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Ma JG, O’Neill MJ, Richardson E, Thomson KL, Ingles J, Muhammad A, Solus JF, Davogustto G, Anderson KC, Benjamin Shoemaker M, Stergachis AB, Floyd BJ, Dunn K, Parikh VN, Chubb H, Perrin MJ, Roden DM, Vandenberg JI, Ng CA, Glazer AM. Multisite Validation of a Functional Assay to Adjudicate SCN5A Brugada Syndrome-Associated Variants. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004569. [PMID: 38953211 PMCID: PMC11335442 DOI: 10.1161/circgen.124.004569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Brugada syndrome is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging, and ≈79% of SCN5A missense variants in ClinVar are currently classified as variants of uncertain significance. Automated patch clamp technology enables high-throughput functional studies of ion channel variants and can provide evidence for variant reclassification. METHODS An in vitro SCN5A-Brugada syndrome automated patch clamp assay was independently performed at Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute. The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. Odds of pathogenicity values were derived from the experimental results according to ClinGen Sequence Variant Interpretation recommendations. The calibrated assay was then used to study SCN5A variants of uncertain significance observed in 4 families with Brugada syndrome and other arrhythmia phenotypes associated with SCN5A loss-of-function. RESULTS Variant channel parameters generated independently at the 2 research sites showed strong correlations, including peak INa density (R2=0.86). The assay accurately distinguished benign controls (24/25 concordant variants) from pathogenic controls (23/24 concordant variants). Odds of pathogenicity values were 0.042 for normal function and 24.0 for abnormal function, corresponding to strong evidence for both American College of Medical Genetics and Genomics/Association for Molecular Pathology benign and pathogenic functional criteria (BS3 and PS3, respectively). Application of the assay to 4 clinical SCN5A variants of uncertain significance revealed loss-of-function for 3/4 variants, enabling reclassification to likely pathogenic. CONCLUSIONS This validated high-throughput assay provides clinical-grade functional evidence to aid the classification of current and future SCN5A-Brugada syndrome variants of uncertain significance.
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Affiliation(s)
- Joanne G. Ma
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | | | - Ebony Richardson
- Clinical Genomics Laboratory, Ctr for Population Genomics, Garvan Inst of Medical Rsrch, Darlinghurst, NSW & Australia & Murdoch Children’s Research Inst, Melbourne, Australia
| | - Kate L. Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Jodie Ingles
- Clinical Genomics Laboratory, Ctr for Population Genomics, Garvan Inst of Medical Rsrch, Darlinghurst, NSW & Australia & Murdoch Children’s Research Inst, Melbourne, Australia
| | | | - Joseph F. Solus
- Vanderbilt Ctr for Arrhythmia Research & Therapeutics (VanCART), Division of Clinical Pharmacology, Dept of Medicine, Nashville, TN
| | | | | | | | | | - Brendan J. Floyd
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Kyla Dunn
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Victoria N. Parikh
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Henry Chubb
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Mark J. Perrin
- Dept of Genomic Medicine, Royal Melbourne Hospital, Victoria, Australia
| | - Dan M. Roden
- Depts of Pharmacology, and Biomedical Informatics, Vanderbilt Univ Medical Ctr, Nashville, TN
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Andrew M. Glazer
- Vanderbilt Ctr for Arrhythmia Research & Therapeutics (VanCART), Division of Clinical Pharmacology, Dept of Medicine, Nashville, TN
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Gallego-Delgado M, Cámara-Checa A, Rubio-Alarcón M, Heredero-Jung D, de la Fuente-Blanco L, Rapún J, Plata-Izquierdo B, Pérez-Martín S, Cebrián J, Moreno de Redrojo L, García-Berrocal B, Delpón E, Sánchez PL, Villacorta E, Caballero R. Variable Penetrance and Expressivity of a Rare Pore Loss-of-Function Mutation (p.L889V) of Nav1.5 Channels in Three Spanish Families. Int J Mol Sci 2024; 25:4686. [PMID: 38731905 PMCID: PMC11083067 DOI: 10.3390/ijms25094686] [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: 02/27/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 05/13/2024] Open
Abstract
A novel rare mutation in the pore region of Nav1.5 channels (p.L889V) has been found in three unrelated Spanish families that produces quite diverse phenotypic manifestations (Brugada syndrome, conduction disease, dilated cardiomyopathy, sinus node dysfunction, etc.) with variable penetrance among families. We clinically characterized the carriers and recorded the Na+ current (INa) generated by p.L889V and native (WT) Nav1.5 channels, alone or in combination, to obtain further insight into the genotypic-phenotypic relationships in patients carrying SCN5A mutations and in the molecular determinants of the Nav1.5 channel function. The variant produced a strong dominant negative effect (DNE) since the peak INa generated by p.L889V channels expressed in Chinese hamster ovary cells, either alone (-69.4 ± 9.0 pA/pF) or in combination with WT (-62.2 ± 14.6 pA/pF), was significantly (n ≥ 17, p < 0.05) reduced compared to that generated by WT channels alone (-199.1 ± 44.1 pA/pF). The mutation shifted the voltage dependence of channel activation and inactivation to depolarized potentials, did not modify the density of the late component of INa, slightly decreased the peak window current, accelerated the recovery from fast and slow inactivation, and slowed the induction kinetics of slow inactivation, decreasing the fraction of channels entering this inactivated state. The membrane expression of p.L889V channels was low, and in silico molecular experiments demonstrated profound alterations in the disposition of the pore region of the mutated channels. Despite the mutation producing a marked DNE and reduction in the INa and being located in a critical domain of the channel, its penetrance and expressivity are quite variable among the carriers. Our results reinforce the argument that the incomplete penetrance and phenotypic variability of SCN5A loss-of-function mutations are the result of a combination of multiple factors, making it difficult to predict their expressivity in the carriers despite the combination of clinical, genetic, and functional studies.
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Affiliation(s)
- María Gallego-Delgado
- Department of Cardiology, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain; (M.G.-D.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
| | - Anabel Cámara-Checa
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - Marcos Rubio-Alarcón
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - David Heredero-Jung
- Department of Biochemistry, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain
| | - Laura de la Fuente-Blanco
- Department of Cardiology, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain; (M.G.-D.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
| | - Josu Rapún
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - Beatriz Plata-Izquierdo
- Department of Pediatrics, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y Leon (SACYL), CIBERCV, 37007 Salamaca, Spain;
| | - Sara Pérez-Martín
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - Jorge Cebrián
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - Lucía Moreno de Redrojo
- Department of Cardiology, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain; (M.G.-D.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
| | - Belén García-Berrocal
- Department of Biochemistry, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain
| | - Eva Delpón
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
| | - Pedro L. Sánchez
- Department of Cardiology, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain; (M.G.-D.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
| | - Eduardo Villacorta
- Department of Cardiology, CSUR Cardiopatías Familiares, Institute of Biomedical Research of Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), 37007 Salamaca, Spain; (M.G.-D.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
| | - Ricardo Caballero
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain (M.R.-A.); (J.R.); (J.C.); (R.C.)
- Department of Pharmacology, School of Medicine, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, 28040 Madrid, Spain
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O'Neill MJ, Yang T, Laudeman J, Calandranis M, Solus J, Roden DM, Glazer AM. ParSE-seq: A Calibrated Multiplexed Assay to Facilitate the Clinical Classification of Putative Splice-altering Variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.04.23295019. [PMID: 37732247 PMCID: PMC10508793 DOI: 10.1101/2023.09.04.23295019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Background Interpreting the clinical significance of putative splice-altering variants outside 2-base pair canonical splice sites remains difficult without functional studies. Methods We developed Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed minigene-based assay, to test variant effects on RNA splicing quantified by high-throughput sequencing. We studied variants in SCN5A, an arrhythmia-associated gene which encodes the major cardiac voltage-gated sodium channel. We used the computational tool SpliceAI to prioritize exonic and intronic candidate splice variants, and ClinVar to select benign and pathogenic control variants. We generated a pool of 284 barcoded minigene plasmids, transfected them into Human Embryonic Kidney (HEK293) cells and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), sequenced the resulting pools of splicing products, and calibrated the assay to the American College of Medical Genetics and Genomics scheme. Variants were interpreted using the calibrated functional data, and experimental data were compared to SpliceAI predictions. We further studied some splice-altering missense variants by cDNA-based automated patch clamping (APC) in HEK cells and assessed splicing and sodium channel function in CRISPR-edited iPSC-CMs. Results ParSE-seq revealed the splicing effect of 224 SCN5A variants in iPSC-CMs and 244 variants in HEK293 cells. The scores between the cell types were highly correlated (R2=0.84). In iPSCs, the assay had concordant scores for 21/22 benign/likely benign and 24/25 pathogenic/likely pathogenic control variants from ClinVar. 43/112 exonic variants and 35/70 intronic variants with determinate scores disrupted splicing. 11 of 42 variants of uncertain significance were reclassified, and 29 of 34 variants with conflicting interpretations were reclassified using the functional data. SpliceAI computational predictions correlated well with experimental data (AUC = 0.96). We identified 20 unique SCN5A missense variants that disrupted splicing, and 2 clinically observed splice-altering missense variants of uncertain significance had normal function when tested with the cDNA-based APC assay. A splice-altering intronic variant detected by ParSE-seq, c.1891-5C>G, also disrupted splicing and sodium current when introduced into iPSC-CMs at the endogenous locus by CRISPR editing. Conclusions ParSE-seq is a calibrated, multiplexed, high-throughput assay to facilitate the classification of candidate splice-altering variants.
