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O'Neill MJ, Sala L, Denjoy I, Wada Y, Kozek K, Crotti L, Dagradi F, Kotta MC, Spazzolini C, Leenhardt A, Salem JE, Kashiwa A, Ohno S, Tao R, Roden DM, Horie M, Extramiana F, Schwartz PJ, Kroncke BM. Continuous Bayesian variant interpretation accounts for incomplete penetrance among Mendelian cardiac channelopathies. Genet Med 2023; 25:100355. [PMID: 36496179 PMCID: PMC9992222 DOI: 10.1016/j.gim.2022.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The congenital Long QT Syndrome (LQTS) and Brugada Syndrome (BrS) are Mendelian autosomal dominant diseases that frequently precipitate fatal cardiac arrhythmias. Incomplete penetrance is a barrier to clinical management of heterozygotes harboring variants in the major implicated disease genes KCNQ1, KCNH2, and SCN5A. We apply and evaluate a Bayesian penetrance estimation strategy that accounts for this phenomenon. METHODS We generated Bayesian penetrance models for KCNQ1-LQT1 and SCN5A-LQT3 using variant-specific features and clinical data from the literature, international arrhythmia genetic centers, and population controls. We analyzed the distribution of posterior penetrance estimates across 4 genotype-phenotype relationships and compared continuous estimates with ClinVar annotations. Posterior estimates were mapped onto protein structure. RESULTS Bayesian penetrance estimates of KCNQ1-LQT1 and SCN5A-LQT3 are empirically equivalent to 10 and 5 clinically phenotype heterozygotes, respectively. Posterior penetrance estimates were bimodal for KCNQ1-LQT1 and KCNH2-LQT2, with a higher fraction of missense variants with high penetrance among KCNQ1 variants. There was a wide distribution of variant penetrance estimates among identical ClinVar categories. Structural mapping revealed heterogeneity among "hot spot" regions and featured high penetrance estimates for KCNQ1 variants in contact with calmodulin and the S6 domain. CONCLUSIONS Bayesian penetrance estimates provide a continuous framework for variant interpretation.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Krystian Kozek
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Maria-Christina Kotta
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Carla Spazzolini
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Antoine Leenhardt
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Joe-Elie Salem
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Ran Tao
- Department of Biostatistics, 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
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Peter J Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Brett M Kroncke
- 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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2
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Next-generation sequencing of postmortem molecular markers to support for medicolegal autopsy. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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3
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Phul S, Kuenze G, Vanoye CG, Sanders CR, George AL, Meiler J. Predicting the functional impact of KCNQ1 variants with artificial neural networks. PLoS Comput Biol 2022; 18:e1010038. [PMID: 35442947 PMCID: PMC9060377 DOI: 10.1371/journal.pcbi.1010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/02/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022] Open
Abstract
Recent advances in experimental and computational protein structure determination have provided access to high-quality structures for most human proteins and mutants thereof. However, linking changes in structure in protein mutants to functional impact remains an active area of method development. If successful, such methods can ultimately assist physicians in taking appropriate treatment decisions. This work presents three artificial neural network (ANN)-based predictive models that classify four key functional parameters of KCNQ1 variants as normal or dysfunctional using PSSM-based evolutionary and/or biophysical descriptors. Recent advances in predicting protein structure and variant properties with artificial intelligence (AI) rely heavily on the availability of evolutionary features and thus fail to directly assess the biophysical underpinnings of a change in structure and/or function. The central goal of this work was to develop an ANN model based on structure and physiochemical properties of KCNQ1 potassium channels that performs comparably or better than algorithms using only on PSSM-based evolutionary features. These biophysical features highlight the structure-function relationships that govern protein stability, function, and regulation. The input sensitivity algorithm incorporates the roles of hydrophobicity, polarizability, and functional densities on key functional parameters of the KCNQ1 channel. Inclusion of the biophysical features outperforms exclusive use of PSSM-based evolutionary features in predicting activation voltage dependence and deactivation time. As AI is increasingly applied to problems in biology, biophysical understanding will be critical with respect to 'explainable AI', i.e., understanding the relation of sequence, structure, and function of proteins. Our model is available at www.kcnq1predict.org.
