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Graça R, Zimon M, Alves AC, Pepperkok R, Bourbon M. High-Throughput Microscopy Characterization of Rare LDLR Variants. JACC Basic Transl Sci 2023; 8:1010-1021. [PMID: 37719435 PMCID: PMC10504398 DOI: 10.1016/j.jacbts.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 09/19/2023]
Abstract
Familial hypercholesterolemia (FH) is the most common inherited life-threatening disorder of lipid metabolism. Early diagnosis and treatment are the key to reduce the cumulative life-long cardiovascular burden of patients with FH. The high number of LDLR variants described as variants of unknown significance is the largest obstacle to achieve a definitive FH diagnosis. This study established a time- and cost-effective high-throughput cell-based assay to functionally profile LDLR variants, which allowed us to discriminate disruptive rare variants from silent ones. This work generated a valuable resource for systematic functional characterization of LDLR variants solving 1 of the major issues to achieve a definitive FH diagnosis.
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Affiliation(s)
- Rafael Graça
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Magdalena Zimon
- Roche Diabetes Care GmbH, Mannheim, Germany
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Ana C. Alves
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Rainer Pepperkok
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
- Advanced Light Microscopy Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Mafalda Bourbon
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Santos RD. Sailing the Uncharted Waters of Familial Hypercholesterolemia LDL Receptor Genetic-Related Variants: Land in Sight? JACC Basic Transl Sci 2023; 8:1022-1024. [PMID: 37719432 PMCID: PMC10504392 DOI: 10.1016/j.jacbts.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Affiliation(s)
- Raul D. Santos
- Address for correspondence: Dr Raul D. Santos, Unidade Clínica de Lipides InCor HCMFUSP, Av Dr Eneas Carvalho Aguiar 44, CEP 05403-000, São Paulo, São Paulo, Brazil.
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Alesci RS, Hecking C, Racké B, Janssen D, Dempfle CE. Utility of ACMG classification to support interpretation of molecular genetic test results in patients with factor VII deficiency. Front Med (Lausanne) 2023; 10:1220813. [PMID: 37521340 PMCID: PMC10382174 DOI: 10.3389/fmed.2023.1220813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/16/2023] [Indexed: 08/01/2023] Open
Abstract
Background The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have introduced an internationally shared framework for variant classification in genetic disorders. FVII deficiency is a rare inherited autosomal recessive bleeding disorder with sparse data concerning ACMG classification. Methods To develop an approach which may improve the utility of molecular genetic test results, 129 patients with FVII deficiency were retrospectively assigned to six subgroups for exploratory analysis: F7 gene wildtype (group 1), ACMG 1 (benign variant) or ACMG 2 (likely benign variant), only (group 2), ACMG 3 (variant of uncertain significance) ± ACMG 1-2 heterozygous or not classified variant (group 3), ACMG 4 (likely pathogenic variant), or ACMG 5 (pathogenic variant) single heterozygous ± ACMG 1-3 single heterozygous (group 4), ACMG 4-5 homozygous or ≥2 ACMG 4-5 heterozygous or ≥1 ACMG 4-5 heterozygous plus either ACMG 1 c.1238G>A modifying variant homozygous or ≥2 ACMG 1-3 (group 5), FVII deficiency and another bleeding disorder (group 6). Results Eleven of 31 patients (35.5%) in group 5 had abnormal ISTH-BS (n = 7) and/or history of substitution with recombinant factor VIIa (n = 5) versus 4 of 80 patients (5.0%, n = 1 abnormal ISTH-BS, n = 3 substitution) in groups 1 (n = 2/22), 2 (n = 1/29), 3 (n = 0/9), and 4 (n = 1/20). Four of 18 patients (22.2%) with FVII deficiency and another bleeding disorder (group 6) had an abnormal ISTH-BS (n = 2) and/or history of substitution with recombinant factor VIIa (n = 3). Conclusion Patients with a homozygous ACMG 4-5 variant or with specific combinations of heterozygous ACMG 4-5 ± ACMG 1-3 variants exhibited a high-risk bleeding phenotype in contrast to the remaining patients without another bleeding disorder. This result may serve as a basis to develop a genotype/phenotype prediction model in future studies.
