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Holm LL, Doktor TK, Flugt KK, Petersen US, Petersen R, Andresen B. All exons are not created equal-exon vulnerability determines the effect of exonic mutations on splicing. Nucleic Acids Res 2024; 52:4588-4603. [PMID: 38324470 PMCID: PMC11077056 DOI: 10.1093/nar/gkae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/05/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
It is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affecting cis-acting splicing regulatory elements (SREs), but there is a misconception that all exons have an equal dependency on SREs and thus a similar vulnerability to aberrant splicing. We demonstrate that some exons are more likely to be affected by exonic splicing mutations (ESMs) due to an inherent vulnerability, which is context dependent and influenced by the strength of exon definition. We have developed VulExMap, a tool which is based on empirical data that can designate whether a constitutive exon is vulnerable. Using VulExMap, we find that only 25% of all exons can be categorized as vulnerable, whereas two-thirds of 359 previously reported ESMs in 75 disease genes are located in vulnerable exons. Because VulExMap analysis is based on empirical data on splicing of exons in their endogenous context, it includes all features important in determining the vulnerability. We believe that VulExMap will be an important tool when assessing the effect of exonic mutations by pinpointing whether they are located in exons vulnerable to ESMs.
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Affiliation(s)
- Lise L Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Katharina K Flugt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Rikke Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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2
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clin Chem 2024; 70:319-338. [PMID: 37725924 DOI: 10.1093/clinchem/hvad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Disrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast cancer susceptibility gene CHEK2 by splicing reporter minigenes. METHODS A total of 128 CHEK2 splice-site variants identified in the Breast Cancer After Diagnostic Gene Sequencing (BRIDGES) project (https://cordis.europa.eu/project/id/634935) were analyzed with MaxEntScan and subsetted to 52 variants predicted to impact splicing. Three CHEK2 minigenes, which span all 15 exons, were constructed and validated. The 52 selected variants were then genetically engineered into the minigenes and assayed in MCF-7 (human breast adenocarcinoma) cells. RESULTS Of 52 variants, 46 (88.5%) impaired splicing. Some of them led to complex splicing patterns with up to 11 different transcripts. Thirty-four variants induced splicing anomalies without any trace or negligible amounts of the full-length transcript. A total of 89 different transcripts were annotated, which derived from different events: single- or multi-exon skipping, alternative site-usage, mutually exclusive exon inclusion, intron retention or combinations of the abovementioned events. Fifty-nine transcripts were predicted to introduce premature termination codons, 7 kept the original open-reading frame, 5 removed the translation start codon, 6 affected the 5'UTR (Untranslated Region), and 2 included missense variations. Analysis of variant c.684-2A > G revealed the activation of a non-canonical TG-acceptor site and exon 6 sequences critical for its recognition. CONCLUSIONS Incorporation of minigene read-outs into an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme allowed us to classify 32 CHEK2 variants (27 pathogenic/likely pathogenic and 5 likely benign). However, 20 variants (38%) remained of uncertain significance, reflecting in part the complex splicing patterns of this gene.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, Cambridge, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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3
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Shchagina O, Gracheva E, Chukhrova A, Bliznets E, Bychkov I, Kutsev S, Polyakov A. Functional Characterization of Two Novel Intron 4 SERPING1 Gene Splice Site Pathogenic Variants in Families with Hereditary Angioedema. Biomedicines 2023; 12:72. [PMID: 38255179 PMCID: PMC10813231 DOI: 10.3390/biomedicines12010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Variants that affect splice sites comprise 14.3% of all pathogenic variants in the SERPING1 gene; more than half of them are located outside the canonical sites. To make a clinical decision concerning patients with such variants, it is essential to know the exact way in which the effect of the variant would be realized. The optimal approach to determine the consequences is considered to be mRNA analysis. In the current study, we present the results of functional analysis of two previously non-described variants in the SERPING1 gene (NM_000062.3) affecting intron 4: c.686-1G>A and c.685+4dup, which were detected in members of two Russian families with autosomal dominant inheritance of angioedema type 1. Analysis of the patients' mRNA (extracted from whole blood) showed that the SERPING1(NM_000062.3):c.685+4dup variant leads to the loss of the donor splice site and the activation of the cryptic site in exon 4: r.710_745del (p.Gly217_Pro228del), while the SERPING1(NM_000062.3):c.686-1G>A variant leads to the skipping of exon 5: r.746_949del (p.Asp229_Ser296del).
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Affiliation(s)
- Olga Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Elena Gracheva
- Department of Health of Vologda Region, Budgetary Healthcare Institution, Vologda Region Regional Clinical Hospital, 160002 Vologda, Russia;
| | - Alyona Chukhrova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Elena Bliznets
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Igor Bychkov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Sergey Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Aleksander Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
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4
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Rozza R, Janoš P, Magistrato A. Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. J Chem Inf Model 2023; 63:7508-7517. [PMID: 37967032 DOI: 10.1021/acs.jcim.3c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
RNA recognition motifs (RRMs) play a pivotal role in RNA metabolism and the regulation of gene expression. Owing to their plasticity and fuzziness, targeting RRM/RNA interfaces with small molecules is a daunting challenge for drug discovery campaigns. The U2AF2 splicing factor, which recognizes the polypyrimidine (polyPy) sequence of premature messenger (pre-m)RNA, exhibits a dynamic architecture consisting of two RRMs joined by a disordered linker. An inhibitor, NSC-194308, was shown to enhance the binding of pre-mRNA to U2AF2, selectively triggering cell death in leukemia cell lines containing spliceosome mutations. The NSC-194308 binding mode remains elusive; yet, unraveling its knowledge may offer intriguing insights for effectively targeting U2AF2 and other flexible protein/protein/RNA interfaces with small molecules. To infer plausible NSC-194308 binding poses to U2AF2, here, we applied and benchmarked the performance of static and dynamic docking approaches, elucidating the molecular basis of the NSC-194308-induced pre-mRNA stabilization on U2AF2. We demonstrate that introducing dynamic effects is mandatory to assess the binding mode of the inhibitors when they target plastic and modular architectures, such as those formed by interacting RRMs. The latter are widespread across RNA binding proteins; therefore, this mechanism may be broadly applicable to discover new therapeutics aimed at selectively modulating the RNA function by targeting protein/protein/RNA interfaces.
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Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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5
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Sullivan PJ, Gayevskiy V, Davis RL, Wong M, Mayoh C, Mallawaarachchi A, Hort Y, McCabe MJ, Beecroft S, Jackson MR, Arts P, Dubowsky A, Laing N, Dinger ME, Scott HS, Oates E, Pinese M, Cowley MJ. Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biol 2023; 24:118. [PMID: 37198692 PMCID: PMC10190034 DOI: 10.1186/s13059-023-02936-7] [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: 03/30/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .
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Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Ryan L Davis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- Department of Neurogenetics, Kolling Institute, St. Leonards, NSW, Australia
- Sydney Medical School-Northern, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marie Wong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Amali Mallawaarachchi
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
- Clinical Genetics Unit, Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Sydney, Australia
| | - Yvonne Hort
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Sarah Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Matilda R Jackson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Andrew Dubowsky
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Emily Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
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6
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Rozza R, Janoš P, Magistrato A. Monovalent Ionic Atmosphere Modulates the Selection of Suboptimal RNA Sequences by Splicing Factors' RNA Recognition Motifs. J Chem Inf Model 2023; 63:3086-3093. [PMID: 37129986 DOI: 10.1021/acs.jcim.3c00110] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The U2AF2 splicing factor is involved in the RNA recognition of the pre-mRNA poly-pyrimidine signaling sequence. This protein contains two RRM domains connected by a flexible linker, which ensure the preferential selection of a poly-uridine sequence over a poly-cytosine one. In this work, all-atom simulations provide insights into the U2AF2 recognition mechanism and on the features underlying its selectivity. Our outcomes show that U2AF2's RNA recognition is driven by cooperative events modulated by RNA-protein and RNA-ion interactions. Stunningly, monovalent ions contribute to mediating the binding of the weakly binding polyC strand, thus contributing to the selection of suboptimal poly-pyrimidine tracts. This finding broadens our understanding of the diverse traits tuning splicing factors' selectivity and adaptability to precisely handle and process diverse pre-mRNA sequences.
