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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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Kalyta K, Stelmaszczyk W, Szczęśniak D, Kotuła L, Dobosz P, Mroczek M. The Spectrum of the Heterozygous Effect in Biallelic Mendelian Diseases-The Symptomatic Heterozygote Issue. Genes (Basel) 2023; 14:1562. [PMID: 37628614 PMCID: PMC10454578 DOI: 10.3390/genes14081562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Heterozygous carriers of pathogenic/likely pathogenic variants in autosomal recessive disorders seem to be asymptomatic. However, in recent years, an increasing number of case reports have suggested that mild and unspecific symptoms can occur in some heterozygotes, as symptomatic heterozygotes have been identified across different disease types, including neurological, neuromuscular, hematological, and pulmonary diseases. The symptoms are usually milder in heterozygotes than in biallelic variants and occur "later in life". The status of symptomatic heterozygotes as separate entities is often disputed, and alternative diagnoses are considered. Indeed, often only a thin line exists between dual, dominant, and recessive modes of inheritance and symptomatic heterozygosity. Interestingly, recent population studies have found global disease effects in heterozygous carriers of some genetic variants. What makes the few heterozygotes symptomatic, while the majority show no symptoms? The molecular basis of this phenomenon is still unknown. Possible explanations include undiscovered deep-splicing variants, genetic and environmental modifiers, digenic/oligogenic inheritance, skewed methylation patterns, and mutational burden. Symptomatic heterozygotes are rarely reported in the literature, mainly because most did not undergo the complete diagnostic procedure, so alternative diagnoses could not be conclusively excluded. However, despite the increasing accessibility to high-throughput technologies, there still seems to be a small group of patients with mild symptoms and just one variant of autosomes in biallelic diseases. Here, we present some examples, the current state of knowledge, and possible explanations for this phenomenon, and thus argue against the existing dominant/recessive classification.
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Affiliation(s)
- Kateryna Kalyta
- School of Life Sciences, FHNW—University of Applied Sciences, 4132 Muttenz, Switzerland;
| | - Weronika Stelmaszczyk
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK;
| | - Dominika Szczęśniak
- Institute of Psychiatry and Neurology in Warsaw, Genetics Department, 02-957 Warsaw, Poland;
| | - Lidia Kotuła
- Department of Genetics, Medical University, 20-080 Lublin, Poland;
| | - Paula Dobosz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland;
| | - Magdalena Mroczek
- University Hospital Basel, University of Basel, 4031 Basel, Switzerland
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Zhong H, Yu M, Lin P, Zhao Z, Zheng X, Xi J, Zhu W, Zheng Y, Zhang W, Lv H, Yan C, Hu J, Wang Z, Lu J, Zhao C, Luo S, Yuan Y. Molecular landscape of DYSF mutations in dysferlinopathy: From a Chinese multicenter analysis to a worldwide perspective. Hum Mutat 2021; 42:1615-1623. [PMID: 34559919 DOI: 10.1002/humu.24284] [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: 04/10/2021] [Revised: 08/10/2021] [Accepted: 09/04/2021] [Indexed: 01/07/2023]
Abstract
Dysferlinopathy is one of the most common subgroup of autosomal recessive limb-girdle muscular dystrophies that is caused by mutations in DYSF gene. However, there is currently no worldwide comprehensive genetic analysis of DYSF variants. Through a national multicenter collaborative effort in China, we identified 222 DYSF variants with 40 novel variants from 245 patients. We then integrated DYSF variants from disease-related genetic databases including LOVD (n = 1020) and Clinvar (n = 1179), to depict the global landscape of disease-related DYSF variants. Normal-population-derived DSYF variants from gnomAD (n = 4318) and ChinaMAP (n = 13,330) were also analyzed in comparison. In Chinese patients, gender instead of genotype showed influence on the onset age of dysferlinopathy, with males showing an earlier age of onset. After integrative analysis, we identified two hotspot DYSF mutations, c.2997G>T in world patients and c.1375dup in Chinese patients, respectively. Both the pathogenic and likely pathogenic variants scattered on the whole gene length of DYSF. However, three specific domains (C2F-C2G-TM, DysF, and C2B-Ferl-C2C) contained variants at higher frequencies than reported in both the databases and Chinese patients. This study comprehensively collected available DYSF variant data, which may pave way for genetic counselling and future clinical trial design for gene therapies in dysferlinopathy.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Pengfei Lin
- Department of Neurology, Shandong University Qilu Hospital, Jinan, Shandong Province, China
| | - Zhe Zhao
- Department of Neuromuscular Disorders, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Xueying Zheng
- Department of Biostatistics, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chuanzhu Yan
- Department of Neurology, Shandong University Qilu Hospital, Jinan, Shandong Province, China
| | - Jing Hu
- Department of Neuromuscular Disorders, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China.,National Center for Neurological Disorders, Shanghai, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
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Gergics P, Smith C, Bando H, Jorge AAL, Rockstroh-Lippold D, Vishnopolska SA, Castinetti F, Maksutova M, Carvalho LRS, Hoppmann J, Martínez Mayer J, Albarel F, Braslavsky D, Keselman A, Bergadá I, Martí MA, Saveanu A, Barlier A, Abou Jamra R, Guo MH, Dauber A, Nakaguma M, Mendonca BB, Jayakody SN, Ozel AB, Fang Q, Ma Q, Li JZ, Brue T, Pérez Millán MI, Arnhold IJP, Pfaeffle R, Kitzman JO, Camper SA. High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency. Am J Hum Genet 2021; 108:1526-1539. [PMID: 34270938 DOI: 10.1016/j.ajhg.2021.06.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary hormone deficiency occurs in ∼1:4,000 live births. Approximately 3% of the cases are due to mutations in the alpha isoform of POU1F1, a pituitary-specific transcriptional activator. We found four separate heterozygous missense variants in unrelated individuals with hypopituitarism that were predicted to affect a minor isoform, POU1F1 beta, which can act as a transcriptional repressor. These variants retain repressor activity, but they shift splicing to favor the expression of the beta isoform, resulting in dominant-negative loss of function. Using a high-throughput splicing reporter assay, we tested 1,070 single-nucleotide variants in POU1F1. We identified 96 splice-disruptive variants, including 14 synonymous variants. In separate cohorts, we found two additional synonymous variants nominated by this screen that co-segregate with hypopituitarism. This study underlines the importance of evaluating the impact of variants on splicing and provides a catalog for interpretation of variants of unknown significance in POU1F1.
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Affiliation(s)
- Peter Gergics
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Cathy Smith
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Hironori Bando
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Alexander A L Jorge
- Genetic Endocrinology Unit (LIM25), Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Denise Rockstroh-Lippold
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany
| | - Sebastian A Vishnopolska
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Frederic Castinetti
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - Mariam Maksutova
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Luciani Renata Silveira Carvalho
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Julia Hoppmann
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany
| | - Julián Martínez Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Frédérique Albarel
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - Debora Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ana Keselman
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, CABA C1428EHA, Argentina
| | - Alexandru Saveanu
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Laboratory of Molecular Biology, Marseille 13385, France
| | - Anne Barlier
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Laboratory of Molecular Biology, Marseille 13385, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Michael H Guo
- Division of Endocrinology, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Dauber
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marilena Nakaguma
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Berenice B Mendonca
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Sajini N Jayakody
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - A Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Qing Fang
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Thierry Brue
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - María Ines Pérez Millán
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ivo J P Arnhold
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Roland Pfaeffle
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany; Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA.
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