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Canchi Sistla H, Talluri S, Rajagopal T, Venkatabalasubramanian S, Rao Dunna N. Genomic instability in ovarian cancer: Through the lens of single nucleotide polymorphisms. Clin Chim Acta 2025; 565:119992. [PMID: 39395774 DOI: 10.1016/j.cca.2024.119992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/04/2024] [Accepted: 10/04/2024] [Indexed: 10/14/2024]
Abstract
Ovarian cancer (OC) is the deadliest gynecological malignancy among all female reproductive cancers. It is characterized by high mortality rate and poor prognosis. Genomic instability caused by mutations, single nucleotide polymorphisms (SNPs), copy number variations (CNVs), microsatellite instability (MSI), and chromosomal instability (CIN) are associated with OC predisposition. SNPs, which are highly prevalent in the general population, show a greater relative risk contribution, particularly in sporadic cancers. Understanding OC etiology in terms of genetic basis can increase the use of molecular diagnostics and provide promising approaches for designing novel treatment modalities. This will help deliver personalized medicine to OC patients, which may soon be within reach. Given the pivotal impact of SNPs in cancers, the primary emphasis of this review is to shed light on their prevalence in key caretaker genes that closely monitor genomic integrity, viz., DNA damage response, repair, cell cycle checkpoints, telomerase maintenance, and apoptosis and their clinical implications in OC. We highlight the current challenges faced in different SNP-based studies. Various computational methods and bioinformatic tools employed to predict the functional impact of SNPs have also been comprehensively reviewed concerning OC research. Overall, this review identifies that variants in the DDR and HRR pathways are the most studied, implying their critical role in the disease. Conversely, variants in other pathways, such as NHEJ, MMR, cell cycle, apoptosis, telomere maintenance, and PARP genes, have been explored the least.
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Affiliation(s)
- Harshavardhani Canchi Sistla
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA 02215, USA; Veterans Administration Boston Healthcare System, West Roxbury, MA 02132, USA
| | | | - Sivaramakrishnan Venkatabalasubramanian
- Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai 603 203, India
| | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India.
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Liu X, Teng L, Sun J. Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites. Comput Biol Chem 2024; 115:108321. [PMID: 39675189 DOI: 10.1016/j.compbiolchem.2024.108321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 11/29/2024] [Accepted: 12/10/2024] [Indexed: 12/17/2024]
Abstract
Hearing impairment is a major global health problem, affecting more than 5 % of the world's population at various ages, from neonates to the elderly. Among the common genetic variations in humans, single nucleotide variations and small insertions or deletions predominate. The study of hearing loss resulting from these variations is proving invaluable in the analysis and diagnosis of hearing disorders. The identification of pathogenic mutations is frequently a lengthy and laborious process. Existing computational prediction tools have been developed primarily for common diseases and genome-wide analyses, with less focus on deafness. This study proposes a novel approach that focuses on the regions surrounding mutation sites. Mutation sites associated with deafness and their flanking regions of different lengths were extracted from relevant databases and combined into seven distinct segments of different lengths. The information-theoretic features of these segments were computed. Five machine learning algorithms were then used for training, resulting in the construction of a model capable of classifying and predicting deafness-related mutations. For fragments encompassing the 250 bp regions upstream and downstream of the mutations, the average AUC of the five classifiers on the independent test set is 0.89 and the average ACC is 0.85, indicating that the model has a high recognition rate of the pathogenic deafness mutation site. An ensemble approach was also applied to predict variants of uncertain significance (VUS) that may be associated with deafness. These variants were then scored and ranked to assess their likelihood of contributing to the condition.
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Affiliation(s)
- Xiao Liu
- School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 401331, China.
| | - Li Teng
- School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 401331, China
| | - Jing Sun
- School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 401331, China
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Clowes V, Taylor JC, Pagnamenta AT. Hiding in plain sight: a partial deletion of BRCA1 exon 7 undetectable by MLPA is a Nepali founder variant. J Med Genet 2024:jmg-2024-110422. [PMID: 39663108 DOI: 10.1136/jmg-2024-110422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 11/17/2024] [Indexed: 12/13/2024]
Affiliation(s)
- Virginia Clowes
- North West Thames Regional Genetics Service, Northwick Park Hospital, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, Devon, UK
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Perrin A, Garcia-Uzquiano R, Stojkovic T, Tard C, Metay C, Bergougnoux A, Van Goethem C, Thèze C, Larrieux M, Faure-Gautron H, Laporte J, Lefebvre G, Krahn M, Juntas-Morales R, Titin's Network Collaborators, Koenig M, Quijano-Roy S, Carlier RY, Cossée M. Congenital Titinopathies Linked to Mutations in TTN Metatranscript-Only Exons. Int J Mol Sci 2024; 25:12994. [PMID: 39684706 DOI: 10.3390/ijms252312994] [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: 10/31/2024] [Revised: 11/28/2024] [Accepted: 11/29/2024] [Indexed: 12/18/2024] Open
Abstract
Congenital titinopathies reported to date show autosomal recessive inheritance and are caused by a variety of genomic variants, most of them located in metatranscript (MTT)-only exons. The aim of this study was to describe additional patients and establish robust genotype-phenotype associations in titinopathies. This study involved analyzing molecular, clinical, pathological, and muscle imaging features in 20 patients who had at least one pathogenic or likely pathogenic TTN variant in MTT-only exons, with onset occurring antenatally or in the early postnatal stages. The 20 patients with recessive inheritance exhibited a heterogeneous range of phenotypes. These included fetal lethality, progressive weakness, cardiac or respiratory complications, hyper-CKemia, or dystrophic muscle biopsies. MRI revealed variable abnormalities in different muscles. All patients presented severe congenital myopathy at birth, characterized by arthrogryposis (either multiplex or axial-distal) or neonatal hypotonia in most cases. This study provides detailed genotype-phenotype correlations in congenital titinopathies caused by mutations in MTT-only exons. The findings highlight the variability in clinical presentation and the severity of phenotypes associated with these specific genetic alterations. RNA-seq analyses provided valuable insights into the molecular consequences of TTN variants, particularly in relation to splicing defects and nonsense-mediated RNA decay. In conclusion, this study reinforces the genotype-phenotype correlations between congenital myopathies and variants in TTN MTT-only exons, improves their molecular diagnosis, and provides a better understanding of their pathophysiology.
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Affiliation(s)
- Aurélien Perrin
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, 34093 Montpellier, France
| | - Rocio Garcia-Uzquiano
- AP-HP, GHU Université Paris-Saclay, Neuromuscular Center, Child Neurology and ICU Department, Raymond Poincare Hospital, 92380 Garches, France
| | - Tanya Stojkovic
- AP-HP, Centre de Référence des Maladies Neuromusculaires Nord/Est/Île-de-France, Sorbonne Université, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Céline Tard
- Département de Neurologie et des Troubles du Mouvement, U1172, Centre Hospitalo Universitaire (CHU) de Lille, CT, Centre de Référence des Maladies Neuromusculaires Nord/Est/Île-de-France, 59000 Lille, France
| | - Corinne Metay
- AP-HP, UF Molecular Cardiogenetics and Myogenetics, Sorbonne Université and Sorbonne Université UPMC Paris 06, Inserm UMRS974, Research Center in Myology, Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, 34093 Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
| | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
| | - Marion Larrieux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
| | - Héloise Faure-Gautron
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, 34093 Montpellier, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, CNRS UMR 7104, Université de Strasbourg, 67400 Illkirch, France
| | - Guillaume Lefebvre
- Service d'Imagerie Musculo-Squelettique, CCIAL, CHU de Lille, Rue Emile Laine, 59037 Lille, France
| | - Martin Krahn
- INSERM, Marseille Medical Genetics, U1251, Aix-Marseille Université, 13385 Marseille, France
- Département de Génétique Médicale, Hôpital Timone Enfants, APHM, 13385 Marseille, France
| | - Raul Juntas-Morales
- Neurology Department, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | | | - Michel Koenig
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, 34093 Montpellier, France
| | - Susana Quijano-Roy
- AP-HP, GHU Université Paris-Saclay, Neuromuscular Center, Child Neurology and ICU Department, Raymond Poincare Hospital, 92380 Garches, France
- U1179 INSERM-UVSQ, Université de Versailles, 78180 Montigny, France
| | - Robert-Yves Carlier
- U1179 INSERM-UVSQ, Université de Versailles, 78180 Montigny, France
- AP-HP, GHU Université Paris-Saclay, DMU Smart Imaging, Radiology Department, Raymond Poincaré Teaching Hospital, 92380 Garches, France
| | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, 34093 Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, 34093 Montpellier, France
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Hoe RHM, Zhao Y, Ong HL, Tay KSS, Tan NCK, Khor MJY, Fan BE, Peikert K, Hermann A, Neo S, Chen Z. Novel Biallelic Synonymous Exonic Variant in VPS13A Affecting mRNA Splicing: Case Report. Neurol Genet 2024; 10:e200207. [PMID: 39588054 PMCID: PMC11588019 DOI: 10.1212/nxg.0000000000200207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/11/2024] [Indexed: 11/27/2024]
Abstract
Objectives Chorea-acanthocytosis is an autosomal recessively inherited condition caused by loss-of-function pathogenic variants in VPS13A. We identified a novel synonymous exonic variant leading to abnormal mRNA splicing in a patient with chorea-acanthocytosis. Methods A patient with focal epilepsy developed generalized chorea with orolingual dystonia, cognitive decline, and peripheral neuropathy, consistent with chorea-acanthocytosis. Her parents were first cousins, but there was otherwise no family history. Targeted gene sequencing for variants in VPS13A, mRNA splicing analysis, and Western blot for chorein were performed. Results A homozygous synonymous variant in exon 41 of VPS13A (NM_033305.3): c.5157C>T; p.Gly1719 = was identified; this was previously classified as a variant of uncertain significance. SpliceAI predicted a splice donor gain with a score of 0.75 2 base pairs upstream of the reported variant. RNA splicing analysis revealed the creation of a type III splice variant, resulting in a frameshift and a premature termination codon. Western blot showed absent chorein/VPS13A protein. Discussion The variant is reclassified as likely pathogenic based on the American College of Medical Genetics criteria. This is the first reported case of ChAc caused by a synonymous variant in VPS13A proven to affect splicing. Our report further expands the spectrum of variants known to cause ChAc.
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Affiliation(s)
- Rebecca Hui Min Hoe
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Yi Zhao
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Helen Lisa Ong
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Karine Su Shan Tay
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Nigel Choon Kiat Tan
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Mikaelea Jia Yi Khor
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Bingwen Eugene Fan
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Kevin Peikert
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Andreas Hermann
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Shermyn Neo
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
| | - Zhiyong Chen
- From the Department of Neurology (R.H.M.H., K.S.S.T., N.C.K.T., S.N., Z.C.), National Neuroscience Institute (Tan Tock Seng Hospital Campus); Departments of Anatomical Pathology (Y.Z.), and Clinical Translational Research (H.L.O.), Singapore General Hospital; Departments of Laboratory Medicine (M.J.Y.K.), and Haematology (B.E.F.), Tan Tock Seng Hospital; Lee Kong Chian School of Medicine (B.E.F.), Nanyang Technological University, Singapore; Translational Neurodegeneration Section "Albrecht Kossel" (K.P., A.H.), Department of Neurology, Rostock University Medical Center, University of Rostock; Center for Transdisciplinary Neurosciences Rostock (CTNR) (K.P., A.H.), University Medical Center Rostock; United Neuroscience Campus Lund-Rostock (UNC) (K.P., A.H.); and Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald (A.H.), Germany
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Munteanu CV, Marian C, Chiriță-Emandi A, Puiu M, Trifa AP. In silico splicing analysis of the PMS2 gene: exploring alternative molecular mechanisms in PMS2-associated Lynch syndrome. BMC Genom Data 2024; 25:100. [PMID: 39592919 PMCID: PMC11600730 DOI: 10.1186/s12863-024-01281-3] [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: 07/01/2024] [Accepted: 11/14/2024] [Indexed: 11/28/2024] Open
Abstract
Lynch syndrome (LS) is one of the most common hereditary cancer syndrome in human populations, associated with germline variants in MLH1, MSH2/EPCAM, MSH6 and PMS2 genes. The advent of next generation sequencing has proven a significant impact in germline variant detection in the causative genes; however, a large proportion of patients with clinical criteria still receive uncertain or negative results. PMS2 is the least frequent reported gene, associated with up to 15% of LS cases with late-onset disease and low penetrance phenotype; however, the proportion of PMS2-LS cases is considered to be highly underestimated. In this context, our analysis aimed to improve the current diagnostic yield by focusing on missense and intronic PMS2 variants available in public clinical databases (ClinVar, LOVD). We performed an in silico assessment of the wild-type DNA sequence and the reported genetic variants, employing splicing bioinformatics tools known for their effectiveness in other genes. Splicing variants were predicted in silico and using GTEx short-read RNA expression data. Out of the 2384 missense variants discovered, 90% were classified with uncertain significance (VUS). 4.9% of missense variants were shown to have a potential splicing consequence (DS > 0.2) using SpliceAI. As described in the original publication, SpliceAI-visual was proven effective in annotation of short intronic variants (< 50 bp). Four short intronic variants were identified using SpliceAI-visual as potentially splicing disturbing, in spite of using a lower threshold (DS > 0.1). Exons 2, 3, 4, 5, 6, 7, 8, 11, 12 and 14 were consistently predicted in at least three out of eight software with weak canonical splice sites. Additionally, we noted that both Exonic Splicing Enhancers (ESEs) and Exonic Splicing Silencers (ESSs) contribute significantly to alternative splicing and exonic selection in PMS2 gene. Specifically, ESE motifs were consistently more abundant in highly expressed exons 5, 11 and 14, while ESS motifs played a fundamental role in exons 6, 7 and 10. Computational analysis performed in our study serves as a valuable filtering step for guiding further RNA experiments. Additional functional data is necessary to validate our findings.
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Affiliation(s)
- Cătălin Vasile Munteanu
- Doctoral School, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania.