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Affiliation(s)
| | - Pavel Janoš
- CNR-IOM at SISSA via Bonomea 265, 34136 Trieste, Italy
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7
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Rayani K, Davies B, Cheung M, Comber D, Roberts JD, Tadros R, Green MS, Healey JS, Simpson CS, Sanatani S, Steinberg C, MacIntyre C, Angaran P, Duff H, Hamilton R, Arbour L, Leather R, Seifer C, Fournier A, Atallah J, Kimber S, Makanjee B, Alqarawi W, Cadrin-Tourigny J, Joza J, Gardner M, Talajic M, Bagnall RD, Krahn AD, Laksman ZWM. Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry. Eur J Hum Genet 2023; 31:512-520. [PMID: 36138163 PMCID: PMC10172209 DOI: 10.1038/s41431-022-01193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Splice-site variants in cardiac genes may predispose carriers to potentially lethal arrhythmias. To investigate, we screened 1315 probands and first-degree relatives enrolled in the Canadian Hearts in Rhythm Organization (HiRO) registry. 10% (134/1315) of patients in the HiRO registry carry variants within 10 base-pairs of the intron-exon boundary with 78% (104/134) otherwise genotype negative. These 134 probands were carriers of 57 unique variants. For each variant, American College of Medical Genetics and Genomics (ACMG) classification was revisited based on consensus between nine in silico tools. Due in part to the in silico algorithms, seven variants were reclassified from the original report, with the majority (6/7) downgraded. Our analyses predicted 53% (30/57) of variants to be likely/pathogenic. For the 57 variants, an average of 9 tools were able to score variants within splice sites, while 6.5 tools responded for variants outside these sites. With likely/pathogenic classification considered a positive outcome, the ACMG classification was used to calculate sensitivity/specificity of each tool. Among these, Combined Annotation Dependent Depletion (CADD) had good sensitivity (93%) and the highest response rate (131/134, 98%), dbscSNV was also sensitive (97%), and SpliceAI was the most specific (64%) tool. Splice variants remain an important consideration in gene elusive inherited arrhythmia syndromes. Screening for intronic variants, even when restricted to the ±10 positions as performed here may improve genetic testing yield. We compare 9 freely available in silico tools and provide recommendations regarding their predictive capabilities. Moreover, we highlight several novel cardiomyopathy-associated variants which merit further study.
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Affiliation(s)
- Kaveh Rayani
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brianna Davies
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Cheung
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Drake Comber
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Martin S Green
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | | | | | | | - Christian Steinberg
- Institut Universitaire de Cardiologie et Pneumologie de Quebec, Laval University, Quebec City, QC, Canada
| | - Ciorsti MacIntyre
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Paul Angaran
- St Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Henry Duff
- Libin Cardiovascular Institute, University of Calgary, Calgary, AB, Canada
| | - Robert Hamilton
- Division of Cardiology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
| | - Laura Arbour
- Division of Medical Genetics, Island Health, Victoria, BC, Canada
| | | | - Colette Seifer
- Section of Cardiology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Anne Fournier
- Division of Pediatric Cardiology, CHU Sainte-Justine, Universite de Montreal, Montreal, QC, Canada
| | - Joseph Atallah
- Division of Pediatric Cardiology, University of Alberta Stollery Children's Hospital, Edmonton, AB, Canada
| | - Shane Kimber
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Bhavanesh Makanjee
- Heart Health Institute, Scarborough Health Network, Scarborough, ON, Canada
| | - Wael Alqarawi
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - Julia Cadrin-Tourigny
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Jacqueline Joza
- Division of Cardiology, McGill University Health Centre, Montreal, QC, Canada
| | - Martin Gardner
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Mario Talajic
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Andrew D Krahn
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Zachary W M Laksman
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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8
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Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022; 14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
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Affiliation(s)
- Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Susana Gómez-Barrero
- Facultad de Ciencias de la Salud, Universidad Alfonso X “El Sabio”, Avda. de la Universidad 1, Villanueva de la Cañada, 28691 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Eladio A. Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
- Correspondence:
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9
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Bueno‐Martínez E, Sanoguera‐Miralles L, Valenzuela‐Palomo A, Esteban‐Sánchez A, Lorca V, Llinares‐Burguet I, Allen J, García‐Álvarez A, Pérez‐Segura P, Durán M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco‐Sampedro EA. Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants. J Pathol 2022; 258:83-101. [PMID: 35716007 PMCID: PMC9541484 DOI: 10.1002/path.5979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 12/29/2022]
Abstract
The ataxia telangiectasia-mutated (ATM) protein is a major coordinator of the DNA damage response pathway. ATM loss-of-function variants are associated with 2-fold increased breast cancer risk. We aimed at identifying and classifying spliceogenic ATM variants detected in subjects of the large-scale sequencing project BRIDGES. A total of 381 variants at the intron-exon boundaries were identified, 128 of which were predicted to be spliceogenic. After further filtering, we ended up selecting 56 variants for splicing analysis. Four functional minigenes (mgATM) spanning exons 4-9, 11-17, 25-29, and 49-52 were constructed in the splicing plasmid pSAD. Selected variants were genetically engineered into the four constructs and assayed in MCF-7/HeLa cells. Forty-eight variants (85.7%) impaired splicing, 32 of which did not show any trace of the full-length (FL) transcript. A total of 43 transcripts were identified where the most prevalent event was exon/multi-exon skipping. Twenty-seven transcripts were predicted to truncate the ATM protein. A tentative ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme that integrates mgATM data allowed us to classify 29 ATM variants as pathogenic/likely pathogenic and seven variants as likely benign. Interestingly, the likely pathogenic variant c.1898+2T>G generated 13% of the minigene FL-transcript due to the use of a noncanonical GG-5'-splice-site (0.014% of human donor sites). Circumstantial evidence in three ATM variants (leakiness uncovered by our mgATM analysis together with clinical data) provides some support for a dosage-sensitive expression model in which variants producing ≥30% of FL-transcripts would be predicted benign, while variants producing ≤13% of FL-transcripts might be pathogenic. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Inés Llinares‐Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética MolecularValladolidSpain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco‐Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
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10
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Rosenberger FA, Tang JX, Sergeant K, Moedas MF, Zierz CM, Moore D, Smith C, Lewis D, Guha N, Hopton S, Falkous G, Lam A, Pyle A, Poulton J, Gorman GS, Taylor RW, Freyer C, Wredenberg A. Pathogenic SLC25A26 variants impair SAH transport activity causing mitochondrial disease. Hum Mol Genet 2022; 31:2049-2062. [PMID: 35024855 PMCID: PMC9239748 DOI: 10.1093/hmg/ddac002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/28/2021] [Accepted: 12/31/2021] [Indexed: 01/14/2023] Open
Abstract
The SLC25A26 gene encodes a mitochondrial inner membrane carrier that transports S-adenosylmethionine (SAM) into the mitochondrial matrix in exchange for S-adenosylhomocysteine (SAH). SAM is the predominant methyl-group donor for most cellular methylation processes, of which SAH is produced as a by-product. Pathogenic, biallelic SLC25A26 variants are a recognized cause of mitochondrial disease in children, with a severe neonatal onset caused by decreased SAM transport activity. Here, we describe two, unrelated adult cases, one of whom presented with recurrent episodes of severe abdominal pain and metabolic decompensation with lactic acidosis. Both patients had exercise intolerance and mitochondrial myopathy associated with biallelic variants in SLC25A26, which led to marked respiratory chain deficiencies and mitochondrial histopathological abnormalities in skeletal muscle that are comparable to those previously described in early-onset cases. We demonstrate using both mouse and fruit fly models that impairment of SAH, rather than SAM, transport across the mitochondrial membrane is likely the cause of this milder, late-onset phenotype. Our findings associate a novel pathomechanism with a known disease-causing protein and highlight the quests of precision medicine in optimizing diagnosis, therapeutic intervention and prognosis.
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Affiliation(s)
- Florian A Rosenberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Jia Xin Tang
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kate Sergeant
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Marco F Moedas
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Charlotte M Zierz
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Moore
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Conrad Smith
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - David Lewis
- Department of General Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nishan Guha
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Sila Hopton
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Gavin Falkous
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Amanda Lam
- Neurometabolic Unit, Institute of Neurology, Queen Square House, London WC1N 3BG, UK
| | - Angela Pyle
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Joanna Poulton
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Gráinne S Gorman
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Robert W Taylor
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
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11
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Deng H, Zhang Y, Ding J, Wang F. Presumed COL4A3/COL4A4 Missense/Synonymous Variants Induce Aberrant Splicing. Front Med (Lausanne) 2022; 9:838983. [PMID: 35386907 PMCID: PMC8977549 DOI: 10.3389/fmed.2022.838983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/07/2022] [Indexed: 12/27/2022] Open
Abstract
Background The incorrect interpretation of missense and synonymous variants can lead to improper molecular diagnosis and subsequent faulty genetic counselling. The aim of this study was to evaluate the pathogenicity of presumed COL4A3/COL4A4 missense and synonymous variants detected by next-generation sequencing to provide evidence for diagnosis and genetic counselling. Methods Patients' clinical findings and genetic data were analysed retrospectively. An in vitro minigene assay was conducted to assess the effect of presumed COL4A3/COL4A4 missense and synonymous variants on RNA splicing. Results Five unclassified COL4A3/COL4A4 variants, which were detected in five of 343 patients with hereditary kidney diseases, were analysed. All of them were predicted to affect splicing by Human Splicing Finder. The presumed COL4A3 missense variant c.4793T > G [p. (Leu1598Arg)] resulted in a loss of alternative full-length transcript during the splicing process. The COL4A3 transcript carried synonymous variant c.765G > A [p. (Thr255Thr)], led to an in-frame deletion of exon 13. Nevertheless, variants c.3566G > A [p. (Gly1189Glu)] in COL4A3 and c.3990G > A [p. (Pro1330Pro)], c.4766C > T [p. (Pro1589Leu)] in COL4A4 exhibited no deleterious effect on splicing. Among the five patients harbouring the abovementioned COL4A3/COL4A4 variants, three patients were genetically diagnosed with autosomal recessive Alport syndrome, one patient was highly suspected of having thin basement membrane nephropathy, and the other patient was clinically diagnosed with Alport syndrome. Conclusions COL4A3 presumed missense variant p. (Leu1598Arg) and synonymous variant p. (Thr255Thr) affect RNA splicing, which highlights the prime importance of transcript analysis of unclassified exonic sequence variants for better molecular diagnosis and genetic counselling. Meanwhile, the reliability of splicing predictions by predictive tools for exonic substitutions needs to be improved.
