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O’Neill MJ, Ng CA, Aizawa T, Sala L, Bains S, Denjoy I, Winbo A, Ullah R, Shen Q, Tan CY, Kozek K, Vanags LR, Mitchell DW, Shen A, Wada Y, Kashiwa A, Crotti L, Dagradi F, Musu G, Spazzolini C, Neves R, Bos JM, Giudicessi JR, Bledsoe X, Lancaster M, Glazer AM, Roden DM, Leenhardt A, Salem JE, Earle N, Stiles R, Agee T, Johnson CN, Horie M, Skinner J, Extramiana F, Ackerman MJ, Schwartz PJ, Ohno S, Vandenberg JI, Kroncke BM. Prognostic Value of Multiplexed Assays of Variant Effect and Automated Patch-clamping for KCNH2-LQTS Risk Stratification. medRxiv 2024:2024.02.01.24301443. [PMID: 38370760 PMCID: PMC10871451 DOI: 10.1101/2024.02.01.24301443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Long QT syndrome (LQTS) is a lethal arrhythmia condition, frequently caused by rare loss-of-function variants in the cardiac potassium channel encoded by KCNH2. Variant-based risk stratification is complicated by heterogenous clinical data, incomplete penetrance, and low-throughput functional data. Objective To test the utility of variant-specific features, including high-throughput functional data, to predict cardiac events among KCNH2 variant heterozygotes. Methods We quantified cell-surface trafficking of 18,323 variants in KCNH2 and recorded potassium current densities for 506 KCNH2 variants. Next, we deeply phenotyped 1150 KCNH2 missense variant patients, including ECG features, cardiac event history (528 total cardiac events), and mortality. We then assessed variant functional, in silico, structural, and LQTS penetrance data to stratify event-free survival for cardiac events in the study cohort. Results Variant-specific current density (HR 0.28 [0.13-0.60]) and estimates of LQTS penetrance incorporating MAVE data (HR 3.16 [1.59-6.27]) were independently predictive of severe cardiac events when controlling for patient-specific features. Risk prediction models incorporating these data significantly improved prediction of 20 year cardiac events (AUC 0.79 [0.75-0.82]) over patient-only covariates (QTc and sex) (AUC 0.73 [0.70-0.77]). Conclusion We show that high-throughput functional data, and other variant-specific features, meaningfully contribute to both diagnosis and prognosis of a clinically actionable monogenic disease.
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Affiliation(s)
- Matthew J. O’Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
- These authors contributed equally
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
- These authors contributed equally
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Sahej Bains
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Annika Winbo
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Rizwan Ullah
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qianyi Shen
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Chek-Ying Tan
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Krystian Kozek
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loren R. Vanags
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Devyn W. Mitchell
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alex Shen
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
- Department of Medicine and Surgery, University Milano Bicocca, Milan, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Giulia Musu
- 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
| | - Raquel Neves
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - J. Martijn Bos
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - John R. Giudicessi
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Xavier Bledsoe
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
| | - Megan Lancaster
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - 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
| | - Nikki Earle
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Rachael Stiles
- Department of Cardiology, Waikato Hospital, Hamilton, New Zealand
| | - Taylor Agee
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA
| | | | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Jonathan Skinner
- Sydney Children’s Hospital Network, University of Sydney, Sydney, Australia
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Michael J. Ackerman
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Peter J. Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Brett M. Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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