- Regional Center of Medical Genetics Timiș, Louis Țurcanu Clinical Emergency Hospital for Children, 2 Iosif Nemoianu Street, Timișoara, 300011, Romania.
| | - Cătălin Marian
- Department of Biochemistry and Pharmacology, Biochemistry Discipline, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Center for Research and Innovation in Personalized Medicine of Respiratory Diseases, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Center of Expertise on Rare Pulmonary Diseases, Victor Babeș Clinical Hospital of Infectious Diseases and Pneumophysiology, 13 Gheorghe Adam Street, Timișoara, 300310, Romania
| | - Adela Chiriță-Emandi
- Department of Microscopic Morphology, Genetics Discipline, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Regional Center of Medical Genetics Timiș, Louis Țurcanu Clinical Emergency Hospital for Children, 2 Iosif Nemoianu Street, Timișoara, 300011, Romania
- Center for Genomic Medicine, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timisoara, 300041, Romania
| | - Maria Puiu
- Department of Microscopic Morphology, Genetics Discipline, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Regional Center of Medical Genetics Timiș, Louis Țurcanu Clinical Emergency Hospital for Children, 2 Iosif Nemoianu Street, Timișoara, 300011, Romania
- Center for Genomic Medicine, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timisoara, 300041, Romania
| | - Adrian Pavel Trifa
- Department of Microscopic Morphology, Genetics Discipline, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Center for Research and Innovation in Personalized Medicine of Respiratory Diseases, Victor Babeș University of Medicine and Pharmacy, 2 Eftimie Murgu Square Street, Timișoara, 300041, Romania
- Center of Expertise on Rare Pulmonary Diseases, Victor Babeș Clinical Hospital of Infectious Diseases and Pneumophysiology, 13 Gheorghe Adam Street, Timișoara, 300310, Romania
- Breast Cancer Center, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, Cluj-Napoca, 400015, Romania
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7
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Zhao W, Tao Y, Xiong J, Liu L, Wang Z, Shao C, Shang L, Hu Y, Xu Y, Su Y, Yu J, Feng T, Xie J, Xu H, Zhang Z, Peng J, Wu J, Zhang Y, Zhu S, Xia K, Tang B, Zhao G, Li J, Li B. GoFCards: an integrated database and analytic platform for gain of function variants in humans. Nucleic Acids Res 2024:gkae1079. [PMID: 39578693 DOI: 10.1093/nar/gkae1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 10/20/2024] [Accepted: 10/28/2024] [Indexed: 11/24/2024] Open
Abstract
Gain-of-function (GOF) variants, which introduce new or amplify protein functions, are essential for understanding disease mechanisms. Despite advances in genomics and functional research, identifying and analyzing pathogenic GOF variants remains challenging owing to fragmented data and database limitations, underscoring the difficulty in accessing critical genetic information. To address this challenge, we manually reviewed the literature, pinpointing 3089 single-nucleotide variants and 72 insertions and deletions in 579 genes associated with 1299 diseases from 2069 studies, and integrated these with the 3.5 million predicted GOF variants. Our approach is complemented by a proprietary scoring system that prioritizes GOF variants on the basis of the evidence supporting their GOF effects and provides predictive scores for variants that lack existing documentation. We then developed a database named GoFCards for general geneticists and clinicians to easily obtain GOF variants in humans (http://www.genemed.tech/gofcards). This database also contains data from >150 sources and offers comprehensive variant-level and gene-level annotations, with the aim of providing users with convenient access to detailed and relevant genetic information. Furthermore, GoFCards empowers users with limited bioinformatic skills to analyze and annotate genetic data, and prioritize GOF variants. GoFCards offers an efficient platform for interpreting GOF variants and thereby advancing genetic research.
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Affiliation(s)
- Wenjing Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
- Department of Medical Genetics, NHC Key Laboratory of Healthy Birth and Birth Defect Prevention in Western China, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, Yunnan 650000, China
- School of Medicinie, Kunming University of Science and Technology, No. 727 Jingming South Road, Chenggong District, Kunming, Yunnan 650000, China
| | - Youfu Tao
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Jiayi Xiong
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
| | - Lei Liu
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Zhongqing Wang
- School of Medicinie, Kunming University of Science and Technology, No. 727 Jingming South Road, Chenggong District, Kunming, Yunnan 650000, China
| | - Chuhan Shao
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Ling Shang
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Yue Hu
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Yishu Xu
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Yingluo Su
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Jiahui Yu
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Tianyi Feng
- Xiangya School of Medicine, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Junyi Xie
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Huijuan Xu
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Zijun Zhang
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Jiayi Peng
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Jianbin Wu
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Yuchang Zhang
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Shaobo Zhu
- School of Life Science, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410008, China
| | - Kun Xia
- MOE Key Laboratory of Pediatric Rare Diseases & Hunan Key Laboratory of Medical Genetics, Central South University, No. 110 Xiangya Road, Furong District, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
- Department of Neurology & Multi-omics Research Center for Brain Disorders, The First Affiliated Hospital University of South China, 69 Chuan Shan Road, Shi Gu District, Hengyang, Hunan 421000, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Furong District, Changsha,Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Furong District, Changsha,Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, No. 87 Xiangya Road, Furong District, Changsha, Hunan 410008, China
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8
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Zanetti A, Dujardin G, Fares-Taie L, Amiel J, Roger JE, Audo I, Robert MP, David P, Jung V, Goudin N, Guerrera IC, Moriceau S, Amana D, Assia Batzir N, Bachar-Zipori A, Basel Salmon L, Boddaert N, Briault S, Bruel AL, Costet-Fighiera C, Coutinho Santos L, Gitiaux C, Kaminska K, Kuentz P, Orenstein N, Philip-Sarles N, Plutino M, Quinodoz M, Santos C, Sigaudy S, Soeiro E Sá M, Sofrin E, Sousa AB, Sousa-Luis R, Thauvin-Robinet C, van Dijk EL, Zaafrane-Khachnaoui K, Zur D, Kaplan J, Rivolta C, Rozet JM, Perrault I. GPATCH11 variants cause mis-splicing and early-onset retinal dystrophy with neurological impairment. Nat Commun 2024; 15:10096. [PMID: 39572588 PMCID: PMC11582697 DOI: 10.1038/s41467-024-54549-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/13/2024] [Indexed: 11/24/2024] Open
Abstract
Here we conduct a study involving 12 individuals with retinal dystrophy, neurological impairment, and skeletal abnormalities, with special focus on GPATCH11, a lesser-known G-patch domain-containing protein, regulator of RNA metabolism. To elucidate its role, we study fibroblasts from unaffected individuals and patients carrying the recurring c.328+1 G > T mutation, which specifically removes the main part of the G-patch domain while preserving the other domains. Additionally, we generate a mouse model replicating the patients' phenotypic defects, including retinal dystrophy and behavioral abnormalities. Our results reveal a subcellular localization of GPATCH11 characterized by a diffuse presence in the nucleoplasm, as well as centrosomal localization, suggesting potential functions in RNA and cilia metabolism. Transcriptomic analysis performed on mouse retina detect dysregulation in both gene expression and splicing activity, impacting key processes such as photoreceptor light responses, RNA regulation, and primary cilia-associated metabolism. Proteomic analysis of mouse retina confirms the roles GPATCH11 plays in RNA processing, splicing, and transcription regulation, while also suggesting additional functions in synaptic plasticity and nuclear stress response. Our research provides insights into the diverse roles of GPATCH11 and identifies that the mutations affecting this protein are responsible for a recently characterized described syndrome.
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Affiliation(s)
- Andrea Zanetti
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France
| | - Gwendal Dujardin
- Génétique, Génomique fonctionnelle et Biotechnologies (GGB), Université de Brest, INSERM UMR1078, EFS, Brest, France
| | - Lucas Fares-Taie
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France
| | - Jérôme E Roger
- Paris-Saclay Institute of Neurosciences, CERTO-Retina France, CNRS, Paris-Saclay University, Saclay, France
| | - Isabelle Audo
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET F-, Paris, France
| | - Matthieu P Robert
- Ophthalmology Department, University Hospital Necker-Enfants Malades, APHP, Paris, France
| | - Pierre David
- Transgenesis platform, Laboratory of Animal Experimentation and Transgenesis (LEAT) of the Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMSS3633, Institute of Genetic Diseases, Imagine, Paris, France
| | - Vincent Jung
- Proteomic Platform Necker, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR 3633, Paris, France
| | - Nicolas Goudin
- Necker Bioimage Analysis Core Facility of the Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR 3633, Paris, France
| | - Ida Chiara Guerrera
- Proteomic Platform Necker, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR 3633, Paris, France
| | - Stéphanie Moriceau
- Platform for Neurobehavioral and metabolism, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR 3633, Institute of Genetic Diseases, Imagine, Paris, France
| | - Danielle Amana
- Ophthalmology Department, Hospital Center of Orleans, Orleans, France
| | - Nurit Assia Batzir
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Anat Bachar-Zipori
- Ophthalmology Division, Tel Aviv Medical Center; Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Lina Basel Salmon
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
| | - Nathalie Boddaert
- Pediatric-Radiology Department, University Hospital Necker-Enfants Malades, APHP, Paris Cité University, INSERM UMR1163, Paris, France
| | - Sylvain Briault
- Genetics Department, Regional Hospital of Orleans (CHRO), Orleans, France
| | - Ange-Line Bruel
- INSERM UMR1231, GAD team Université de Bourgogne-Franche Comté, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | | | | | - Cyril Gitiaux
- Department of Clinical Neurophysiology, Reference center for neuromuscular pathologies Paris Nord Est, University Hospital Necker-Enfants Malades, Paris Cité University, Paris, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Paul Kuentz
- INSERM UMR1231, GAD team Université de Bourgogne-Franche Comté, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Naama Orenstein
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Morgane Plutino
- Service de Génétique Médicale, Hôpital l'Archet 2, CHU de Nice, Nice, France
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Cristina Santos
- Instituto de Oftalmologia Dr. Gama Pinto (IOGP), Lisboa, Portugal
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Sabine Sigaudy
- Medical Genetics Department, Hospital Timone Enfant, Marseille, France
| | - Mariana Soeiro E Sá
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Efrat Sofrin
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
- Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Rui Sousa-Luis
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christel Thauvin-Robinet
- INSERM UMR1231, GAD team Université de Bourgogne-Franche Comté, FHU-TRANSLAD, CHU Dijon, Dijon, France
- Reference Center for Rare Diseases "Developmental Abnormalities and Malformation Syndromes" of the East, Genetic center, Hopital d'Enfants, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette Cedex, France
| | | | - Dinah Zur
- Ophthalmology Division, Tel Aviv Medical Center; Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Cité University, Paris, France.
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9
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Martinez-Mayer J, Vishnopolska S, Perticarari C, Iglesias Garcia L, Hackbartt M, Martinez M, Zaiat J, Jacome-Alvarado A, Braslavsky D, Keselman A, Bergadá I, Marino R, Ramírez P, Pérez Garrido N, Ciaccio M, Di Palma MI, Belgorosky A, Forclaz MV, Benzrihen G, D'Amato S, Cirigliano ML, Miras M, Paez Nuñez A, Castro L, Mallea-Gil MS, Ballarino C, Latorre-Villacorta L, Casiello AC, Hernandez C, Figueroa V, Alonso G, Morin A, Guntsche Z, Lee H, Lee E, Song Y, Marti MA, Perez-Millan MI. Exome Sequencing Has a High Diagnostic Rate in Sporadic Congenital Hypopituitarism and Reveals Novel Candidate Genes. J Clin Endocrinol Metab 2024; 109:3196-3210. [PMID: 38717911 DOI: 10.1210/clinem/dgae320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 06/23/2024]
Abstract
CONTEXT The pituitary gland is key for childhood growth, puberty, and metabolism. Pituitary dysfunction is associated with a spectrum of phenotypes, from mild to severe. Congenital hypopituitarism (CH) is the most commonly reported pediatric endocrine dysfunction, with an incidence of 1:4000, yet low rates of genetic diagnosis have been reported. OBJECTIVE We aimed to unveil the genetic etiology of CH in a large cohort of patients from Argentina. METHODS We performed whole exome sequencing of 137 unrelated cases of CH, the largest cohort examined with this method to date. RESULTS Of the 137 cases, 19.1% and 16% carried pathogenic or likely pathogenic variants in known and new genes, respectively, while 28.2% carried variants of uncertain significance. This high yield was achieved through the integration of broad gene panels (genes described in animal models and/or other disorders), an unbiased candidate gene screen with a new bioinformatics pipeline (including genes with high loss-of-function intolerance), and analysis of copy number variants. Three novel findings emerged. First, the most prevalent affected gene encodes the cell adhesion factor ROBO1. Affected children had a spectrum of phenotypes, consistent with a role beyond pituitary stalk interruption syndrome. Second, we found that CHD7 mutations also produce a phenotypic spectrum, not always associated with full CHARGE syndrome. Third, we add new evidence of pathogenicity in the genes PIBF1 and TBC1D32, and report 13 novel candidate genes associated with CH (eg, PTPN6, ARID5B). CONCLUSION Overall, these results provide an unprecedented insight into the diverse genetic etiology of hypopituitarism.
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Affiliation(s)
- Julian Martinez-Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Sebastian Vishnopolska
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Catalina Perticarari
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Lucia Iglesias Garcia
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Martina Hackbartt
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Marcela Martinez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Jonathan Zaiat
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Andrea Jacome-Alvarado
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Debora Braslavsky
- Centro de Investigaciones "Dr. Cesar Bergadá" (CEDIE)-CONICET-FEI-División Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, C1425EFD, Buenos Aires, Argentina
| | - Ana Keselman
- Centro de Investigaciones "Dr. Cesar Bergadá" (CEDIE)-CONICET-FEI-División Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, C1425EFD, Buenos Aires, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones "Dr. Cesar Bergadá" (CEDIE)-CONICET-FEI-División Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, C1425EFD, Buenos Aires, Argentina
| | - Roxana Marino
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Pablo Ramírez
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Natalia Pérez Garrido
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Marta Ciaccio
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Maria Isabel Di Palma
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Alicia Belgorosky
- Servicio de Endocrinología-CONICET, Hospital de Pediatría Prof. Dr. J. P. Garrahan, C1245AAM, Buenos Aires, Argentina
| | - Maria Veronica Forclaz
- Servicio de Endocrinología Pediátrica, Hospital Nacional Profesor Alejandro Posadas, 1684, Buenos Aires, Argentina
| | - Gabriela Benzrihen
- Servicio de Endocrinología Pediátrica, Hospital Nacional Profesor Alejandro Posadas, 1684, Buenos Aires, Argentina
| | - Silvia D'Amato
- Servicio de Endocrinología Pediátrica, Hospital Nacional Profesor Alejandro Posadas, 1684, Buenos Aires, Argentina
| | - Maria Lujan Cirigliano
- Servicio de Endocrinología Pediátrica, Hospital Nacional Profesor Alejandro Posadas, 1684, Buenos Aires, Argentina
| | - Mirta Miras
- Hospital De Niños de la Santísima Trinidad, CP5000, Córdoba, Argentina
- Centro Privado de Endocrinologia Infanto Juvenil Crecer, CP5000, Cordoba, Argentina
| | - Alejandra Paez Nuñez
- Centro Privado de Endocrinologia Infanto Juvenil Crecer, CP5000, Cordoba, Argentina
| | - Laura Castro
- Hospital De Niños de la Santísima Trinidad, CP5000, Córdoba, Argentina
| | | | - Carolina Ballarino
- Servicio de Endocrinología, Hospital Militar Central, C1426BOS, Buenos Aires, Argentina
| | | | - Ana Clara Casiello
- Servicio de Endocrinología, Hospital General de Niños Pedro de Elizalde, C1270AAN, Buenos Aires, Argentina
| | - Claudia Hernandez
- Servicio de Endocrinología, Hospital General de Niños Pedro de Elizalde, C1270AAN, Buenos Aires, Argentina
| | - Veronica Figueroa
- Servicio de Endocrinología, Hospital General de Niños Pedro de Elizalde, C1270AAN, Buenos Aires, Argentina
| | - Guillermo Alonso
- Sección Endocrinología Pediátrica, Hospital Italiano, C1199ABB, Buenos Aires, Argentina
| | - Analia Morin
- Sala de Endocrinología, Hospital de Niños Sor Maria Ludovica de La Plata, B1904, La Plata, Argentina
| | | | - Hane Lee
- 3Billion Inc., 14th, 416 Teheran-ro, Gangnam-gu, Seoul, South Korea
| | - Eugene Lee
- 3Billion Inc., 14th, 416 Teheran-ro, Gangnam-gu, Seoul, South Korea
| | - Yongjun Song
- 3Billion Inc., 14th, 416 Teheran-ro, Gangnam-gu, Seoul, South Korea
| | - Marcelo Adrian Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Maria Ines Perez-Millan
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
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10
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Frederiksen JH, Birkedal U, Bachmann S, Eliesen EV, Rasmussen LJ, Pedersen KV, Al‐Zehhawi L, Boonen SE, Krogh L, Rønlund K, Graversen L, Assenholt J, Schmiegelow K, Wadt K, Gerdes A, Hansen TVO. Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data. Mol Genet Genomic Med 2024; 12:e70026. [PMID: 39548353 PMCID: PMC11567815 DOI: 10.1002/mgg3.70026] [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: 06/17/2024] [Revised: 08/29/2024] [Accepted: 09/25/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND Pathogenic variants in the mismatch repair genes are associated with an elevated lifetime risk of colorectal cancer (CRC). We previously identified two variants of uncertain significance (VUS) in the MLH1 gene, c.696_698del, p.(Cys233del) and c.1919C > G, p.(Pro640Arg), in Danish families with numerous occurrences of CRC. METHODS To reclassify the variants we collected clinical data, initiated tumor and co-segregation analysis, and performed RNA splicing analysis, subcellular localization, and protein stability studies. RESULTS The functional analysis revealed that the c.696_698del, p.(Cys233del) variant had an effect at the RNA level, on subcellular localization, and on protein stability, while the c.1919C > G, p.(Pro640Arg) variant showed decreased expression in localization studies and decreased protein stability. These results suggest both variants disrupt DNA mismatch repair. CONCLUSION By applying all collected data and functional results we propose to reclassify the c.696_698del, p.(Cys233del) and the c.1919C > G, p.(Pro640Arg) variants as likely pathogenic (class 4) using MMR gene-specific ACMG/AMP guidelines. Consequently, the two MLH1 variants can now be used for risk assessment of variant carriers, while family members without the variants can be excluded from intensified cancer surveillance and follow population recommendations.