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Affiliation(s)
- Haiyue Deng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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12
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Drouet C, López-Lera A, Ghannam A, López-Trascasa M, Cichon S, Ponard D, Parsopoulou F, Grombirikova H, Freiberger T, Rijavec M, Veronez CL, Pesquero JB, Germenis AE. SERPING1 Variants and C1-INH Biological Function: A Close Relationship With C1-INH-HAE. FRONTIERS IN ALLERGY 2022; 3:835503. [PMID: 35958943 PMCID: PMC9361472 DOI: 10.3389/falgy.2022.835503] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Hereditary angioedema with C1 Inhibitor deficiency (C1-INH-HAE) is caused by a constellation of variants of the SERPING1 gene (n = 809; 1,494 pedigrees), accounting for 86.8% of HAE families, showing a pronounced mutagenic liability of SERPING1 and pertaining to 5.6% de novo variants. C1-INH is the major control serpin of the kallikrein–kinin system (KKS). In addition, C1-INH controls complement C1 and plasminogen activation, both systems contributing to inflammation. Recognizing the failed control of C1s protease or KKS provides the diagnosis of C1-INH-HAE. SERPING1 variants usually behave in an autosomal-dominant character with an incomplete penetrance and a low prevalence. A great majority of variants (809/893; 90.5%) that were introduced into online database have been considered as pathogenic/likely pathogenic. Haploinsufficiency is a common feature in C1-INH-HAE where a dominant-negative variant product impacts the wild-type allele and renders it inactive. Small (36.2%) and large (8.3%) deletions/duplications are common, with exon 4 as the most affected one. Point substitutions with missense variants (32.2%) are of interest for the serpin structure–function relationship. Canonical splice sites can be affected by variants within introns and exons also (14.3%). For noncanonical sequences, exon skipping has been confirmed by splicing analyses of patients' blood-derived RNAs (n = 25). Exonic variants (n = 6) can affect exon splicing. Rare deep-intron variants (n = 6), putatively acting as pseudo-exon activating mutations, have been characterized as pathogenic. Some variants have been characterized as benign/likely benign/of uncertain significance (n = 74). This category includes some homozygous (n = 10) or compound heterozygous variants (n = 11). They are presenting with minor allele frequency (MAF) below 0.00002 (i.e., lower than C1-INH-HAE frequency), and may be quantitatively unable to cause haploinsufficiency. Rare benign variants could contribute as disease modifiers. Gonadal mosaicism in C1-INH-HAE is rare and must be distinguished from a de novo variant. Situations with paternal or maternal disomy have been recorded (n = 3). Genotypes must be interpreted with biological investigation fitting with C1-INH expression and typing. Any SERPING1 variant reminiscent of the dysfunctional phenotype of serpin with multimerization or latency should be identified as serpinopathy.
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Affiliation(s)
- Christian Drouet
- Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM UMR1016, Université de Paris, Paris, France
- Univ. Grenoble-Alpes & Centre Hospitalier Universitaire de Grenoble, Grenoble, France
- *Correspondence: Christian Drouet
| | - Alberto López-Lera
- Hospital La Paz Institute for Health Research (IdiPAZ), CIBERER U-754, Madrid, Spain
| | | | - Margarita López-Trascasa
- Hospital La Paz Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid, Madrid, Spain
| | - Sven Cichon
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Denise Ponard
- Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | | | - Hana Grombirikova
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation Brno and Medical Faculty, Masaryk University, Brno, Czechia
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation Brno and Medical Faculty, Masaryk University, Brno, Czechia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Camila L. Veronez
- Department of Biophysics, Centre for Research and Genetic Diagnosis of Genetic Diseases, Federal University of São Paolo, São Paolo, Brazil
| | - João Bosco Pesquero
- Department of Biophysics, Centre for Research and Genetic Diagnosis of Genetic Diseases, Federal University of São Paolo, São Paolo, Brazil
| | - Anastasios E. Germenis
- CeMIA SA, Larissa, Greece
- Department of Immunology & Histocompatibility, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larissa, Greece
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13
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Valenzuela‐Palomo A, Bueno‐Martínez E, Sanoguera‐Miralles L, Lorca V, Fraile‐Bethencourt E, Esteban‐Sánchez A, Gómez‐Barrero S, Carvalho S, Allen J, García‐Álvarez A, Pérez‐Segura P, Dorling L, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants. J Pathol 2022; 256:321-334. [PMID: 34846068 PMCID: PMC9306493 DOI: 10.1002/path.5839] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
PALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing project Breast Cancer After Diagnostic Gene Sequencing (BRIDGES; https://bridges-research.eu/). Eighty-two PALB2 variants at the intron-exon boundaries were analyzed with MaxEntScan. Forty-two variants were selected for the subsequent splicing functional assays. For this purpose, three splicing reporter minigenes comprising exons 1-12 were constructed. The 42 potential spliceogenic variants were introduced into the minigenes by site-directed mutagenesis and assayed in MCF-7/MDA-MB-231 cells. Splicing anomalies were observed in 35 variants, 23 of which showed no traces or minimal amounts of the expected full-length transcripts of each minigene. More than 30 different variant-induced transcripts were characterized, 23 of which were predicted to truncate the PALB2 protein. The pathogenicity of all variants was interpreted according to an in-house adaptation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) variant classification scheme. Up to 23 variants were classified as pathogenic/likely pathogenic. Remarkably, three ±1,2 variants (c.49-2A>T, c.108+2T>C, and c.211+1G>A) were classified as variants of unknown significance, as they produced significant amounts of either in-frame transcripts of unknown impact on the PALB2 protein function or the minigene full-length transcripts. In conclusion, we have significantly contributed to the ongoing effort of identifying spliceogenic variants in the clinically relevant PALB2 cancer susceptibility gene. Moreover, we suggest some approaches to classify the findings in accordance with the ACMG-AMP rationale. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eugenia Fraile‐Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
- Knight Cancer Research BuildingPortlandORUSA
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
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14
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Qian P, Bao Y, Huang HM, Suo L, Han Y, Li ZJ, Zhang M. A deep intronic splice variant of the COL4A5 gene in a Chinese family with X-linked Alport syndrome. Front Pediatr 2022; 10:1009188. [PMID: 36714647 PMCID: PMC9880855 DOI: 10.3389/fped.2022.1009188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/26/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND X-linked Alport syndrome (XLAS) is caused by pathogenic variants in COL4A5 and is characterized by progressive kidney disease, hearing loss, and ocular abnormalities.The aim of this study was to identify gene mutations in a Chinese family with XLAS, confirm a diagnosis, and provide an accurate genetic counseling. METHODS The proband was a 5-year-old male with microscopic hematuria and a family history of renal disease in 5 relatives.His relatives had microhematuria with or without proteinuria. His maternal uncle developed renal failure at the age of 35 years. He was evaluated by renal biopsy,whole-exome sequencing (WES) and whole-genome sequencing (WGS) for Alport syndrome. RT-PCR and cDNA Sanger sequencing were performed on RNA extracted from the skin of the proband. Then, a splicing reporter minigene assay was used to examine the effect of the variation on the splicing of the primary transcript in transfected cells. RESULTS Pathological examination of the kidney of the proband revealed diffuse thinning of the glomerular basement membrane, and immunofluorescence analysis indicated normal expression of the α5 chain in the basement membrane. No phenotype-associated candidate variant was detected in the proband via WES. A novel deep intronic COL4A5 variant (c.385-716G > A), which is segregated with disease in this family, was identified using WGS. In-vitro minigene assay and in-vivo RT-PCR analysis demonstrated that the variant could produce both normal and abnormal transcripts. The abnormal transcripts showed that the variant activated a cryptic splice site, introducing a 147 bp pseudoexon into the mRNA sequence and consequently generating a premature termination codon (p.G129Afs*38) and leading to frameshifting and truncation of the α5 (collagen IV) protein. CONCLUSION This is the first report of the novel c.385-716G > A splicing mutation in the COL4A5 gene, which illustrates the importance of performing WGS to find additional mutations in WES-negative patients with highly suspected forms of genetic diseases. The same results obtained from the in-vitro and in-vivo splicing experiments confirm the consistency between the minigene assay and RT-PCR analysis. In addition, this study highlights the importance of functional analysis in diagnosis and genetic counseling in AS.
