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Tamayo-Trujillo R, Paz-Cruz E, Cadena-Ullauri S, Guevara-Ramirez P, Ruiz-Pozo VA, Ibarra-Castillo R, Laso-Bayas JL, Zambrano AK. Exploring Atrial Fibrillation: Understanding the Complex Relation Between Lifestyle and Genetic Factors. J Med Cases 2024; 15:186-194. [PMID: 39091575 PMCID: PMC11287905 DOI: 10.14740/jmc4250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/21/2024] [Indexed: 08/04/2024] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide across diverse ethnic groups. Among these, atrial fibrillation (AF) stands as one of the most prevalent types of arrhythmias and the primary cause of stroke. Risk factors associated with AF include alcohol consumption, aging, high blood pressure, hypertension, inflammation, and genetic factors. A family history of CVD could indicate an increased risk. Consequently, genetic, and genomic testing should be performed to identify the molecular etiology of CVDs and assess at-risk patients. It is important to note that CVDs are the results of the complex interplay of genes and environmental factors, including ethnicity. In this case, the proband's clinic story includes a history of smoking abuse for 10 years (10 cigarettes per day), obesity, hypertension, and an associated familial history. These risk factors, along with genetic variants, could trigger the early onset of AF. In recent years, genetic and genomic studies have significantly advanced our understanding of CVD etiology, given that next-generation sequencing (NGS) allows for the identification of genetic variants that could contribute to these pathologies. Furthermore, NGS facilitates early diagnosis, personalized pharmacological approaches, and identification of novel biomarkers. Thus, NGS is a valuable tool in CVD management. However, such studies are limited in Ecuador, a low- and middle-income country. Several challenges contribute to this gap, encompassing economic, infrastructural, and educational obstacles. Notably, the cost of genetic and genomic studies may also pose a barrier, restricting access to a portion of the population. In this case report, we present a 56-year-old Ecuadorian woman, who has been diagnosed with AF; however, after performing NGS no disease-associated variants were found, despite having strong clinical signs and symptoms. In summary, this case report contributes valuable insights into the complex interplay between genetic and lifestyle factors in the development and management of AF. The case report aims to underscore the potential impact of genetic variants on disease risk, even when classified as variants of uncertain significance, and the importance of an integral approach to patient care that includes genetic screening, lifestyle interventions, and tailored pharmacological treatment.
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Affiliation(s)
- Rafael Tamayo-Trujillo
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- These authors contributed equally to this work and share first authorship
| | - Elius Paz-Cruz
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- These authors contributed equally to this work and share first authorship
| | - Santiago Cadena-Ullauri
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- These authors contributed equally to this work and share first authorship
| | - Patricia Guevara-Ramirez
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- These authors contributed equally to this work and share first authorship
| | - Viviana A. Ruiz-Pozo
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | | | - Ana Karina Zambrano
- Centro de Investigacion Genetica y Genomica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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Owais A, Barney M, Ly OT, Brown G, Chen H, Sridhar A, Pavel A, Khetani SR, Darbar D. Genetics and Pharmacogenetics of Atrial Fibrillation: A Mechanistic Perspective. JACC Basic Transl Sci 2024; 9:918-934. [PMID: 39170958 PMCID: PMC11334418 DOI: 10.1016/j.jacbts.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 08/23/2024]
Abstract
The heritability of atrial fibrillation (AF) is well established. Over the last decade genetic architecture of AF has been unraveled by genome-wide association studies and family-based studies. However, the translation of these genetic discoveries has lagged owing to an incomplete understanding of the pathogenic mechanisms underlying the genetic variants, challenges in classifying variants of uncertain significance (VUS), and limitations of existing disease models. We review the mechanistic insight provided by basic science studies regarding AF mechanisms, recent developments in high-throughput classification of VUS, and advances in bioengineered cardiac models for developing personalized therapy for AF.