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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
| | - Julie Laudeman
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Maria Calandranis
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joseph Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
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4
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Verkerk AO, Wilders R. The Action Potential Clamp Technique as a Tool for Risk Stratification of Sinus Bradycardia Due to Loss-of-Function Mutations in HCN4: An In Silico Exploration Based on In Vitro and In Vivo Data. Biomedicines 2023; 11:2447. [PMID: 37760888 PMCID: PMC10525944 DOI: 10.3390/biomedicines11092447] [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: 07/11/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
These days, in vitro functional analysis of gene variants is becoming increasingly important for risk stratification of cardiac ion channelopathies. So far, such risk stratification has been applied to SCN5A, KCNQ1, and KCNH2 gene variants associated with Brugada syndrome and long QT syndrome types 1 and 2, respectively, but risk stratification of HCN4 gene variants related to sick sinus syndrome has not yet been performed. HCN4 is the gene responsible for the hyperpolarization-activated 'funny' current If, which is an important modulator of the spontaneous diastolic depolarization underlying the sinus node pacemaker activity. In the present study, we carried out a risk classification assay on those loss-of-function mutations in HCN4 for which in vivo as well as in vitro data have been published. We used the in vitro data to compute the charge carried by If (Qf) during the diastolic depolarization phase of a prerecorded human sinus node action potential waveform and assessed the extent to which this Qf predicts (1) the beating rate of the comprehensive Fabbri-Severi model of a human sinus node cell with mutation-induced changes in If and (2) the heart rate observed in patients carrying the associated mutation in HCN4. The beating rate of the model cell showed a very strong correlation with Qf from the simulated action potential clamp experiments (R2 = 0.95 under vagal tone). The clinically observed minimum or resting heart rates showed a strong correlation with Qf (R2 = 0.73 and R2 = 0.71, respectively). While a translational perspective remains to be seen, we conclude that action potential clamp on transfected cells, without the need for further voltage clamp experiments and data analysis to determine individual biophysical parameters of If, is a promising tool for risk stratification of sinus bradycardia due to loss-of-function mutations in HCN4. In combination with an If blocker, this tool may also prove useful when applied to human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) obtained from mutation carriers and non-carriers.
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Affiliation(s)
- Arie O. Verkerk
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Ronald Wilders
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
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Salvarani N, Peretto G, Silvia C, Villatore A, Thairi C, Santoni A, Galli C, Carrera P, Sala S, Benedetti S, Di Pasquale E, Di Resta C. Functional Characterisation of the Rare SCN5A p.E1225K Variant, Segregating in a Brugada Syndrome Familial Case, in Human Cardiomyocytes from Pluripotent Stem Cells. Int J Mol Sci 2023; 24:ijms24119548. [PMID: 37298497 DOI: 10.3390/ijms24119548] [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: 04/19/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Brugada syndrome (BrS) is an inherited autosomal dominant cardiac channelopathy. Pathogenic rare mutations in the SCN5A gene, encoding the alpha-subunit of the voltage-dependent cardiac Na+ channel protein (Nav1.5), are identified in 20% of BrS patients, affecting the correct function of the channel. To date, even though hundreds of SCN5A variants have been associated with BrS, the underlying pathogenic mechanisms are still unclear in most cases. Therefore, the functional characterization of the SCN5A BrS rare variants still represents a major hurdle and is fundamental to confirming their pathogenic effect. Human cardiomyocytes (CMs) differentiated from pluripotent stem cells (PSCs) have been extensively demonstrated to be reliable platforms for investigating cardiac diseases, being able to recapitulate specific traits of disease, including arrhythmic events and conduction abnormalities. Based on this, in this study, we performed a functional analysis of the BrS familial rare variant NM_198056.2:c.3673G>A (NP_932173.1:p.Glu1225Lys), which has been never functionally characterized before in a cardiac-relevant context, as the human cardiomyocyte. Using a specific lentiviral vector encoding a GFP-tagged SCN5A gene carrying the specific c.3673G>A variant and CMs differentiated from control PSCs (PSC-CMs), we demonstrated an impairment of the mutated Nav1.5, thus suggesting the pathogenicity of the rare BrS detected variant. More broadly, our work supports the application of PSC-CMs for the assessment of the pathogenicity of gene variants, the identification of which is increasing exponentially due to the advances in next-generation sequencing methods and their massive use in genetic testing.
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Affiliation(s)
- Nicolò Salvarani
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, 20138 Milan, Italy
- IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Giovanni Peretto
- Department of Cardiac Electrophysiology and Arrhythmology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Faculty of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Crasto Silvia
- IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Andrea Villatore
- Faculty of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Cecilia Thairi
- IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Anna Santoni
- Genomic Unit for the Diagnosis of Human Pathologies, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Camilla Galli
- IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Paola Carrera
- Genomic Unit for the Diagnosis of Human Pathologies, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Laboratory of Clinical Molecular Biology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Simone Sala
- Department of Cardiac Electrophysiology and Arrhythmology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Benedetti
- Genomic Unit for the Diagnosis of Human Pathologies, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Elisa Di Pasquale
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, 20138 Milan, Italy
- IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Chiara Di Resta
- Faculty of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Genomic Unit for the Diagnosis of Human Pathologies, IRCCS San Raffaele Hospital, 20132 Milan, Italy
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6
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Melgari D, Calamaio S, Frosio A, Prevostini R, Anastasia L, Pappone C, Rivolta I. Automated Patch-Clamp and Induced Pluripotent Stem Cell-Derived Cardiomyocytes: A Synergistic Approach in the Study of Brugada Syndrome. Int J Mol Sci 2023; 24:ijms24076687. [PMID: 37047659 PMCID: PMC10095337 DOI: 10.3390/ijms24076687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
The development of high-throughput automated patch-clamp technology is a recent breakthrough in the field of Brugada syndrome research. Brugada syndrome is a heart disorder marked by abnormal electrocardiographic readings and an elevated risk of sudden cardiac death due to arrhythmias. Various experimental models, developed either in animals, cell lines, human tissue or computational simulation, play a crucial role in advancing our understanding of this condition, and developing effective treatments. In the perspective of the pathophysiological role of ion channels and their pharmacology, automated patch-clamp involves a robotic system that enables the simultaneous recording of electrical activity from multiple single cells at once, greatly improving the speed and efficiency of data collection. By combining this approach with the use of patient-derived cardiomyocytes, researchers are gaining a more comprehensive view of the underlying mechanisms of heart disease. This has led to the development of more effective treatments for those affected by cardiovascular conditions.
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Affiliation(s)
- Dario Melgari
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
| | - Serena Calamaio
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
| | - Anthony Frosio
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
| | - Rachele Prevostini
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
- Faculty of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
- Faculty of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Arrhythmology Department, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Ilaria Rivolta
- Institute of Molecular and Translational Cardiology (IMTC), San Donato Milanese, 20097 Milan, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore, 48, 20900 Monza, Italy
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7
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O'Neill MJ, Muhammad A, Li B, Wada Y, Hall L, Solus JF, Short L, Roden DM, Glazer AM. Dominant negative effects of SCN5A missense variants. Genet Med 2022; 24:1238-1248. [PMID: 35305865 DOI: 10.1016/j.gim.2022.02.010] [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: 10/12/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Up to 30% of patients with Brugada syndrome (BrS) carry loss-of-function (LoF) variants in the cardiac sodium channel gene SCN5A encoding for the protein NaV1.5. Recent studies suggested that NaV1.5 can dimerize, and some variants exert dominant negative effects. In this study, we sought to explore the generality of missense variant NaV1.5 dominant negative effects and their clinical severity. METHODS We identified 35 LoF variants (<10% of wild type [WT] peak current) and 15 partial LoF variants (10%-50% of WT peak current) that we assessed for dominant negative effects. SCN5A variants were studied in HEK293T cells, alone or in heterozygous coexpression with WT SCN5A using automated patch clamp. To assess the clinical risk, we compared the prevalence of dominant negative vs putative haploinsufficient (frameshift, splice, or nonsense) variants in a BrS consortium and the Genome Aggregation Database population database. RESULTS In heterozygous expression with WT, 32 of 35 LoF and 6 of 15 partial LoF variants showed reduction to <75% of WT-alone peak current, showing a dominant negative effect. Individuals with dominant negative LoF variants had an elevated disease burden compared with the individuals with putative haploinsufficient variants (2.7-fold enrichment in BrS cases, P = .019). CONCLUSION Most SCN5A missense LoF variants exert a dominant negative effect. This class of variant confers an especially high burden of BrS.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Ayesha Muhammad
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Bian Li
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Lynn Hall
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Joseph F Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Laura Short
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN; Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN; Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN.