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Affiliation(s)
| | - Ulf Birkedal
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Sarah Bachmann
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | | | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Katja Venborg Pedersen
- Department of Clinical Genetics, Hospital LittlebeltUniversity of Southern DenmarkVejleDenmark
| | - Lana Al‐Zehhawi
- Department of Clinical Genetics, Zealand University HospitalRegion ZealandRoskildeDenmark
| | - Susanne E. Boonen
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
| | - Lotte Krogh
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
| | - Karina Rønlund
- Department of Clinical Genetics, Hospital LittlebeltUniversity of Southern DenmarkVejleDenmark
| | - Lise Graversen
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
| | | | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent MedicineCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Karin Wadt
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Anne‐Marie Gerdes
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Thomas v. O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
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11
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Cogan G, Zaki MS, Issa M, Keren B, Guillaud-Bataille M, Renaldo F, Isapof A, Lallemant P, Stevanin G, Guillot-Noel L, Courtin T, Buratti J, Freihuber C, Gleeson JG, Howarth R, Durr A, de Sainte Agathe JM, Mignot C. Biallelic variants in ERLIN1: a series of 13 individuals with spastic paraparesis. Hum Genet 2024; 143:1353-1362. [PMID: 39367212 DOI: 10.1007/s00439-024-02702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/09/2024] [Indexed: 10/06/2024]
Abstract
Biallelic variants in the ERLIN1 gene were recently reported as the cause of two motor neuron degeneration diseases, SPG62 and a recessive form of amyotrophic lateral sclerosis. However, only 12 individuals from five pedigrees have been identified so far. Thus, the description of the disease remains limited. Following the discovery of a homozygous pathogenic variant in a girl with SPG62, presenting with intellectual disability, and epilepsy, we gathered the largest series of SPG62 cases reported so far (13 individuals) to better understand the phenotype associated with ERLIN1. We collected molecular and clinical data for 13 individuals from six families with ERLIN1 biallelic variants. We performed RNA-seq analyses to characterize intronic variants and used Alphafold and a transcripts database to characterize the molecular consequences of the variants. We identified three new variants suspected to alter the bell-shaped ring formed by the ERLIN1/ERLIN2 complex. Affected individuals had childhood-onset paraparesis with slow progression. Six individuals presented with gait ataxia and three had superficial sensory loss. Aside from our proband, none had intellectual disability or epilepsy. Biallelic pathogenic ERLIN1 variants induce a rare, predominantly pure, spastic paraparesis, with possible cerebellar and peripheral nerve involvement.
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Affiliation(s)
- Guillaume Cogan
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mahmoud Issa
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Marine Guillaud-Bataille
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Florence Renaldo
- APHP Sorbonne Université, Service de Neuropédiatrie, Centre de Référence Neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Arnaud Isapof
- APHP Sorbonne Université, Service de Neuropédiatrie, Centre de Référence Neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Pauline Lallemant
- APHP Sorbonne Université, Service de Médecine Physique et de Réadaptation Pédiatrique, Hôpital Armand Trousseau, Paris, France
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Giovanni Stevanin
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
- Bordeaux University, INCIA, UMR5287, CNRS, EPHE, 33000, Bordeaux, France
| | - Lena Guillot-Noel
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Thomas Courtin
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Julien Buratti
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Cécile Freihuber
- APHP Sorbonne Université, Service de Neuropédiatrie, Centre de Référence Neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92130, USA
| | - Robyn Howarth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92130, USA
| | - Alexandra Durr
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Jean-Madeleine de Sainte Agathe
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau, Centre de Référence Déficiences Intellectuelles de Causes Rares, ERN-ITHACA, 47-83 Boulevard de l'hôpital, 75013, Paris, France.
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.
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12
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Rivera IS, French JD, Bitar M, Sivakumaran H, Nair S, Kaufmann S, Hillman KM, Moradi Marjaneh M, Beesley J, Edwards SL. GWAS and 3D chromatin mapping identifies multicancer risk genes associated with hormone-dependent cancers. PLoS Genet 2024; 20:e1011490. [PMID: 39585897 PMCID: PMC11627375 DOI: 10.1371/journal.pgen.1011490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 12/09/2024] [Accepted: 11/06/2024] [Indexed: 11/27/2024] Open
Abstract
Hormone-dependent cancers (HDCs) share several risk factors, suggesting a common aetiology. Using data from genome-wide association studies, we showed spatial clustering of risk variants across four HDCs (breast, endometrial, ovarian and prostate cancers), contrasting with genetically uncorrelated traits. We identified 44 multi-HDC risk regions across the genome, defined as overlapping risk regions for at least two HDCs: two regions contained risk variants for all four HDCs, 13 for three HDCs and 28 for two HDCs. Integrating GWAS data, epigenomic profiling and promoter capture HiC maps from diverse cell line models, we annotated 53 candidate risk genes at 22 multi-HDC risk regions. These targets were enriched for established genes from the COSMIC Cancer Gene Census, but many had no previously reported pleiotropic roles. Additionally, we pinpointed lncRNAs as potential HDC targets and identified risk alleles in several regions that altered transcription factors motifs, suggesting regulatory mechanisms. Known drug targets were over-represented among the candidate multi-HDC risk genes, implying that some may serve as targets for therapeutic development or facilitate the repurposing of existing treatments for HDC. Our approach provides a framework for identifying common target genes driving complex traits and enhances understanding of HDC susceptibility.
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Affiliation(s)
- Isela Sarahi Rivera
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Juliet D French
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Mainá Bitar
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Haran Sivakumaran
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sneha Nair
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kristine M Hillman
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jonathan Beesley
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Stacey L Edwards
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
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13
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Diallo M, Sylla O, Sidibé MK, Plaisant C, Mercier E, Sequeira A, Javerzat S, Hadid A, Lasseaux E, Michaud V, Arveiler B. Genotypic spectrum of albinism in Mali. Pigment Cell Melanoma Res 2024; 37:752-761. [PMID: 38720644 DOI: 10.1111/pcmr.13175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 10/29/2024]
Abstract
Albinism is a phenotypically and genetically heterogeneous condition characterized by a variable degree of hypopigmentation and by ocular features leading to reduced visual acuity. Whereas numerous genotypic studies have been conducted throughout the world, very little is known about the genotypic spectrum of albinism in Africa and especially in sub-Saharan Western Africa. Here we report the analysis of all known albinism genes in a series a 23 patients originating from Mali. Four were diagnosed with OCA 1 (oculocutaneous albinism type 1), 17 with OCA 2, and two with OCA 4. OCA2 variant NM_000275.3:c.819_822delinsGGTC was most frequently encountered. Four novel variants were identified (two in TYR, two in OCA2). A deep intronic variant was found to alter splicing of the OCA2 RNA by inclusion of a pseudo exon. Of note, the OCA2 exon 7 deletion commonly found in eastern, central, and southern Africa was absent from this series. African patients with OCA 1 and OCA 4 had only been reported twice and once, respectively, in previous publications. This study constitutes the first report of the genotypic spectrum of albinism in a western sub-Saharan country.
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Affiliation(s)
- Modibo Diallo
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
| | | | | | | | - Elina Mercier
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
| | - Angèle Sequeira
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
| | - Sophie Javerzat
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
| | | | | | - Vincent Michaud
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
- Service de Génétique Médicale, CHU, Bordeaux, France
| | - Benoit Arveiler
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University INSERM U1211, Bordeaux, France
- Service de Génétique Médicale, CHU, Bordeaux, France
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14
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Abid F, Khan K, Ashraf NM, Badshah Y, Shabbir M, Trembley JH, Afsar T, Almajwal A, Razak S. Genetic Variants at PRKCG Splice and UTR Sites Promote Cancer Susceptibility by Disrupting Epigenetic and miRNA Regulatory Network. J Cancer 2024; 15:6644-6657. [PMID: 39668814 PMCID: PMC11632988 DOI: 10.7150/jca.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 10/14/2024] [Indexed: 12/14/2024] Open
Abstract
The changes in the protein kinase C gamma gene (PRKCG) expression are associated with both coding and non-coding variants. No studies have specifically established the association between PRKCG 3'UTR, 5'UTR, donor and acceptor splice variants with post-transcriptional changes through utilizing in-silico tools. The current study intends to uncover this linkage. In total, 419 3' and 5'UTR variants were retrieved. 325 of these variant IDs were annotated as functionally significant. 18 variants impacted the transcription factors binding and therefore influenced the post-transcriptional regulatory activity while 7 variants affected regulatory mechanisms through histone modifications. 2 rsIDs (rs373228, rs446795) potentially impacted the interactions with RNA binding proteins. In addition to that, PRKCG showed high expression in brain cells and had variable expression in TCGA tumors, respectively. Furthermore, 5 3' UTR variants were identified to be targeted by miRNAs. In total, 5 of these miRNAs (hsa-miR-663a, hsa-miR-324-5p, hsa-miR-646, hsa-miR-1205 and hsa-miR-4270) that targeted 3'UTRs (rs57483118, rs181418157 and rs60891969) showed differential expressions in distinct cancer types. The presence of 3'UTR variants likely altered the secondary structure of mRNA. The 7 rsIDs at 3' UTR site caused the loss of function of authentic splice site at 10 positions was noted; at 1 position, gain of function was observed while at 2 positions no effect was identified. Moreover, the loss of donor and acceptor splice site was evident. Our results highlight the importance of non-coding regions that might boost our research capacity to predict and construct targeted therapeutic approaches.
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Affiliation(s)
- Fizzah Abid
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Khushbukhat Khan
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Yasmin Badshah
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Maria Shabbir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Janeen H Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, 55111 USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN,55405 USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN,55407 USA
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11421, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11421, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11421, Saudi Arabia
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15
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Karimi N, Ghasemi A, Panahi A, Ziaadini B, Nafissi S. CHRNE-related congenital myasthenic syndrome in Iran: Clinical and molecular insights. Neuromuscul Disord 2024; 46:105234. [PMID: 39550999 DOI: 10.1016/j.nmd.2024.105234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 10/03/2024] [Accepted: 10/24/2024] [Indexed: 11/19/2024]
Abstract
Variants in the CHRNE gene can lead to a condition called congenital myasthenic syndrome (CMS), which affects the neuromuscular junction (NMJ). CHRNE mutations are the most common cause of CMS. Seventy-seven patients with a possible diagnosis of CMS were referred to the neuromuscular clinic of Shariati Hospital affiliated with the Tehran University of Medical Sciences. We performed whole-exome sequencing (WES) to determine the underlying defect in a group of individuals with a possible diagnosis of CMS. Clinical features and morphological and molecular data on 33 patients with mutations in CHRNE were described. Age of onset, age at diagnosis, consanguinity, family history, motor milestone delay, ophthalmoparesis, generalized fatigue, dysphagia, neurophysiologic findings, and response to treatment of the patients were assessed. Nineteen CHRNE variants including 10 novel ones were identified. The most common mutations were c.1327del; (p.Glu443LysfsTer64) in four different families and c.1252-1267dup; (p.Cys423SerfsTer38) in three families. Clinical onset was mostly at birth or under one year with bilateral fatigable ptosis, ophthalmoplegia, bulbar weakness, and proximal muscle weakness. All patients were treated with pyridostigmine ± salbutamol, which resulted in improvement of motor function, dysphagia, and breathing.
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Affiliation(s)
- Narges Karimi
- Immunogenetics Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Aida Ghasemi
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Panahi
- Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Bentolhoda Ziaadini
- Neurology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Nafissi
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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16
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Keefer-Jacques E, Valente N, Jacko AM, Matwijec G, Reese A, Tekriwal A, Loomes KM, Spinner NB, Gilbert MA. Investigation of cryptic JAG1 splice variants as a cause of Alagille syndrome and performance evaluation of splice predictor tools. HGG ADVANCES 2024; 5:100351. [PMID: 39244638 PMCID: PMC11440345 DOI: 10.1016/j.xhgg.2024.100351] [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: 07/02/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024] Open
Abstract
Haploinsufficiency of JAG1 is the primary cause of Alagille syndrome (ALGS), a rare, multisystem disorder. The identification of JAG1 intronic variants outside of the canonical splice region as well as missense variants, both of which lead to uncertain associations with disease, confuses diagnostics. Strategies to determine whether these variants affect splicing include the study of patient RNA or minigene constructs, which are not always available or can be laborious to design, as well as the utilization of computational splice prediction tools. These tools, including SpliceAI and Pangolin, use algorithms to calculate the probability that a variant results in a splice alteration, expressed as a Δ score, with higher Δ scores (>0.2 on a 0-1 scale) positively correlated with aberrant splicing. We studied the consequence of 10 putative splice variants in ALGS patient samples through RNA analysis and compared this to SpliceAI and Pangolin predictions. We identified eight variants with aberrant splicing, seven of which had not been previously validated. Combining these data with non-canonical and missense splice variants reported in the literature, we identified a predictive threshold for SpliceAI and Pangolin with high sensitivity (Δ score >0.6). Moreover, we showed reduced specificity for variants with low Δ scores (<0.2), highlighting a limitation of these tools that results in the misidentification of true splice variants. These results improve genomic diagnostics for ALGS by confirming splice effects for seven variants and suggest that the integration of splice prediction tools with RNA analysis is important to ensure accurate clinical variant classifications.