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Affiliation(s)
- Asia Owais
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Miles Barney
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Olivia Thao Ly
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
- Department of Biomedical Engineering, University of Illinois, Chicago, Illinois, USA
| | - Grace Brown
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
- Department of Biomedical Engineering, University of Illinois, Chicago, Illinois, USA
| | - Hanna Chen
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Arvind Sridhar
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Arif Pavel
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Salman R. Khetani
- Department of Biomedical Engineering, University of Illinois, Chicago, Illinois, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, Illinois, USA
- Department of Biomedical Engineering, University of Illinois, Chicago, Illinois, USA
- Department of Physiology and Biophysics, University of Illinois, Chicago, Illinois, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois, Chicago, Illinois, USA
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3
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Wada Y, Wang L, Hall LD, Yang T, Short LL, Solus JF, Glazer AM, Roden DM. The electrophysiologic effects of KCNQ1 extend beyond expression of IKs: evidence from genetic and pharmacologic block. Cardiovasc Res 2024; 120:735-744. [PMID: 38442735 PMCID: PMC11135641 DOI: 10.1093/cvr/cvae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
AIMS While variants in KCNQ1 are the commonest cause of the congenital long QT syndrome, we and others find only a small IKs in cardiomyocytes from human-induced pluripotent stem cells (iPSC-CMs) or human ventricular myocytes. METHODS AND RESULTS We studied population control iPSC-CMs and iPSC-CMs from a patient with Jervell and Lange-Nielsen (JLN) syndrome due to compound heterozygous loss-of-function (LOF) KCNQ1 variants. We compared the effects of pharmacologic IKs block to those of genetic KCNQ1 ablation, using JLN cells, cells homozygous for the KCNQ1 LOF allele G643S, or siRNAs reducing KCNQ1 expression. We also studied the effects of two blockers of IKr, the other major cardiac repolarizing current, in the setting of pharmacologic or genetic ablation of KCNQ1: moxifloxacin, associated with a very low risk of drug-induced long QT, and dofetilide, a high-risk drug. In control cells, a small IKs was readily recorded but the pharmacologic IKs block produced no change in action potential duration at 90% repolarization (APD90). In contrast, in cells with genetic ablation of KCNQ1 (JLN), baseline APD90 was markedly prolonged compared with control cells (469 ± 20 vs. 310 ± 16 ms). JLN cells displayed increased sensitivity to acute IKr block: the concentration (μM) of moxifloxacin required to prolong APD90 100 msec was 237.4 [median, interquartile range (IQR) 100.6-391.6, n = 7] in population cells vs. 23.7 (17.3-28.7, n = 11) in JLN cells. In control cells, chronic moxifloxacin exposure (300 μM) mildly prolonged APD90 (10%) and increased IKs, while chronic exposure to dofetilide (5 nM) produced greater prolongation (67%) and no increase in IKs. However, in the siRNA-treated cells, moxifloxacin did not increase IKs and markedly prolonged APD90. CONCLUSION Our data strongly suggest that KCNQ1 expression modulates baseline cardiac repolarization, and the response to IKr block, through mechanisms beyond simply generating IKs.
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Affiliation(s)
- Yuko Wada
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Lili Wang
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Lynn D Hall
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Laura L Short
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Joseph F Solus
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Andrew M Glazer
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232, USA
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Ryan T, Roberts JD. Stem cell models of inherited arrhythmias. NATURE CARDIOVASCULAR RESEARCH 2024; 3:420-430. [PMID: 39196215 DOI: 10.1038/s44161-024-00451-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 08/29/2024]
Abstract
Inherited arrhythmias are a heterogeneous group of conditions that confer risk of sudden death. Many inherited arrhythmias have been linked to pathogenic genetic variants that result in ion channel dysfunction, although current genetic testing panels fail to identify variants in many patients, potentially secondary to their underlying substrates being oligogenic or polygenic. Here we review the current state of knowledge surrounding the cellular mechanisms of inherited arrhythmias generated from stem cell models with a focus on integrating genetic and mechanistic data. The utility and limitations of human induced pluripotent stem cell models in disease modeling and drug development are also explored with a particular focus on examples of pharmacogenetics and precision medicine. We submit that progress in understanding inherited arrhythmias is likely to be made by using human induced pluripotent stem cells to model probable polygenic cases as well as to interrogate the diverse and potentially complex molecular networks implicated by genome-wide association studies.
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Affiliation(s)
- Tammy Ryan
- McMaster University, Hamilton, Ontario, Canada.