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Affiliation(s)
| | | | - Benjamin Racké
- Institute of Immunology and Genetics, Kaiserslautern, Germany
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Stalke A, Behrendt A, Hennig F, Gohlke H, Buhl N, Reinkens T, Baumann U, Schlegelberger B, Illig T, Pfister ED, Skawran B. Functional characterization of novel or yet uncharacterized ATP7B missense variants detected in patients with clinical Wilson's disease. Clin Genet 2023. [PMID: 37157876 DOI: 10.1111/cge.14352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023]
Abstract
Wilson's disease (WD, MIM#277900) is an autosomal recessive disorder resulting in copper excess caused by biallelic variants in the ATP7B gene (MIM#606882) encoding a copper transporting P-type ATPase. ATP7B variants of unknown significance (VUS) are detected frequently, sometimes impeding a clear diagnosis. Functional analyses can help to classify these variants as benign or pathogenic. Additionally, variants already classified as (likely) pathogenic benefit from functional analyses to understand their pathomechanism, thus contribute to the development of personalized treatment approaches in the future. We described clinical features of six WD patients and functionally characterized five ATP7B missense variants (two VUS, three yet uncharacterized likely pathogenic variants), detected in these patients. We determined the protein level, copper export capacity, and cellular localization in an in vitro model and potential structural consequences using an ATP7B protein model based on AlphaFold. Our analyses give insight into the pathomechanism and allowed reclassification for the two VUS to likely pathogenic and for two of the three likely pathogenic variants to pathogenic.
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Affiliation(s)
- Amelie Stalke
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- Department of Pediatric Gastroenterology and Hepatology, Division of Kidney, Liver, and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Annika Behrendt
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Finja Hennig
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Nicole Buhl
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- Department of Pediatric Gastroenterology and Hepatology, Division of Kidney, Liver, and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Thea Reinkens
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ulrich Baumann
- Department of Pediatric Gastroenterology and Hepatology, Division of Kidney, Liver, and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | | | - Thomas Illig
- Hannover Unified Bank, Hannover Medical School, Hannover, Germany
| | - Eva-Doreen Pfister
- Department of Pediatric Gastroenterology and Hepatology, Division of Kidney, Liver, and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Britta Skawran
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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Mansard L, Baux D, Vaché C, Blanchet C, Meunier I, Willems M, Faugère V, Baudoin C, Moclyn M, Bianchi J, Dollfus H, Gilbert-Dussardier B, Dupin-Deguine D, Bonneau D, Drumare I, Odent S, Zanlonghi X, Claustres M, Koenig M, Kalatzis V, Roux AF. The Study of a 231 French Patient Cohort Significantly Extends the Mutational Spectrum of the Two Major Usher Genes MYO7A and USH2A. Int J Mol Sci 2021; 22:ijms222413294. [PMID: 34948090 PMCID: PMC8703989 DOI: 10.3390/ijms222413294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 01/06/2023] Open
Abstract
Usher syndrome is an autosomal recessive disorder characterized by congenital hearing loss combined with retinitis pigmentosa, and in some cases, vestibular areflexia. Three clinical subtypes are distinguished, and MYO7A and USH2A represent the two major causal genes involved in Usher type I, the most severe form, and type II, the most frequent form, respectively. Massively parallel sequencing was performed on a cohort of patients in the context of a molecular diagnosis to confirm clinical suspicion of Usher syndrome. We report here 231 pathogenic MYO7A and USH2A genotypes identified in 73 Usher type I and 158 Usher type II patients. Furthermore, we present the ACMG classification of the variants, which comprise all types. Among them, 68 have not been previously reported in the literature, including 12 missense and 16 splice variants. We also report a new deep intronic variant in USH2A. Despite the important number of molecular studies published on these two genes, we show that during the course of routine genetic diagnosis, undescribed variants continue to be identified at a high rate. This is particularly pertinent in the current era, where therapeutic strategies based on DNA or RNA technologies are being developed.