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Affiliation(s)
- Ernest Keefer-Jacques
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicolette Valente
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anastasia M Jacko
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Grace Matwijec
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Apsara Reese
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Aarna Tekriwal
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melissa A Gilbert
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Nóbrega PR, Paiva ARB, Amorim Junior AD, Lima PLGSB, Cabral KSS, Barcelos IP, Pessoa ALS, Souza-Lima CFL, Castro MAA, Freua F, Santos EDS, Rocha MMV, Maia RE, Araújo RS, Ramos JDG, Resende RG, Carvalho GDS, Valença LPA, Lima de Carvalho JR, Melo ES, Pedroso JL, Barsottini OGP, Houlden H, Kok F, Lynch DS. Further description of the phenotypic spectrum of neuronal ceroid lipofuscinosis type 11. Genet Med 2024; 27:101291. [PMID: 39394881 DOI: 10.1016/j.gim.2024.101291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 10/01/2024] [Accepted: 10/01/2024] [Indexed: 10/14/2024] Open
Abstract
PURPOSE Ceroid lipofuscinosis type 11 (CLN11) is a very rare disease, being reported in only 13 unrelated families so far. Further reports are necessary to comprehend the clinical phenotype of this condition. This article aims to report 9 additional cases of CLN11 from 9 unrelated Latin American families presenting with relatively slow disease progression. METHODS This was a retrospective observational study including patients with CLN11. Patients were identified through an active search for granulin precursor gene (GRN) pathogenic variants across the entire database of next-generation sequencing of a commercial laboratory and by contacting attending physicians to check for clinical and radiologic findings compatible with a neuronal ceroid lipofuscinosis phenotype. RESULTS Nine CLN11 patients from unrelated families were evaluated. Age of onset varied between 3 to 17 years. The most common findings were visual impairment, cerebellar ataxia, seizures, myoclonus, and cognitive decline. One patient had a previously unreported finding of cervical, perioral, and tongue myoclonus. Most of the patients were able to walk unassisted after an average of 14.2 years (SD 4.76 y) from disease onset. CONCLUSION We describe 9 new cases of a very rare type of neuronal ceroid lipofuscinosis (CLN11) from Latin America with a recurrent p.(Gln257ProfsTer27) and a novel p.(Cys83Ter) nonsense variant. Our findings suggest that a slowly progressive neuronal ceroid lipofuscinosis might be a clue for the diagnosis of CLN11.
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Affiliation(s)
- Paulo Ribeiro Nóbrega
- Division of Neurology, Universidade Federal do Ceara, Fortaleza, CE, Brazil; Centro Universitário Christus, Fortaleza, CE, Brazil
| | - Anderson Rodrigues Brandão Paiva
- Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil; Mendelics Genomic Analysis, São Paulo, SP, Brazil
| | - Antonio Duarte Amorim Junior
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Katiane Sayão Souza Cabral
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Isabella Peixoto Barcelos
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - André Luis Santos Pessoa
- Hospital Infantil Albert Sabin, Fortaleza, CE, Brazil; Universidade Estadual do Ceara, Fortaleza, CE, Brazil
| | | | - Matheus Augusto Araújo Castro
- Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil; Mendelics Genomic Analysis, São Paulo, SP, Brazil
| | - Fernando Freua
- Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Rayana Elias Maia
- Departamento de Pediatria e Genética, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Rodrigo Santos Araújo
- Hospital Universitário de Lagarto, Universidade Federal de Sergipe, Aracaju, SE, Brazil; Hospital de Urgência de Sergipe, Aracaju, SE, Brazil
| | | | | | - Gerson da Silva Carvalho
- Centro de Referência em Doenças Raras do Distrito Federal, Hospital de Apoio de Brasília, Brasília, DF, Brazil
| | | | | | - Eduardo Sousa Melo
- Centro de Ciências Médicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - José Luiz Pedroso
- Universidade Federal de São Paulo, Departamento de Neurologia, São Paulo, SP, Brazil
| | | | - Henry Houlden
- Dept of Neuromuscular Disease, UCL Institute of Neurology, Queen Sq, London; National Hospital for Neurology and Neurosurgery, Queen Sq, London
| | - Fernando Kok
- Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil; Mendelics Genomic Analysis, São Paulo, SP, Brazil
| | - David S Lynch
- Dept of Neuromuscular Disease, UCL Institute of Neurology, Queen Sq, London; National Hospital for Neurology and Neurosurgery, Queen Sq, London; National Institute for Health and Care Research (NIHR) and University College London Hospitals, Biomedical Research Centre, London.
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18
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Blair DR, Risch N. Dissecting the Reduced Penetrance of Putative Loss-of-Function Variants in Population-Scale Biobanks. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.23.24314008. [PMID: 39399029 PMCID: PMC11469360 DOI: 10.1101/2024.09.23.24314008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Loss-of-function variants (LoFs) disrupt the activity of their impacted gene. They are often associated with clinical phenotypes, including autosomal dominant diseases driven by haploinsufficiency. Recent analyses using biobanks have suggested that LoF penetrance for some haploinsufficient disorders may be low, an observation that has important implications for population genomic screening. However, biobanks are also rife with missing data, and the reliability of these findings remains uncertain. Here, we examine the penetrance of putative LoFs (pLoFs) using a cohort of ≈24,000 carriers derived from two population-scale biobanks: the UK Biobank and the All of Us Research Program. We investigate several possible etiologies for reduced pLoF penetrance, including biobank recruitment biases, annotation artifacts, missed diagnoses, and incomplete clinical records. Systematically accounting for these factors increased penetrance, but widespread reduced penetrance remained. Therefore, we hypothesized that other factors must be driving this phenomenon. To test this, we trained machine learning models to identify pLoFs with high penetrance using the genomic features specific to each variant. These models were predictive of penetrance across a range of diseases and ploF types, including those with prior evidence for pathogenicity. This suggests that reduced ploF penetrance is in fact common, and care should be taken when counseling asymptomatic carriers.
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Affiliation(s)
- David R. Blair
- Division of Medical Genetics, Department of Pediatrics
- University of California San Francisco
| | - Neil Risch
- Department of Epidemiology & Biostatistics
- University of California San Francisco
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19
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Doedens A, Skarp S, Holmström L, Pakanen L, Saarimäki S, Kerkelä R, Pylkäs K, Huikuri HV, Junttila J. Genetic variants associated with cardiac hypertrophy-related sudden cardiac death and cardiovascular outcomes in a Finnish population. Heart 2024:heartjnl-2024-324623. [PMID: 39362746 DOI: 10.1136/heartjnl-2024-324623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/14/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Hypertrophic cardiomyopathy is a common cause of non-ischaemic sudden cardiac death (SCD). Left ventricular hypertrophy (LVH) without cardiomyopathy-related myocardial disarray is a common autopsy finding and is often associated with prior hypertension in SCD subjects. Our aim was to investigate novel rare gene variants among SCD subjects with presumably hypertension-related LVH and myocardial fibrosis at autopsy. METHODS Whole exome sequencing was used to study rare variants (minor allele frequency<0.005) estimated to be deleterious in 96 non-ischaemic SCD subjects with presumably hypertension-related LVH and myocardial fibrosis. Associations of the identified variants with cardiac disease endpoints were replicated in the Finnish national genetic study (FinnGen) dataset. RESULTS 18 variants were estimated likely to affect protein function and 14 of these were associated with cardiomyopathies, heart failure, conduction abnormalities, hypertension and/or cardiac arrest in Finnish population (FinnGen). Three of the variants were classified as pathogenic or likely pathogenic. These include the splice site variant NM_000449.3:c.234-1G>A in regulatory factor X5 and frameshift variants NM_000449.3:c.234-1G>A in dehydrogenase/reductase 7C and NM_015873.3:c.1164del in villin like. CONCLUSIONS We identified rare deleterious variants associated with LVH in SCD subjects. Several of the identified rare variants associated with cardiovascular endpoints including heart failure, cardiomyopathies, cardiac arrest and hypertension in general population.
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Affiliation(s)
- Anne Doedens
- Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Sini Skarp
- Faculty of Medicine, University of Oulu, Oulu, Finland
| | | | - Lasse Pakanen
- Department of Forensic Medicine, Oulu University Hospital, Oulu, Finland
| | | | - Risto Kerkelä
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Heikki V Huikuri
- Department of Internal Medicine, University of Oulu, Oulu, Finland
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20
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O'Neill MJ, Yang T, Laudeman J, Calandranis ME, Harvey ML, Solus JF, Roden DM, Glazer AM. ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants. Nat Commun 2024; 15:8320. [PMID: 39333091 PMCID: PMC11437130 DOI: 10.1038/s41467-024-52474-4] [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: 09/13/2023] [Accepted: 09/10/2024] [Indexed: 09/29/2024] Open
Abstract
Interpreting the clinical significance of putative splice-altering variants outside canonical splice sites remains difficult without time-intensive experimental studies. To address this, we introduce Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed assay to quantify variant effects on RNA splicing. We first apply this technique to study hundreds of variants in the arrhythmia-associated gene SCN5A. Variants are studied in 'minigene' plasmids with molecular barcodes to allow pooled variant effect quantification. We perform experiments in two cell types, including disease-relevant induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The assay strongly separates known control variants from ClinVar, enabling quantitative calibration of the ParSE-seq assay. Using these evidence strengths and experimental data, we reclassify 29 of 34 variants with conflicting interpretations and 11 of 42 variants of uncertain significance. In addition to intronic variants, we show that many synonymous and missense variants disrupted RNA splicing. Two splice-altering variants in the assay also disrupt splicing and sodium current when introduced into iPSC-CMs by CRISPR-Cas9 editing. ParSE-seq provides high-throughput experimental data for RNA-splicing to support precision medicine efforts and can be readily adopted to study other loss-of-function genotype-phenotype relationships.
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Affiliation(s)
| | - Tao Yang
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie Laudeman
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maria E Calandranis
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Lorena Harvey
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph F Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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21
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Gaschignard M, Domenach L, Lamireau D, Guibet C, Roche S, Richard E, Redonnet-Vernhet I, Mesli S, Lebreton L. Case report: Two siblings with very late onset of holocarboxylase synthase deficiency and a mini-review. Front Genet 2024; 15:1249480. [PMID: 39391064 PMCID: PMC11464450 DOI: 10.3389/fgene.2024.1249480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/28/2024] [Indexed: 10/12/2024] Open
Abstract
Holocarboxylase synthase (HCS) deficiency is an extremely rare metabolic disorder typically presenting as severe neonatal metabolic acidosis, lethargy, hypotonia, vomiting, and seizures. This report describes two siblings in a family with late-onset forms of HCS deficiency. The younger sister presented at the age of 11 years and manifested as acute metabolic acidosis, which promptly resolved following rehydration and biotin administration. The results of the organic urine profile confirmed multiple carboxylase deficiency, and genetic testing revealed a novel pathogenic variant in the HLCS gene (NM_000411.8) in the homozygous state: c.995A>G; p. (Gln332Arg). No further decompensation was observed for her during the 3-year follow-up period. His older brother was diagnosed at the age of 23 years-old through biochemical tests, without any history of acidotic decompensation. A mini-review of HCS deficiency with late onset (>1 year) or early onset (<1 month) revealed that splice variants are associated with late onset, while both variants p. (Leu216Arg) and p. (Leu237Pro) are associated with early onset. However, the majority of genotypes do not show a clear correlation with the timing of HCS deficiency onset. The most significant point here is the description of extremely late-onset cases of HCS deficiency. This can prompt metabolic investigations and raise suspicion of this rare disease in cases of unexplained metabolic acidosis, even beyond early childhood.
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Affiliation(s)
| | - Louis Domenach
- Laboratoire de Biochimie, Pôle de Biologie et Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Delphine Lamireau
- Hôpital Pédiatrique, Pôle Pédiatrique, CHU de Bordeaux, Bordeaux, France
| | - Claire Guibet
- Laboratoire de Biochimie, Pôle de Biologie et Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Sandrine Roche
- Hôpital Pédiatrique, Pôle Pédiatrique, CHU de Bordeaux, Bordeaux, France
| | - Emmanuel Richard
- Laboratoire de Biochimie, Pôle de Biologie et Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Isabelle Redonnet-Vernhet
- Hôpital Pédiatrique, Pôle Pédiatrique, CHU de Bordeaux, Bordeaux, France
- lNSERM MRGM U1211, Université de Bordeaux, Bordeaux, France
| | - Samir Mesli
- Laboratoire de Biochimie, Pôle de Biologie et Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Louis Lebreton
- Laboratoire de Biochimie, Pôle de Biologie et Pathologie, CHU de Bordeaux, Bordeaux, France
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22
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Akram R, Anwar H, Muzaffar H, Turchetti V, Lau T, Vona B, Makhdoom EUH, Iqbal J, Mahmood Baig S, Hussain G, Efthymiou S, Houlden H. A Novel MAG Variant Causes Hereditary Spastic Paraplegia in a Consanguineous Pakistani Family. Genes (Basel) 2024; 15:1203. [PMID: 39336794 PMCID: PMC11431006 DOI: 10.3390/genes15091203] [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: 08/23/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
Background and objectives: Hereditary spastic paraplegia (HSP) is characterized by unsteady gait, motor incoordination, speech impairment, abnormal eye movement, progressive spasticity and lower limb weakness. Spastic paraplegia 75 (SPG75) results from a mutation in the gene that encodes myelin associated glycoprotein (MAG). Only a limited number of MAG variants associated with SPG75 in families of European, Middle Eastern, North African, Turkish and Palestinian ancestry have been documented so far. This study aims to provide further insight into the clinical and molecular manifestations of HSP. Methods: Using whole-exome sequencing, we investigated a consanguineous Pakistani family where three individuals presented with clinical signs of HSP. Sanger sequencing was used to carry out segregation analysis on available family members, and a minigene splicing assay was utilized to evaluate the effect of the splicing variant. Results: We identified a novel homozygous pathogenic splice donor variant in MAG (c.46 + 1G > T) associated with SPG75. RNA analysis revealed exon skipping that resulted in the loss of a start codon for ENST00000361922.8 isoform. Affected individuals exhibited variable combinations of nystagmus, developmental delay, cognitive impairments, spasticity, dysarthria, delayed gait and ataxia. The proband displayed a quadrupedal stride, and his siblings experienced frequent falls and ataxic gait as one of the prominent features that have not been previously reported in SPG75. Conclusions: Thus, the present study presents an uncommon manifestation of SPG75, the first from the Pakistani population, and broadens the spectrum of MAG variants.