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8
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Abstract
Brugada syndrome is a heritable channelopathy characterized by a peculiar electrocardiogram (ECG) pattern and increased risk of cardiac arrhythmias and sudden death. The arrhythmias originate because of an imbalance between the repolarizing and depolarizing currents that modulate the cardiac action potential. Even if an overt structural cardiomyopathy is not typical of Brugada syndrome, fibrosis and structural changes in the right ventricle contribute to a conduction slowing, which ultimately facilitates ventricular arrhythmias. Currently, Mendelian autosomal dominant transmission is detected in less than 25% of all clinical confirmed cases. Although 23 genes have been associated with the condition, only SCN5A, encoding the cardiac sodium channel, is considered clinically actionable and disease causing. The limited monogenic inheritance has pointed toward new perspectives on the possible complex genetic architecture of the disease, involving polygenic inheritance and a polygenic risk score that can influence penetrance and risk stratification. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marina Cerrone
- Leon H. Charney Division of Cardiology, Grossman School of Medicine, New York University, New York, NY, USA;
| | - Sarah Costa
- Department of Internal Medicine, Kantonsspital Baden, Baden, Switzerland
| | - Mario Delmar
- Leon H. Charney Division of Cardiology, Grossman School of Medicine, New York University, New York, NY, USA;
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9
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Tomar S, Klinzing DC, Chen CK, Gan LH, Moscarello T, Reuter C, Ashley EA, Foo R. Causative Variants for Inherited Cardiac Conditions in a Southeast Asian Population Cohort. Circ Genom Precis Med 2022; 15:e003536. [DOI: 10.1161/circgen.121.003536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Variable penetrance and late-onset phenotypes are key challenges for classifying causal as well as incidental findings in inherited cardiac conditions. Allele frequencies of variants in ancestry-specific populations, along with clinical variant analysis and interpretation, are critical to determine their true significance.
Methods:
Here, we carefully reviewed and classified variants in genes associated with inherited cardiac conditions based on a population whole-genome sequencing cohort of 4810 Singaporeans representing Southeast Asian ancestries.
Results:
Eighty-nine (1.85%) individuals carried either pathogenic or likely pathogenic variants across 25 genes. Forty-six (51.7%) had variants in causal genes for familial hyperlipidemia, but there were also recurrent variants in
SCN5A
and
MYBPC3
, causal genes for inherited arrhythmia and cardiomyopathy, which, despite previous reports, we determined to lack criteria for pathogenicity.
Conclusions:
Our findings highlight the incidence of disease-related variants in inherited cardiac conditions and emphasize the value of large-scale sequencing in specific ancestries. Follow-up detailed phenotyping and analysis of pedigrees are crucial because assigning pathogenicity will significantly affect clinical management for individuals and their family members.
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Affiliation(s)
- Swati Tomar
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University Singapore (S.T., D.C.K., C.K.C., L.H.G., R.F.)
- Cardiovascular Research Institute, National University Heart Centre (S.T., D.C.K., C.K.C., L.H.G., R.F.), National University Health System, Singapore
| | - David C. Klinzing
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University Singapore (S.T., D.C.K., C.K.C., L.H.G., R.F.)
- Cardiovascular Research Institute, National University Heart Centre (S.T., D.C.K., C.K.C., L.H.G., R.F.), National University Health System, Singapore
- Khoo Teck Puat National University Children’s Medical Institute (C.K.C.), National University Health System, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Singapore, Singapore (C.K.C.)
| | - Ching Kit Chen
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University Singapore (S.T., D.C.K., C.K.C., L.H.G., R.F.)
- Cardiovascular Research Institute, National University Heart Centre (S.T., D.C.K., C.K.C., L.H.G., R.F.), National University Health System, Singapore
| | - Louis Hanqiang Gan
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University Singapore (S.T., D.C.K., C.K.C., L.H.G., R.F.)
- Cardiovascular Research Institute, National University Heart Centre (S.T., D.C.K., C.K.C., L.H.G., R.F.), National University Health System, Singapore
| | - Tia Moscarello
- Centre for Inherited Cardiovascular Disease, Stanford University Medical Center, CA (T.M., C.R., E.A.A.)
| | - Chloe Reuter
- Centre for Inherited Cardiovascular Disease, Stanford University Medical Center, CA (T.M., C.R., E.A.A.)
| | - Euan A. Ashley
- Centre for Inherited Cardiovascular Disease, Stanford University Medical Center, CA (T.M., C.R., E.A.A.)
| | - Roger Foo
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University Singapore (S.T., D.C.K., C.K.C., L.H.G., R.F.)
- Cardiovascular Research Institute, National University Heart Centre (S.T., D.C.K., C.K.C., L.H.G., R.F.), National University Health System, Singapore
- Genome Institute of Singapore (R.F.)
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10
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Glazer AM, Davogustto G, Shaffer CM, Vanoye CG, Desai RR, Farber-Eger EH, Dikilitas O, Shang N, Pacheco JA, Yang T, Muhammad A, Mosley JD, Van Driest SL, Wells QS, Shaffer LL, Kalash OR, Wada Y, Bland S, Yoneda ZT, Mitchell DW, Kroncke BM, Kullo IJ, Jarvik GP, Gordon AS, Larson EB, Manolio TA, Mirshahi T, Luo JZ, Schaid D, Namjou B, Alsaied T, Singh R, Singhal A, Liu C, Weng C, Hripcsak G, Ralston JD, McNally EM, Chung WK, Carrell DS, Leppig KA, Hakonarson H, Sleiman P, Sohn S, Glessner J, Denny J, Wei WQ, George AL, Shoemaker MB, Roden DM. Arrhythmia Variant Associations and Reclassifications in the eMERGE-III Sequencing Study. Circulation 2022; 145:877-891. [PMID: 34930020 PMCID: PMC8940719 DOI: 10.1161/circulationaha.121.055562] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Sequencing Mendelian arrhythmia genes in individuals without an indication for arrhythmia genetic testing can identify carriers of pathogenic or likely pathogenic (P/LP) variants. However, the extent to which these variants are associated with clinically meaningful phenotypes before or after return of variant results is unclear. In addition, the majority of discovered variants are currently classified as variants of uncertain significance, limiting clinical actionability. METHODS The eMERGE-III study (Electronic Medical Records and Genomics Phase III) is a multicenter prospective cohort that included 21 846 participants without previous indication for cardiac genetic testing. Participants were sequenced for 109 Mendelian disease genes, including 10 linked to arrhythmia syndromes. Variant carriers were assessed with electronic health record-derived phenotypes and follow-up clinical examination. Selected variants of uncertain significance (n=50) were characterized in vitro with automated electrophysiology experiments in HEK293 cells. RESULTS As previously reported, 3.0% of participants had P/LP variants in the 109 genes. Herein, we report 120 participants (0.6%) with P/LP arrhythmia variants. Compared with noncarriers, arrhythmia P/LP carriers had a significantly higher burden of arrhythmia phenotypes in their electronic health records. Fifty-four participants had variant results returned. Nineteen of these 54 participants had inherited arrhythmia syndrome diagnoses (primarily long-QT syndrome), and 12 of these 19 diagnoses were made only after variant results were returned (0.05%). After in vitro functional evaluation of 50 variants of uncertain significance, we reclassified 11 variants: 3 to likely benign and 8 to P/LP. CONCLUSIONS Genome sequencing in a large population without indication for arrhythmia genetic testing identified phenotype-positive carriers of variants in congenital arrhythmia syndrome disease genes. As the genomes of large numbers of people are sequenced, the disease risk from rare variants in arrhythmia genes can be assessed by integrating genomic screening, electronic health record phenotypes, and in vitro functional studies. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier; NCT03394859.