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Affiliation(s)
- Pei Qian
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Ying Bao
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Hui-Mei Huang
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Lei Suo
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Yan Han
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Zhi-Juan Li
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
| | - Min Zhang
- Department of Nephrology, Xi'an Children's Hospital, Xi'an, China
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15
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Wu J, Zhang J, Liu L, Zhang B, Yamamura T, Nozu K, Matsuo M, Zhao J. A disease-causing variant of COL4A5 in a Chinese family with Alport syndrome: a case series. BMC Nephrol 2021; 22:380. [PMID: 34774011 PMCID: PMC8590243 DOI: 10.1186/s12882-021-02585-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Alport syndrome (AS), which is a rare hereditary disease caused by mutations of genes including COL4A3, COL4A4 and COL4A5, has a wide spectrum of phenotypes. Most disease-causing variants of AS are located in the exons or the conservative splicing sites of these genes, while little is known about the intronic disease-causing variants. METHODS A Chinese AS family was recruited in this study. All the clinical data of AS patient were collected from medical records. After pedigree analysis, the pathogenic variants were studied by the whole exome sequencing (WES). Minigene assay and in vivo RT-PCR analysis were performed to validate the functions of the variants. RESULTS Renal biopsy showed a typical histopathology changes of AS. WES revealed compound heterozygous substitution, NM_033380 c.991-14(IVS17) A > G, in the intron 17 of the COL4A5 gene, which were confirmed by Sanger sequencing. Moreover, the variant was co-segregated with the phenotype in this family. Minigene assay in cultured cell lines showed that a splicing error was induced by this intronic variant, which further confirmed by in vivo RT-PCR analysis. CONCLUSION A novel intronic disease-causing variant in COL4A5 gene was identified by WES, which was the molecular pathogenic basis of AS.
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Affiliation(s)
- Jing Wu
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Jun Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Li Liu
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Bo Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518, Arise, Ikawadani-cho, Nishi, Kobe, Hyogo, 651-2180, Japan
| | - Jinghong Zhao
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China.
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16
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Towards Splicing Therapy for Lysosomal Storage Disorders: Methylxanthines and Luteolin Ameliorate Splicing Defects in Aspartylglucosaminuria and Classic Late Infantile Neuronal Ceroid Lipofuscinosis. Cells 2021; 10:cells10112813. [PMID: 34831035 PMCID: PMC8616534 DOI: 10.3390/cells10112813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 12/22/2022] Open
Abstract
Splicing defects caused by mutations in the consensus sequences at the borders of introns and exons are common in human diseases. Such defects frequently result in a complete loss of function of the protein in question. Therapy approaches based on antisense oligonucleotides for specific gene mutations have been developed in the past, but they are very expensive and require invasive, life-long administration. Thus, modulation of splicing by means of small molecules is of great interest for the therapy of genetic diseases resulting from splice-site mutations. Using minigene approaches and patient cells, we here show that methylxanthine derivatives and the food-derived flavonoid luteolin are able to enhance the correct splicing of the AGA mRNA with a splice-site mutation c.128-2A>G in aspartylglucosaminuria, and result in increased AGA enzyme activity in patient cells. Furthermore, we also show that one of the most common disease causing TPP1 gene variants in classic late infantile neuronal ceroid lipofuscinosis may also be amenable to splicing modulation using similar substances. Therefore, our data suggest that splice-modulation with small molecules may be a valid therapy option for lysosomal storage disorders.
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17
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Rossanti R, Horinouchi T, Yamamura T, Nagano C, Sakakibara N, Ishiko S, Aoto Y, Kondo A, Nagai S, Okada E, Ishimori S, Nagase H, Matsui S, Tamagaki K, Ubara Y, Nagahama M, Shima Y, Nakanishi K, Ninchoji T, Matsuo M, Iijima K, Nozu K. Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants. KIDNEY360 2021; 3:497-505. [PMID: 35582193 PMCID: PMC9034806 DOI: 10.34067/kid.0005252021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023]
Abstract
Background Alport syndrome is an inherited disorder characterized by progressive renal disease, variable sensorineural hearing loss, and ocular abnormalities. Although many pathogenic variants in COL4A3 and COL4A4 have been identified in patients with autosomal Alport syndrome, synonymous mutations in these genes have rarely been identified. Methods We conducted in silico splicing analysis using Human Splicing Finder (HSF) and Alamut to predict splicing domain strength and disruption of the sites. Furthermore, we performed in vitro splicing assays using minigene constructs and mRNA analysis of patient samples to determine the pathogenicity of four synonymous variants detected in four patients with suspected autosomal dominant Alport syndrome (COL4A3 [c.693G>A (p.Val231=)] and COL4A4 [c.1353C>T (p.Gly451=), c.735G>A (p.Pro245=), and c.870G>A (p.Lys290=)]). Results Both in vivo and in vitro splicing assays showed exon skipping in two out of the four synonymous variants identified (c.735G>A and c.870G>A in COL4A4). Prediction analysis of wild-type and mutated COL4A4 sequences using HSF and Alamut suggested these two variants may lead to the loss of binding sites for several splicing factors, e.g., in acceptor sites and exonic splicing enhancers. The other two variants did not induce aberrant splicing. Conclusions This study highlights the pitfalls of classifying the functional consequences of variants by a simple approach. Certain synonymous variants, although they do not alter the amino acid sequence of the encoded protein, can dramatically affect pre-mRNA splicing, as shown in two of our patients. Our findings indicate that transcript analysis should be carried out to evaluate synonymous variants detected in patients with autosomal dominant Alport syndrome.
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Affiliation(s)
- Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan,Department of Child Health, Nephrology Division, Dr. Hasan Sadikin General Hospital/Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsushi Kondo
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sadayuki Nagai
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Matsui
- Department of Nephrology and Hypertension, Mitsubishi Kyoto Hospital, Kyoto, Japan
| | - Keiichi Tamagaki
- Department of Nephrology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshifumi Ubara
- Nephrology Center, Okinaka Memorial Institute for Medical Research, Tokyo, Japan
| | | | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan
| | - Kazumoto Iijima
- Hyogo Prefectural Kobe Children’s Hospital, Kobe, Japan,Department of Advanced Pediatric Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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18
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Abrahams L, Savisaar R, Mordstein C, Young B, Kudla G, Hurst LD. Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption. Nucleic Acids Res 2021; 49:9665-9685. [PMID: 34469537 PMCID: PMC8464065 DOI: 10.1093/nar/gkab750] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
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Affiliation(s)
- Liam Abrahams
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Aarhus University, Department of Molecular Biology and Genetics, C F Møllers Allé 3, 8000 Aarhus, Denmark
| | - Bethan Young
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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19
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Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021; 4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learning-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to validate the predictive analyses are defined, distinguishing between methods testing RNA (transcriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as suggestions on which approaches are more suitable in diagnostic rather than in clinical research.
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Affiliation(s)
| | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.)
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20
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Frederiksen JH, Jensen SB, Tümer Z, Hansen TVO. Classification of MSH6 Variants of Uncertain Significance Using Functional Assays. Int J Mol Sci 2021; 22:ijms22168627. [PMID: 34445333 PMCID: PMC8395337 DOI: 10.3390/ijms22168627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
Lynch syndrome (LS) is one of the most common hereditary cancer predisposition syndromes worldwide. Individuals with LS have a high risk of developing colorectal or endometrial cancer, as well as several other cancers. LS is caused by autosomal dominant pathogenic variants in one of the DNA mismatch repair (MMR) genes MLH1, MSH2, PMS2 or MSH6, and typically include truncating variants, such as frameshift, nonsense or splicing variants. However, a significant number of missense, intronic, or silent variants, or small in-frame insertions/deletions, are detected during genetic screening of the MMR genes. The clinical effects of these variants are often more difficult to predict, and a large fraction of these variants are classified as variants of uncertain significance (VUS). It is pivotal for the clinical management of LS patients to have a clear genetic diagnosis, since patients benefit widely from screening, preventive and personal therapeutic measures. Moreover, in families where a pathogenic variant is identified, testing can be offered to family members, where non-carriers can be spared frequent surveillance, while carriers can be included in cancer surveillance programs. It is therefore important to reclassify VUSs, and, in this regard, functional assays can provide insight into the effect of a variant on the protein or mRNA level. Here, we briefly describe the disorders that are related to MMR deficiency, as well as the structure and function of MSH6. Moreover, we review the functional assays that are used to examine VUS identified in MSH6 and discuss the results obtained in relation to the ACMG/AMP PS3/BS3 criterion. We also provide a compiled list of the MSH6 variants examined by these assays. Finally, we provide a future perspective on high-throughput functional analyses with specific emphasis on the MMR genes.
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Affiliation(s)
- Jane H. Frederiksen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
- Correspondence: (J.H.F.); (T.v.O.H.)
| | - Sara B. Jensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
| | - Zeynep Tümer
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Thomas v. O. Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
- Correspondence: (J.H.F.); (T.v.O.H.)