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Affiliation(s)
- Luke Mansard
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - David Baux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
| | - Christel Vaché
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
| | - Catherine Blanchet
- National Reference Centre for Inherited Sensory Diseases, University Montpellier, CHU Montpellier, F-34000 Montpellier, France;
- Oto Laryngology Department, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
- National Reference Centre for Inherited Sensory Diseases, University Montpellier, CHU Montpellier, F-34000 Montpellier, France;
| | - Marjolaine Willems
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
- Medical Genetics Department, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France
| | - Valérie Faugère
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Corinne Baudoin
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Melody Moclyn
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Julie Bianchi
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Helene Dollfus
- Reference Center for Rare Affections in Ophthalmology Genetics (CARGO), Institute of Medical Genetics of Alsace, University of Strasbourg, CHU Strasbourg, F-67000 Strasbourg, France;
| | | | - Delphine Dupin-Deguine
- Medical Genetics Department, University of Toulouse, CHU Purpan, F-31000 Toulouse, France;
| | - Dominique Bonneau
- Medical Genetics Department, University of Angers, CHU Angers, F-49000 Angers, France;
| | - Isabelle Drumare
- Vision and Neuro-Ophthalmology Department, University of Lille, CHU Lille, F-59000 Lille, France;
| | - Sylvie Odent
- Clinical Genetics Service, University Hospital, Genetics and Development Institute of Rennes IDGDR, UMR6290 University of Rennes, F-35000 Rennes, France;
| | - Xavier Zanlonghi
- Center of Competence for Rare Diseases, Jules Verne Clinic, F-44000 Nantes, France;
| | - Mireille Claustres
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Michel Koenig
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
| | - Anne-Françoise Roux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, F-34000 Montpellier, France; (L.M.); (D.B.); (C.V.); (V.F.); (C.B.); (M.M.); (J.B.); (M.C.); (M.K.)
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, F-34000 Montpellier, France; (I.M.); (M.W.); (V.K.)
- Correspondence:
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Sun Y, Xiao L, Li K, Wang H, Song X, Li Z, Li C, Chen Y, Li S, Huang J, Tan L, Hu D, Yu T, Li R, Wang H, Jin L, Shi L, Marian AJ, Wang DW. Shared Genetic Etiology of Primary Dilated Cardiomyopathy and Ischemic Dilated Cardiomyopathy. Front Cardiovasc Med 2021; 8:752662. [PMID: 37273834 PMCID: PMC10236477 DOI: 10.3389/fcvm.2021.752662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/26/2021] [Indexed: 06/06/2023] Open
Abstract
Background: Mutations in genes encoding sarcomere and cytoskeletal proteins are major causes of primary dilated cardiomyopathy (DCM). Likewise, ischemic myocardial injury is a major cause of secondary cardiac remodeling, which, in a subset, is severe and resembles DCM. The latter is referred to as ischemic dilated cardiomyopathy (IDCM). We postulated the presence of pathogenic and likely pathogenic variants (PVs and LPVs, respectively) in genes known to cause primary DCM might predispose the heart to severe cardiac dilatation and dysfunction post myocardial ischemic injury, i.e., IDCM. Methods: We performed whole-exome sequencing in 1,041 patients with primary DCM, 215 patients with IDCM, and 414 healthy controls. Indices of cardiac size and function were similar between those with primary and ischemic DCM. PVs and LPVs, including the truncating variants in 36 genes known to cause primary DCM were identified and compared among the three groups. Results: Pathogenic variants and LPVs were detected in 266 individuals, comprised of 215/1,041 (20.7%) patients with DCM, 27/215 (12.6%) patients with IDCM, and 24/414 (5.8%) control individuals. PVs and LPVs in the TTN gene were the most common and detected in 130/1,041 (12.5%) of patients with DCM, 15/215 (7.0%) of cases with IDCM, and 10/414 (2.4%) control individuals. Of 135 TTNtv, 118 involved exons that were >90% spliced in. These variants were found in 120/1,041 (11.5%) of DCM patients, 6/215 (2.8%) of IDCM cases, and only in 1/414 (0.2%) of the control population (p < 0.001 among the three groups). Conclusions: Pathogenic variants and LPVs in genes known to cause primary DCM are enriched in patients with IDCM, suggesting that such variants function as susceptibility alleles for cardiac dilatation and dysfunction in post myocardial ischemic injury. Thus, IDCM shares a partial genetic etiology with the primary DCM.