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Affiliation(s)
- Saksham Phul
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
| | - Carlos G. Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
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4
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Kozek K, Wada Y, Sala L, Denjoy I, Egly C, O'Neill MJ, Aiba T, Shimizu W, Makita N, Ishikawa T, Crotti L, Spazzolini C, Kotta MC, Dagradi F, Castelletti S, Pedrazzini M, Gnecchi M, Leenhardt A, Salem JE, Ohno S, Zuo Y, Glazer AM, Mosley JD, Roden DM, Knollmann BC, Blume JD, Extramiana F, Schwartz PJ, Horie M, Kroncke BM. Estimating the Posttest Probability of Long QT Syndrome Diagnosis for Rare KCNH2 Variants. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003289. [PMID: 34309407 DOI: 10.1161/circgen.120.003289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The proliferation of genetic profiling has revealed many associations between genetic variations and disease. However, large-scale phenotyping efforts in largely healthy populations, coupled with DNA sequencing, suggest variants currently annotated as pathogenic are more common in healthy populations than previously thought. In addition, novel and rare variants are frequently observed in genes associated with disease both in healthy individuals and those under suspicion of disease. This raises the question of whether these variants can be useful predictors of disease. To answer this question, we assessed the degree to which the presence of a variant in the cardiac potassium channel gene KCNH2 was diagnostically predictive for the autosomal dominant long QT syndrome. METHODS We estimated the probability of a long QT diagnosis given the presence of each KCNH2 variant using Bayesian methods that incorporated variant features such as changes in variant function, protein structure, and in silico predictions. We call this estimate the posttest probability of disease. Our method was applied to over 4000 individuals heterozygous for 871 missense or in-frame insertion/deletion variants in KCNH2 and validated against a separate international cohort of 933 individuals heterozygous for 266 missense or in-frame insertion/deletion variants. RESULTS Our method was well-calibrated for the observed fraction of heterozygotes diagnosed with long QT syndrome. Heuristically, we found that the innate diagnostic information one learns about a variant from 3-dimensional variant location, in vitro functional data, and in silico predictors is equivalent to the diagnostic information one learns about that same variant by clinically phenotyping 10 heterozygotes. Most importantly, these data can be obtained in the absence of any clinical observations. CONCLUSIONS We show how variant-specific features can inform a prior probability of disease for rare variants even in the absence of clinically phenotyped heterozygotes.
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Affiliation(s)
- Krystian Kozek
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN.,Department of Cardiovascular Medicine, Shiga University of Medical Science, Otsu, Japan (Y.W., S.O., M.H.)
| | - Luca Sala
- Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy (L.S., L.C., C.K., M.P., P.J.S.)
| | - Isabelle Denjoy
- CNMR Maladies Cardiaques Héréditaires Rares, AP-HP, Hôpital Bichat, Paris, France (I.D., A.L., F.E.)
| | - Christian Egly
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
| | - Matthew J O'Neill
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
| | - Takeshi Aiba
- Department of Cardiovascular Medicine (T.A., N.M., S.O.), National Cerebral and Cardiovascular Center, Suita
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan (W.S.)
| | - Naomasa Makita
- Department of Cardiovascular Medicine (T.A., N.M., S.O.), National Cerebral and Cardiovascular Center, Suita.,7Omics Research Center (N.M., T.I.), National Cerebral and Cardiovascular Center, Suita
| | - Taisuke Ishikawa
- 7Omics Research Center (N.M., T.I.), National Cerebral and Cardiovascular Center, Suita
| | - Lia Crotti
- Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy (L.S., L.C., C.K., M.P., P.J.S.).,Department of Cardiovascular, Neural & Metabolic Sciences, San Luca Hospital (L.C.), Istituto Auxologico Italiano IRCCS.,Center for Cardiac Arrhythmias of Genetic Origin (L.C., C.S., F.D., S.C., P.J.S.), Istituto Auxologico Italiano IRCCS.,Department of Medicine and Surgery, University Milano Bicocca, Milan (L.C.)