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21
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MLH1 intronic variants mapping to + 5 position of splice donor sites lead to deleterious effects on RNA splicing. Fam Cancer 2021; 19:323-336. [PMID: 32363481 DOI: 10.1007/s10689-020-00182-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Germline pathogenic variants in the DNA mismatch repair genes (MMR): MLH1, MSH2, MSH6, and PMS2, are causative of Lynch syndrome (LS). However, many of the variants mapping outside the invariant splice site positions (IVS ± 1, IVS ± 2) are classified as variants of unknown significance (VUS). Three such variants (MLH1 c.588+5G>C, c.588+5G>T and c.677+5G>A) were identified in 8 unrelated LS families from Argentina, Brazil and Chile. Herein, we collected clinical information on these families and performed segregation analysis and RNA splicing studies to assess the implication of these VUS in LS etiology. Pedigrees showed a clear pattern of variant co-segregation with colorectal cancer and/or other LS-associated malignancies. Tumors presented deficient expression of MLH1-PMS2 proteins in 7/7 of the LS families, and MSI-high status in 3/3 cases. Moreover, RNA analyses revealed that c.588+5G>C and c.588+5G>T induce skipping of exon 7 whereas c.677+5G>A causes skipping of exon 8. In sum, we report that the combined clinical findings in the families and the molecular studies provided the evidences needed to demonstrate that the three MLH1 variants are causative of LS and to classify c.588+5G>C and c.677+5G>A as class 5 (pathogenic), and c.588+5G>T as class 4 (likely-pathogenic). Our findings underline the importance of performing clinical and family analyses, as well as RNA splicing assays in order to determine the clinical significance of intronic variants, and contribute to the genetic counseling and clinical management of patients and their relatives.
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22
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Saint-Martin C, Cauchois-Le Mière M, Rex E, Soukarieh O, Arnoux JB, Buratti J, Bouvet D, Frébourg T, Gaildrat P, Shyng SL, Bellanné-Chantelot C, Martins A. Functional characterization of ABCC8 variants of unknown significance based on bioinformatics predictions, splicing assays, and protein analyses: Benefits for the accurate diagnosis of congenital hyperinsulinism. Hum Mutat 2021; 42:408-420. [PMID: 33410562 DOI: 10.1002/humu.24164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
ABCC8 encodes the SUR1 subunit of the β-cell ATP-sensitive potassium channel whose loss of function causes congenital hyperinsulinism (CHI). Molecular diagnosis is critical for optimal management of CHI patients. Unfortunately, assessing the impact of ABCC8 variants on RNA splicing remains very challenging as this gene is poorly expressed in leukocytes. Here, we performed bioinformatics analysis and cell-based minigene assays to assess the impact on splicing of 13 ABCC8 variants identified in 20 CHI patients. Next, channel properties of SUR1 proteins expected to originate from minigene-detected in-frame splicing defects were analyzed after ectopic expression in COSm6 cells. Out of the analyzed variants, seven induced out-of-frame splicing defects and were therefore classified as recessive pathogenic, whereas two led to skipping of in-frame exons. Channel functional analysis of the latter demonstrated their pathogenicity. Interestingly, the common rs757110 SNP increased exon skipping in our system suggesting that it may act as a disease modifier factor. Our strategy allowed determining the pathogenicity of all selected ABCC8 variants, and CHI-inheritance pattern for 16 out of the 20 patients. This study highlights the value of combining RNA and protein functional approaches in variant interpretation and reveals the minigene splicing assay as a new tool for CHI molecular diagnostics.
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Affiliation(s)
- Cécile Saint-Martin
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Marine Cauchois-Le Mière
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Emily Rex
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Omar Soukarieh
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jean-Baptiste Arnoux
- Department of Inherited Metabolic Disease, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Julien Buratti
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Delphine Bouvet
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Thierry Frébourg
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | | | - Alexandra Martins
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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23
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
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24
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Le Tertre M, Ka C, Raud L, Berlivet I, Gourlaouen I, Richard G, Uguen K, Chen JM, Férec C, Fichou Y, Le Gac G. Splicing analysis of SLC40A1 missense variations and contribution to hemochromatosis type 4 phenotypes. Blood Cells Mol Dis 2020; 87:102527. [PMID: 33341511 DOI: 10.1016/j.bcmd.2020.102527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/09/2023]
Abstract
Hemochromatosis type 4, or ferroportin disease, is considered as the second leading cause of primary iron overload after HFE-related hemochromatosis. The disease, which is predominantly associated with missense variations in the SLC40A1 gene, is characterized by wide clinical heterogeneity. We tested the possibility that some of the reported missense mutations, despite their positions within exons, cause splicing defects. Fifty-eight genetic variants were selected from the literature based on two criteria: a precise description of the nucleotide change and individual evidence of iron overload. The selected variants were investigated by different in silico prediction tools and prioritized for midigene splicing assays. Of the 15 variations tested in vitro, only two were associated with splicing changes. We confirm that the c.1402G>A transition (p.Gly468Ser) disrupts the exon 7 donor site, leading to the use of an exonic cryptic splicing site and the generation of a truncated reading frame. We observed, for the first time, that the p.Gly468Ser substitution has no effect on the ferroportin iron export function. We demonstrate alternative splicing of exon 5 in different cell lines and show that the c.430A>G (p.Asn144Asp) variant promotes exon 5 inclusion. This could be part of a gain-of-function mechanism. We conclude that splicing mutations rarely contribute to hemochromatosis type 4 phenotypes. An in-depth investigation of exon 5 auxiliary splicing sequences may help to elucidate the mechanism by which splicing regulatory proteins regulate the production of the full length SLC40A1 transcript and to clarify its physiological importance.
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Affiliation(s)
- Marlène Le Tertre
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Loann Raud
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Association Gaétan Saleün, F-29200, France
| | | | - Isabelle Gourlaouen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | | | - Kévin Uguen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Association Gaétan Saleün, F-29200, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Gérald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France.
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25
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Hsiao HHT, Crichlow GV, Murphy JW, Folta-Stogniew EJ, Lolis EJ, Braddock DT. Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60. PLoS One 2020; 15:e0242725. [PMID: 33253191 PMCID: PMC7703929 DOI: 10.1371/journal.pone.0242725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML3’). We found that the PUF60–AdML3’ dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60’s two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML3’ revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF602:AdML3’) stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3’ splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3’ splice sites.
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Affiliation(s)
- Hsin-hao T. Hsiao
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Gregg V. Crichlow
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - James W. Murphy
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ewa J. Folta-Stogniew
- W.M. Keck Biotechnology Research Laboratory, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Elias J. Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Demetrios T. Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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26
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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27
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Denzer L, Schroten H, Schwerk C. From Gene to Protein-How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection. Int J Mol Sci 2020; 21:ijms21103730. [PMID: 32466312 PMCID: PMC7279228 DOI: 10.3390/ijms21103730] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteria evolved many strategies to survive and persist within host cells. Secretion of bacterial effectors enables bacteria not only to enter the host cell but also to manipulate host gene expression to circumvent clearance by the host immune response. Some effectors were also shown to evade the nucleus to manipulate epigenetic processes as well as transcription and mRNA procession and are therefore classified as nucleomodulins. Others were shown to interfere downstream with gene expression at the level of mRNA stability, favoring either mRNA stabilization or mRNA degradation, translation or protein stability, including mechanisms of protein activation and degradation. Finally, manipulation of innate immune signaling and nutrient supply creates a replicative niche that enables bacterial intracellular persistence and survival. In this review, we want to highlight the divergent strategies applied by intracellular bacteria to evade host immune responses through subversion of host gene expression via bacterial effectors. Since these virulence proteins mimic host cell enzymes or own novel enzymatic functions, characterizing their properties could help to understand the complex interactions between host and pathogen during infections. Additionally, these insights could propose potential targets for medical therapy.
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28
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Horinouchi T, Nozu K, Yamamura T, Minamikawa S, Nagano C, Sakakibara N, Nakanishi K, Shima Y, Morisada N, Ishiko S, Aoto Y, Nagase H, Takeda H, Rossanti R, Kaito H, Matsuo M, Iijima K. Determination of the pathogenicity of known COL4A5 intronic variants by in vitro splicing assay. Sci Rep 2019; 9:12696. [PMID: 31481700 PMCID: PMC6722096 DOI: 10.1038/s41598-019-48990-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023] Open
Abstract
X-linked Alport syndrome (XLAS) is a congenital renal disease caused by mutations in COL4A5. In XLAS cases suspected of being caused by aberrant splicing, transcript analysis needs to be conducted to determine splicing patterns and assess the pathogenicity. However, such analysis is not always available. We conducted a functional splicing assay using a hybrid minigene for seven COL4A5 intronic mutations: one was identified by us and six were found in the Human Gene Mutation Database. The minigene assay revealed exon skipping in four variants, exon skipping and a 10-bp insertion in one variant, and no change in one variant, which appeared not to be pathogenic. For one variant, our assay did not work. The results of all three cases for which transcript data were available were consistent with our assay results. Our findings may help to increase the accuracy of genetic test results and clarify the mechanisms causing aberrant splicing.
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Affiliation(s)
- Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan.