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Affiliation(s)
- Yang Sun
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Xiao
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Xiuli Song
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Zongzhe Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Chenze Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Yanghui Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Shiyang Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Huang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Lun Tan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Hu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Yu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Jin
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
- Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Leming Shi
- Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Ali J. Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, United States
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, China
- Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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Graça R, Fernandes R, Alves AC, Menezes J, Romão L, Bourbon M. Characterization of Two Variants at Met 1 of the Human LDLR Gene Encoding the Same Amino Acid but Causing Different Functional Phenotypes. Biomedicines 2021; 9:1219. [PMID: 34572405 PMCID: PMC8467959 DOI: 10.3390/biomedicines9091219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Familial hypercholesterolemia (FH) is the most common genetic disorder of lipid metabolism, characterized by increased levels of total and LDL plasma cholesterol, which leads to premature atherosclerosis and coronary heart disease. FH phenotype has considerable genetic heterogeneity and phenotypic variability, depending on LDL receptor activity and lifestyle. To improve diagnosis and patient management, here, we characterized two single nucleotide missense substitutions at Methionine 1 of the human LDLR gene (c.1A>T/p.(Met1Leu) and c.1A>C/p.(Met1Leu)). We used a combination of Western blot, flow cytometry, and luciferase assays to determine the effects of both variants on the expression, activity, and synthesis of LDLR. Our data show that both variants can mediate translation initiation, although the expression of variant c.1A>T is very low. Both variants are in the translation initiation codon and codify for the same amino acid p.(Met1Leu), yet they lead to different levels of impairment on LDLR expression and activity, corroborating different efficiencies of the translation initiation at these non-canonical initiation codons. The functional data of these variants allowed for an improved American College of Medical Genetics (ACMG) classification for both variants, which can allow a more personalized choice of the lipid-lowering treatment and dyslipidemia management, ultimately improving patients' prognosis.
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Affiliation(s)
- Rafael Graça
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
| | - Rafael Fernandes
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Ana Catarina Alves
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
| | - Juliane Menezes
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Luísa Romão
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Mafalda Bourbon
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
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Mhaske A, Dileep K, Kumar M, Poojary M, Pandhare K, Zhang KY, Scaria V, Binukumar B. ATP7A Clinical Genetics Resource - A comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput Struct Biotechnol J 2020; 18:2347-2356. [PMID: 32994893 PMCID: PMC7501406 DOI: 10.1016/j.csbj.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
ATP7A is a critical copper transporter involved in Menkes Disease, Occipital horn Syndrome and X-linked distal spinal muscular atrophy type 3 which are X linked genetic disorders. These are rare diseases and their genetic epidemiology of the diseases is unknown. A number of genetic variants in the genes have been reported in published literature as well as databases, however, understanding the pathogenicity of variants and genetic epidemiology requires the data to be compiled in a unified format. To this end, we systematically compiled genetic variants from published literature and datasets. Each of the variants were systematically evaluated for evidences with respect to their pathogenicity and classified as per the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG-AMP) guidelines into Pathogenic, Likely Pathogenic, Benign, Likely Benign and Variants of Uncertain Significance. Additional integrative analysis of population genomic datasets provides insights into the genetic epidemiology of the disease through estimation of carrier frequencies in global populations. To deliver a mechanistic explanation for the pathogenicity of selected variants, we also performed molecular modeling studies. Our modeling studies concluded that the small structural distortions observed in the local structures of the protein may lead to the destabilization of the global structure. To the best of our knowledge, ATP7A Clinical Genetics Resource is one of the most comprehensive compendium of variants in the gene providing clinically relevant annotations in gene.
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Affiliation(s)
- Aditi Mhaske
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - K.V. Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kam Y.J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
| | - B.K. Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
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Malikova J, Kaci A, Dusatkova P, Aukrust I, Torsvik J, Vesela K, Kankova PD, Njølstad PR, Pruhova S, Bjørkhaug L. Functional Analyses of HNF1A-MODY Variants Refine the Interpretation of Identified Sequence Variants. J Clin Endocrinol Metab 2020; 105:5722353. [PMID: 32017842 DOI: 10.1210/clinem/dgaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022]
Abstract
CONTEXT While rare variants of the hepatocyte nuclear factor-1 alpha (HNF1A) gene can cause maturity-onset diabetes of the young (HNF1A-MODY), other variants can be risk factors for the development of type 2 diabetes. As has been suggested by the American College of Medical Genetics (ACMG) guidelines for variant interpretation, functional studies provide strong evidence to classify a variant as pathogenic. OBJECTIVE We hypothesized that a functional evaluation can improve the interpretation of the HNF1A variants in our Czech MODY Registry. DESIGN, SETTINGS, AND PARTICIPANTS We studied 17 HNF1A variants that were identified in 48 individuals (33 female/15 male) from 20 Czech families with diabetes, using bioinformatics in silico tools and functional protein analyses (transactivation, protein expression, DNA binding, and nuclear localization). RESULTS Of the 17 variants, 12 variants (p.Lys120Glu, p.Gln130Glu, p.Arg131Pro, p.Leu139Pro, p.Met154Ile, p.Gln170Ter, p.Glu187SerfsTer40, p.Phe215SerfsTer18, p.Gly253Arg, p.Leu383ArgfsTer3, p.Gly437Val, and p.Thr563HisfsTer85) exhibited significantly reduced transcriptional activity or DNA binding (< 40%) and were classified as (likely) pathogenic, 2/17 variants were (likely) benign and 3/17 remained of uncertain significance. Functional analyses allowed for the reclassification of 10/17 variants (59%). Diabetes treatment was improved in 20/29 (69%) carriers of (likely) pathogenic HNF1A variants. CONCLUSION Functional evaluation of the HNF1A variants is necessary to better predict the pathogenic effects and to improve the diagnostic interpretation and treatment, particularly in cases where the cosegregation or family history data are not available or where the phenotype is more diverse and overlaps with other types of diabetes.