| | - Jason D Roberts
- McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute and Hamilton Health Sciences, Hamilton, Ontario, Canada
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Glazer AM, Yang T, Li B, Page D, Fouda M, Wada Y, Lancaster MC, O’Neill MJ, Muhammad A, Gao X, Ackerman MJ, Sanatani S, Ruben PC, Roden DM. Multifocal Ectopic Purkinje Premature Contractions due to neutralization of an SCN5A negative charge: structural insights into the gating pore hypothesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580021. [PMID: 38405820 PMCID: PMC10888965 DOI: 10.1101/2024.02.13.580021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background We identified a novel SCN5A variant, E171Q, in a neonate with very frequent ectopy and reduced ejection fraction which normalized after arrhythmia suppression by flecainide. This clinical picture is consistent with multifocal ectopic Purkinje-related premature contractions (MEPPC). Most previous reports of MEPPC have implicated SCN5A variants such as R222Q that neutralize positive charges in the S4 voltage sensor helix of the channel protein NaV1.5 and generate a gating pore current. Methods and Results E171 is a highly conserved negatively-charged residue located in the S2 transmembrane helix of NaV1.5 domain I. E171 is a key component of the Gating Charge Transfer Center, a region thought to be critical for normal movement of the S4 voltage sensor helix. We used heterologous expression, CRISPR-edited induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), and molecular dynamics simulations to demonstrate that E171Q generates a gating pore current, which was suppressed by a low concentration of flecainide (IC50 = 0.71±0.07 µM). R222Q shifts voltage dependence of activation and inactivation in a negative direction but we observed positive shifts with E171Q. E171Q iPSC-CMs demonstrated abnormal spontaneous activity and prolonged action potentials. Molecular dynamics simulations revealed that both R222Q and E171Q proteins generate a water-filled permeation pathway that underlies generation of the gating pore current. Conclusion Previously identified MEPPC-associated variants that create gating pore currents are located in positively-charged residues in the S4 voltage sensor and generate negative shifts in the voltage dependence of activation and inactivation. We demonstrate that neutralizing a negatively charged S2 helix residue in the Gating Charge Transfer Center generates positive shifts but also create a gating pore pathway. These findings implicate the gating pore pathway as the primary functional and structural determinant of MEPPC and widen the spectrum of variants that are associated with gating pore-related disease in voltage-gated ion channels.
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Affiliation(s)
| | - Tao Yang
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bian Li
- Vanderbilt University Medical Center, Nashville, TN, USA
- Current address: Regeneron Pharmaceuticals Inc., Tarrytown NY, USA. Bian Li contributed to this article as an employee of Vanderbilt University Medical Center and the views expressed do not necessarily represent the views of Regeneron Pharmaceuticals Inc
| | - Dana Page
- Simon Fraser University, Burnaby, BC, Canada
| | | | - Yuko Wada
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Xiaozhi Gao
- Mayo Clinic College of Medicine and Science, Mayo Foundation, Rochester, MN, USA
| | - Michael J. Ackerman
- Mayo Clinic College of Medicine and Science, Mayo Foundation, Rochester, MN, USA
| | | | | | - Dan M. Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
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Asatryan B, Murray B, Gasperetti A, McClellan R, Barth AS. Unraveling Complexities in Genetically Elusive Long QT Syndrome. Circ Arrhythm Electrophysiol 2024; 17:e012356. [PMID: 38264885 DOI: 10.1161/circep.123.012356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Genetic testing has become standard of care for patients with long QT syndrome (LQTS), providing diagnostic, prognostic, and therapeutic information for both probands and their family members. However, up to a quarter of patients with LQTS do not have identifiable Mendelian pathogenic variants in the currently known LQTS-associated genes. This absence of genetic confirmation, intriguingly, does not lessen the severity of LQTS, with the prognosis in these gene-elusive patients with unequivocal LQTS mirroring genotype-positive patients in the limited data available. Such a conundrum instigates an exploration into the causes of corrected QT interval (QTc) prolongation in these cases, unveiling a broad spectrum of potential scenarios and mechanisms. These include multiple environmental influences on QTc prolongation, exercise-induced repolarization abnormalities, and the profound implications of the constantly evolving nature of genetic testing and variant interpretation. In addition, the rapid advances in genetics have the potential to uncover new causal genes, and polygenic risk factors may aid in the diagnosis of high-risk patients. Navigating this multifaceted landscape requires a systematic approach and expert knowledge, integrating the dynamic nature of genetics and patient-specific influences for accurate diagnosis, management, and counseling of patients. The role of a subspecialized expert cardiogenetic clinic is paramount in evaluation to navigate this complexity. Amid these intricate aspects, this review outlines potential causes of gene-elusive LQTS. It also provides an outline for the evaluation of patients with negative and inconclusive genetic test results and underscores the need for ongoing adaptation and reassessment in our understanding of LQTS, as the complexities of gene-elusive LQTS are increasingly deciphered.
