Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants

Katneni, Upendra K.; Liss, Aaron; Holcomb, David; Katagiri, Nobuko H.; Hunt, Ryan; Bar, Haim; Ismail, Amra; Komar, Anton A.; Kimchi‐Sarfaty, Chava

doi:10.1002/mgg3.840

Title: Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants

Journal Article · 30 June 2019 · Molecular Genetics & Genomic Medicine

DOI: https://doi.org/10.1002/mgg3.840 · OSTI ID:1559339

Katneni, Upendra K. ^[1]; Liss, Aaron ^[1]; Holcomb, David ^[1]; Katagiri, Nobuko H. ^[1]; Hunt, Ryan ^[1]; Bar, Haim ^[2]; Ismail, Amra ^[3]; Komar, Anton A. ^[3];

^[1]

US Food and Drug Administration, Silver Spring MD (United States). Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research
University of Connecticut, Storrs, CT (United States). Department of Statistics
Cleveland State University, Cleveland, OH (United States). Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease

Background: Pre-mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease-inducing mechanism of synonymous variants, its contribution toward disease phenotype of non-synonymous variants is underappreciated. Methods: In this study, we analyzed 415 disease-causing and 120 neutral F9 exonic point variants including both synonymous and non-synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. Results: The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. Conclusion: Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non=synonymous variants.

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Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; US Food and Drug Administration

Grant/Contract Number:: SC0014664

OSTI ID:: 1559339

Alternate ID(s):: OSTI ID: 1559340; OSTI ID: 1623575

Journal Information:: Molecular Genetics & Genomic Medicine, Vol. 7, Issue 8; ISSN 2324-9269

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 9 works

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References (68)