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Grants
- WT093205MA, WT104033AIA; MR/S01165X/1, MR/S005021/1, G0601943 The Wellcome Trust, The MRC, The MSA Trust, The National Institute for Health Research University College London Hospitals Biomedical Research Centre NIHR-BRC), The Michael J Fox Foundation (MJFF), The Fidelity Trust, Rosetrees Trust, The Dolby Family fun
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Affiliation(s)
- Rabia Akram
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan; (R.A.); (H.A.); (H.M.); (E.U.H.M.)
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (V.T.); (T.L.); (H.H.)
| | - Haseeb Anwar
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan; (R.A.); (H.A.); (H.M.); (E.U.H.M.)
| | - Humaira Muzaffar
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan; (R.A.); (H.A.); (H.M.); (E.U.H.M.)
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (V.T.); (T.L.); (H.H.)
| | - Tracy Lau
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (V.T.); (T.L.); (H.H.)
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany;
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Ehtisham Ul Haq Makhdoom
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan; (R.A.); (H.A.); (H.M.); (E.U.H.M.)
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, Faisalabad 38000, Pakistan;
| | - Javed Iqbal
- Department of Neurology, Allied Hospital, Faisalabad Medical University, Faisalabad 38000, Pakistan;
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, Faisalabad 38000, Pakistan;
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi 74000, Pakistan
| | - Ghulam Hussain
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan; (R.A.); (H.A.); (H.M.); (E.U.H.M.)
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (V.T.); (T.L.); (H.H.)
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (V.T.); (T.L.); (H.H.)
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23
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Chi CS, Tsai CR, Lee HF. Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study. Arch Dis Child 2024; 109:730-735. [PMID: 38789118 PMCID: PMC11347223 DOI: 10.1136/archdischild-2024-326985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE To resolve unsolved whole-genome sequencing (WGS) data in individuals with paediatric neurological disorders. DESIGN A cohort study method using updated bioinformatic tools, new analysis targets, clinical information and literature databases was employed to reanalyse existing unsolved genome data. PARTICIPANTS From January 2016 to September 2023, a total of 615 individuals who aged under 18 years old, exhibited neurological disorders and received singleton WGS were recruited. 364 cases were unsolved during initial WGS analysis, in which 102 consented to reanalyse existing singleton WGS data. RESULTS Median duration for reanalysis after initial negative WGS results was 2 years and 4 months. The diagnostic yield was 29 of 102 individuals (28.4%) through reanalysis. New disease gene discovery and new target acquisitions contributed to 13 of 29 solved cases (44.8%). The reasons of non-detected causative variants during initial WGS analysis were variant reclassification in 9 individuals (31%), analytical issue in 9 (31%), new emerging disease-gene association in 8 (27.6%) and clinical update in 3 (10.3%). The 29 new diagnoses increased the cumulative diagnostic yield of clinical WGS in the entire study cohort to 45.5% after reanalysis. CONCLUSIONS Unsolved paediatric WGS individuals with neurological disorders could obtain molecular diagnoses through reanalysis within a timeframe of 2-2.5 years. New disease gene, structural variations and deep intronic splice variants make a significant contribution to diagnostic yield. This approach can provide precise genetic counselling to positive reanalysis results and end a diagnostic odyssey.
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Affiliation(s)
- Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsiu-Fen Lee
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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24
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De Paolis E, Raspaglio G, Ciferri N, Zangrilli I, Ricciardi Tenore C, Urbani A, Ferraro PM, Minucci A, Concolino P. Single-Base Substitution Causing Dual-Exon Skipping Event in PKD2 Gene: Unusual Molecular Finding from Exome Sequencing in a Patient with Autosomal Dominant Polycystic Kidney Disease. J Clin Med 2024; 13:4682. [PMID: 39200828 PMCID: PMC11355194 DOI: 10.3390/jcm13164682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Background: Pathogenic variants in the Polycystic Kidney Disease 2 (PKD2) gene are associated with Autosomal Dominant Polycystic Kidney Disease (ADPKD) in approximately 30% of cases. In recent years, the high-throughput sequencing techniques have significantly increased the number of variants identified in affected patients. Here, we described the peculiar effect of a PKD2 splicing variant, the c.1717-2A>G, identified in an Italian male patient with ADPKD. This variant led to the unusual and rare skipping of two consecutive exons, causing a large in-frame deletion. Methods: The genetic evaluation of the patient was performed using the Next-Generation Sequencing (NGS) assay Clinical Exome Solution® (SOPHiA Genetics). Bioinformatics analysis was performed using the SOPHiA DDM platform (SOPHiA Genetics). Prediction of pathogenicity was carried out by integrating several in silico tools. RNA evaluation was performed to test the effect of the variant on the PKD2 splicing using a Reverse-Transcription PCR coupled with cDNA sequencing. Results: NGS revealed the presence of the PKD2 c.1717-2A>G variant that lies in the canonical splice site of intron 7. This rare variant was predicted to have a significant impact on the splicing, proved by the RNA-based analysis. We identified the presence of a transcript characterised by the simultaneous skipping of exons 8 and 9, with a retained reading frame and the merging of exons 7-10. Conclusions: We described for the first time a dual-exon skip event related to the presence of a single-base substitution in the PKD2 gene in an ADPKD-affected patient. We assumed that the molecular basis of such a rare mechanism lies in the specific order of intron removal. The finding represents novel evidence of an alternative and unusual splicing mechanism in the PKD2 gene, adding insights to the pathogenesis of the ADPKD.
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Affiliation(s)
- Elisa De Paolis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Giuseppina Raspaglio
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Nunzia Ciferri
- Nephrology Unit, Departement of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Ilaria Zangrilli
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
| | - Claudio Ricciardi Tenore
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
| | - Andrea Urbani
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Pietro Manuel Ferraro
- Section of Nephrology, Department of Medicine, Università degli Studi di Verona, 37127 Verona, Italy;
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
| | - Paola Concolino
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (G.R.); (I.Z.); (C.R.T.); (A.M.)
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
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25
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Diallo M, Courdier C, Mercier E, Sequeira A, Defay-Stinat A, Plaisant C, Mesdaghi S, Rigden D, Javerzat S, Lasseaux E, Bourgeade L, Audebert-Bellanger S, Dollfus H, Hadj-Rabia S, Morice-Picard F, Philibert M, Sidibé MK, Smirnov V, Sylla O, Michaud V, Arveiler B. Functional Characterization of Splice Variants in the Diagnosis of Albinism. Int J Mol Sci 2024; 25:8657. [PMID: 39201349 PMCID: PMC11355033 DOI: 10.3390/ijms25168657] [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: 07/02/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 09/02/2024] Open
Abstract
Albinism is a genetically heterogeneous disease in which 21 genes are known so far. Its inheritance mode is autosomal recessive except for one X-linked form. The molecular analysis of exonic sequences of these genes allows for about a 70% diagnostic rate. About half (15%) of the unsolved cases are heterozygous for one pathogenic or probably pathogenic variant. Assuming that the missing variant may be located in non-coding regions, we performed sequencing for 122 such heterozygous patients of either the whole genome (27 patients) or our NGS panel (95 patients) that includes, in addition to all exons of the 21 genes, the introns and flanking sequences of five genes, TYR, OCA2, SLC45A2, GPR143 and HPS1. Rare variants (MAF < 0.01) in trans to the first variant were tested by RT-PCR and/or minigene assay. Of the 14 variants tested, nine caused either exon skipping or the inclusion of a pseudoexon, allowing for the diagnosis of 11 patients. This represents 9.8% (12/122) supplementary diagnosis for formerly unsolved patients and 75% (12/16) of those in whom the candidate variant was in trans to the first variant. Of note, one missense variant was demonstrated to cause skipping of the exon in which it is located, thus shedding new light on its pathogenic mechanism. Searching for non-coding variants and testing them for an effect on RNA splicing is warranted in order to increase the diagnostic rate.
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Affiliation(s)
- Modibo Diallo
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
| | - Cécile Courdier
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
| | - Elina Mercier
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
| | - Angèle Sequeira
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
| | - Alicia Defay-Stinat
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
| | - Claudio Plaisant
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
| | - Shahram Mesdaghi
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.M.); (D.R.)
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Daniel Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.M.); (D.R.)
| | - Sophie Javerzat
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
| | - Eulalie Lasseaux
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
| | - Laetitia Bourgeade
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
| | | | - Hélène Dollfus
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Strasbourg, 67091 Strasbourg, France;
| | - Smail Hadj-Rabia
- Service de Dermatologie, Hôpital Necker-Enfants Malades, 75015 Paris, France;
| | - Fanny Morice-Picard
- Service de Dermatologie, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France;
| | | | | | - Vasily Smirnov
- Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Centre Hospitalier Universitaire de Lille, 59037 Lille, France;
| | - Ousmane Sylla
- Infirmerie Hôpital Militaire, Bamako BP 236, Mali; (M.K.S.); (O.S.)
| | - Vincent Michaud
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
| | - Benoit Arveiler
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux University, INSERM U1211, 33076 Bordeaux, France; (M.D.); (C.C.); (E.M.); (A.S.); (A.D.-S.); (S.J.); (V.M.)
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France; (C.P.); (E.L.); (L.B.)
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26
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María Del Rocío PB, Palomares Bralo M, Vanhooydonck M, Hamerlinck L, D'haene E, Leimbacher S, Jacobs EZ, De Cock L, D'haenens E, Dheedene A, Malfait Z, Vantomme L, Silva A, Rooney K, Santos-Simarro F, Lleuger-Pujol R, García-Miñaúr S, Losantos-García I, Menten B, Gestri G, Ragge N, Sadikovic B, Bogaert E, Syx D, Callewaert B, Vergult S. Loss-of-function of the Zinc Finger Homeobox 4 ( ZFHX4) gene underlies a neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.07.24311381. [PMID: 39148819 PMCID: PMC11326360 DOI: 10.1101/2024.08.07.24311381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
8q21.11 microdeletions encompassing the gene encoding transcription factor ZFHX4, have previously been associated by us with a syndromic form of intellectual disability, hypotonia, decreased balance and hearing loss. Here, we report on 57 individuals, 52 probands and 5 affected family members, with protein truncating variants (n=36), (micro)deletions (n=20) or an inversion (n=1) affecting ZFHX4 with variable developmental delay and intellectual disability, distinctive facial characteristics, morphological abnormalities of the central nervous system, behavioral alterations, short stature, hypotonia, and occasionally cleft palate and anterior segment dysgenesis. The phenotypes associated with 8q21.11 microdeletions and ZFHX4 intragenic loss-of-function variants largely overlap, identifying ZFHX4 as the main driver for the microdeletion syndrome, although leukocyte-derived DNA shows a mild common methylation profile for (micro)deletions only. We identify ZFHX4 as a transcription factor that is increasingly expressed during human brain development and neuronal differentiation. Furthermore, ZFHX4 interacting factors identified via IP-MS in neural progenitor cells, suggest an important role for ZFHX4 in cellular and developmental pathways, especially during histone modifications, cytosolic transport and development. Additionally, using CUT&RUN, we observed that ZFHX4 binds with the promoter regions of genes with crucial roles in embryonic, neuron and axon development. Since loss-of-function variants in ZFHX4 are found with consistent dysmorphic facial features, we investigated whether the disruption of zfhx4 causes craniofacial abnormalities in zebrafish. First-generation (F0) zfhx4 crispant zebrafish, (mosaic) mutant for zfhx4 loss-of-function variants, have significantly shorter Meckel's cartilages and smaller ethmoid plates compared to control zebrafish. Furthermore, behavioral assays show a decreased movement frequency in the zfhx4 crispant zebrafish in comparison with control zebrafish larvae. Although further research is needed, our in vivo work suggests a role for zfhx4 in facial skeleton patterning, palatal development and behavior.
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Affiliation(s)
- Pérez Baca María Del Rocío
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - María Palomares Bralo
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Hamerlinck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva D'haene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sebastian Leimbacher
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Erika D'haenens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Zoë Malfait
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ananilia Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Fernando Santos-Simarro
- Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain
| | - Roser Lleuger-Pujol
- Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital; Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain
| | - Sixto García-Miñaúr
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | | | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gaia Gestri
- University College London, London, England, Great Britain
| | - Nicola Ragge
- Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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27
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Zeuli R, Karali M, de Bruijn SE, Rodenburg K, Scarpato M, Capasso D, Astuti GDN, Gilissen C, Rodríguez-Hidalgo M, Ruiz-Ederra J, Testa F, Simonelli F, Cremers FPM, Banfi S, Roosing S. Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients. HGG ADVANCES 2024; 5:100314. [PMID: 38816995 PMCID: PMC11225895 DOI: 10.1016/j.xhgg.2024.100314] [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: 03/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.
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Affiliation(s)
- Roberta Zeuli
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marianthi Karali
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margherita Scarpato
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, Naples, Italy
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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28
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Oh RY, AlMail A, Cheerie D, Guirguis G, Hou H, Yuki KE, Haque B, Thiruvahindrapuram B, Marshall CR, Mendoza-Londono R, Shlien A, Kyriakopoulou LG, Walker S, Dowling JJ, Wilson MD, Costain G. A systematic assessment of the impact of rare canonical splice site variants on splicing using functional and in silico methods. HGG ADVANCES 2024; 5:100299. [PMID: 38659227 PMCID: PMC11144818 DOI: 10.1016/j.xhgg.2024.100299] [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: 07/11/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
Canonical splice site variants (CSSVs) are often presumed to cause loss-of-function (LoF) and are assigned very strong evidence of pathogenicity (according to American College of Medical Genetics/Association for Molecular Pathology criterion PVS1). The exact nature and predictability of splicing effects of unselected rare CSSVs in blood-expressed genes are poorly understood. We identified 168 rare CSSVs in blood-expressed genes in 112 individuals using genome sequencing, and studied their impact on splicing using RNA sequencing (RNA-seq). There was no evidence of a frameshift, nor of reduced expression consistent with nonsense-mediated decay, for 25.6% of CSSVs: 17.9% had wildtype splicing only and normal junction depths, 3.6% resulted in cryptic splice site usage and in-frame insertions or deletions, 3.6% resulted in full exon skipping (in frame), and 0.6% resulted in full intron inclusion (in frame). Blind to these RNA-seq data, we attempted to predict the precise impact of CSSVs by applying in silico tools and the ClinGen Sequence Variant Interpretation Working Group 2018 guidelines for applying PVS1 criterion. The predicted impact on splicing using (1) SpliceAI, (2) MaxEntScan, and (3) AutoPVS1, an automatic classification tool for PVS1 interpretation of null variants that utilizes Ensembl Variant Effect Predictor and MaxEntScan, was concordant with RNA-seq analyses for 65%, 63%, and 61% of CSSVs, respectively. In summary, approximately one in four rare CSSVs did not show evidence for LoF based on analysis of RNA-seq data. Predictions from in silico methods were often discordant with findings from RNA-seq. More caution may be warranted in applying PVS1-level evidence to CSSVs in the absence of functional data.