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Shogo Minamikawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, 207, Uehara, Nishihara-cho, Tyutou, Okinawa, 903-0125, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, 811-1, Kimiidera, Wakayama, Wakayama Prefecture, 641-8510, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Hiroki Takeda
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518, Arise, Ikawadani-cho, Nishi, Kobe, Hyogo, 651-2180, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
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29
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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30
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Bitsori M, Vergadi E, Galanakis E. A Novel CLCN5 Splice Site Mutation in a Boy with Incomplete Phenotype of Dent Disease. J Pediatr Genet 2019; 8:235-239. [PMID: 31687264 DOI: 10.1055/s-0039-1692172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/22/2019] [Indexed: 12/15/2022]
Abstract
Dent disease is a rare X-linked renal proximal tubulopathy presenting with low-molecular-weight proteinuria (LMWP), hypercalciuria, and nephrocalcinosis, other signs of incomplete renal Fanconi syndrome, and renal failure. Early identification of patients who harbor disease-associated mutations is important for effective medical care and avoidance of unnecessary interventions. We report the case of an asymptomatic 9-year-old boy who presented with proteinuria in routine examination. Further investigation revealed the presence of nephrotic range proteinuria, mostly LMWP and mild hypercalciuria without nephrocalcinosis, or other features of tubular dysfunction. Renal function, growth, and bone mineral density were within regular limits. The male gender and the presence of LMWP and hypercalciuria even in the absence of other findings prompted us to genetic investigation for Dent disease. A novel splice site mutation (c.416-2A > G) of the chloride voltage-gated channel 5 ( CLCN5 ) gene, responsible for Dent disease type 1 was identified. In silico analysis revealed that this mutation interferes with the mating of exons 4 and 5. Due to early molecular diagnosis, our patient did not undergo a renal biopsy, neither required aggressive pharmacological interventions. This case underscores the diversity and complexity of CLCN5 mutations and highlights the importance of early molecular testing in male patients with incomplete phenotype of Dent disease.
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Affiliation(s)
- Maria Bitsori
- Department of Paediatrics, Heraklion University Hospital, Crete, Greece
| | - Eleni Vergadi
- Department of Paediatrics, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Emmanouil Galanakis
- Department of Paediatrics, School of Medicine, University of Crete, Heraklion, Crete, Greece
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Goina E, Acedo A, Buratti E, Velasco EA. Mis-splicing in breast cancer: identification of pathogenic BRCA2 variants by systematic minigene assays. J Pathol 2019; 248:409-420. [PMID: 30883759 DOI: 10.1002/path.5268] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/21/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022]
Abstract
Splicing disruption is a common mechanism of gene inactivation associated with germline variants of susceptibility genes. To study the role of BRCA2 mis-splicing in hereditary breast/ovarian cancer (HBOC), we performed a comprehensive analysis of variants from BRCA2 exons 2-9, as well as the initial characterization of the regulatory mechanisms of such exons. A pSAD-based minigene with exons 2-9 was constructed and validated in MCF-7 cells, producing the expected transcript (1016-nt/V1-BRCA2_exons_2-9-V2). DNA variants from mutational databases were analyzed by NNSplice and Human Splicing Finder softwares. To refine ESE-variant prediction, we mapped the regulatory regions through a functional strategy whereby 26 exonic microdeletions were introduced into the minigene and tested in MCF-7 cells. Thus, we identified nine spliceogenic ESE-rich intervals where ESE-variants may be located. Combining bioinformatics and microdeletion assays, 83 variants were selected and genetically engineered in the minigene. Fifty-three changes impaired splicing: 28 variants disrupted the canonical sites, four created new ones, 10 abrogated enhancers, eight created silencers and three caused a double-effect. Notably, nine spliceogenic-ESE variants were located within ESE-containing intervals. Capillary electrophoresis and sequencing revealed more than 23 aberrant transcripts, where exon skipping was the most common event. Interestingly, variant c.67G>A triggered the usage of a noncanonical GC-donor 4-nt upstream. Thirty-six variants that induced severe anomalies (>60% aberrant transcripts) were analyzed according to the ACMG guidelines. Thus, 28 variants were classified as pathogenic, five as likely pathogenic and three as variants of uncertain significance. Interestingly, 13 VUS were reclassified as pathogenic or likely pathogenic variants. In conclusion, a large fraction of BRCA2 variants (∼64%) provoked splicing anomalies lending further support to the high prevalence of this disease-mechanism. The low accuracy of ESE-prediction algorithms may be circumvented by functional ESE-mapping that represents an optimal strategy to identify spliceogenic ESE-variants. Finally, systematic functional assays by minigenes depict a valuable tool for the initial characterization of splicing anomalies and the clinical interpretation of variants. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Elisa Goina
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Emanuele Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Zhou Y, Fujikura K, Mkrtchian S, Lauschke VM. Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data. Front Pharmacol 2018; 9:1437. [PMID: 30564131 PMCID: PMC6288784 DOI: 10.3389/fphar.2018.01437] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Up to half of all patients do not respond to pharmacological treatment as intended. A substantial fraction of these inter-individual differences is due to heritable factors and a growing number of associations between genetic variations and drug response phenotypes have been identified. Importantly, the rapid progress in Next Generation Sequencing technologies in recent years unveiled the true complexity of the genetic landscape in pharmacogenes with tens of thousands of rare genetic variants. As each individual was found to harbor numerous such rare variants they are anticipated to be important contributors to the genetically encoded inter-individual variability in drug effects. The fundamental challenge however is their functional interpretation due to the sheer scale of the problem that renders systematic experimental characterization of these variants currently unfeasible. Here, we review concepts and important progress in the development of computational prediction methods that allow to evaluate the effect of amino acid sequence alterations in drug metabolizing enzymes and transporters. In addition, we discuss recent advances in the interpretation of functional effects of non-coding variants, such as variations in splice sites, regulatory regions and miRNA binding sites. We anticipate that these methodologies will provide a useful toolkit to facilitate the integration of the vast extent of rare genetic variability into drug response predictions in a precision medicine framework.
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Affiliation(s)
- Yitian Zhou
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kohei Fujikura
- Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Souren Mkrtchian
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M. Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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Impact, Characterization, and Rescue of Pre-mRNA Splicing Mutations in Lysosomal Storage Disorders. Genes (Basel) 2018; 9:genes9020073. [PMID: 29415500 PMCID: PMC5852569 DOI: 10.3390/genes9020073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/19/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage disorders (LSDs) represent a group of more than 50 severe metabolic diseases caused by the deficiency of specific lysosomal hydrolases, activators, carriers, or lysosomal integral membrane proteins, leading to the abnormal accumulation of substrates within the lysosomes. Numerous mutations have been described in each disease-causing gene; among them, about 5-19% affect the pre-mRNA splicing process. In the last decade, several strategies to rescue/increase normal splicing of mutated transcripts have been developed and LSDs represent excellent candidates for this type of approach: (i) most of them are inherited in an autosomic recessive manner and patients affected by late-onset (LO) phenotypes often retain a fair amount of residual enzymatic activity; thus, even a small recovery of normal splicing may be beneficial in clinical settings; (ii) most LSDs still lack effective treatments or are currently treated with extremely expensive approaches; (iii) in few LSDs, a single splicing mutation accounts for up to 40-70% of pathogenic alleles. At present, numerous preclinical studies support the feasibility of reverting the pathological phenotype by partially rescuing splicing defects in LSDs. This review provides an overview of the impact of splicing mutations in LSDs and the related therapeutic approaches currently under investigation in these disorders.
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de Calais FL, Smith LD, Raponi M, Maciel-Guerra AT, Guerra-Junior G, de Mello MP, Baralle D. A study of splicing mutations in disorders of sex development. Sci Rep 2017; 7:16202. [PMID: 29176693 PMCID: PMC5701223 DOI: 10.1038/s41598-017-16296-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
The presence of splicing sequence variants in genes responsible for sex development in humans may compromise correct biosynthesis of proteins involved in the normal development of gonads and external genitalia. In a cohort of Brazilian patients, we identified mutations in HSD17B3 and SRD5A2 which are both required for human sexual differentiation. A number of these mutations occurred within regions potentially critical for splicing regulation. Minigenes were used to validate the functional effect of mutations in both genes. We evaluated the c.277 + 2 T > G mutation in HSD17B3, and the c.544 G > A, c.548-44 T > G and c.278delG mutations in SRD5A2. We demonstrated that these mutations altered the splicing pattern of these genes. In a genomic era these results illustrate, and remind us, that sequence variants within exon-intron boundaries, which are primarily identified for diagnostic purposes and have unknown pathogenicity, need to be assessed with regards to their impact not only on protein expression, but also on mRNA splicing.
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Affiliation(s)
- Flavia Leme de Calais
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Lindsay D Smith
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Michela Raponi
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andréa Trevas Maciel-Guerra
- Departamento de Genética, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gil Guerra-Junior
- Departamento de Pediatria, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
- Wessex Clinical Genetics Service, Southampton University Hospitals NHS Trust, Southampton, UK.