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Affiliation(s)
- Jana Malikova
- Department of Pediatrics, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Alba Kaci
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
| | - Petra Dusatkova
- Department of Pediatrics, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Ingvild Aukrust
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Janniche Torsvik
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
| | - Klara Vesela
- Department of Pediatrics, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Pavla Dvorakova Kankova
- Department of Pediatrics, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
| | - Stepanka Pruhova
- Department of Pediatrics, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Lise Bjørkhaug
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
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Zanetti A, D’Avanzo F, Rigon L, Rampazzo A, Concolino D, Barone R, Volpi N, Santoro L, Lualdi S, Bertola F, Scarpa M, Tomanin R. Molecular diagnosis of patients affected by mucopolysaccharidosis: a multicenter study. Eur J Pediatr 2019; 178:739-753. [PMID: 30809705 PMCID: PMC6459791 DOI: 10.1007/s00431-019-03341-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 11/25/2022]
Abstract
Mucopolysaccharidoses (MPS) are a subgroup of 11 monogenic lysosomal storage disorders due to the deficit of activity of the lysosomal hydrolases deputed to the degradation of mucopolysaccharides. Although individually rare, all together they account for at least 1:25,000 live births. In this study, we present the genetic analysis of a population of 71 MPS patients enrolled in a multicenter Italian study. We re-annotated all variants, according to the latest recommendations, and re-classified them as suggested by the American College of Medical Genetics and Genomics. Variant distribution per type was mainly represented by missense mutations. Overall, 10 patients had received no molecular diagnosis, although 6 of them had undergone either HSCT or ERT, based on clinical and enzymatic evaluations. Moreover, nine novel variants are reported.Conclusions: Our analysis underlines the need to complete the molecular diagnosis in patients previously diagnosed only on a biochemical basis, suggests a periodical re-annotation of the variants and solicits their deposition in public databases freely available to clinicians and researchers. We strongly recommend a molecular diagnosis based on the analysis of the "trio" instead of the sole proband. These recommendations will help to obtain a complete and correct diagnosis of mucopolysaccharidosis, rendering also possible genetic counseling. What is known • MPS are a group of 11 metabolic genetic disorders due to deficits of enzymes involved in the mucopolysaccharides degradation. • Molecular analysis is commonly performed to confirm enzymatic assays. What is new • Eighty-six percent of the 71 patients we collected received a molecular diagnosis; among them, 9 novel variants were reported. • We stress the importance of molecular diagnosis in biochemically diagnosed patients, encourage a periodical re-annotation of variants according to the recent nomenclature and their publication in open databases.
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Affiliation(s)
- Alessandra Zanetti
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Francesca D’Avanzo
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Laura Rigon
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Angelica Rampazzo
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | | | - Rita Barone
- Department of Clinical and Experimental Medicine, Child Neurology and Psychiatry, University of Catania, Catania, Italy
| | - Nicola Volpi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Lucia Santoro
- Department of Clinical Sciences, Division of Pediatrics, Polytechnic University of Marche, Ospedali Riuniti, Presidio Salesi, Ancona, Italy
| | - Susanna Lualdi
- Laboratorio di Genetica Medica e Biobanche, Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Bertola
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Maurizio Scarpa
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Rosella Tomanin
- Laboratorio di Diagnosi e Terapia delle Malattie Lisosomiali, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
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