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Affiliation(s)
- Rachel Y Oh
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ali AlMail
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - David Cheerie
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - George Guirguis
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Huayun Hou
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Kyoko E Yuki
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada
| | - Bushra Haque
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Christian R Marshall
- Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lianna G Kyriakopoulou
- Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Susan Walker
- The Centre for Applied Genomics, SickKids Research Institute, Toronto, ON, Canada
| | - James J Dowling
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada; Division of Neurology, Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
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29
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Zheng H, Kang H, Qiu Y, Xie L, Wu J, Lai P, Kang J. Novel PRKAR1A mutation in Carney complex: a case report and literature review. Front Endocrinol (Lausanne) 2024; 15:1384956. [PMID: 39050568 PMCID: PMC11266075 DOI: 10.3389/fendo.2024.1384956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Objective Carney complex is a rare autosomal dominant syndrome that has been shown to be associated with inactivation due to PRKAR1A mutations. We revealed a novel PRKAR1A gene mutation in Chinese patient with Carney complex and review the literature to enhance understanding of Carney complex. Case presentation A 23-year-old Chinese male patient with a family history cardiac myxoma was admitted to our Department of Endocrinology because of central obesity and hyperpigmentation. Physical examination revealed a maximum blood pressure of 150/93mmHg, a waist circumference of 102cm, a weight of 70kg, a height of 170cm, and a BMI of 24.22kg/m2. Additionally, there was spotty skin pigmentation on the lip mucosa, purple striae on the abdomen, thin skin on both legs, and visible veins. Blood examination revealed hypercortisolemia, decreased adrenocorticotropic hormone (ACTH) levels and failure to suppress cortisol with low and high-dose dexamethasone suppression tests. Magnetic resonance imaging (MRI) scan revealed multiple small adrenal nodules and Retroperitoneal neurogenic tumor. Genetic testing showed a novel heterozygous mutation in exon 5 of PRKAR1A (c.500_502 + 8delAAGGTAAGGGC). The patient underwent resection of the right adrenal gland and retroperitoneal neoplasms in 2020. Postoperative pathology following the right adrenal gland resection showed nodular hyperplasia of the adrenal cortex. The pathology from the retroperitoneal tumor resection revealed spindle cell tumors rich in pigment and cells. The patient was diagnosed as Carney complex according to Stratakis CA in 2001 guidelines. After long-term follow-up, the patient's condition was stable, with weight loss, waist circumference reduction, significantly lower cortisol levels, and normal blood lipids. Conclusion This case reported a Carney complex in a Chinese patient, characterized clinically by non-ACTH-dependent Cushing's syndrome, familial recurrent cardiac myxomas, psammomatous melanotic schwannoma (PMS) and skin and mucosal pigmentation. A novel subtype of PRKAR1A mutation was discovered, which may affect the characteristics of the PRKAR1A protein and contribute to the development of Carney complex.
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Affiliation(s)
- Huaqiang Zheng
- Department of Endocrinology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Hong Kang
- Department of Dermatology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Yizhen Qiu
- Department of Neurology Critical Care Medicine, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Liangxiao Xie
- Department of Endocrinology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Jinzhi Wu
- Department of Endocrinology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Pengbin Lai
- Department of Endocrinology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
| | - Jiapeng Kang
- Department of Medical Oncology, Zhangzhou Municipal Hospital, Zhangzhou Municipal Hospital Affiliated of Fujian Medical University, Zhangzhou, China
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30
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Rudrabhatla PK, Divya KP, Fasaludeen A, Menon RN, Cherian A, Urulangodi M, Sundaram S. Generalized Stiffness in Hereditary Hyperekplexia Responsive to Trihexyphenidyl: A Novel Finding. Clin Pediatr (Phila) 2024; 63:885-888. [PMID: 37899614 DOI: 10.1177/00099228231203300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Affiliation(s)
- Pavan Kumar Rudrabhatla
- R Madhavan Nayar Centre for Comprehensive Epilepsy Care, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - K P Divya
- Comprehensive Care Centre for Movement Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Alfiya Fasaludeen
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Ramshekhar N Menon
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Ajith Cherian
- R Madhavan Nayar Centre for Comprehensive Epilepsy Care, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Soumya Sundaram
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
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31
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Huang AC, Su JY, Hung YJ, Chiang HL, Chen YT, Huang YT, Yu CHA, Lin HN, Lin CL. SpliceAPP: an interactive web server to predict splicing errors arising from human mutations. BMC Genomics 2024; 25:600. [PMID: 38877417 PMCID: PMC11179192 DOI: 10.1186/s12864-024-10512-x] [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: 03/01/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Splicing variants are a major class of pathogenic mutations, with their severity equivalent to nonsense mutations. However, redundant and degenerate splicing signals hinder functional assessments of sequence variations within introns, particularly at branch sites. We have established a massively parallel splicing assay to assess the impact on splicing of 11,191 disease-relevant variants. Based on the experimental results, we then applied regression-based methods to identify factors determining splicing decisions and their respective weights. RESULTS Our statistical modeling is highly sensitive, accurately annotating the splicing defects of near-exon intronic variants, outperforming state-of-the-art predictive tools. We have incorporated the algorithm and branchpoint information into a web-based tool, SpliceAPP, to provide an interactive application. This user-friendly website allows users to upload any genetic variants with genome coordinates (e.g., chr15 74,687,208 A G), and the tool will output predictions for splicing error scores and evaluate the impact on nearby splice sites. Additionally, users can query branch site information within the region of interest. CONCLUSIONS In summary, SpliceAPP represents a pioneering approach to screening pathogenic intronic variants, contributing to the development of precision medicine. It also facilitates the annotation of splicing motifs. SpliceAPP is freely accessible using the link https://bc.imb.sinica.edu.tw/SpliceAPP . Source code can be downloaded at https://github.com/hsinnan75/SpliceAPP .
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Affiliation(s)
- Ang-Chu Huang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Jia-Ying Su
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Jen Hung
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hung-Lun Chiang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yi-Ting Chen
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsin Albert Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hsin-Nan Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
| | - Chien-Ling Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan.
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Barbotin AL, Boursier A, Jourdain AS, Moerman A, Rabat B, Chehimi M, Thuillier C, Ghoumid J, Smol T. Identification of a novel CFAP61 homozygous splicing variant associated with multiple morphological abnormalities of the flagella. J Assist Reprod Genet 2024; 41:1499-1505. [PMID: 38775994 PMCID: PMC11224159 DOI: 10.1007/s10815-024-03139-0] [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: 01/25/2024] [Accepted: 05/07/2024] [Indexed: 07/05/2024] Open
Abstract
In this study, we investigated the role of a newly identified homozygous variant (c.1245 + 6T > C) in the CFAP61 gene in the development of multiple morphologically abnormal flagella (MMAF) in an infertile patient. Using exome sequencing, we identified this variant, which led to exon 12 skipping and the production of a truncated CFAP61 protein. Transmission electron microscopy analysis of the patient's spermatozoa revealed various flagellar abnormalities, including defective nuclear chromatin condensation, axoneme disorganization, and mitochondria embedded in residual cytoplasmic droplets. Despite a fertilization rate of 83.3% through ICSI, there was no successful pregnancy due to poor embryo quality.Our findings suggest a link between the identified CFAP61 variant and MMAF, indicating potential disruption in radial spokes' assembly or function crucial for normal ciliary motility. Furthermore, nearly half of the observed sperm heads displayed chromatin condensation defects, possibly contributing to the low blastulation rate. This case underscores the significance of genetic counseling and testing, particularly for couples dealing with infertility and MMAF. Early identification of such genetic variants can guide appropriate interventions and improve reproductive outcomes.
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Affiliation(s)
- Anne-Laure Barbotin
- UMRS1172 Development and Plasticity of the Neuroendocrine Brain, University of Lille, Lille, France
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Angèle Boursier
- UMRS1172 Development and Plasticity of the Neuroendocrine Brain, University of Lille, Lille, France
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Anne-Sophie Jourdain
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | | | - Baptiste Rabat
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
| | - Mariam Chehimi
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Caroline Thuillier
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | - Jamal Ghoumid
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | - Thomas Smol
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France.
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France.
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Al-Saei O, Malka S, Owen N, Aliyev E, Vempalli FR, Ocieczek P, Al-Khathlan B, Fakhro K, Moosajee M. Increasing the diagnostic yield of childhood glaucoma cases recruited into the 100,000 Genomes Project. BMC Genomics 2024; 25:484. [PMID: 38755526 PMCID: PMC11097485 DOI: 10.1186/s12864-024-10353-8] [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: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Childhood glaucoma (CG) encompasses a heterogeneous group of genetic eye disorders that is responsible for approximately 5% of childhood blindness worldwide. Understanding the molecular aetiology is key to improving diagnosis, prognosis and unlocking the potential for optimising clinical management. In this study, we investigated 86 CG cases from 78 unrelated families of diverse ethnic backgrounds, recruited into the Genomics England 100,000 Genomes Project (GE100KGP) rare disease cohort, to improve the genetic diagnostic yield. Using the Genomics England/Genomic Medicine Centres (GE/GMC) diagnostic pipeline, 13 unrelated families were solved (13/78, 17%). Further interrogation using an expanded gene panel yielded a molecular diagnosis in 7 more unrelated families (7/78, 9%). This analysis effectively raises the total number of solved CG families in the GE100KGP to 26% (20/78 families). Twenty-five percent (5/20) of the solved families had primary congenital glaucoma (PCG), while 75% (15/20) had secondary CG; 53% of this group had non-acquired ocular anomalies (including iris hypoplasia, megalocornea, ectopia pupillae, retinal dystrophy, and refractive errors) and 47% had non-acquired systemic diseases such as cardiac abnormalities, hearing impairment, and developmental delay. CYP1B1 was the most frequently implicated gene, accounting for 55% (11/20) of the solved families. We identified two novel likely pathogenic variants in the TEK gene, in addition to one novel pathogenic copy number variant (CNV) in FOXC1. Variants that passed undetected in the GE100KGP diagnostic pipeline were likely due to limitations of the tiering process, the use of smaller gene panels during analysis, and the prioritisation of coding SNVs and indels over larger structural variants, CNVs, and non-coding variants.
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Affiliation(s)
- Omayma Al-Saei
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | | | - Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
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Zhang Y, Ahsan MU, Wang K. Noncoding de novo mutations in SCN2A are associated with autism spectrum disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.05.24306908. [PMID: 38766206 PMCID: PMC11100849 DOI: 10.1101/2024.05.05.24306908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Coding de novo mutations (DNMs) contribute to the risk for autism spectrum disorders (ASD), but the contribution of noncoding DNMs remains relatively unexplored. Here we use whole genome sequencing (WGS) data of 12,411 individuals (including 3,508 probands and 2,218 unaffected siblings) from 3,357 families collected in Simons Foundation Powering Autism Research for Knowledge (SPARK) to detect DNMs associated with ASD, while examining Simons Simplex Collection (SSC) with 6383 individuals from 2274 families to replicate the results. For coding DNMs, SCN2A reached exome-wide significance (p=2.06×10-11) in SPARK. The 618 known dominant ASD genes as a group are strongly enriched for coding DNMs in cases than sibling controls (fold change=1.51, p =1.13×10-5 for SPARK; fold change=1.86, p =2.06×10-9 for SSC). For noncoding DNMs, we used two methods to assess statistical significance: a point-based test that analyzes sites with a Combined Annotation Dependent Depletion (CADD) score ≥15, and a segment-based test that analyzes 1kb genomic segments with segment-specific background mutation rates (inferred from expected rare mutations in Gnocchi genome constraint scores). The point-based test identified SCN2A as marginally significant (p=6.12×10-4) in SPARK, yet segment-based test identified CSMD1, RBFOX1 and CHD13 as exome-wide significant. We did not identify significant enrichment of noncoding DNMs (in all 1kb segments or those with Gnocchi>4) in the 618 known ASD genes as a group in cases than sibling controls. When combining evidence from both coding and noncoding DNMs, we found that SCN2A with 11 coding and 5 noncoding DNMs exhibited the strongest significance (p=4.15×10-13). In summary, we identified both coding and noncoding DNMs in SCN2A associated with ASD, while nominating additional candidates for further examination in future studies.
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Affiliation(s)
- Yuan Zhang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Kronzer VL, Sparks JA, Raychaudhuri S, Cerhan JR. Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nat Rev Rheumatol 2024; 20:290-300. [PMID: 38538758 DOI: 10.1038/s41584-024-01096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Rheumatoid arthritis (RA) has an estimated heritability of nearly 50%, which is particularly high in seropositive RA. HLA alleles account for a large proportion of this heritability, in addition to many common single-nucleotide polymorphisms with smaller individual effects. Low-frequency and rare variants, such as those captured by next-generation sequencing, can also have a large role in heritability in some individuals. Rare variant discovery has informed the development of drugs such as inhibitors of PCSK9 and Janus kinases. Some 34 low-frequency and rare variants are currently associated with RA risk. One variant (19:10352442G>C in TYK2) was identified in five separate studies, and might therefore represent a promising therapeutic target. Following a set of best practices in future studies, including studying diverse populations, using large sample sizes, validating RA and serostatus, replicating findings, adjusting for other variants and performing functional assessment, could help to ensure the relevance of identified variants. Exciting opportunities are now on the horizon for genetics in RA, including larger datasets and consortia, whole-genome sequencing and direct applications of findings in the management, and especially treatment, of RA.
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Affiliation(s)
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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Danaeifar M, Najafi A. Artificial Intelligence and Computational Biology in Gene Therapy: A Review. Biochem Genet 2024:10.1007/s10528-024-10799-1. [PMID: 38635012 DOI: 10.1007/s10528-024-10799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
One of the trending fields in almost all areas of science and technology is artificial intelligence. Computational biology and artificial intelligence can help gene therapy in many steps including: gene identification, gene editing, vector design, development of new macromolecules and modeling of gene delivery. There are various tools used by computational biology and artificial intelligence in this field, such as genomics, transcriptomic and proteomics data analysis, machine learning algorithms and molecular interaction studies. These tools can introduce new gene targets, novel vectors, optimized experiment conditions, predict the outcomes and suggest the best solutions to avoid undesired immune responses following gene therapy treatment.
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Affiliation(s)
- Mohsen Danaeifar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran.
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Mackeh R, El Bsat Y, Elmi A, Bibawi H, Karim MY, Hassan A, Lo B. Novel Synonymous Variant in IL7R Causes Preferential Expression of the Soluble Isoform. J Clin Immunol 2024; 44:96. [PMID: 38587703 PMCID: PMC11001715 DOI: 10.1007/s10875-024-01688-8] [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: 08/28/2023] [Accepted: 03/08/2024] [Indexed: 04/09/2024]
Abstract
PURPOSE The interleukin-7 receptor (IL-7R) is primarily expressed on lymphoid cells and plays a crucial role in the development, proliferation, and survival of T cells. Autosomal recessive mutations that disrupt IL-7Rα chain expression give rise to a severe combined immunodeficiency (SCID), which is characterized by lymphopenia and a T-B+NK+ phenotype. The objective here was to diagnose two siblings displaying the T-B+NK+ SCID phenotype as initial clinical genetic testing did not detect any variants in known SCID genes. METHODS Whole genome sequencing (WGS) was utilized to identify potential variants causing the SCID phenotype. Splicing prediction tools were employed to assess the deleterious impact of the mutation. Polymerase Chain Reaction (PCR), Sanger sequencing, flow cytometry, and ELISA were then used to validate the pathogenicity of the detected mutation. RESULTS We discovered a novel homozygous synonymous mutation in the IL7R gene. Our functional studies indicate that this variant is pathogenic, causing exon 6, which encodes the transmembrane domain, to be preferentially spliced out. CONCLUSION In this study, we identified a novel rare synonymous mutation causing a loss of IL-7Rα expression at the cellular membrane. This case demonstrates the value of reanalyzing genetic data based on the clinical phenotype and highlights the significance of functional studies in determining the pathogenicity of genetic variants.