Spliceosomal UsnRNP biogenesis, structure and function Will, Cindy L.; Lührmann, Reinhard Current Opinion in Cell Biology, Vol. 13, Issue 3 https://doi.org/10.1016/S0955-0674(00)00211-8	journal	June 2001
Nomenclature of genetic variants in hemostasis: Scientific and Standardisation Committee communication Goodeve, A. C.; Reitsma, P. H.; Mcvey, J. H. Journal of Thrombosis and Haemostasis, Vol. 9, Issue 4 https://doi.org/10.1111/j.1538-7836.2011.04191.x	journal	April 2011
A Gene-Specific Method for Predicting Hemophilia-Causing Point Mutations Hamasaki-Katagiri, Nobuko; Salari, Raheleh; Wu, Andrew Journal of Molecular Biology, Vol. 425, Issue 21 https://doi.org/10.1016/j.jmb.2013.07.037	journal	November 2013
Quantitative evaluation of all hexamers as exonic splicing elements Ke, Shengdong; Shang, Shulian; Kalachikov, Sergey M. Genome Research, Vol. 21, Issue 8 https://doi.org/10.1101/gr.119628.110	journal	June 2011
An exon-specific U1 small nuclear RNA (snRNA) strategy to correct splicing defects Fernandez Alanis, Eugenio; Pinotti, Mirko; Dal Mas, Andrea Human Molecular Genetics, Vol. 21, Issue 11 https://doi.org/10.1093/hmg/dds045	journal	February 2012
Genome-wide discovery of human splicing branchpoints Mercer, Tim R.; Clark, Michael B.; Andersen, Stacey B. Genome Research, Vol. 25, Issue 2 https://doi.org/10.1101/gr.182899.114	journal	January 2015
Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta -tropomyosin gene Chen, C. D.; Kobayashi, R.; Helfman, D. M. Genes & Development, Vol. 13, Issue 5 https://doi.org/10.1101/gad.13.5.593	journal	March 1999
Human Splicing Finder: an online bioinformatics tool to predict splicing signals Desmet, François-Olivier; Hamroun, Dalil; Lalande, Marine Nucleic Acids Research, Vol. 37, Issue 9 https://doi.org/10.1093/nar/gkp215	journal	April 2009
Prediction of single‐nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6 Raponi, Michela; Kralovicova, Jana; Copson, Ellen Human Mutation, Vol. 32, Issue 4 https://doi.org/10.1002/humu.21458	journal	February 2011
Definitions in Hemophilia: Recommendation of the Scientific Subcommittee on Factor VIII and Factor IX of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis White, Gilbert; Rosendaal, Frits; Aledort, Louis Thrombosis and Haemostasis, Vol. 85, Issue 03 https://doi.org/10.1055/s-0037-1615621	journal	January 2001
Exposing synonymous mutations Hunt, Ryan C.; Simhadri, Vijaya L.; Iandoli, Matthew Trends in Genetics, Vol. 30, Issue 7 https://doi.org/10.1016/j.tig.2014.04.006	journal	July 2014
Analysis of canonical and non-canonical splice sites in mammalian genomes Burset, M. Nucleic Acids Research, Vol. 28, Issue 21 https://doi.org/10.1093/nar/28.21.4364	journal	November 2000
Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B Simhadri, Vijaya L.; Hamasaki-Katagiri, Nobuko; Lin, Brian C. Journal of Medical Genetics, Vol. 54, Issue 5 https://doi.org/10.1136/jmedgenet-2016-104072	journal	December 2016
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions Tang, Rongying; Prosser, Debra O.; Love, Donald R. Advances in Bioinformatics, Vol. 2016 https://doi.org/10.1155/2016/5614058	journal	January 2016
In silico tools for splicing defect prediction: a survey from the viewpoint of end users Jian, Xueqiu; Boerwinkle, Eric; Liu, Xiaoming Genetics in Medicine, Vol. 16, Issue 7 https://doi.org/10.1038/gim.2013.176	journal	November 2013
An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B Rallapalli, P. M.; Kemball-Cook, G.; Tuddenham, E. G. Journal of Thrombosis and Haemostasis, Vol. 11, Issue 7 https://doi.org/10.1111/jth.12276	journal	July 2013
Genomic HEXploring allows landscaping of novel potential splicing regulatory elements Erkelenz, Steffen; Theiss, Stephan; Otte, Marianne Nucleic Acids Research, Vol. 42, Issue 16 https://doi.org/10.1093/nar/gku736	journal	August 2014
Sorting out the complexity of SR protein functions Graveley, Brenton R. RNA, Vol. 6, Issue 9 https://doi.org/10.1017/S1355838200000960	journal	September 2000
Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function Tajnik, Mojca; Rogalska, Malgorzata Ewa; Bussani, Erica PLOS Genetics, Vol. 12, Issue 5 https://doi.org/10.1371/journal.pgen.1006082	journal	May 2016
Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis Caminsky, Natasha G.; Mucaki, Eliseos J.; Rogan, Peter K. F1000Research, Vol. 3 https://doi.org/10.12688/f1000research.5654.2	journal	January 2014
dbSNP: the NCBI database of genetic variation Sherry, S. T. Nucleic Acids Research, Vol. 29, Issue 1 https://doi.org/10.1093/nar/29.1.308	journal	January 2001
Correction: Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools Soukarieh, Omar; Gaildrat, Pascaline; Hamieh, Mohamad PLOS Genetics, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pgen.1005971	journal	April 2016
Improved Splice Site Detection in Genie Reese, Martin G.; Eeckman, Frank H.; Kulp, David Journal of Computational Biology, Vol. 4, Issue 3 https://doi.org/10.1089/cmb.1997.4.311	journal	January 1997