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Affiliation(s)
- Babken Asatryan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Brittney Murray
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alessio Gasperetti
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rebecca McClellan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andreas S Barth
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Sharma AK, Singh S, Bhat M, Gill K, Zaid M, Kumar S, Shakya A, Tantray J, Jose D, Gupta R, Yangzom T, Sharma RK, Sahu SK, Rathore G, Chandolia P, Singh M, Mishra A, Raj S, Gupta A, Agarwal M, Kifayat S, Gupta A, Gupta P, Vashist A, Vaibhav P, Kathuria N, Yadav V, Singh RP, Garg A. New drug discovery of cardiac anti-arrhythmic drugs: insights in animal models. Sci Rep 2023; 13:16420. [PMID: 37775650 PMCID: PMC10541452 DOI: 10.1038/s41598-023-41942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023] Open
Abstract
Cardiac rhythm regulated by micro-macroscopic structures of heart. Pacemaker abnormalities or disruptions in electrical conduction, lead to arrhythmic disorders may be benign, typical, threatening, ultimately fatal, occurs in clinical practice, patients on digitalis, anaesthesia or acute myocardial infarction. Both traditional and genetic animal models are: In-vitro: Isolated ventricular Myocytes, Guinea pig papillary muscles, Patch-Clamp Experiments, Porcine Atrial Myocytes, Guinea pig ventricular myocytes, Guinea pig papillary muscle: action potential and refractory period, Langendorff technique, Arrhythmia by acetylcholine or potassium. Acquired arrhythmia disorders: Transverse Aortic Constriction, Myocardial Ischemia, Complete Heart Block and AV Node Ablation, Chronic Tachypacing, Inflammation, Metabolic and Drug-Induced Arrhythmia. In-Vivo: Chemically induced arrhythmia: Aconitine antagonism, Digoxin-induced arrhythmia, Strophanthin/ouabain-induced arrhythmia, Adrenaline-induced arrhythmia, and Calcium-induced arrhythmia. Electrically induced arrhythmia: Ventricular fibrillation electrical threshold, Arrhythmia through programmed electrical stimulation, sudden coronary death in dogs, Exercise ventricular fibrillation. Genetic Arrhythmia: Channelopathies, Calcium Release Deficiency Syndrome, Long QT Syndrome, Short QT Syndrome, Brugada Syndrome. Genetic with Structural Heart Disease: Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia, Dilated Cardiomyopathy, Hypertrophic Cardiomyopathy, Atrial Fibrillation, Sick Sinus Syndrome, Atrioventricular Block, Preexcitation Syndrome. Arrhythmia in Pluripotent Stem Cell Cardiomyocytes. Conclusion: Both traditional and genetic, experimental models of cardiac arrhythmias' characteristics and significance help in development of new antiarrhythmic drugs.
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Affiliation(s)
- Ashish Kumar Sharma
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India.
| | - Shivam Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Mehvish Bhat
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Kartik Gill
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Mohammad Zaid
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Sachin Kumar
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Anjali Shakya
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Junaid Tantray
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Divyamol Jose
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Rashmi Gupta
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Tsering Yangzom
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Rajesh Kumar Sharma
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | | | - Gulshan Rathore
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Priyanka Chandolia
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Mithilesh Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Anurag Mishra
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Shobhit Raj
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Archita Gupta
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Mohit Agarwal
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Sumaiya Kifayat
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Anamika Gupta
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Prashant Gupta
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Ankit Vashist
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Parth Vaibhav
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Nancy Kathuria
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Vipin Yadav
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Ravindra Pal Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, 303121, India
| | - Arun Garg
- MVN University, Palwal, Haryana, India
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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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Padmanabhan S, du Toit C, Dominiczak AF. Cardiovascular precision medicine - A pharmacogenomic perspective. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e28. [PMID: 38550953 PMCID: PMC10953758 DOI: 10.1017/pcm.2023.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 05/16/2024]
Abstract
Precision medicine envisages the integration of an individual's clinical and biological features obtained from laboratory tests, imaging, high-throughput omics and health records, to drive a personalised approach to diagnosis and treatment with a higher chance of success. As only up to half of patients respond to medication prescribed following the current one-size-fits-all treatment strategy, the need for a more personalised approach is evident. One of the routes to transforming healthcare through precision medicine is pharmacogenomics (PGx). Around 95% of the population is estimated to carry one or more actionable pharmacogenetic variants and over 75% of adults over 50 years old are on a prescription with a known PGx association. Whilst there are compelling examples of pharmacogenomic implementation in clinical practice, the case for cardiovascular PGx is still evolving. In this review, we shall summarise the current status of PGx in cardiovascular diseases and look at the key enablers and barriers to PGx implementation in clinical practice.