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Grodecká L, Buratti E, Freiberger T. Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics? Int J Mol Sci 2017; 18:ijms18081668. [PMID: 28758972 PMCID: PMC5578058 DOI: 10.3390/ijms18081668] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023] Open
Abstract
For more than three decades, researchers have known that consensus splice sites alone are not sufficient regulatory elements to provide complex splicing regulation. Other regulators, so-called splicing regulatory elements (SREs) are needed. Most importantly, their sequence variants often underlie the development of various human disorders. However, due to their variable location and high degeneracy, these regulatory sequences are also very difficult to recognize and predict. Many different approaches aiming to identify SREs have been tried, often leading to the development of in silico prediction tools. While these tools were initially expected to be helpful to identify splicing-affecting mutations in genetic diagnostics, we are still quite far from meeting this goal. In fact, most of these tools are not able to accurately discern the SRE-affecting pathological variants from those not affecting splicing. Nonetheless, several recent evaluations have given appealing results (namely for EX-SKIP, ESRseq and Hexplorer predictors). In this review, we aim to summarize the history of the different approaches to SRE prediction, and provide additional validation of these tools based on patients' clinical data. Finally, we evaluate their usefulness for diagnostic settings and discuss the challenges that have yet to be met.
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Affiliation(s)
- Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic.
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic.
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.
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37
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Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes. Clin Immunol 2017; 180:33-44. [DOI: 10.1016/j.clim.2017.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/03/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
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Álvarez-Satta M, Castro-Sánchez S, Pousada G, Valverde D. Functional analysis by minigene assay of putative splicing variants found in Bardet-Biedl syndrome patients. J Cell Mol Med 2017; 21:2268-2275. [PMID: 28502102 PMCID: PMC5618670 DOI: 10.1111/jcmm.13147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/30/2017] [Indexed: 01/05/2023] Open
Abstract
Bardet–Biedl syndrome (BBS) and Alström syndrome (ALMS) are rare diseases belonging to the group of ciliopathies. Although mutational screening studies of BBS/ALMS cohorts have been extensively reported, little is known about the functional effect of those changes. Thus, splicing variants are estimated to represent 15% of disease‐causing mutations, and there is growing evidence that many exonic changes are really splicing variants misclassified. In this study, we aimed to analyse for the first time several variants in BBS2,ARL6/BBS3,BBS4 and ALMS1 genes predicted to produce aberrant splicing by minigene assay. We found discordance between bioinformatics analysis and experimental data when comparing wild‐type and mutant constructs. Remarkably, we identified nonsense variants presumably resistant to nonsense‐mediated decay, even when a premature termination codon would be introduced in the second amino acid (p.(G2*) mutation in ARL6/BBS3 gene). As a whole, we report one of the first functional studies of BBS/ALMS1 variants using minigene assay, trying to elucidate their role in disease. Functional studies of variants identified in BBS and ALMS patients are essential for their proper classification and subsequent genetic counselling and could also be the start point for new therapeutic approaches, currently based only on symptomatic treatment.
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Affiliation(s)
- María Álvarez-Satta
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Sheila Castro-Sánchez
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Guillermo Pousada
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Diana Valverde
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
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Mthembu NN, Mbita Z, Hull R, Dlamini Z. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:77-93. [PMID: 28694706 PMCID: PMC5490432 DOI: 10.2147/hiv.s124911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies.
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Affiliation(s)
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa
| | - Rodney Hull
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
| | - Zodwa Dlamini
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
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Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18. PLoS Genet 2017; 13:e1006691. [PMID: 28339459 PMCID: PMC5384790 DOI: 10.1371/journal.pgen.1006691] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 04/07/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022] Open
Abstract
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants. A splicing reporter minigene with BRCA2 exons 14 to-20 (MGBR2_ex14-20) was constructed in the pSAD vector. Fifty-two candidate variants were selected with splicing prediction programs, introduced in MGBR2_ex14-20 by site-directed mutagenesis and assayed in triplicate in MCF-7 cells. Wild type MGBR2_ex14-20 produced a stable transcript of the expected size (1,806 nucleotides) and structure (V1-[BRCA2_exons_14–20]–V2). Functional mapping by microdeletions revealed essential sequences for exon recognition on the 3’ end of exon 17 (c.7944-7973) and the 5’ end of exon 18 (c.7979-7988, c.7999-8013). Thirty out of the 52 selected variants induced anomalous splicing in minigene assays with >16 different aberrant transcripts, where exon skipping was the most common event. A wide range of splicing motifs were affected including the canonical splice sites (15 variants), novel alternative sites (3 variants), the polypyrimidine tract (3 variants) and enhancers/silencers (9 variants). According to the guidelines of the American College of Medical Genetics and Genomics (ACMG), 20 variants could be classified as pathogenic (c.7806-2A>G, c.7806-1G>A, c.7806-1G>T, c.7806-1_7806-2dup, c.7976+1G>A, c.7977-3_7978del, c.7977-2A>T, c.7977-1G>T, c.7977-1G>C, c.8009C>A, c.8331+1G>T and c.8331+2T>C) or likely pathogenic (c.7806-9T>G, c.7976G>C, c.7976G>A, c.7977-7C>G, c.7985C>G, c.8023A>G, c.8035G>T and c.8331G>A), accounting for 30.8% of all pathogenic/likely pathogenic variants of exons 17–18 at the BRCA Share database. The remaining 8 variants (c.7975A>G, c.7977-6T>G, c.7988A>T, c.7992T>A, c.8007A>G, c.8009C>T, c.8009C>G, and c.8072C>T) induced partial splicing anomalies with important ratios of the full-length transcript (≥70%), so that they remained classified as VUS. Aberrant splicing is therefore especially prevalent in BRCA2 exons 17 and 18 due to the presence of active ESEs involved in exon recognition. Splicing functional assays with minigenes are a valuable strategy for the initial characterization of the splicing outcomes and the subsequent clinical interpretation of variants of any disease-gene, although these results should be checked, whenever possible, against patient RNA. A significant proportion of disease-causing mutations of inherited disorders impair splicing. Massive sequencing projects of genetic diseases generate thousands of sequence variations that require functional and clinical interpretations. We have shown that splicing reporter minigenes of the breast cancer genes BRCA1 and BRCA2 are useful tools to functionally test DNA variants. In this work, we have constructed a 7-exon BRCA2 minigene (exons 14 to 20) where we mapped critical splicing regulatory sequences and tested 52 selected variants of exons 17 and 18 detected in breast cancer patients. We finely located three DNA segments on both exons that presumably contain splicing enhancer sequences. We observed that a total of 30 variants of any type disrupted the splicing patterns and, given the severity of their outcomes, we classified 20 of them as pathogenic or likely pathogenic. We also showed that a wide range of splicing elements were affected including canonical and novel 5’ and 3’ splice sites, the polypyrimidine tract and enhancer and silencer sequences. We concluded that splicing aberrations are frequent in Hereditary Breast and Ovarian Cancer and that minigenes are valuable tools to functionally classify DNA variants of any human disease gene under the splicing viewpoint.
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41
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Balestra D, Scalet D, Pagani F, Rogalska ME, Mari R, Bernardi F, Pinotti M. An Exon-Specific U1snRNA Induces a Robust Factor IX Activity in Mice Expressing Multiple Human FIX Splicing Mutants. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e370. [PMID: 27701399 PMCID: PMC5095682 DOI: 10.1038/mtna.2016.77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/21/2016] [Indexed: 12/30/2022]
Abstract
In cellular models we have demonstrated that a unique U1snRNA targeting an intronic region downstream of a defective exon (Exon-specific U1snRNA, ExSpeU1) can rescue multiple exon-skipping mutations, a relevant cause of genetic disease. Here, we explored in mice the ExSpeU1 U1fix9 toward two model Hemophilia B-causing mutations at the 5′ (c.519A > G) or 3′ (c.392-8T > G) splice sites of F9 exon 5. Hydrodynamic injection of wt-BALB/C mice with plasmids expressing the wt and mutant (hFIX-2G5′ss and hFIX-8G3′ss) splicing-competent human factor IX (hFIX) cassettes resulted in the expression of hFIX transcripts lacking exon 5 in liver, and in low plasma levels of inactive hFIX. Coinjection of U1fix9, but not of U1wt, restored exon inclusion of variants and in the intrinsically weak FIXwt context. This resulted in appreciable circulating hFIX levels (mean ± SD; hFIX-2G5′ss, 1.0 ± 0.5 µg/ml; hFIX-8G3′ss, 1.2 ± 0.3 µg/ml; and hFIXwt, 1.9 ± 0.6 µg/ml), leading to a striking shortening (from ~100 seconds of untreated mice to ~80 seconds) of FIX-dependent coagulation times, indicating a hFIX with normal specific activity. This is the first proof-of-concept in vivo that a unique ExSpeU1 can efficiently rescue gene expression impaired by distinct exon-skipping variants, which extends the applicability of ExSpeU1s to panels of mutations and thus cohort of patients.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Daniela Scalet
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Franco Pagani
- Internation Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Rosella Mari
- Haemostasis & Thrombosis Center, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.,LTTA Center, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.,LTTA Center, University of Ferrara, Ferrara, Italy
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Gaweda-Walerych K, Mohagheghi F, Zekanowski C, Buratti E. Parkinson's disease-related gene variants influence pre-mRNA splicing processes. Neurobiol Aging 2016; 47:127-138. [PMID: 27574110 DOI: 10.1016/j.neurobiolaging.2016.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 12/27/2022]
Abstract
We have analyzed the impact of Parkinson's disease (PD)-related genetic variants on splicing using dedicated minigene assays. Out of 14 putative splicing variants in 5 genes (PINK1, [PTEN induced kinase 1]; LRPPRC, [leucine-rich pentatricopeptide repeat containing protein]; TFAM, [mitochondrial transcription factor A]; PARK2, [parkin RBR E3 ubiquitin protein ligase]; and HSPA9, [heat shock protein family A (Hsp70) member 9]), 4 LRPPRC variants, (IVS32-3C>T, IVS35+14C>T, IVS35+15C>T, and IVS9+30A>G) influenced, pre-messenger RNA splicing by modulating the inclusion of the respective exons. In addition, 1-Methyl-4-phenylpyridinium ion-induced splicing changes of endogenous LRPPRC messenger RNA, reproduced the effect of the LRPPRC IVS35+14C>T mutation. Using silencing and overexpression methods, we show that LRPPRC exon 33 splicing is negatively regulated by heterogeneous nuclear ribonucleoprotein A1 both in a minigene and endogenous context. Furthermore, exon 33 exclusion due to PD-associated mutation IVS32-3C>T or heterogeneous nuclear ribonucleoprotein A1 overexpression and exon 35 exclusion due to IVS35+14C>T can be rescued by co-expression of modified U1 small nuclear RNAs, providing a potentially useful therapeutic strategy. Our results indicate for the first time that LRPPRC intronic variants can affect normal splicing of this gene and may influence disease risk in PD and related disorders.