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Affiliation(s)
| | | | | | | | | | | | | | - Ning Shang
- Columbia University Irving Medical Center, New York NY
| | | | - Tao Yang
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | | | | | - Yuko Wada
- Vanderbilt University Medical Center, Nashville TN
| | - Sarah Bland
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | - Gail P. Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | - Bahram Namjou
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | - Tarek Alsaied
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | | | | | - Cong Liu
- Columbia University Irving Medical Center, New York NY
| | - Chunhua Weng
- Columbia University Irving Medical Center, New York NY
| | | | - James D. Ralston
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville TN
| | | | | | - Dan M. Roden
- Vanderbilt University Medical Center, Nashville TN
- Correspondence should be addressed to Dan M. Roden, MD, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232,
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11
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Daimi H, Lozano-Velasco E, Aranega A, Franco D. Genomic and Non-Genomic Regulatory Mechanisms of the Cardiac Sodium Channel in Cardiac Arrhythmias. Int J Mol Sci 2022; 23:1381. [PMID: 35163304 PMCID: PMC8835759 DOI: 10.3390/ijms23031381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Nav1.5 is the predominant cardiac sodium channel subtype, encoded by the SCN5A gene, which is involved in the initiation and conduction of action potentials throughout the heart. Along its biosynthesis process, Nav1.5 undergoes strict genomic and non-genomic regulatory and quality control steps that allow only newly synthesized channels to reach their final membrane destination and carry out their electrophysiological role. These regulatory pathways are ensured by distinct interacting proteins that accompany the nascent Nav1.5 protein along with different subcellular organelles. Defects on a large number of these pathways have a tremendous impact on Nav1.5 functionality and are thus intimately linked to cardiac arrhythmias. In the present review, we provide current state-of-the-art information on the molecular events that regulate SCN5A/Nav1.5 and the cardiac channelopathies associated with defects in these pathways.
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Affiliation(s)
- Houria Daimi
- Biochemistry and Molecular Biology Laboratory, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Estefanía Lozano-Velasco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (A.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento, 34, 18016 Granada, Spain
| | - Amelia Aranega
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (A.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento, 34, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (A.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento, 34, 18016 Granada, Spain
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12
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Papagiannis J, Yang T, Glazer AM, Tisma-Dupanovic S, Avramidis D, Kannankeril PJ, Viskin S, Walsh EP, Roden DM. Incessant atrial and ventricular tachycardias associated with an SCN5A mutation. HeartRhythm Case Rep 2021; 7:806-811. [PMID: 34987964 PMCID: PMC8695285 DOI: 10.1016/j.hrcr.2021.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Ishikawa T, Kimoto H, Mishima H, Yamagata K, Ogata S, Aizawa Y, Hayashi K, Morita H, Nakajima T, Nakano Y, Nagase S, Murakoshi N, Kowase S, Ohkubo K, Aiba T, Morimoto S, Ohno S, Kamakura S, Nogami A, Takagi M, Karakachoff M, Dina C, Schott JJ, Yoshiura KI, Horie M, Shimizu W, Nishimura K, Kusano K, Makita N. Functionally validated SCN5A variants allow interpretation of pathogenicity and prediction of lethal events in Brugada syndrome. Eur Heart J 2021; 42:2854-2863. [PMID: 34219138 DOI: 10.1093/eurheartj/ehab254] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/09/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
AIMS The prognostic value of genetic variants for predicting lethal arrhythmic events (LAEs) in Brugada syndrome (BrS) remains controversial. We investigated whether the functional curation of SCN5A variations improves prognostic predictability. METHODS AND RESULTS Using a heterologous expression system and whole-cell patch clamping, we functionally characterized 22 variants of unknown significance (VUSs) among 55 SCN5A mutations previously curated using in silico prediction algorithms in the Japanese BrS registry (n = 415). According to the loss-of-function (LOF) properties, SCN5A mutation carriers (n = 60) were divided into two groups: LOF-SCN5A mutations and non-LOF SCN5A variations. Functionally proven LOF-SCN5A mutation carriers (n = 45) showed significantly severer electrocardiographic conduction abnormalities and worse prognosis associated with earlier manifestations of LAEs (7.9%/year) than in silico algorithm-predicted SCN5A carriers (5.1%/year) or all BrS probands (2.5%/year). Notably, non-LOF SCN5A variation carriers (n = 15) exhibited no LAEs during the follow-up period. Multivariate analysis demonstrated that only LOF-SCN5A mutations and a history of aborted cardiac arrest were significant predictors of LAEs. Gene-based association studies using whole-exome sequencing data on another independent SCN5A mutation-negative BrS cohort (n = 288) showed no significant enrichment of rare variants in 16 985 genes including 22 non-SCN5A BrS-associated genes as compared with controls (n = 372). Furthermore, rare variations of non-SCN5A BrS-associated genes did not affect LAE-free survival curves. CONCLUSION In vitro functional validation is key to classifying the pathogenicity of SCN5A VUSs and for risk stratification of genetic predictors of LAEs. Functionally proven LOF-SCN5A mutations are genetic burdens of sudden death in BrS, but evidence for other BrS-associated genes is elusive.
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Affiliation(s)
- Taisuke Ishikawa
- Omics Research Center, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Hiroki Kimoto
- Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 8528523, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 8528523, Japan
| | - Kenichiro Yamagata
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Soshiro Ogata
- Department of Preventive Medicine and Epidemiology, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Yoshiyasu Aizawa
- Department of Cardiovascular Medicine, International University of Health and Welfare, 4-3 Kozunomori, Narita 2860048, Japan
| | - Kenshi Hayashi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1 Takaramachi, Kanazawa 9208641, Japan
| | - Hiroshi Morita
- Department of Cardiovascular Therapeutics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Okayama 7008558, Japan
| | - Tadashi Nakajima
- Department of Cardiovascular Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showamachi, Maebashi 3710034, Japan
| | - Yukiko Nakano
- Department of Cardiovascular Medicine, Hiroshima University, 1-2-3 Kasumi, Hiroshima 7348551, Japan
| | - Satoshi Nagase
- Department of Advanced Arrhythmia and Translational Medical Science, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Nobuyuki Murakoshi
- Department of Cardiology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 3058575, Japan
| | - Shinya Kowase
- Department of Heart Rhythm Management, Yokohama Rosai Hospital, 3211 Kozukue-Cho, Yokohama 2220036, Japan
| | - Kimie Ohkubo
- Division of Cardiology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamimachi, Tokyo 1738610, Japan
| | - Takeshi Aiba
- Department of Clinical Laboratory, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Shimpei Morimoto
- Innovation Platform & Office for Precision Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 8528501, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Shiro Kamakura
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Akihiko Nogami
- Department of Cardiology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 3058575, Japan
| | - Masahiko Takagi
- Division of Cardiac Arrhythmia, Kansai Medical University, 10-15 Fumizonomachi, Moriguchi 5708507, Japan
| | - Matilde Karakachoff
- L'institut du Thorax, CHU Nantes, 1 Place Alexis-Ricordeau, Nantes 44007, France
| | - Christian Dina
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, 8 Quai Moncousu, Nantes 44007, France
| | - Jean-Jacques Schott
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, 8 Quai Moncousu, Nantes 44007, France
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 8528523, Japan
| | - Minoru Horie
- Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Setatsukiwa-cho, Ohtsu 5202192, Japan
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Nippon Medical School, 1-1-5 Sendagi, Tokyo 1138603, Japan
| | - Kunihiro Nishimura
- Department of Preventive Medicine and Epidemiology, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Kengo Kusano
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
| | - Naomasa Makita
- Omics Research Center, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita 5648565, Japan
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14
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Arana-Rueda E, Pezzotti MR, Pedrote A, Acosta J, Frutos-López M, Varela LM, García-Fernández N, Castellano A. Brugada syndrome masked by complete left bundle branch block: A clinical and functional study of its association with the p.1449Y>H SCN5A variant. J Cardiovasc Electrophysiol 2021; 32:2785-2790. [PMID: 34411358 DOI: 10.1111/jce.15215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 11/27/2022]
Abstract
SCN5A gene variants are associated with both Brugada syndrome and conduction disturbances, sometimes expressing an overlapping phenotype. Functional consequences of SCN5A variants assessed by patch-clamp electrophysiology are particularly beneficial for correct pathogenic classification and are related to disease penetrance and severity. Here, we identify a novel SCN5A loss of function variant, p.1449Y>H, which presented with high penetrance and complete left bundle branch block, totally masking the typical findings on the electrocardiogram. We highlight the possibility of this overlap combination that makes impossible an electrocardiographic diagnosis and, through a functional analysis, associate the p.1449Y>H variant to SCN5A pathogenicity.