| | - Carla Spazzolini
- Center for Cardiac Arrhythmias of Genetic Origin (L.C., C.S., F.D., S.C., P.J.S.), Istituto Auxologico Italiano IRCCS
| | | | - Federica Dagradi
- Center for Cardiac Arrhythmias of Genetic Origin (L.C., C.S., F.D., S.C., P.J.S.), Istituto Auxologico Italiano IRCCS
| | - Silvia Castelletti
- Center for Cardiac Arrhythmias of Genetic Origin (L.C., C.S., F.D., S.C., P.J.S.), Istituto Auxologico Italiano IRCCS
| | - Matteo Pedrazzini
- Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy (L.S., L.C., C.K., M.P., P.J.S.)
| | - Massimiliano Gnecchi
- Department of Molecular Medicine, Unit of Cardiology, University of Pavia (M.G.).,Intensive Cardiac Care Unit and Lab of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy (M.G.)
| | - Antoine Leenhardt
- CNMR Maladies Cardiaques Héréditaires Rares, AP-HP, Hôpital Bichat, Paris, France (I.D., A.L., F.E.).,University de Paris (A.L., F.E.)
| | - Joe-Elie Salem
- Division of Cardiovascular Medicine, Cardio-oncology Program (J.-E.S.), Vanderbilt University Medical Center, Nashville, TN.,Sorbonne Université, INSERM CIC-1901, AP-HP, Department of Pharmacology, Regional Pharmacovigilance Center, Pitié-Salpêtrière Hospital, Paris, France (J.-E.S.)
| | - Seiko Ohno
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Otsu, Japan (Y.W., S.O., M.H.).,Department of Cardiovascular Medicine (T.A., N.M., S.O.), National Cerebral and Cardiovascular Center, Suita
| | - Yi Zuo
- Department of Biostatistics (Y.Z., J.D.M., D.M.R.), Vanderbilt University, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan D Mosley
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN.,Department of Biostatistics (Y.Z., J.D.M., D.M.R.), Vanderbilt University, Nashville, TN.,Biomedical Informatics (J.D.M.), Vanderbilt University, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN.,Department of Biostatistics (Y.Z., J.D.M., D.M.R.), Vanderbilt University, Nashville, TN
| | - Bjorn C Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
| | | | - Fabrice Extramiana
- CNMR Maladies Cardiaques Héréditaires Rares, AP-HP, Hôpital Bichat, Paris, France (I.D., A.L., F.E.).,University de Paris (A.L., F.E.)
| | - Peter J Schwartz
- Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy (L.S., L.C., C.K., M.P., P.J.S.).,Center for Cardiac Arrhythmias of Genetic Origin (L.C., C.S., F.D., S.C., P.J.S.), Istituto Auxologico Italiano IRCCS
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Otsu, Japan (Y.W., S.O., M.H.)
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine & Pharmacology (K.K., Y.W., C.E., M.J.O., A.M.G., J.D.M., D.M.R., B.C.K., B.M.K.), Vanderbilt University Medical Center, Nashville, TN
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5
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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: 85] [Impact Index Per Article: 21.3] [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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6
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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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7
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Brewer KR, Kuenze G, Vanoye CG, George AL, Meiler J, Sanders CR. Structures Illuminate Cardiac Ion Channel Functions in Health and in Long QT Syndrome. Front Pharmacol 2020; 11:550. [PMID: 32431610 PMCID: PMC7212895 DOI: 10.3389/fphar.2020.00550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The cardiac action potential is critical to the production of a synchronized heartbeat. This electrical impulse is governed by the intricate activity of cardiac ion channels, among them the cardiac voltage-gated potassium (Kv) channels KCNQ1 and hERG as well as the voltage-gated sodium (Nav) channel encoded by SCN5A. Each channel performs a highly distinct function, despite sharing a common topology and structural components. These three channels are also the primary proteins mutated in congenital long QT syndrome (LQTS), a genetic condition that predisposes to cardiac arrhythmia and sudden cardiac death due to impaired repolarization of the action potential and has a particular proclivity for reentrant ventricular arrhythmias. Recent cryo-electron microscopy structures of human KCNQ1 and hERG, along with the rat homolog of SCN5A and other mammalian sodium channels, provide atomic-level insight into the structure and function of these proteins that advance our understanding of their distinct functions in the cardiac action potential, as well as the molecular basis of LQTS. In this review, the gating, regulation, LQTS mechanisms, and pharmacological properties of KCNQ1, hERG, and SCN5A are discussed in light of these recent structural findings.
