Predicting the Functional Impact of KCNQ1 Variants of Unknown Significance

Li, Bian; Mendenhall, Jeffrey L.; Kroncke, Brett M.; Taylor, Keenan C.; Huang, Hui; Vanoye, Carlos G.; Blume, Jeffrey D.; George, Alfred L.; Sanders, Charles R.; Meiler, Jens

doi:10.1161/circgenetics.117.001754

Cited by 40 publications

(57 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach may be extended to study additional SCN5A variants, including gain of function Long QT-associated variants or additional variants observed in population sequencing efforts. Accurate classification of the large number of variants in arrhythmiaassociated genes will require integrating data from multiple different model systems, such as patch clamping, 16,17 induced pluripotent stem cell-derived cardiomyocytes, [49][50][51] structural and computational models, 12,52,53 and ultra-high-throughput multiplexed assays. [54][55][56] Limitations: This study assays variants in a heterologous expression system.…”

Section: High-throughput Approaches To Variant Classificationmentioning

confidence: 99%

High-throughput reclassification ofSCN5Avariants

Glazer

Wada

Bian

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Rationale: 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 (VUS). The designation of VUS is a barrier to the use of sequence data in clinical care. Objective:We selected 83 variants for study: 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 patients 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.Methods and Results: Ten previously studied variants had functional properties concordant with published manual patch clamp data. All 10 suspected benign variants had wildtype-like function. 22 suspected BrS variants had loss of channel function (<10% normalized peak current) and 23 variants had partial loss of function (10-50% normalized peak current). The 73 previously unstudied variants were initially classified as likely benign (n=2), likely pathogenic (n=11), or VUS (n=60). After the patch clamp studies, 16 variants were benign/likely benign, 47 were pathogenic/likely pathogenic, and only 10 were still VUS. 8/22 loss of function variants were partially rescuable by incubation at lower temperature or pretreatment with a sodium channel blocker. Structural modeling identified likely mechanisms for loss of function including altered thermostability, and disruptions to alpha helices, disulfide bonds, or the permeation pore. Conclusions:High-throughput automated patch clamping enabled the reclassification of the majority of tested VUS's in SCN5A.

show abstract

Section: High-throughput Approaches To Variant Classificationmentioning

confidence: 99%

High-throughput reclassification ofSCN5Avariants

Glazer

Wada

Bian

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…While progress in the functional characterization of LQTS-associated mutations has been made (12)(13)(14) the mechanistic molecular basis of channel dysfunction for most KCNQ1 mutations is still unclear. The dearth of direct experimental data that can help to determine how mutations alter KCNQ1 structure and function has prompted computational modeling approaches (16,59).…”

Section: Rosetta-predicted Stability Changes In Kcnq1 Models Correlatmentioning

confidence: 99%

“…About 50% of the genetic cases of long QT syndrome (LQTS), which predispose children and young adults to sudden cardiac death, are associated with dominant mutations in KCNQ1 (type 1 LQTS) (11). While progress in the functional characterization of LQTS-associated mutations has been made (12)(13)(14)(15), the molecular mechanisms underlying channel dysfunction remain difficult to assess without the availability of high-accuracy structural data. A detailed molecular understanding is needed to improve decision making for new unclassified KCNQ1 mutations and to support the development of new anti-arrhythmic therapeutics.…”