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Affiliation(s)
- Eduardo Arana-Rueda
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain.,Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - María R Pezzotti
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Alonso Pedrote
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Juan Acosta
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Manuel Frutos-López
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Lourdes-María Varela
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Noelia García-Fernández
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Antonio Castellano
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain.,CIBERCV, ISCIII, Madrid, Spain
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15
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Functional cross-talk between phosphorylation and disease-causing mutations in the cardiac sodium channel Na v1.5. Proc Natl Acad Sci U S A 2021; 118:2025320118. [PMID: 34373326 PMCID: PMC8379932 DOI: 10.1073/pnas.2025320118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The cardiac sodium channel (Nav1.5) is crucial for generating a regular heartbeat. It is thus not surprising that Nav1.5 mutations have been linked to life-threatening arrhythmias. Interestingly, Nav1.5 activity can also be altered by posttranslational modifications, such as tyrosine phosphorylation. Our combination of protein engineering and molecular modeling has revealed that the detrimental effect of a long QT3 patient mutation is only exposed when a proximal tyrosine is phosphorylated. This suggests a dynamic cross-talk between the genetic mutation and a neighboring phosphorylation, a phenomenon that could be important in other classes of proteins. Additionally, we show that phosphorylation can affect the channel’s sensitivity toward clinically relevant drugs, a finding that may prove important when devising patient-specific treatment plans. The voltage-gated sodium channel Nav1.5 initiates the cardiac action potential. Alterations of its activation and inactivation properties due to mutations can cause severe, life-threatening arrhythmias. Yet despite intensive research efforts, many functional aspects of this cardiac channel remain poorly understood. For instance, Nav1.5 undergoes extensive posttranslational modification in vivo, but the functional significance of these modifications is largely unexplored, especially under pathological conditions. This is because most conventional approaches are unable to insert metabolically stable posttranslational modification mimics, thus preventing a precise elucidation of the contribution by these modifications to channel function. Here, we overcome this limitation by using protein semisynthesis of Nav1.5 in live cells and carry out complementary molecular dynamics simulations. We introduce metabolically stable phosphorylation mimics on both wild-type (WT) and two pathogenic long-QT mutant channel backgrounds and decipher functional and pharmacological effects with unique precision. We elucidate the mechanism by which phosphorylation of Y1495 impairs steady-state inactivation in WT Nav1.5. Surprisingly, we find that while the Q1476R patient mutation does not affect inactivation on its own, it enhances the impairment of steady-state inactivation caused by phosphorylation of Y1495 through enhanced unbinding of the inactivation particle. We also show that both phosphorylation and patient mutations can impact Nav1.5 sensitivity toward the clinically used antiarrhythmic drugs quinidine and ranolazine, but not flecainide. The data highlight that functional effects of Nav1.5 phosphorylation can be dramatically amplified by patient mutations. Our work is thus likely to have implications for the interpretation of mutational phenotypes and the design of future drug regimens.
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16
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Tsumoto K, Ashihara T, Naito N, Shimamoto T, Amano A, Kurata Y, Kurachi Y. Specific decreasing of Na + channel expression on the lateral membrane of cardiomyocytes causes fatal arrhythmias in Brugada syndrome. Sci Rep 2020; 10:19964. [PMID: 33203944 PMCID: PMC7673036 DOI: 10.1038/s41598-020-76681-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Reduced cardiac sodium (Na+) channel current (INa) resulting from the loss-of-function of Na+ channel is a major cause of lethal arrhythmias in Brugada syndrome (BrS). Inspired by previous experimental studies which showed that in heart diseases INa was reduced along with expression changes in Na+ channel within myocytes, we hypothesized that the local decrease in INa caused by the alteration in Na+ channel expression in myocytes leads to the occurrence of phase-2 reentry, the major triggering mechanism of lethal arrhythmias in BrS. We constructed in silico human ventricular myocardial strand and ring models, and examined whether the Na+ channel expression changes in each myocyte cause the phase-2 reentry in BrS. Reducing Na+ channel expression in the lateral membrane of each myocyte caused not only the notch-and-dome but also loss-of-dome type action potentials and slowed conduction, both of which are typically observed in BrS patients. Furthermore, the selective reduction in Na+ channels on the lateral membrane of each myocyte together with spatial tissue heterogeneity of Na+ channel expression caused the phase-2 reentry and phase-2 reentry-mediated reentrant arrhythmias. Our data suggest that the BrS phenotype is strongly influenced by expression abnormalities as well as genetic abnormalities of Na+ channels.
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Affiliation(s)
- Kunichika Tsumoto
- Department of Physiology II, Kanazawa Medical University, 1-1 Daigaku, Uchinada, 920-0293, Japan.
- Department of Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, 565-0871, Japan.
| | - Takashi Ashihara
- Department of Medical Informatics and Biomedical Engineering, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, 520-2192, Japan
| | - Narumi Naito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Japan
| | - Takao Shimamoto
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Japan
| | - Akira Amano
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Japan
| | - Yasutaka Kurata
- Department of Physiology II, Kanazawa Medical University, 1-1 Daigaku, Uchinada, 920-0293, Japan
| | - Yoshihisa Kurachi
- Department of Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, 565-0871, Japan
- Glocal Center for Medical Engineering and Informatics, Osaka University, 2-2 Yamada-oka, Suita, 565-0871, Japan
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17
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Pearman CM, Denham NC, Mills RW, Ding WY, Modi SS, Hall MCS, Todd DM, Mahida S. Relationship between sodium channel function and clinical phenotype in SCN5A variants associated with Brugada syndrome. Hum Mutat 2020; 41:2195-2204. [PMID: 33131149 PMCID: PMC7756571 DOI: 10.1002/humu.24128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/23/2020] [Accepted: 10/09/2020] [Indexed: 12/19/2022]
Abstract
The identification of a pathogenic SCN5A variant confers an increased risk of conduction defects and ventricular arrhythmias (VA) in Brugada syndrome (BrS). However, specific aspects of sodium channel function that influence clinical phenotype have not been defined. A systematic literature search identified SCN5A variants associated with BrS. Sodium current (INa) functional parameters (peak current, decay, steady‐state activation and inactivation, and recovery from inactivation) and clinical features (conduction abnormalities [CA], spontaneous VA or family history of sudden cardiac death [SCD], and spontaneous BrS electrocardiogram [ECG]) were extracted. A total of 561 SCN5A variants associated with BrS were identified, for which data on channel function and clinical phenotype were available in 142. In the primary analysis, no relationship was found between any aspect of channel function and CA, VA/SCD, or spontaneous BrS ECG pattern. Sensitivity analyses including only variants graded pathogenic or likely pathogenic suggested that reduction in peak current and positive shift in steady‐state activation were weakly associated with CA and VA/SCD, although sensitivity and specificity remained low. The relationship between in vitro assessment of channel function and BrS clinical phenotype is weak. The assessment of channel function does not enhance risk stratification. Caution is needed when extrapolating functional testing to the likelihood of variant pathogenicity.
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Affiliation(s)
- Charles M Pearman
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK.,Unit of Cardiac Physiology, Division of Cardiovascular Sciences, Manchester Academic Health Science Centre, Core Technology Facility, University of Manchester, Manchester, UK
| | - Nathan C Denham
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK.,Unit of Cardiac Physiology, Division of Cardiovascular Sciences, Manchester Academic Health Science Centre, Core Technology Facility, University of Manchester, Manchester, UK
| | - Robert W Mills
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Wern Y Ding
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK.,Liverpool Centre for Cardiovascular Science, Faculty of Life Sciences, University of Liverpool, Liverpool, UK
| | - Simon S Modi
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Mark C S Hall
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Derick M Todd
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Saagar Mahida
- Department of Cardiac Electrophysiology and Inherited Cardiac Conditions, Liverpool Heart and Chest Hospital, Liverpool, UK.,Liverpool Centre for Cardiovascular Science, Faculty of Life Sciences, University of Liverpool, Liverpool, UK
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18
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Functional evaluation of gene mutations in Long QT Syndrome: strength of evidence from in vitro assays for deciphering variants of uncertain significance. JOURNAL OF CONGENITAL CARDIOLOGY 2020. [DOI: 10.1186/s40949-020-00037-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Genetic screening is now commonplace for patients suspected of having inherited cardiac conditions. Variants of uncertain significance (VUS) in disease-associated genes pose problems for the diagnostician and reliable methods for evaluating VUS function are required. Although function is difficult to interrogate for some genes, heritable channelopathies have established mechanisms that should be amenable to well-validated evaluation techniques.
The cellular electrophysiology techniques of ‘voltage-’ and ‘patch-’ clamp have a long history of successful use and have been central to identifying both the roles of genes involved in different forms of congenital Long QT Syndrome (LQTS) and the mechanisms by which mutations lead to aberrant ion channel function underlying clinical phenotypes. This is particularly evident for KCNQ1, KCNH2 and SCN5A, mutations in which underlie > 90% of genotyped LQTS cases (the LQT1-LQT3 subtypes). Recent studies utilizing high throughput (HT) planar patch-clamp recording have shown it to discriminate effectively between rare benign and pathological variants, studied through heterologous expression of recombinant channels. In combination with biochemical methods for evaluating channel trafficking and supported by biophysical modelling, patch clamp also provides detailed mechanistic insight into the functional consequences of identified mutations. Whilst potentially powerful, patient-specific stem-cell derived cardiomyocytes and genetically modified animal models are currently not well-suited to high throughput VUS study.