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Affiliation(s)
- K Gaweda-Walerych
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
| | - F Mohagheghi
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - C Zekanowski
- Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - E Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Analysis of mutations within the intron20 splice donor site of CREBBP in patients with and without classical RSTS. Eur J Hum Genet 2016; 24:1639-1643. [PMID: 27165009 DOI: 10.1038/ejhg.2016.47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 11/08/2022] Open
Abstract
Whole-exome sequencing of a patient with intellectual disability and without recognisable phenotype yielded a mutation in the intron20 splice donor site of CREBBP. Mutations at different positions within the same intron20 splice donor site were observed in three patients clinically suspected as having Rubinstein-Taybi syndrome (RSTS). All mutations were de novo and likely disease-causing. To investigate a putative difference in splicing between the patient without RSTS phenotype and the three patients with the RSTS phenotype, we analysed the effects of these mutations on splicing of the pre-mRNA of CREBBP. As no RNA of patients was available, we generated a new and improved exon-trap vector, pCDNAGHE, and tested the effect of the various mutations on splicing in vitro. All mutations lead to skipping of exon20. In one of the patients with an RSTS phenotype, there was also some normal splicing detectable. We conclude that the splicing pattern obtained by exon-trapping cannot explain the difference in phenotype between the patient without the RSTS phenotype and the patients with clinical RSTS. Patient or tissue-specific splice effects as well as modifying genes likely will explain the difference in phenotype.
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44
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Schleit J, Bailey SS, Tran T, Chen D, Stowers S, Schwarze U, Byers PH. Molecular Outcome, Prediction, and Clinical Consequences of Splice Variants in COL1A1, Which Encodes the proα1(I) Chains of Type I Procollagen. Hum Mutat 2016; 36:728-39. [PMID: 25963598 DOI: 10.1002/humu.22812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/28/2015] [Indexed: 11/09/2022]
Abstract
Approximately 10%-20% of germline pathogenic variants alter mRNA splicing, with phenotypes often dependent on the stability of the mRNA produced by the mutant allele. To better understand the relationships between genotype, mRNA splicing, and phenotype, we examined clinical and molecular data from 243 probands with osteogenesis imperfecta (OI) representing 145 unique splicing variants within the type I procollagen gene, COL1A1. All individuals with IVSX-1G>A mutations had OI type I because the substitution shifted the splice acceptor site 1 nt downstream and destabilized the mRNA. OI phenotypes were not consistent for any other splice variant identified. We sequenced all cDNA species from cultured dermal fibroblasts from 40 individuals to identify splice outcome and compared those results to splice predictions from Human Splice Finder (HSF), Spliceport (SP), and Automatic Splice Site and Exon Definition Analyses (ASSEDA). Software-based splice predictions were correct in 42%, 55%, and 74% instances for HSF, SP, and ASSEDA, respectively. As molecular diagnostics move increasingly to DNA sequence analysis, the need to understand the effects of splice site variants will increase. These data demonstrate that caution must be exercised when using splice prediction software to predict splice outcome.
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Affiliation(s)
- Jennifer Schleit
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Samuel S Bailey
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Thao Tran
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Diana Chen
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Susan Stowers
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Ulrike Schwarze
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Peter H Byers
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
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Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools. PLoS Genet 2016; 12:e1005756. [PMID: 26761715 PMCID: PMC4711968 DOI: 10.1371/journal.pgen.1005756] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient's RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants), including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs). We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZEI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases.
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46
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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47
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Acedo A, Hernández-Moro C, Curiel-García Á, Díez-Gómez B, Velasco EA. Functional classification of BRCA2 DNA variants by splicing assays in a large minigene with 9 exons. Hum Mutat 2015; 36:210-21. [PMID: 25382762 PMCID: PMC4371643 DOI: 10.1002/humu.22725] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/27/2014] [Indexed: 01/04/2023]
Abstract
Numerous pathogenic DNA variants impair the splicing mechanism in human genetic diseases. Minigenes are optimal approaches to test variants under the splicing viewpoint without the need of patient samples. We aimed to design a robust minigene construct of the breast cancer gene BRCA2 in order to investigate the impact of variants on splicing. BRCA2 exons 19-27 (MGBR2_ex19-27) were cloned in the new vector pSAD. It produced a large transcript of the expected size (2,174 nucleotides) and exon structure (V1-ex19-27-V2). Splicing assays showed that 18 (17 splice-site and 1 silencer variants) out of 40 candidate DNA variants induced aberrant patterns. Twenty-four anomalous transcripts were accurately detected by fluorescent-RT-PCR that were generated by exon-skipping, alternative site usage, and intron-retention events. Fourteen variants induced major anomalies and were predicted to disrupt protein function so they could be classified as pathogenic. Furthermore, minigene mimicked previously reported patient RNA outcomes of seven variants supporting the reproducibility of minigene assays. Therefore, a relevant fraction of variants are involved in breast cancer through splicing alterations. MGBR2_ex19-27 is the largest reported BRCA2 minigene and constitutes a valuable tool for the functional and clinical classification of sequence variations.
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Affiliation(s)
- Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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48
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Velho RV, Sperb-Ludwig F, Schwartz IVD. New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals. AN ACAD BRAS CIENC 2015; 87:1375-88. [PMID: 26247150 DOI: 10.1590/0001-3765201520140711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.
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Affiliation(s)
- Renata V Velho
- Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, BR
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49
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Pal LR, Yu CH, Mount SM, Moult J. Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease. BMC Genomics 2015; 16 Suppl 8:S4. [PMID: 26110739 PMCID: PMC4480957 DOI: 10.1186/1471-2164-16-s8-s4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, there must be some molecular level mechanism relevant to the disease. What are these mechanisms and how do they contribute to disease? RESULTS Here we consider the roles of three primary mechanism classes: changes that directly alter protein function (missense SNPs), changes that alter transcript abundance as a consequence of variants close-by in sequence, and changes that affect splicing. Missense SNPs are divided into those predicted to have a high impact on in vivo protein function, and those with a low impact. Splicing is divided into SNPs with a direct impact on splice sites, and those with a predicted effect on auxiliary splicing signals. The analysis was based on associations found for seven complex trait diseases in the classic Wellcome Trust Case Control Consortium (WTCCC1) GWA study and subsequent studies and meta-analyses, collected from the GWAS catalog. Linkage disequilibrium information was used to identify possible candidate SNPs for involvement in disease mechanism in each of the 356 loci associated with these seven diseases. With the parameters used, we find that 76% of loci have at least of these mechanisms. Overall, except for the low incidence of direct impact on splice sites, the mechanisms are found at similar frequencies, with changes in transcript abundance the most common. But the distribution of mechanisms over diseases varies markedly, as does the fraction of loci with assigned mechanisms. Many of the implicated proteins have previously been suggested as relevant, but the specific mechanism assignments are new. In addition, a number of new disease relevant proteins are proposed. CONCLUSIONS The high fraction of GWAS loci with proposed mechanisms suggests that these classes of mechanism play a major role. Other mechanism types, such as variants affecting expression of genes remote in the DNA sequence, will contribute in other loci. Each of the identified putative mechanisms provides a hypothesis for further investigation.
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Affiliation(s)
- Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
| | - Chen-Hsin Yu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
- Molecular and Cellular Biology Program, University of Maryland, College Park, MD, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
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50
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van der Klift HM, Jansen AML, van der Steenstraten N, Bik EC, Tops CMJ, Devilee P, Wijnen JT. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med 2015; 3:327-45. [PMID: 26247049 PMCID: PMC4521968 DOI: 10.1002/mgg3.145] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants.
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Affiliation(s)
- Heleen M van der Klift
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Anne M L Jansen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands
| | | | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Pathology, Leiden University Medical Center Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
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