Section: Introductionmentioning

confidence: 99%

Upgraded molecular models of the human KCNQ1 potassium channel

Künze

Duran

Woods

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

The voltage-gated potassium channel KCNQ1 (KV7.1) assembles with the KCNE1 accessory protein to generate the slow delayed rectifier current, IKS, which is critical for membrane repolarization as part of the cardiac action potential. Loss-of-function (LOF) mutations in KCNQ1 are the most common cause of congenital long QT syndrome (LQTS), type 1 LQTS, an inherited genetic predisposition to cardiac arrhythmia and sudden cardiac death. A detailed structural understanding of KCNQ1 is needed to elucidate the molecular basis for KCNQ1 LOF in disease and to enable structure-guided design of new anti-arrhythmic drugs. In this work, advanced structural models of human KCNQ1 in the resting/closedand activated/open states were developed by Rosetta homology modeling guided by newly available experimentally-based templates: X. leavis KCNQ1 and resting voltage sensor structures. Using molecular dynamics (MD) simulations, the models' capability to describe experimentally established channel properties including state-dependent voltage sensor gating charge interactions and pore conformations, PIP2 binding sites, and voltage sensorpore domain interactions were validated. Rosetta energy calculations were applied to assess the models' utility in interpreting mutation-evoked KCNQ1 dysfunction by predicting the change in protein thermodynamic stability for 50 characterized KCNQ1 variants with mutations located in the voltage-sensing domain. Energetic destabilization was successfully predicted for folding-defective KCNQ1 LOF mutants whereas wild type-like mutants had no significant energetic frustrations, which supports growing evidence that mutation-induced protein destabilization is an especially common cause of KCNQ1 dysfunction. The new KCNQ1 Rosetta models provide helpful tools in the study of the structural mechanisms of KCNQ1 function and can be used to generate structurebased hypotheses to explain KCNQ1 dysfunction. Author SummaryCardiac rhythm is maintained by synchronized electrical impulses conducted throughout the heart. The potassium ion channel KCNQ1 is important for the repolarization phase of the cardiac action potential that underlies these electrical impulses. Heritable mutations in KCNQ1 can lead to channel loss-offunction (LOF) and predisposition to a life-threatening cardiac arrhythmia. Knowledge of the threedimensional structure of KCNQ1 is important to understand how mutations lead to LOF and to support structurally-guided design of new anti-arrhythmic drugs. In this work, we present the development and validation of molecular models of human KCNQ1 inferred by homology from the structure of frog KCNQ1.Models were developed for the open channel state in which potassium ions can pass through the channel and the closed state in which the channel is not conductive. Using molecular dynamics simulations, interactions in the voltage-sensing and pore domain of KCNQ1 and with the membrane lipid PIP2 were analyzed. Energy calculations for KCNQ1 mutations in the voltage-sensing domain reveled that most of 3 the mutations t...

show abstract

“…The EP data identified 32 KCNQ1 mutants that failed to yield at least 65% of peak WT K + channel current and were therefore classified as LOF. The 65% value chosen for the cutoff is based on the approximate boundary between the range of currents observed for known LQTS mutants and benign mutants based on an extensive literature review (see also (16)). The underlying mechanisms for LOF in these 32 mutants were not established by the functional data alone, leading to the experiments of the present study.…”

Section: Structure Mapping Of 51 Human Kcnq1 Variantsmentioning

confidence: 99%

“…More than 600 KCNQ1 mutations associated with LQTS have been identified and this number continues to grow (8)(9)(10). While progress in functional characterization of LQTS-associated KCNQ1 mutations has been made (11)(12)(13)(14)(15)(16), the mechanistic basis of channel dysfunction for most mutations is not known.…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of KCNQ1 Channel Dysfunction in Long QT Syndrome Involving Voltage Sensor Domain Mutations

Huang

Kuenze

Smith

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

Loss-of-function (LOF) mutations in human KCNQ1 are responsible for susceptibility to a lifethreatening heart rhythm disorder, the congenital long-QT syndrome (LQTS). Hundreds of KCNQ1 mutations have been identified, but the molecular mechanisms responsible for impaired function are poorly understood. Here, we investigated the impact of 51 KCNQ1 variants located within the voltage sensor domain (VSD), with an emphasis on elucidating effects on cell surface expression, protein folding and structure. For each variant, the efficiency of trafficking to the plasma membrane, the impact of proteasome inhibition, and protein stability were assayed. The results of these experiments, combined with channel functional data, provided the basis for classifying each mutation into one of 6 mechanistic categories. More than half of the KCNQ1 LOF mutations destabilize the structure of the VSD, resulting in mistrafficking and degradation by the proteasome, an observation that underscores the growing appreciation that mutation-induced destabilization of membrane proteins may be a common human disease mechanism. Finally, we observed that 5 of the folding-defective LQTS mutants are located in the VSD S0 helix, where they interact with a number of other LOF mutation sites in other segments of the VSD. These observations reveal a critical role for the S0 helix as a central scaffold to help organize and stabilize the KCNQ1 VSD and, most likely, the corresponding domain of many other ion channels.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

show abstract

Predicting the Functional Impact of KCNQ1 Variants of Unknown Significance

Cited by 40 publications

References 48 publications

High-throughput reclassification ofSCN5Avariants

High-throughput reclassification ofSCN5Avariants

Upgraded molecular models of the human KCNQ1 potassium channel

Mechanisms of KCNQ1 Channel Dysfunction in Long QT Syndrome Involving Voltage Sensor Domain Mutations

Contact Info

Product

Resources

About