Conclusion
The widely adopted 2015 American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP) guidelines for the interpretation of sequence variants include the PS3 criterion for consideration of evidence from well-established in vitro or in vivo assays. The wealth of information on underlying mechanisms of LQT1-LQT3 and recent HT patch clamp data support consideration of patch clamp data together (for LQT1 and LQT2) with information from biochemical trafficking assays as meeting the PS3 criterion of well established assays, able to provide ‘strong’ evidence for functional pathogenicity of identified VUS.
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19
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Campuzano O, Sarquella-Brugada G, Cesar S, Arbelo E, Brugada J, Brugada R. Update on Genetic Basis of Brugada Syndrome: Monogenic, Polygenic or Oligogenic? Int J Mol Sci 2020; 21:ijms21197155. [PMID: 32998306 PMCID: PMC7582739 DOI: 10.3390/ijms21197155] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Brugada syndrome is a rare inherited arrhythmogenic disease leading to ventricular fibrillation and high risk of sudden death. In 1998, this syndrome was linked with a genetic variant with an autosomal dominant pattern of inheritance. To date, rare variants identified in more than 40 genes have been potentially associated with this disease. Variants in regulatory regions, combinations of common variants and other genetic alterations are also proposed as potential origins of Brugada syndrome, suggesting a polygenic or oligogenic inheritance pattern. However, most of these genetic alterations remain of questionable causality; indeed, rare pathogenic variants in the SCN5A gene are the only established cause of Brugada syndrome. Comprehensive analysis of all reported genetic alterations identified the origin of disease in no more than 40% of diagnosed cases. Therefore, identifying the cause of this rare arrhythmogenic disease in the many families without a genetic diagnosis is a major current challenge in Brugada syndrome. Additional challenges are interpretation/classification of variants and translation of genetic data into clinical practice. Further studies focused on unraveling the pathophysiological mechanisms underlying the disease are needed. Here we provide an update on the genetic basis of Brugada syndrome.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Centre, University of Girona-IDIBGI, 17190 Girona, Spain
- Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain;
- Centro Investigación Biomédica en Red: Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain; (E.A.); (J.B.)
- Correspondence: (O.C.); (R.B.)
| | - Georgia Sarquella-Brugada
- Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain;
- Arrhythmia Unit, Hospital Sant Joan de Déu, University of Barcelona, 08950 Barcelona, Spain;
| | - Sergi Cesar
- Arrhythmia Unit, Hospital Sant Joan de Déu, University of Barcelona, 08950 Barcelona, Spain;
| | - Elena Arbelo
- Centro Investigación Biomédica en Red: Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain; (E.A.); (J.B.)
- Arrhythmia Unit, Hospital Sant Joan de Déu, University of Barcelona, 08950 Barcelona, Spain;
| | - Josep Brugada
- Centro Investigación Biomédica en Red: Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain; (E.A.); (J.B.)
- Arrhythmia Unit, Hospital Sant Joan de Déu, University of Barcelona, 08950 Barcelona, Spain;
- Arrhythmia Section, Cardiovascular Institute, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Centre, University of Girona-IDIBGI, 17190 Girona, Spain
- Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain;
- Centro Investigación Biomédica en Red: Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain; (E.A.); (J.B.)
- Familial Cardiomyopathies Unit, Hospital Josep Trueta de Girona, 17007 Girona, Spain
- Correspondence: (O.C.); (R.B.)
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20
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Heyne HO, Baez-Nieto D, Iqbal S, Palmer DS, Brunklaus A, May P, Johannesen KM, Lauxmann S, Lemke JR, Møller RS, Pérez-Palma E, Scholl UI, Syrbe S, Lerche H, Lal D, Campbell AJ, Wang HR, Pan J, Daly MJ. Predicting functional effects of missense variants in voltage-gated sodium and calcium channels. Sci Transl Med 2020; 12:eaay6848. [PMID: 32801145 DOI: 10.1126/scitranslmed.aay6848] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/20/2019] [Accepted: 07/22/2020] [Indexed: 12/30/2022]
Abstract
Malfunctions of voltage-gated sodium and calcium channels (encoded by SCNxA and CACNA1x family genes, respectively) have been associated with severe neurologic, psychiatric, cardiac, and other diseases. Altered channel activity is frequently grouped into gain or loss of ion channel function (GOF or LOF, respectively) that often corresponds not only to clinical disease manifestations but also to differences in drug response. Experimental studies of channel function are therefore important, but laborious and usually focus only on a few variants at a time. On the basis of known gene-disease mechanisms of 19 different diseases, we inferred LOF (n = 518) and GOF (n = 309) likely pathogenic variants from the disease phenotypes of variant carriers. By training a machine learning model on sequence- and structure-based features, we predicted LOF or GOF effects [area under the receiver operating characteristics curve (ROC) = 0.85] of likely pathogenic missense variants. Our LOF versus GOF prediction corresponded to molecular LOF versus GOF effects for 87 functionally tested variants in SCN1/2/8A and CACNA1I (ROC = 0.73) and was validated in exome-wide data from 21,703 cases and 128,957 controls. We showed respective regional clustering of inferred LOF and GOF nucleotide variants across the alignment of the entire gene family, suggesting shared pathomechanisms in the SCNxA/CACNA1x family genes.
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Affiliation(s)
- Henrike O Heyne
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 5WR36M Helsinki, Finland
| | - David Baez-Nieto
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sumaiya Iqbal
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S Palmer
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andreas Brunklaus
- Paediatric Neurosciences Research Group, Royal Hospital for Sick Children, Glasgow G51 4TF, UK
- School of Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, Belvaux, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Centre, 4293 Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Stephan Lauxmann
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Centre, 4293 Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Eduardo Pérez-Palma
- Cologne Center for Genomics (CCG), University of Cologne, 50923, Germany
- Genomic Medicine Institute, Lemer Research Institute Cleveland Clinic, OH G92J47, USA
| | - Ute I Scholl
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care and BIH Center for Regenerative Therapies, 10178 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Center for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany
| | - Dennis Lal
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Cologne Center for Genomics (CCG), University of Cologne, 50923, Germany
- Genomic Medicine Institute, Lemer Research Institute Cleveland Clinic, OH G92J47, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH G92J47, USA
| | - Arthur J Campbell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hao-Ran Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jen Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 5WR36M Helsinki, Finland
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21
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Glazer AM, Wada Y, Li B, Muhammad A, Kalash OR, O'Neill MJ, Shields T, Hall L, Short L, Blair MA, Kroncke BM, Capra JA, Roden DM. High-Throughput Reclassification of SCN5A Variants. Am J Hum Genet 2020; 107:111-123. [PMID: 32533946 PMCID: PMC7332654 DOI: 10.1016/j.ajhg.2020.05.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Partial or complete loss-of-function variants in SCN5A are the most common genetic cause of the arrhythmia disorder Brugada syndrome (BrS1). However, the pathogenicity of SCN5A variants is often unknown or disputed; 80% of the 1,390 SCN5A missense variants observed in at least one individual to date are variants of uncertain significance (VUSs). The designation of VUS is a barrier to the use of sequence data in clinical care. We selected 83 variants: 10 previously studied control variants, 10 suspected benign variants, and 63 suspected Brugada syndrome-associated variants, selected on the basis of their frequency in the general population and in individuals with Brugada syndrome. We used high-throughput automated patch clamping to study the function of the 83 variants, with the goal of reclassifying variants with functional data. The ten previously studied controls had functional properties concordant with published manual patch clamp data. All 10 suspected benign variants had wild-type-like function. 22 suspected BrS variants had loss of channel function (<10% normalized peak current) and 22 variants had partial loss of function (10%-50% normalized peak current). The previously unstudied variants were initially classified as likely benign (n = 2), likely pathogenic (n = 10), or VUSs (n = 61). After the patch clamp studies, 16 variants were benign/likely benign, 45 were pathogenic/likely pathogenic, and only 12 were still VUSs. Structural modeling identified likely mechanisms for loss of function including altered thermostability and disruptions to alpha helices, disulfide bonds, or the permeation pore. High-throughput patch clamping enabled reclassification of the majority of tested VUSs in SCN5A.