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Affiliation(s)
| | | | - Asha Elmi
- Research Branch, Sidra Medicine, Doha, Qatar
| | - Hani Bibawi
- Division of Hematopathology, Sidra Medicine, Doha, Qatar
| | - Mohammed Yousuf Karim
- Division of Hematopathology, Sidra Medicine, Doha, Qatar
- College of Medicine, Qatar University, Doha, Qatar
| | - Amel Hassan
- Pediatric Allergy and Immunology Department, Sidra Medicine, Ar-Rayyan, Qatar
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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Mori T, Fujimaru T, Liu C, Patterson K, Yamamoto K, Suzuki T, Chiga M, Sekine A, Ubara Y, Miller DE, Zalusky MPG, Mandai S, Ando F, Mori Y, Kikuchi H, Susa K, Chong JX, Bamshad MJ, Tan YQ, Zhang F, Uchida S, Sohara E. CFAP47 is a novel causative gene implicated in X-linked polycystic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24304760. [PMID: 38633811 PMCID: PMC11023651 DOI: 10.1101/2024.04.05.24304760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a well-described condition in which ~80% of cases have a genetic explanation, while the genetic basis of sporadic cystic kidney disease in adults remains unclear in ~30% of cases. This study aimed to identify novel genes associated with polycystic kidney disease (PKD) in patients with sporadic cystic kidney disease in which a clear genetic change was not identified in established genes. A next-generation sequencing panel analyzed known genes related to renal cysts in 118 sporadic cases, followed by whole-genome sequencing on 47 unrelated individuals without identified candidate variants. Three male patients were found to have rare missense variants in the X-linked gene Cilia And Flagella Associated Protein 47 (CFAP47). CFAP47 was expressed in primary cilia of human renal tubules, and knockout mice exhibited vacuolation of tubular cells and tubular dilation, providing evidence that CFAP47 is a causative gene involved in cyst formation. This discovery of CFAP47 as a newly identified gene associated with PKD, displaying X-linked inheritance, emphasizes the need for further cases to understand the role of CFAP47 in PKD.
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Affiliation(s)
- Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chunyu Liu
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kohei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takefumi Suzuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinari Sekine
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Miranda PG Zalusky
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Feng Zhang
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Mudau MM, Dillon B, Smal C, Feben C, Honey E, Carstens N, Krause A. Mutation analysis and clinical profile of South African patients with Neurofibromatosis type 1 (NF1) phenotype. Front Genet 2024; 15:1331278. [PMID: 38596211 PMCID: PMC11002079 DOI: 10.3389/fgene.2024.1331278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients. In the present study, NF1 patients were screened using a next-generation sequencing (NGS) assay targeting NF1 exons and intron/exon boundaries for SNV and NF1 multiple ligation-dependent probe amplification (MLPA) analysis for CNV detection. Twenty-six unrelated Southern African patients clinically suspected of having NF1, based on the clinical diagnostic criteria developed by the National Institute of Health (NIH), were included in the current study. A detection rate of 58% (15/26) was obtained, with SNVs identified in 80% (12/15) using a targeted gene panel and NF1 gene deletion in 20% (3/15) identified using MLPA. Ten patients (38%) had no variants identified, although they met NF1 diagnostic criteria. One VUS was identified in this study in a patient that met NF1 diagnostic criteria, however there was no sufficient information to classify variant as pathogenic. The clinical features of Southern African patients with NF1 are similar to that of the known NF1 phenotype, with the exception of a lower frequency of plexiform neurofibromas and a higher frequency of developmental/intellectual disability compared to other cohorts. This is the first clinical and molecular characterisation of a Southern African ancestry NF1 cohort using both next-generation sequencing and MLPA analysis. A significant number of patients remained without a diagnosis following DNA-level testing. The current study offers a potential molecular testing strategy for our low resource environment that could benefit a significant proportion of patients who previously only received a clinical diagnosis without molecular confirmation.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwyn Dillon
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clarice Smal
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Knauer C, Haltern H, Schoger E, Kügler S, Roos L, Zelarayán LC, Hasenfuss G, Zimmermann WH, Wollnik B, Cyganek L. Preclinical evaluation of CRISPR-based therapies for Noonan syndrome caused by deep-intronic LZTR1 variants. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102123. [PMID: 38333672 PMCID: PMC10851011 DOI: 10.1016/j.omtn.2024.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Gene variants in LZTR1 are implicated to cause Noonan syndrome associated with a severe and early-onset hypertrophic cardiomyopathy. Mechanistically, LZTR1 deficiency results in accumulation of RAS GTPases and, as a consequence, in RAS-MAPK signaling hyperactivity, thereby causing the Noonan syndrome-associated phenotype. Despite its epidemiological relevance, pharmacological as well as invasive therapies remain limited. Here, personalized CRISPR-Cas9 gene therapies might offer a novel alternative for a curative treatment in this patient cohort. In this study, by utilizing a patient-specific screening platform based on iPSC-derived cardiomyocytes from two Noonan syndrome patients, we evaluated different clinically translatable therapeutic approaches using small Cas9 orthologs targeting a deep-intronic LZTR1 variant to cure the disease-associated molecular pathology. Despite high editing efficiencies in cardiomyocyte cultures transduced with lentivirus or all-in-one adeno-associated viruses, we observed crucial differences in editing outcomes in proliferative iPSCs vs. non-proliferative cardiomyocytes. While editing in iPSCs rescued the phenotype, the same editing approaches did not robustly restore LZTR1 function in cardiomyocytes, indicating critical differences in the activity of DNA double-strand break repair mechanisms between proliferative and non-proliferative cell types and highlighting the importance of cell type-specific screens for testing CRISPR-Cas9 gene therapies.
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Affiliation(s)
- Carolin Knauer
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
| | - Henrike Haltern
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
| | - Eric Schoger
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Sebastian Kügler
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Lennart Roos
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Laura C. Zelarayán
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Cardiology and Angiology, University of Giessen, 35390 Giessen, Germany
| | - Gerd Hasenfuss
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Wolfram-Hubertus Zimmermann
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 37075 Göttingen, Germany
- DZNE (German Center for Neurodegenerative Diseases), 37075 Göttingen, Germany
| | - Bernd Wollnik
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 37075 Göttingen, Germany
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Chafai N, Bonizzi L, Botti S, Badaoui B. Emerging applications of machine learning in genomic medicine and healthcare. Crit Rev Clin Lab Sci 2024; 61:140-163. [PMID: 37815417 DOI: 10.1080/10408363.2023.2259466] [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: 06/19/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
The integration of artificial intelligence technologies has propelled the progress of clinical and genomic medicine in recent years. The significant increase in computing power has facilitated the ability of artificial intelligence models to analyze and extract features from extensive medical data and images, thereby contributing to the advancement of intelligent diagnostic tools. Artificial intelligence (AI) models have been utilized in the field of personalized medicine to integrate clinical data and genomic information of patients. This integration allows for the identification of customized treatment recommendations, ultimately leading to enhanced patient outcomes. Notwithstanding the notable advancements, the application of artificial intelligence (AI) in the field of medicine is impeded by various obstacles such as the limited availability of clinical and genomic data, the diversity of datasets, ethical implications, and the inconclusive interpretation of AI models' results. In this review, a comprehensive evaluation of multiple machine learning algorithms utilized in the fields of clinical and genomic medicine is conducted. Furthermore, we present an overview of the implementation of artificial intelligence (AI) in the fields of clinical medicine, drug discovery, and genomic medicine. Finally, a number of constraints pertaining to the implementation of artificial intelligence within the healthcare industry are examined.
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Affiliation(s)
- Narjice Chafai
- Laboratory of Biodiversity, Ecology, and Genome, Faculty of Sciences, Department of Biology, Mohammed V University in Rabat, Rabat, Morocco
| | - Luigi Bonizzi
- Department of Biomedical, Surgical and Dental Science, University of Milan, Milan, Italy
| | - Sara Botti
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology, and Genome, Faculty of Sciences, Department of Biology, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
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Wu H, Lin JH, Tang XY, Marenne G, Zou WB, Schutz S, Masson E, Génin E, Fichou Y, Le Gac G, Férec C, Liao Z, Chen JM. Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants. Hum Genomics 2024; 18:21. [PMID: 38414044 PMCID: PMC10898081 DOI: 10.1186/s40246-024-00586-9] [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: 11/09/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Single-nucleotide variants (SNVs) within gene coding sequences can significantly impact pre-mRNA splicing, bearing profound implications for pathogenic mechanisms and precision medicine. In this study, we aim to harness the well-established full-length gene splicing assay (FLGSA) in conjunction with SpliceAI to prospectively interpret the splicing effects of all potential coding SNVs within the four-exon SPINK1 gene, a gene associated with chronic pancreatitis. RESULTS Our study began with a retrospective analysis of 27 SPINK1 coding SNVs previously assessed using FLGSA, proceeded with a prospective analysis of 35 new FLGSA-tested SPINK1 coding SNVs, followed by data extrapolation, and ended with further validation. In total, we analyzed 67 SPINK1 coding SNVs, which account for 9.3% of the 720 possible coding SNVs. Among these 67 FLGSA-analyzed SNVs, 12 were found to impact splicing. Through detailed comparison of FLGSA results and SpliceAI predictions, we inferred that the remaining 653 untested coding SNVs in the SPINK1 gene are unlikely to significantly affect splicing. Of the 12 splice-altering events, nine produced both normally spliced and aberrantly spliced transcripts, while the remaining three only generated aberrantly spliced transcripts. These splice-impacting SNVs were found solely in exons 1 and 2, notably at the first and/or last coding nucleotides of these exons. Among the 12 splice-altering events, 11 were missense variants (2.17% of 506 potential missense variants), and one was synonymous (0.61% of 164 potential synonymous variants). Notably, adjusting the SpliceAI cut-off to 0.30 instead of the conventional 0.20 would improve specificity without reducing sensitivity. CONCLUSIONS By integrating FLGSA with SpliceAI, we have determined that less than 2% (1.67%) of all possible coding SNVs in SPINK1 significantly influence splicing outcomes. Our findings emphasize the critical importance of conducting splicing analysis within the broader genomic sequence context of the study gene and highlight the inherent uncertainties associated with intermediate SpliceAI scores (0.20 to 0.80). This study contributes to the field by being the first to prospectively interpret all potential coding SNVs in a disease-associated gene with a high degree of accuracy, representing a meaningful attempt at shifting from retrospective to prospective variant analysis in the era of exome and genome sequencing.
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Affiliation(s)
- Hao Wu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jin-Huan Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Xin-Ying Tang
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
- Department of Prevention and Health Care, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Gaëlle Marenne
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Sacha Schutz
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | | | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
- Shanghai Institute of Pancreatic Diseases, Shanghai, China.
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France.
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Uctepe E, Vona B, Esen FN, Sonmez FM, Smol T, Tümer S, Mancılar H, Geylan Durgun DE, Boute O, Moghbeli M, Ghayoor Karimiani E, Hashemi N, Bakhshoodeh B, Kim HG, Maroofian R, Yesilyurt A. Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly. Eur J Hum Genet 2024; 32:52-60. [PMID: 37880421 PMCID: PMC10772072 DOI: 10.1038/s41431-023-01461-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
Lissencephaly (LIS) is a malformation of cortical development due to deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. Thirty-one LIS-associated genes have been previously described. Recently, biallelic pathogenic variants in CRADD and PIDD1, have associated with LIS impacting the previously established role of the PIDDosome in activating caspase-2. In this report, we describe biallelic truncating variants in CASP2, another subunit of PIDDosome complex. Seven patients from five independent families presenting with a neurodevelopmental phenotype were identified through GeneMatcher-facilitated international collaborations. Exome sequencing analysis was carried out and revealed two distinct novel homozygous (NM_032982.4:c.1156delT (p.Tyr386ThrfsTer25), and c.1174 C > T (p.Gln392Ter)) and compound heterozygous variants (c.[130 C > T];[876 + 1 G > T] p.[Arg44Ter];[?]) in CASP2 segregating within the families in a manner compatible with an autosomal recessive pattern. RNA studies of the c.876 + 1 G > T variant indicated usage of two cryptic splice donor sites, each introducing a premature stop codon. All patients from whom brain MRIs were available had a typical fronto-temporal LIS and pachygyria, remarkably resembling the CRADD and PIDD1-related neuroimaging findings. Other findings included developmental delay, attention deficit hyperactivity disorder, hypotonia, seizure, poor social skills, and autistic traits. In summary, we present patients with CASP2-related ID, anterior-predominant LIS, and pachygyria similar to previously reported patients with CRADD and PIDD1-related disorders, expanding the genetic spectrum of LIS and lending support that each component of the PIDDosome complex is critical for normal development of the human cerebral cortex and brain function.
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Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara, Türkiye
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | | | - F Mujgan Sonmez
- Department of Child Neurology, Faculty of Medicine, Retired lecturer, Karadeniz Technical University, Trabzon, Türkiye
- Private Office, Ankara, Türkiye
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Sait Tümer
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye
| | | | | | - Odile Boute
- Clinique de Génétique, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hyung Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ahmet Yesilyurt
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye.
- Acibadem Maslak Hospital, Istanbul, Türkiye.
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Kulsirichawaroj P, Suksangkharn Y, Nam DE, Pho-iam T, Limwongse C, Chung KW, Sanmaneechai O, Zuchner SL, Choi BO. Gene Distribution in Pediatric-Onset Inherited Peripheral Neuropathy: A Single Tertiary Center in Thailand. J Neuromuscul Dis 2024; 11:191-199. [PMID: 37927275 PMCID: PMC10789325 DOI: 10.3233/jnd-230174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Inherited peripheral neuropathy presents a diagnostic and therapeutic challenge due to its association with mutations in over 100 genes. This condition leads to long-term disability and poses a substantial healthcare burden on society. OBJECTIVE This study aimed to investigate the distribution of genes and establish the genotype-phenotype correlations, focusing on pediatric-onset cases. METHODS Exome sequencing and other analytical techniques were employed to identify pathogenic variants, including duplication analysis of the PMP22 gene. Each patient underwent physical examination and electrophysiological studies. Genotypes were correlated with phenotypic features, such as age at disease onset and ulnar motor nerve conduction velocity. RESULTS We identified 35 patients with pediatric-onset inherited peripheral neuropathy. Pathogenic or likely pathogenic variants were confirmed in 24 out of 35 (68.6%) patients, with 4 of these variants being novel. A confirmed molecular diagnosis was achieved in 90.9% (10/11) of patients with demyelinating Charcot-Marie-Tooth disease (CMT) and 56.3% (9/16) of patients with axonal CMT. Among patients with infantile-onset CMT (≤2 years), the most common causative genes were MFN2 and NEFL, while GDAP1 and MFN2 were frequent causes among patients with childhood- or adolescent-onset CMT (3-9 years). CONCLUSIONS The MFN2 gene was the most commonly implicated gene, and the axonal type was predominant in this cohort of Thai patients with pediatric-onset inherited peripheral neuropathy.