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Affiliation(s)
- Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Clea du Toit
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
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10
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O’Neill MJ, Wada Y, Hall LD, Mitchell DW, Glazer AM, Roden DM. Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003782. [PMID: 36197721 PMCID: PMC9772980 DOI: 10.1161/circgen.122.003782] [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: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Rare protein-altering variants in SCN5A, KCNQ1, and KCNH2 are major causes of Brugada syndrome and the congenital long QT syndrome. While splice-altering variants lying outside 2-bp canonical splice sites can cause these diseases, their role remains poorly described. We implemented 2 functional assays to assess 12 recently reported putative splice-altering variants of uncertain significance and 1 likely pathogenic variant without functional data observed in Brugada syndrome and long QT syndrome probands. METHODS We deployed minigene assays to assess the splicing consequences of 10 variants. Three variants incompatible with the minigene approach were introduced into control induced pluripotent stem cells by CRISPR genome editing. We differentiated cells into induced pluripotent stem cell-derived cardiomyocytes and studied splicing outcomes by reverse transcription-polymerase chain reaction. We used the American College of Medical Genetics and Genomics functional assay criteria (PS3/BS3) to reclassify variants. RESULTS We identified aberrant splicing, with presumed disruption of protein sequence, in 8/10 variants studied using the minigene assay and 1/3 studied in induced pluripotent stem cell-derived cardiomyocytes. We reclassified 8 variants of uncertain significance to likely pathogenic, 1 variant of uncertain significance to likely benign, and 1 likely pathogenic variant to pathogenic. CONCLUSIONS Functional assays reclassified splice-altering variants outside canonical splice sites in Brugada Syndrome- and long QT syndrome-associated genes.
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Affiliation(s)
- Matthew J. O’Neill
- Vanderbilt University School of Medicine, Medical Scientist
Training Program, Vanderbilt University
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics
(VanCART), Division of Clinical Pharmacology, Department of Medicine
| | - Lynn D. Hall
- Vanderbilt Center for Arrhythmia Research and Therapeutics
(VanCART), Division of Clinical Pharmacology, Department of Medicine
| | - Devyn W. Mitchell
- Vanderbilt Center for Arrhythmia Research and Therapeutics
(VanCART), Division of Clinical Pharmacology, Department of Medicine
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics
(VanCART), Division of Clinical Pharmacology, Department of Medicine
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics
(VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics,
Vanderbilt University Medical Center, Nashville, TN
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11
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Blackwell DJ, Schmeckpeper J, Knollmann BC. Animal Models to Study Cardiac Arrhythmias. Circ Res 2022; 130:1926-1964. [PMID: 35679367 DOI: 10.1161/circresaha.122.320258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cardiac arrhythmias are a significant cause of morbidity and mortality worldwide, accounting for 10% to 15% of all deaths. Although most arrhythmias are due to acquired heart disease, inherited channelopathies and cardiomyopathies disproportionately affect children and young adults. Arrhythmogenesis is complex, involving anatomic structure, ion channels and regulatory proteins, and the interplay between cells in the conduction system, cardiomyocytes, fibroblasts, and the immune system. Animal models of arrhythmia are powerful tools for studying not only molecular and cellular mechanism of arrhythmogenesis but also more complex mechanisms at the whole heart level, and for testing therapeutic interventions. This review summarizes basic and clinical arrhythmia mechanisms followed by an in-depth review of published animal models of genetic and acquired arrhythmia disorders.
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Affiliation(s)
- Daniel J Blackwell
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN
| | - Jeffrey Schmeckpeper
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN
| | - Bjorn C Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN
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12
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Song Y, Zheng Z, Lian J. Deciphering Common Long QT Syndrome Using CRISPR/Cas9 in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Front Cardiovasc Med 2022; 9:889519. [PMID: 35647048 PMCID: PMC9136094 DOI: 10.3389/fcvm.2022.889519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
From carrying potentially pathogenic genes to severe clinical phenotypes, the basic research in the inherited cardiac ion channel disease such as long QT syndrome (LQTS) has been a significant challenge in explaining gene-phenotype heterogeneity. These have opened up new pathways following the parallel development and successful application of stem cell and genome editing technologies. Stem cell-derived cardiomyocytes and subsequent genome editing have allowed researchers to introduce desired genes into cells in a dish to replicate the disease features of LQTS or replace causative genes to normalize the cellular phenotype. Importantly, this has made it possible to elucidate potential genetic modifiers contributing to clinical heterogeneity and hierarchically manage newly identified variants of uncertain significance (VUS) and more therapeutic options to be tested in vitro. In this paper, we focus on and summarize the recent advanced application of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) combined with clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9) in the interpretation for the gene-phenotype relationship of the common LQTS and presence challenges, increasing our understanding of the effects of mutations and the physiopathological mechanisms in the field of cardiac arrhythmias.
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Affiliation(s)
- Yongfei Song
- Department of Cardiovascular, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
- Yongfei Song
| | - Zequn Zheng
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
- Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
| | - Jiangfang Lian
- Department of Cardiovascular, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
- Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
- *Correspondence: Jiangfang Lian
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