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Affiliation(s)
- Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bian Li
- Department of Biological Sciences, Center for Structural Biology, and Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - Ayesha Muhammad
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Olivia R Kalash
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J O'Neill
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tiffany Shields
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lynn Hall
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Laura Short
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Marcia A Blair
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John A Capra
- Department of Biological Sciences, Center for Structural Biology, and Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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22
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Kroncke BM, Smith DK, Zuo Y, Glazer AM, Roden DM, Blume JD. A Bayesian method to estimate variant-induced disease penetrance. PLoS Genet 2020; 16:e1008862. [PMID: 32569262 PMCID: PMC7347235 DOI: 10.1371/journal.pgen.1008862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/09/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
A major challenge emerging in genomic medicine is how to assess best disease risk from rare or novel variants found in disease-related genes. The expanding volume of data generated by very large phenotyping efforts coupled to DNA sequence data presents an opportunity to reinterpret genetic liability of disease risk. Here we propose a framework to estimate the probability of disease given the presence of a genetic variant conditioned on features of that variant. We refer to this as the penetrance, the fraction of all variant heterozygotes that will present with disease. We demonstrate this methodology using a well-established disease-gene pair, the cardiac sodium channel gene SCN5A and the heart arrhythmia Brugada syndrome. From a review of 756 publications, we developed a pattern mixture algorithm, based on a Bayesian Beta-Binomial model, to generate SCN5A penetrance probabilities for the Brugada syndrome conditioned on variant-specific attributes. These probabilities are determined from variant-specific features (e.g. function, structural context, and sequence conservation) and from observations of affected and unaffected heterozygotes. Variant functional perturbation and structural context prove most predictive of Brugada syndrome penetrance.
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Affiliation(s)
- Brett M. Kroncke
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pharmacology Vanderbilt University, Nashville, Tennessee, United States of America
| | - Derek K. Smith
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yi Zuo
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew M. Glazer
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dan M. Roden
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pharmacology Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jeffrey D. Blume
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
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23
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Rowe MK, Roberts JD. The evolution of gene-guided management of inherited arrhythmia syndromes: Peering beyond monogenic paradigms towards comprehensive genomic risk scores. J Cardiovasc Electrophysiol 2020; 31:2998-3008. [PMID: 32107815 DOI: 10.1111/jce.14415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 12/19/2022]
Abstract
Inherited arrhythmia syndromes have traditionally been viewed as monogenic forms of disease whose pathophysiology is driven by a single highly penetrant rare genetic variant. Although an accurate depiction of a proportion of genetic variants, the variable penetrance frequently noted in genotype positive families and the presence of sporadic genotype negative cases have long highlighted a more nuanced truth being operative. Coupled with our more recent recognition that many rare variants implicated in inherited arrhythmia syndromes possess unexpectedly high allele frequencies within the general population, these observations have contributed to the realization that a spectrum of pathogenicity exists among clinically relevant genetic variants. Notably, variable mutation pathogenicity and corresponding variable degrees of penetrance emphasize a limitation of contemporary guidelines, which attempt to dichotomize genetic variants as pathogenic or benign. Recognition of the existence of low and intermediate penetrant variants insufficient to be causative for disease in isolation has served to emphasize the importance of additional genetic, clinical, and environmental factors in the pathogenesis of rare inherited arrhythmia syndromes. Despite being rare, it has also become increasingly evident that common genetic variants play critical roles in both heritable channelopathies and cardiomyopathies and in aggregate may even be the primary drivers in certain instances, such as genotype negative Brugada syndrome. Our growing realization that the genetic substrates of inherited arrhythmia syndromes have intricacies that extend beyond traditionally perceived monogenic paradigms has highlighted a potential value of leveraging more comprehensive genomic risk scores for predicting disease development and arrhythmic risk.
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Affiliation(s)
- Matthew K Rowe
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, Ontario, Canada
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, Ontario, Canada
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24
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Glazer AM, Kroncke BM, Matreyek KA, Yang T, Wada Y, Shields T, Salem JE, Fowler DM, Roden DM. Deep Mutational Scan of an SCN5A Voltage Sensor. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e002786. [PMID: 31928070 DOI: 10.1161/circgen.119.002786] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Variants in ion channel genes have classically been studied in low throughput by patch clamping. Deep mutational scanning is a complementary approach that can simultaneously assess function of thousands of variants. METHODS We have developed and validated a method to perform a deep mutational scan of variants in SCN5A, which encodes the major voltage-gated sodium channel in the heart. We created a library of nearly all possible variants in a 36 base region of SCN5A in the S4 voltage sensor of domain IV and stably integrated the library into HEK293T cells. RESULTS In preliminary experiments, challenge with 3 drugs (veratridine, brevetoxin, and ouabain) could discriminate wild-type channels from gain- and loss-of-function pathogenic variants. High-throughput sequencing of the pre- and postdrug challenge pools was used to count the prevalence of each variant and identify variants with abnormal function. The deep mutational scan scores identified 40 putative gain-of-function and 33 putative loss-of-function variants. For 8 of 9 variants, patch clamping data were consistent with the scores. CONCLUSIONS These experiments demonstrate the accuracy of a high-throughput in vitro scan of SCN5A variant function, which can be used to identify deleterious variants in SCN5A and other ion channel genes.
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Affiliation(s)
- Andrew M Glazer
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Brett M Kroncke
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle (K.A.M., D.M.F.)
| | - Tao Yang
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Yuko Wada
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Tiffany Shields
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Joe-Elie Salem
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN.,Department of Clinical Pharmacology, APHP, Sorbonne Université, INSERM, CIC-1421, Hôpital Pitié-Salpêtrière, Paris, France (J.-E.S.)
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle (K.A.M., D.M.F.)
| | - Dan M Roden
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt Center for Arrhythmia Research and Therapeutics (A.M.G., B.M.K., T.Y., Y.W., T.S., J.-E.S., D.M.R.), Vanderbilt University Medical Center, Nashville, TN.,Department of Biomedical Informatics (D.M.R.), Vanderbilt University Medical Center, Nashville, TN.,Department of Pharmacology (D.M.R.), Vanderbilt University Medical Center, Nashville, TN
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25
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Barbieri R, Bertelli S, Pusch M, Gavazzo P. Late sodium current blocker GS967 inhibits persistent currents induced by familial hemiplegic migraine type 3 mutations of the SCN1A gene. J Headache Pain 2019; 20:107. [PMID: 31730442 PMCID: PMC6858687 DOI: 10.1186/s10194-019-1056-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/29/2019] [Indexed: 01/31/2023] Open
Abstract
Background Familial hemiplegic migraine (FHM) is a group of genetic migraine, associated with hemiparesis and aura. Three causative different genes have been identified, all of which are involved in membrane ion transport. Among these, SCN1A encodes the voltage-gated Na+ channel Nav1.1, and FHM caused by mutations of SCN1A is named FHM3. For 7 of the 12 known FHM3-causing SCNA1 mutations functional consequences have been investigated, and even if gain of function effect seems to be a predominant phenotype, for several mutations conflicting results have been obtained and the available data do not reveal a univocal FHM3 pathomechanism. Methods To obtain a more complete picture, here, we characterized by patch clamp approach the remaining 5 mutations (Q1489H, I1498M, F1499 L, M1500 V, F1661 L) in heterologous expression systems. Results With the exception of I1498M, all mutants exhibited the same current density as WT and exhibited a shift of the steady state inactivation to more positive voltages, an accelerated recovery from inactivation, and an increase of the persistent current, revealing that most FHM3 mutations induce a gain of function. We also determined the effect of GS967, a late Na+ current blocker, on the above mentioned mutants as well as on previously characterized ones (L1649Q, L1670 W, F1774S). GS967 inhibited persistent currents of all SCNA1 FMH3-related mutants and dramatically slowed the recovery from fast inactivation of WT and mutants, consistent with the hypothesis that GS967 specifically binds to and thereby stabilizes the fast inactivated state. Simulation of neuronal firing showed that enhanced persistent currents cause an increase of ionic fluxes during action potential repolarization and consequent accumulation of K+ and/or exhaustion of neuronal energy resources. In silico application of GS967 largely reduced net ionic currents in neurons without impairing excitability. Conclusion In conclusion, late Na+ current blockers appear a promising specific pharmacological treatment of FHM3.
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Affiliation(s)
- R Barbieri
- Biophysics Institute, National Research Council, Via De Marini 6, Genoa, Italy
| | - S Bertelli
- Biophysics Institute, National Research Council, Via De Marini 6, Genoa, Italy.,International School of Advanced Studies (SISSA), Via Bonomea, 265, Trieste, Italy
| | - M Pusch
- Biophysics Institute, National Research Council, Via De Marini 6, Genoa, Italy
| | - P Gavazzo
- Biophysics Institute, National Research Council, Via De Marini 6, Genoa, Italy.