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Affiliation(s)
- Pimchanok Kulsirichawaroj
- Department of Pediatrics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - Yanin Suksangkharn
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Da Eun Nam
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Theeraphong Pho-iam
- Siriraj Genomics, Office of the Dean, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - Chanin Limwongse
- Siriraj Genomics, Office of the Dean, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Oranee Sanmaneechai
- Department of Pediatrics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
- Center of Research Excellence for Neuromuscular Diseases, Faculty of Medicine, Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - Stephan L. Zuchner
- Department of Human Genetics, University of Miami Health System, Miami, FL, USA
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, and Samsung Advanced Institute for Health Science & Tech, Sungkyunkwan University School of Medicine, Seoul, Korea
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Lin Y, Xu J, Yang T. [Genetic and phenotypic analysis of MYO15A rare variants associated with autosomal recessive hearing loss]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2024; 38:38-43. [PMID: 38297847 PMCID: PMC11116157 DOI: 10.13201/j.issn.2096-7993.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Indexed: 02/02/2024]
Abstract
Objective:To analyze the phenotype and genotype characteristics of autosomal recessive hearing loss caused by MYO15A gene variants, and to provide genetic diagnosis and genetic counseling for patients and their families. Methods:Identification of MYO15A gene variants by next generation sequencing in two sporadic cases of hearing loss at Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine. The sequence variants were verified by Sanger sequencing.The pathogenicity of these variants was determined according to the American College of Medical Genetics and Genomics(ACMG) variant classification guidelines, in conjuction with clinical data. Results:The probands of the two families have bilateral,severe or complete hearing loss.Four variants of MYO15A were identified, including one pathogenic variant that has been reported, two likely pathogenic variants,and one splicing variant of uncertain significance. Patient I carries c. 3524dupA(p. Ser1176Valfs*14), a reported pathogenic variant, and a splicing variant c. 10082+3G>A of uncertain significance according to the ACMG guidelines. Patient I was treated with bilateral hearing aids with satisfactory effect, demonstrated average hearing thresholds of 37.5 dB in the right ear and 33.75 dB in the left ear. Patient Ⅱ carries c. 7441_7442del(p. Leu2481Glufs*86) and c. 10250_10252del(p. Ser3417del),a pair of as likely pathogenic variants according to the ACMG guidelines. Patient Ⅱ, who underwent right cochlear implantation eight years ago, achieved scores of 9 on the Categorical Auditory Performance-Ⅱ(CAP-Ⅱ) and 5 on the Speech Intelligibility Rating(SIR). Conclusion:This study's discovery of the rare c. 7441_7442del variant and the splicing variant c. 10082+3G>A in the MYO15A gene is closely associated with autosomal recessive hearing loss, expanding the MYO15A variant spectrum. Additionally, the pathogenicity assessment of the splicing variant facilitates classification of splicing variations.
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Affiliation(s)
- Yun Lin
- Department of Otolaryngology-Head and Neck Surgery,Shanghai Ninth People's Hospital,Shanghai Jiao Tong University School of Medicine,Shanghai,200125,China
- Ear Institute,Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases
| | - Jun Xu
- Department of Otolaryngology-Head and Neck Surgery,Shanghai Ninth People's Hospital,Shanghai Jiao Tong University School of Medicine,Shanghai,200125,China
- Ear Institute,Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery,Shanghai Ninth People's Hospital,Shanghai Jiao Tong University School of Medicine,Shanghai,200125,China
- Ear Institute,Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases
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Gorcenco S, Kafantari E, Wallenius J, Karremo C, Alinder E, Dobloug S, Landqvist Waldö M, Englund E, Ehrencrona H, Wictorin K, Karrman K, Puschmann A. Clinical and genetic analyses of a Swedish patient series diagnosed with ataxia. J Neurol 2024; 271:526-542. [PMID: 37787810 PMCID: PMC10770240 DOI: 10.1007/s00415-023-11990-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/04/2023]
Abstract
Hereditary ataxia is a heterogeneous group of complex neurological disorders. Next-generation sequencing methods have become a great help in clinical diagnostics, but it may remain challenging to determine if a genetic variant is the cause of the patient's disease. We compiled a consecutive single-center series of 87 patients from 76 families with progressive ataxia of known or unknown etiology. We investigated them clinically and genetically using whole exome or whole genome sequencing. Test methods were selected depending on family history, clinical phenotype, and availability. Genetic results were interpreted based on the American College of Medical Genetics criteria. For high-suspicion variants of uncertain significance, renewed bioinformatical and clinical evaluation was performed to assess the level of pathogenicity. Thirty (39.5%) of the 76 families had received a genetic diagnosis at the end of our study. We present the predominant etiologies of hereditary ataxia in a Swedish patient series. In two families, we established a clinical diagnosis, although the genetic variant was classified as "of uncertain significance" only, and in an additional three families, results are pending. We found a pathogenic variant in one family, but we suspect that it does not explain the complete clinical picture. We conclude that correctly interpreting genetic variants in complex neurogenetic diseases requires genetics and clinical expertise. The neurologist's careful phenotyping remains essential to confirm or reject a diagnosis, also by reassessing clinical findings after a candidate genetic variant is suggested. Collaboration between neurology and clinical genetics and combining clinical and research approaches optimizes diagnostic yield.
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Affiliation(s)
- Sorina Gorcenco
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden.
| | - Efthymia Kafantari
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Joel Wallenius
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Christin Karremo
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Erik Alinder
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Sigurd Dobloug
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
- Division of Clinical Sciences Helsingborg, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Maria Landqvist Waldö
- Division of Clinical Sciences Helsingborg, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Elisabet Englund
- Pathology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Hans Ehrencrona
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Klas Wictorin
- Division of Clinical Sciences Helsingborg, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Kristina Karrman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Andreas Puschmann
- Neurology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
- SciLifeLab National Research Infrastructure, Solna, Sweden
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Bertani-Torres W, Lezirovitz K, Alencar-Coutinho D, Pardono E, da Costa SS, Antunes LDN, de Oliveira J, Otto PA, Pingault V, Mingroni-Netto RC. Waardenburg Syndrome: The Contribution of Next-Generation Sequencing to the Identification of Novel Causative Variants. Audiol Res 2023; 14:9-25. [PMID: 38391765 PMCID: PMC10886116 DOI: 10.3390/audiolres14010002] [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: 10/01/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 02/24/2024] Open
Abstract
Waardenburg syndrome (WS) is characterized by hearing loss and pigmentary abnormalities of the eyes, hair, and skin. The condition is genetically heterogeneous, and is classified into four clinical types differentiated by the presence of dystopia canthorum in type 1 and its absence in type 2. Additionally, limb musculoskeletal abnormalities and Hirschsprung disease differentiate types 3 and 4, respectively. Genes PAX3, MITF, SOX10, KITLG, EDNRB, and EDN3 are already known to be associated with WS. In WS, a certain degree of molecularly undetected patients remains, especially in type 2. This study aims to pinpoint causative variants using different NGS approaches in a cohort of 26 Brazilian probands with possible/probable diagnosis of WS1 (8) or WS2 (18). DNA from the patients was first analyzed by exome sequencing. Seven of these families were submitted to trio analysis. For inconclusive cases, we applied a targeted NGS panel targeting WS/neurocristopathies genes. Causative variants were detected in 20 of the 26 probands analyzed, these being five in PAX3, eight in MITF, two in SOX10, four in EDNRB, and one in ACTG1 (type 2 Baraitser-Winter syndrome, BWS2). In conclusion, in our cohort of patients, the detection rate of the causative variant was 77%, confirming the superior detection power of NGS in genetically heterogeneous diseases.
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Affiliation(s)
- William Bertani-Torres
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
- Department of Embryology and Genetics of Malformations, INSERM (Institut National de la Santé et de la Recherche Médicale) UMR (Unité Mixte de Recherche) 1163, Université Paris-Cité and Institut Imagine, 75015 Paris, France
| | - Karina Lezirovitz
- Otorhinolaryngology Lab-LIM 32, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Danillo Alencar-Coutinho
- Otorhinolaryngology Lab-LIM 32, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Eliete Pardono
- Instituto de Ciências da Saúde, Universidade Paulista UNIP, São Paulo 04026-002, Brazil
- Colégio Miguel de Cervantes, São Paulo 05618-001, Brazil
| | - Silvia Souza da Costa
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Larissa do Nascimento Antunes
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Judite de Oliveira
- Médecine Génomique des Maladies Rares, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Paulo Alberto Otto
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Véronique Pingault
- Department of Embryology and Genetics of Malformations, INSERM (Institut National de la Santé et de la Recherche Médicale) UMR (Unité Mixte de Recherche) 1163, Université Paris-Cité and Institut Imagine, 75015 Paris, France
- Médecine Génomique des Maladies Rares, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Regina Célia Mingroni-Netto
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
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Zhou N, Liang W, Zhang Y, Quan G, Li T, Huang S, Huo Y, Cui H, Cheng Y. ODAD1 variants resulting from splice-site mutations retain partial function and cause primary ciliary dyskinesia with outer dynein arm defects. Front Genet 2023; 14:1270278. [PMID: 38028630 PMCID: PMC10651219 DOI: 10.3389/fgene.2023.1270278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder caused by defects in motile ciliary function and/or structure. Outer dynein arm docking complex subunit 1 (ODAD1) is an important component of the outer dynein arm docking complex (ODA-DC). To date, 13 likely pathogenic mutations of ODAD1 have been reported. However, the pathogenesis of ODAD1 mutations remains elusive. To investigate the pathogenesis of splice-site mutations in ODAD1 discovered in this study and those reported previously, molecular and functional analyses were performed. Whole-exome sequencing revealed a compound mutation in ODAD1 (c.71-2A>C; c.598-2A>C) in a patient with PCD, with c.598-2A>C being a novel mutation that resulted in two mutant transcripts. The compound mutation in ODAD1 (c.71-2A>C; c.598-2A>C) led to aberrant splicing that resulted in the absence of the wild-type ODAD1 and defects of the outer dynein arm in ciliary axonemes, causing a decrease in ciliary beat frequency. Furthermore, we demonstrated that the truncated proteins resulting from splice-site mutations in ODAD1 could retain partial function and inhibit the interaction between wild-type ODAD1 and ODAD3. The results of this study expand the mutational and clinical spectrum of PCD, provide more evidence for genetic counseling, and offer new insights into gene-based therapeutic strategies for PCD.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuanxiong Cheng
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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Zeibich R, Kwan P, J. O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research. Int J Mol Sci 2023; 24:14645. [PMID: 37834093 PMCID: PMC10572791 DOI: 10.3390/ijms241914645] [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: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Epilepsy is a group of brain disorders characterised by an enduring predisposition to generate unprovoked seizures. Fuelled by advances in sequencing technologies and computational approaches, more than 900 genes have now been implicated in epilepsy. The development and optimisation of tools and methods for analysing the vast quantity of genomic data is a rapidly evolving area of research. Deep learning (DL) is a subset of machine learning (ML) that brings opportunity for novel investigative strategies that can be harnessed to gain new insights into the genomic risk of people with epilepsy. DL is being harnessed to address limitations in accuracy of long-read sequencing technologies, which improve on short-read methods. Tools that predict the functional consequence of genetic variation can represent breaking ground in addressing critical knowledge gaps, while methods that integrate independent but complimentary data enhance the predictive power of genetic data. We provide an overview of these DL tools and discuss how they may be applied to the analysis of genetic data for epilepsy research.
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Affiliation(s)
- Robert Zeibich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Terence J. O’Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
| | - Zongyuan Ge
- Faculty of Engineering, Monash University, Melbourne, VIC 3800, Australia;
- Monash-Airdoc Research, Monash University, Melbourne, VIC 3800, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
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50
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Hentrich L, Parnes M, Lotze TE, Coorg R, de Koning TJ, Nguyen KM, Yip CK, Jungbluth H, Koy A, Dafsari HS. Novel Genetic and Phenotypic Expansion in GOSR2-Related Progressive Myoclonus Epilepsy. Genes (Basel) 2023; 14:1860. [PMID: 37895210 PMCID: PMC10606070 DOI: 10.3390/genes14101860] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Biallelic variants in the Golgi SNAP receptor complex member 2 gene (GOSR2) have been reported in progressive myoclonus epilepsy with neurodegeneration. Typical clinical features include ataxia and areflexia during early childhood, followed by seizures, scoliosis, dysarthria, and myoclonus. Here, we report two novel patients from unrelated families with a GOSR2-related disorder and novel genetic and clinical findings. The first patient, a male compound heterozygous for the GOSR2 splice site variant c.336+1G>A and the novel c.364G>A,p.Glu122Lys missense variant showed global developmental delay and seizures at the age of 2 years, followed by myoclonus at the age of 8 years with partial response to clonazepam. The second patient, a female homozygous for the GOSR2 founder variant p.Gly144Trp, showed only mild fine motor developmental delay and generalized tonic-clonic seizures triggered by infections during adolescence, with seizure remission on levetiracetam. The associated movement disorder progressed atypically slowly during adolescence compared to its usual speed, from initial intention tremor and myoclonus to ataxia, hyporeflexia, dysmetria, and dystonia. These findings expand the genotype-phenotype spectrum of GOSR2-related disorders and suggest that GOSR2 should be included in the consideration of monogenetic causes of dystonia, global developmental delay, and seizures.
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Affiliation(s)
- Lea Hentrich
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (L.H.)
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Mered Parnes
- Division of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; (M.P.); (T.E.L.)
| | - Timothy Edward Lotze
- Division of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; (M.P.); (T.E.L.)
| | - Rohini Coorg
- Division of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; (M.P.); (T.E.L.)
| | - Tom J. de Koning
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
- Pediatrics, Department of Clinical Sciences, Lund University, 221 00 Lund, Sweden
| | - Kha M. Nguyen
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.M.N.); (C.K.Y.)
| | - Calvin K. Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.M.N.); (C.K.Y.)
| | - Heinz Jungbluth
- Department of Paediatric Neurology, Evelina’s Children Hospital, Guy’s & St. Thomas’ Hospital NHS Foundation Trust, London SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King’s College London, London WC2R 2LS, UK
| | - Anne Koy
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (L.H.)
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (L.H.)
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
- Department of Paediatric Neurology, Evelina’s Children Hospital, Guy’s & St. Thomas’ Hospital NHS Foundation Trust, London SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King’s College London, London WC2R 2LS, UK
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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