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression Shapiro, Marvin B.; Senapathy, Periannan Nucleic Acids Research, Vol. 15, Issue 17 https://doi.org/10.1093/nar/15.17.7155	journal	January 1987
A Synonymous Single Nucleotide Polymorphism in ΔF508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein Bartoszewski, Rafal A.; Jablonsky, Michael; Bartoszewska, Sylwia Journal of Biological Chemistry, Vol. 285, Issue 37 https://doi.org/10.1074/jbc.M110.154575	journal	July 2010
Pick one, but be quick: 5' splice sites and the problems of too many choices Roca, X.; Krainer, A. R.; Eperon, I. C. Genes & Development, Vol. 27, Issue 2 https://doi.org/10.1101/gad.209759.112	journal	January 2013
Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals Yeo, Gene; Burge, Christopher B. Journal of Computational Biology, Vol. 11, Issue 2-3 https://doi.org/10.1089/1066527041410418	journal	March 2004
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12 Pagani, F. Human Molecular Genetics, Vol. 12, Issue 10 https://doi.org/10.1093/hmg/ddg131	journal	May 2003
Unusual expression of the F9 gene in peripheral lymphocytes hinders investigation of F9 mRNA in hemophilia B patients Green, P. M.; Rowley, G.; Giannelli, F. Journal of Thrombosis and Haemostasis, Vol. 1, Issue 12 https://doi.org/10.1111/j.1538-7836.2003.0543a.x	journal	December 2003
Listening to silence and understanding nonsense: exonic mutations that affect splicing Cartegni, Luca; Chew, Shern L.; Krainer, Adrian R. Nature Reviews Genetics, Vol. 3, Issue 4 https://doi.org/10.1038/nrg775	journal	April 2002
The gene structure of human anti-haemophilic factor IX. Anson, D. S.; Choo, K. H.; Rees, D. J. The EMBO Journal, Vol. 3, Issue 5 https://doi.org/10.1002/j.1460-2075.1984.tb01926.x	journal	May 1984
Haemophilia A and haemophilia B: molecular insights Bowen, D. J. Molecular Pathology, Vol. 55, Issue 2 https://doi.org/10.1136/mp.55.2.127	journal	April 2002
miRNAs in the spotlight: Making 'silent' mutations speak up Salzman, David W.; Weidhaas, Joanne B. Nature Medicine, Vol. 17, Issue 8 https://doi.org/10.1038/nm0811-934	journal	August 2011
Loss of exon identity is a common mechanism of human inherited disease Sterne-Weiler, T.; Howard, J.; Mort, M. Genome Research, Vol. 21, Issue 10 https://doi.org/10.1101/gr.118638.110	journal	July 2011
An Exon-Specific U1snRNA Induces a Robust Factor IX Activity in Mice Expressing Multiple Human FIX Splicing Mutants Balestra, Dario; Scalet, Daniela; Pagani, Franco Molecular Therapy - Nucleic Acids, Vol. 5 https://doi.org/10.1038/mtna.2016.77	journal	January 2016
The CDC Hemophilia B mutation project mutation list: a new online resource Li, Tengguo; Miller, Connie H.; Payne, Amanda B. Molecular Genetics & Genomic Medicine, Vol. 1, Issue 4 https://doi.org/10.1002/mgg3.30	journal	August 2013
A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1793-7	journal	September 2017
Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics? Grodecká, Lucie; Buratti, Emanuele; Freiberger, Tomáš International Journal of Molecular Sciences, Vol. 18, Issue 8 https://doi.org/10.3390/ijms18081668	journal	July 2017
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity Kimchi-Sarfaty, C.; Oh, J. M.; Kim, I.-W. Science, Vol. 315, Issue 5811, p. 525-528 https://doi.org/10.1126/science.1135308	journal	January 2007
Haemophilia A and haemophilia B: molecular insights Bowen, D. J. Molecular Pathology, Vol. 55, Issue 1 https://doi.org/10.1136/mp.55.1.1	journal	February 2002
Improved splice site detection in Genie Reese, Martin G.; Eeckman, Frank H.; Kulp, David Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97 https://doi.org/10.1145/267521.267766	conference	January 1997
Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis Caminsky, Natasha G.; Mucaki, Eliseos J.; Rogan, Peter K. F1000Research, Vol. 3 https://doi.org/10.12688/f1000research.5654.1	journal	January 2014
Prediction of single‐nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6 Raponi, Michela; Kralovicova, Jana; Copson, Ellen Human Mutation, Vol. 32, Issue 4 https://doi.org/10.1002/humu.21458	journal	February 2011
The CDC Hemophilia B mutation project mutation list: a new online resource Li, Tengguo; Miller, Connie H.; Payne, Amanda B. Molecular Genetics & Genomic Medicine, Vol. 1, Issue 4 https://doi.org/10.1002/mgg3.30	journal	August 2013
Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly Ullah, Irfan; Kakar, Naseebullah; Schrauwen, Isabelle Human Genetics, Vol. 138, Issue 6 https://doi.org/10.1007/s00439-019-02000-0	journal	April 2019
Activated partial thromboplastin time-based clot waveform analysis enables measurement of very low levels of factor IX activity in patients with severe hemophilia B Nishiyama, Atsuko; Ogiwara, Kenichi; Mizumachi, Kuniyoshi International Journal of Hematology, Vol. 116, Issue 5 https://doi.org/10.1007/s12185-022-03419-4	journal	July 2022