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Affiliation(s)
- Kathryn R. Brewer
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Carlos G. Vanoye
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Alfred L. George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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Tseng GN. Structure-function relationship of the slow delayed rectifier channel: impactful questions in 2020 and beyond. Am J Physiol Heart Circ Physiol 2020; 318:H329-H331. [PMID: 31922891 DOI: 10.1152/ajpheart.00009.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Gea-Ny Tseng
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
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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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10
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Monasky MM, Micaglio E, Giachino D, Ciconte G, Giannelli L, Locati ET, Ramondini E, Cotugno R, Vicedomini G, Borrelli V, Ghiroldi A, Anastasia L, Pappone C. Genotype-Phenotype Correlation in a Family with Brugada Syndrome Harboring the Novel p.Gln371* Nonsense Variant in the SCN5A Gene. Int J Mol Sci 2019; 20:ijms20225522. [PMID: 31698696 PMCID: PMC6888117 DOI: 10.3390/ijms20225522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 12/30/2022] Open
Abstract
Brugada syndrome (BrS) is marked by coved ST-segment elevation and increased risk of sudden cardiac death. The genetics of this syndrome are elusive in over half of the cases. Variants in the SCN5A gene are the single most common known genetic unifier, accounting for about a third of cases. Research models, such as animal models and cell lines, are limited. In the present study, we report the novel NM_198056.2:c.1111C>T (p.Gln371*) heterozygous variant in the SCN5A gene, as well as its segregation with BrS in a large family. The results herein suggest a pathogenic effect of this variant. Functional studies are certainly warranted to characterize the molecular effects of this variant.
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Affiliation(s)
- Michelle M. Monasky
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Emanuele Micaglio
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Daniela Giachino
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano (TO), Italy;
| | - Giuseppe Ciconte
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Luigi Giannelli
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Emanuela T. Locati
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Elisa Ramondini
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Roberta Cotugno
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Gabriele Vicedomini
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Valeria Borrelli
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
| | - Andrea Ghiroldi
- Stem Cells for Tissue Engineering Laboratory, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (A.G.); (L.A.)
| | - Luigi Anastasia
- Stem Cells for Tissue Engineering Laboratory, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (A.G.); (L.A.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Carlo Pappone
- Arrhythmology Department, IRCCS Policlinico San Donato, 20097 San Donato Milanese (MI), Italy; (M.M.M.); (E.M.); (G.C.); (L.G.); (E.T.L.); (E.R.); (R.C.); (G.V.); (V.B.)
- Correspondence: ; Tel./Fax: +39-0252774260/4306
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Le NQK, Yapp EKY, Nagasundaram N, Chua MCH, Yeh HY. Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture. Comput Struct Biotechnol J 2019; 17:1245-1254. [PMID: 31921391 PMCID: PMC6944713 DOI: 10.1016/j.csbj.2019.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/07/2019] [Accepted: 09/11/2019] [Indexed: 11/20/2022] Open
Abstract
Protein function prediction is one of the most well-studied topics, attracting attention from countless researchers in the field of computational biology. Implementing deep neural networks that help improve the prediction of protein function, however, is still a major challenge. In this research, we suggested a new strategy that includes gated recurrent units and position-specific scoring matrix profiles to predict vesicular transportation proteins, a biological function of great importance. Although it is difficult to discover its function, our model is able to achieve accuracies of 82.3% and 85.8% in the cross-validation and independent dataset, respectively. We also solve the problem of imbalance in the dataset via tuning class weight in the deep learning model. The results generated showed sensitivity, specificity, MCC, and AUC to have values of 79.2%, 82.9%, 0.52, and 0.861, respectively. Our strategy shows superiority in results on the same dataset against all other state-of-the-art algorithms. In our suggested research, we have suggested a technique for the discovery of more proteins, particularly proteins connected with vesicular transport. In addition, our accomplishment could encourage the use of gated recurrent units architecture in protein function prediction.
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Affiliation(s)
- Nguyen Quoc Khanh Le
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
- Professional Master Program in Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan
| | - Edward Kien Yee Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, #08-04, Innovis, 138634, Singapore
| | - N. Nagasundaram
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
| | - Matthew Chin Heng Chua
- Institute of Systems Science, 25 Heng Mui Keng Terrace, National University of Singapore, 119615, Singapore
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
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