphic variation in ACADM exon 11 affects splicing efficiency and may affect fatty acid oxidation. Mol Genet Metab 2013; 110:122-8. [PMID: 23810226 DOI: 10.1016/j.ymgme.2013.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/04/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
Abstract
In recent studies combining genome-wide association and tandem-MS based metabolic profiling, a single-nucleotide polymorphism (SNP), rs211718C>T, located far upstream of the MCAD gene (ACADM) was found to be associated with serum concentrations of medium-chain acylcarnitines indicating improved beta-oxidation of medium-chain fatty acids. We examined the functional basis for this association and identified linkage between rs211718 and the intragenic synonymous polymorphic variant c.1161A>G in ACADM exon 11 (rs1061337). Employing minigene studies we show that the c.1161A allele is associated with exon 11 missplicing, and that the c.1161G allele corrects this missplicing. This may result in production of more full length MCAD protein from the c.1161G allele. Our analysis suggests that the improved splicing of the c.1161G allele is due to changes in the relative binding of splicing regulatory proteins SRSF1 and hnRNP A1. Using publicly available pre-aligned RNA-seq data, we find that the ACADM c.1161G allele is expressed at significantly higher levels than the c.1161A allele across different tissues. This supports that c.1161A>G is a functional SNP, which leads to higher MCAD expression, perhaps due to improved splicing. This study is a proof of principle that synonymous SNPs are not neutral. By changing the binding sites for splicing regulatory proteins they can have significant effects on pre-mRNA splicing and thus protein function. In addition, this study shows that for a sequence variation to have an effect, it might need to change the balance in the relative binding of positive and negative splicing factors.
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Affiliation(s)
- Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Novel GUCA1A mutations suggesting possible mechanisms of pathogenesis in cone, cone-rod, and macular dystrophy patients. BIOMED RESEARCH INTERNATIONAL 2013; 2013:517570. [PMID: 24024198 PMCID: PMC3759255 DOI: 10.1155/2013/517570] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/19/2013] [Indexed: 01/06/2023]
Abstract
Here, we report two novel GUCA1A (the gene for guanylate cyclase activating protein 1) mutations identified in unrelated Spanish families affected by autosomal dominant retinal degeneration (adRD) with cone and rod involvement. All patients from a three-generation adRD pedigree underwent detailed ophthalmic evaluation. Total genome scan using single-nucleotide polymorphisms and then the linkage analysis were undertaken on the pedigree. Haplotype analysis revealed a 55.37 Mb genomic interval cosegregating with the disease phenotype on chromosome 6p21.31-q15. Mutation screening of positional candidate genes found a heterozygous transition c.250C>T in exon 4 of GUCA1A, corresponding to a novel mutation p.L84F. A second missense mutation, c.320T>C (p.I107T), was detected by screening of the gene in a Spanish patients cohort. Using bioinformatics approach, we predicted that either haploinsufficiency or dominant-negative effect accompanied by creation of a novel function for the mutant protein is a possible mechanism of the disease due to c.250C>T and c.320T>C. Although additional functional studies are required, our data in relation to the c.250C>T mutation open the possibility that transacting factors binding to de novo created recognition site resulting in formation of aberrant splicing variant is a disease model which may be more widespread than previously recognized as a mechanism causing inherited RD.
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Houdayer C, Caux-Moncoutier V, Krieger S, Barrois M, Bonnet F, Bourdon V, Bronner M, Buisson M, Coulet F, Gaildrat P, Lefol C, Léone M, Mazoyer S, Muller D, Remenieras A, Révillion F, Rouleau E, Sokolowska J, Vert JP, Lidereau R, Soubrier F, Sobol H, Sevenet N, Bressac-de Paillerets B, Hardouin A, Tosi M, Sinilnikova OM, Stoppa-Lyonnet D. Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat 2012; 33:1228-38. [DOI: 10.1002/humu.22101] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/15/2012] [Accepted: 03/30/2012] [Indexed: 01/05/2023]
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Fortugno P, Grosso F, Zambruno G, Pastore S, Faletra F, Castiglia D. A synonymous mutation in SPINK5 exon 11 causes Netherton syndrome by altering exonic splicing regulatory elements. J Hum Genet 2012; 57:311-5. [DOI: 10.1038/jhg.2012.22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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