A Gene-Specific Method for Predicting Hemophilia-Causing Point Mutations Hamasaki-Katagiri, Nobuko; Salari, Raheleh; Wu, Andrew Journal of Molecular Biology, Vol. 425, Issue 21 https://doi.org/10.1016/j.jmb.2013.07.037	journal	November 2013
In silico tools for splicing defect prediction: a survey from the viewpoint of end users Jian, Xueqiu; Boerwinkle, Eric; Liu, Xiaoming Genetics in Medicine, Vol. 16, Issue 7 https://doi.org/10.1038/gim.2013.176	journal	November 2013
An Exon-Specific U1snRNA Induces a Robust Factor IX Activity in Mice Expressing Multiple Human FIX Splicing Mutants Balestra, Dario; Scalet, Daniela; Pagani, Franco Molecular Therapy - Nucleic Acids, Vol. 5 https://doi.org/10.1038/mtna.2016.77	journal	January 2016
miRNAs in the spotlight: Making 'silent' mutations speak up Salzman, David W.; Weidhaas, Joanne B. Nature Medicine, Vol. 17, Issue 8 https://doi.org/10.1038/nm0811-934	journal	August 2011
Listening to silence and understanding nonsense: exonic mutations that affect splicing Cartegni, Luca; Chew, Shern L.; Krainer, Adrian R. Nature Reviews Genetics, Vol. 3, Issue 4 https://doi.org/10.1038/nrg775	journal	April 2002
Definitions in Hemophilia: Recommendation of the Scientific Subcommittee on Factor VIII and Factor IX of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis White, Gilbert; Rosendaal, Frits; Aledort, Louis Thrombosis and Haemostasis, Vol. 85, Issue 03 https://doi.org/10.1055/s-0037-1615621	journal	January 2001
Improved Splice Site Detection in Genie Reese, Martin G.; Eeckman, Frank H.; Kulp, David Journal of Computational Biology, Vol. 4, Issue 3 https://doi.org/10.1089/cmb.1997.4.311	journal	January 1997
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12 Pagani, F. Human Molecular Genetics, Vol. 12, Issue 10 https://doi.org/10.1093/hmg/ddg131	journal	May 2003
An exon-specific U1 small nuclear RNA (snRNA) strategy to correct splicing defects Fernandez Alanis, Eugenio; Pinotti, Mirko; Dal Mas, Andrea Human Molecular Genetics, Vol. 21, Issue 11 https://doi.org/10.1093/hmg/dds045	journal	February 2012
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression Shapiro, Marvin B.; Senapathy, Periannan Nucleic Acids Research, Vol. 15, Issue 17 https://doi.org/10.1093/nar/15.17.7155	journal	January 1987
Analysis of canonical and non-canonical splice sites in mammalian genomes Burset, M. Nucleic Acids Research, Vol. 28, Issue 21 https://doi.org/10.1093/nar/28.21.4364	journal	November 2000
dbSNP: the NCBI database of genetic variation Sherry, S. T. Nucleic Acids Research, Vol. 29, Issue 1 https://doi.org/10.1093/nar/29.1.308	journal	January 2001
Quantitative evaluation of all hexamers as exonic splicing elements Ke, Shengdong; Shang, Shulian; Kalachikov, Sergey M. Genome Research, Vol. 21, Issue 8 https://doi.org/10.1101/gr.119628.110	journal	June 2011
Genome-wide discovery of human splicing branchpoints Mercer, Tim R.; Clark, Michael B.; Andersen, Stacey B. Genome Research, Vol. 25, Issue 2 https://doi.org/10.1101/gr.182899.114	journal	January 2015
Nomenclature of genetic variants in hemostasis: Scientific and Standardisation Committee communication Goodeve, A. C.; Reitsma, P. H.; Mcvey, J. H. Journal of Thrombosis and Haemostasis, Vol. 9, Issue 4 https://doi.org/10.1111/j.1538-7836.2011.04191.x	journal	April 2011
Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B Simhadri, Vijaya L.; Hamasaki-Katagiri, Nobuko; Lin, Brian C. Journal of Medical Genetics, Vol. 54, Issue 5 https://doi.org/10.1136/jmedgenet-2016-104072	journal	December 2016
Haemophilia A and haemophilia B: molecular insights Bowen, D. J. Molecular Pathology, Vol. 55, Issue 1 https://doi.org/10.1136/mp.55.1.1	journal	February 2002
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions Tang, Rongying; Prosser, Debra O.; Love, Donald R. Advances in Bioinformatics, Vol. 2016 https://doi.org/10.1155/2016/5614058	journal	January 2016
A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1793-7	journal	September 2017
Correction: Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools Soukarieh, Omar; Gaildrat, Pascaline; Hamieh, Mohamad PLOS Genetics, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pgen.1005971	journal	April 2016
Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function Tajnik, Mojca; Rogalska, Malgorzata Ewa; Bussani, Erica PLOS Genetics, Vol. 12, Issue 5 https://doi.org/10.1371/journal.pgen.1006082	journal	May 2016
Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics? Grodecká, Lucie; Buratti, Emanuele; Freiberger, Tomáš International Journal of Molecular Sciences, Vol. 18, Issue 8 https://doi.org/10.3390/ijms18081668	journal	July 2017

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity
hemophilia B
in silico splicing analysis
in vitro minigene assay
splicing dysregulation
synonymous variants