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26
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Affiliation(s)
- Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
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27
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Campuzano O, Sarquella-Brugada G, Fernandez-Falgueras A, Cesar S, Coll M, Mates J, Arbelo E, Perez-Serra A, Del Olmo B, Jordá P, Fiol V, Iglesias A, Puigmulé M, Lopez L, Pico F, Brugada J, Brugada R. Genetic interpretation and clinical translation of minor genes related to Brugada syndrome. Hum Mutat 2019; 40:749-764. [PMID: 30821013 DOI: 10.1002/humu.23730] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/19/2022]
Abstract
Brugada syndrome (BrS) is an inherited arrhythmogenic disease associated with sudden cardiac death. The main gene is SCN5A. Additional variants in 42 other genes have been reported as deleterious, although these variants have not yet received comprehensive pathogenic analysis. Our aim was to clarify the role of all currently reported variants in minor genes associated with BrS. We performed a comprehensive analysis according to the American College of Medical Genetics and Genomics guidelines of published clinical and basic data on all genes (other than SCN5A) related to BrS. Our results identified 133 rare variants potentially associated with BrS. After applying current recommendations, only six variants (4.51%) show a conclusive pathogenic role. All definitively pathogenic variants were located in four genes encoding sodium channels or related proteins: SLMAP, SEMA3A, SCNN1A, and SCN2B. In total, 33.83% of variants in 19 additional genes were potentially pathogenic. Beyond SCN5A, we conclude definitive pathogenic variants associated with BrS in four minor genes. The current list of genes associated with BrS, therefore, should include SCN5A, SLMAP, SEMA3A, SCNN1A, and SCN2B. Comprehensive genetic interpretation and careful clinical translation should be done for all variants currently classified as potentially deleterious for BrS.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - Georgia Sarquella-Brugada
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain.,Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Anna Fernandez-Falgueras
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Sergi Cesar
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Monica Coll
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Jesus Mates
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Elena Arbelo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Cardiology Service, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,IDIBAPS, Institut d'Investigació August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alexandra Perez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Bernat Del Olmo
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Paloma Jordá
- Cardiology Service, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,IDIBAPS, Institut d'Investigació August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Victoria Fiol
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Marta Puigmulé
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Laura Lopez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Ferran Pico
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain
| | - Josep Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain.,Cardiology Service, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,IDIBAPS, Institut d'Investigació August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona, University of Girona, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain.,Cardiology Service, Hospital Josep Trueta, University of Girona, Girona, Spain
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28
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Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM. Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1. Comput Struct Biotechnol J 2019; 17:206-214. [PMID: 30828412 PMCID: PMC6383132 DOI: 10.1016/j.csbj.2019.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/28/2022] Open
Abstract
Rare variants in the cardiac potassium channel KV7.1 (KCNQ1) and sodium channel NaV1.5 (SCN5A) are implicated in genetic disorders of heart rhythm, including congenital long QT and Brugada syndromes (LQTS, BrS), but also occur in reference populations. We previously reported two sets of NaV1.5 (n = 356) and KV7.1 (n = 144) variants with in vitro characterized channel currents gathered from the literature. Here we investigated the ability to predict commonly reported NaV1.5 and KV7.1 variant functional perturbations by leveraging diverse features including variant classifiers PROVEAN, PolyPhen-2, and SIFT; evolutionary rate and BLAST position specific scoring matrices (PSSM); and structure-based features including “functional densities” which is a measure of the density of pathogenic variants near the residue of interest. Structure-based functional densities were the most significant features for predicting NaV1.5 peak current (adj. R2 = 0.27) and KV7.1 + KCNE1 half-maximal voltage of activation (adj. R2 = 0.29). Additionally, use of structure-based functional density values improves loss-of-function classification of SCN5A variants with an ROC-AUC of 0.78 compared with other predictive classifiers (AUC = 0.69; two-sided DeLong test p = .01). These results suggest structural data can inform predictions of the effect of uncharacterized SCN5A and KCNQ1 variants to provide a deeper understanding of their burden on carriers.
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Affiliation(s)
- Brett M Kroncke
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey Mendenhall
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Derek K Smith
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37240, USA
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey D Blume
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37240, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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29
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Kroncke BM, Yang T, Roden DM. Multiple mechanisms underlie increased cardiac late sodium current. Heart Rhythm 2019; 16:1091-1097. [PMID: 30677491 DOI: 10.1016/j.hrthm.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND We recently reported a quantitative relationship between the degree of functional perturbation reported in the literature for 356 variants in the cardiac sodium channel gene SCN5A and the penetrance of resulting arrhythmia phenotypes. In the course of that work, we identified multiple SCN5A variants, including R1193Q, that are common in populations but are reported in human embryonic kidney (HEK) cells to generate large late sodium current (INa-L). OBJECTIVE The purpose of this study was to compare the functional properties of R1193Q with those of the well-studied type 3 long QT syndrome mutation ΔKPQ. METHODS We compared functional properties of SCN5A R1193Q with those of ΔKPQ in Chinese hamster ovary (CHO) cells at baseline and after exposure to intracellular phosphatidylinositol (3,4,5)-trisphosphate (PIP3), which inhibits INa-L generated by decreased Phosphoinositide 3-kinase (PI3K) activity. We also used CRISPR/Cas9 editing to generate R1193Q in human-induced pluripotent stem cells differentiated to cardiomyocytes (hiPSC-CMs). RESULTS Both R1193Q and ΔKPQ generated robust INa-L in CHO cells. PIP3 abrogated the late current phenotype in R1193Q cells but had no effect on ΔKPQ. Homozygous R1193Q hiPSC-CMs displayed increased INa-L and long action potentials with frequent triggered beats, which were reversed with the addition of PIP3. CONCLUSION The consistency between the late current produced in HEK cells, CHO cells, and hiPSC-CMs suggests that the late current is a feature of the SCN5A R1193Q variant in human cardiomyocytes but that the mechanism by which the late current is produced is distinct and indirect, as compared with the more highly penetrant ΔKPQ. These data suggest that observing a late current in an in vitro setting does not necessarily translate to highly pathogenic type 3 long QT syndrome phenotype but depends on the underlying mechanism.
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Affiliation(s)
- Brett M Kroncke
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
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30
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Denham NC, Pearman CM, Ding WY, Waktare J, Gupta D, Snowdon R, Hall M, Cooper R, Modi S, Todd D, Mahida S. Systematic re-evaluation of SCN5A variants associated with Brugada syndrome. J Cardiovasc Electrophysiol 2018; 30:118-127. [PMID: 30203441 DOI: 10.1111/jce.13740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/01/2018] [Accepted: 09/07/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND A large number of SCN5A variants have been reported to underlie Brugada syndrome (BrS). However, the evidence supporting individual variants is highly heterogeneous. OBJECTIVE We systematically re-evaluated all SCN5A variants reported in BrS using the 2015 American college of medical genetics and genomics and the association for molecular pathology (ACMG-AMP) guidelines. METHODS A PubMed/Embase search was performed to identify all reported SCN5A variants in BrS. Standardized bioinformatic re-analysis (SIFT, PolyPhen, Mutation Taster, Mutation assessor, FATHMM, GERP, PhyloP, and SiPhy) and re-evaluation of frequency in the gnomAD database were performed. Fourteen ACMG-AMP rules were deemed applicable for SCN5A variant analysis. RESULTS Four hundred and eighty unique SCN5A variants were identified, the majority of which 425 (88%) were coding variants. One hundred and fifty-six of 425 (37%) variants were classified as pathogenic/likely pathogenic. Two hundred and fifty-eight (60%) were classified as variants of uncertain significance, while a further 11 (3%) were classified as benign/likely benign. When considering the subset of variants that were considered "null" variants separately, 95% fulfilled criteria for pathogenicity/likely pathogenicity. In contrast, only 17% of missense variants fulfilled criteria for pathogenicity/likely pathogenicity. Importantly, however, only 25% of missense variants had available functional data, which was a major score driver for pathogenic classification. CONCLUSION Based on contemporary ACMG-AMP guidelines, only a minority of SCN5A variants implicated in BrS fulfill the criteria for pathogenicity or likely pathogenicity.
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Affiliation(s)
- Nathan C Denham
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Charles M Pearman
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Wern Yew Ding
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Johan Waktare
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Dhiraj Gupta
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Richard Snowdon
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Mark Hall
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Robert Cooper
- Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Simon Modi
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Derick Todd
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - Saagar Mahida
- Department of Cardiac Electrophysiology, Liverpool Heart and Chest Hospital, Liverpool, UK.,Department of Inherited Cardiac Diseases, Liverpool Heart and Chest Hospital, Liverpool, UK
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31
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Roberts JD. Predicting Penetrance of SCN5A Rare Variants: Peering Beyond the Black and White and Into the Shades of Grey. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2018; 11:e002166. [PMID: 29728398 DOI: 10.1161/circgen.118.002166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada.
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