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      Plural molecular and cellular mechanisms of pore domain KCNQ2 encephalopathy

      research-article
      1 , 2 , 1 , 1 , 3 , 4 , 5 , 5 , 6 , 5 , 7 , 7 , 1 , 1 , 8 , 1 , 3 , 4 , 9 , 9 , 10 , 11 , 12 , 1 , 8 , 13 , 14 , 14 , 1 , 2 , 8 , 3 , 1 , 8 , 5 , 1 , 2 , 8 ,
      ,
      eLife
      eLife Sciences Publications, Ltd
      channelopathy, axon initial segment, brain development, epilepsy, precision medicine, Human, Mouse

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          Abstract

          KCNQ2 variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, and KCNQ2 G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. Kcnq2 G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal cell KCNQ2 and KCNQ3 immunolabeling was significantly shifted from axon initial segments to neuronal somata. Despite normal mRNA levels, G256W/+ mouse KCNQ2 protein levels were reduced by about 50%. Our findings indicate that G256W pathogenicity results from multiplicative effects, including reductions in intrinsic conduction, subcellular targeting, and protein stability. These studies provide evidence for an unexpected and novel role for the KCNQ2 pore turret and introduce a valid animal model of KCNQ2 encephalopathy. Our results, spanning structure to behavior, may be broadly applicable because the majority of KCNQ2 encephalopathy patients share variants near the selectivity filter.

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          Most cited references102

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            The mutational constraint spectrum quantified from variation in 141,456 humans

            Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes 1 . Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.
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              UCSF ChimeraX: Meeting modern challenges in visualization and analysis

              UCSF ChimeraX is next‐generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting‐edge experimental methods, while providing advanced options for high‐quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax / for Windows, Mac, and Linux.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                06 January 2025
                2025
                : 13
                : RP91204
                Affiliations
                [1 ] Department of Neurology, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [2 ] Department of Molecular and Human Genetics, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [3 ] Department of Neurology, Children’s Colorado, University of Colorado ( https://ror.org/00mj9k629) Aurora United States
                [4 ] Department of Pediatrics, Children’s Colorado, University of Colorado ( https://ror.org/00mj9k629) Aurora United States
                [5 ] Department of Physiology and Neurobiology, University of Connecticut ( https://ror.org/02der9h97) Storrs United States
                [6 ] Department of Pharmacology, Northwestern University Feinberg School of Medicine Chicago United States
                [7 ] KCNQ2 Cure Alliance Denver United States
                [8 ] Department of Neuroscience, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [9 ] The Rare Disease Translational Center & Technology Evaluation and Development, The Jackson Laboratory ( https://ror.org/021sy4w91) Bar Harbor United States
                [10 ] Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [11 ] CryoEM Core, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [12 ] Department of Molecular and Cellular Biology, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [13 ] Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine ( https://ror.org/02pttbw34) Houston United States
                [14 ] Center for Human Genetics Tübingen Tübingen Germany
                Nathan Kline Institute United States
                National Institute of Neurological Disorders and Stroke ( https://ror.org/01s5ya894) United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Baylor College of Medicine Houston United States
                Author notes
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0001-5675-7932
                https://orcid.org/0000-0001-5527-3047
                https://orcid.org/0000-0002-4935-1122
                https://orcid.org/0000-0003-0252-9760
                https://orcid.org/0000-0002-3993-966X
                https://orcid.org/0000-0003-3045-7901
                https://orcid.org/0000-0003-3672-8442
                Article
                91204
                10.7554/eLife.91204
                11703504
                39761077
                e797c723-66c2-4a8d-af2d-46a1b55d8f01
                © 2024, Abreo et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 02 January 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100001454, American Epilepsy Society;
                Award ID: Predoctoral Fellowship
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100002736, Citizens United for Research in Epilepsy;
                Award ID: Pediatric Epilepsy Award
                Award Recipient :
                Funded by: Jack Pribaz Foundation;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R01 NS49119
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R01 NS101596
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R01 NS108874
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: K08 NS096029
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000025, National Institute of Mental Health;
                Award ID: MH126953
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: U54 OD020351
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R01 NS29709
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: U54 NS108874
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: P30 CA034196
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100009633, Eunice Kennedy Shriver National Institute of Child Health and Human Development;
                Award ID: P50 HD103555
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: R01 GM143380
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000050, National Heart, Lung, and Blood Institute;
                Award ID: R01 HL162842
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000928, Welch Foundation;
                Award ID: Q-2173-20230405
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004917, Cancer Prevention and Research Institute of Texas;
                Award ID: RP190602
                Award Recipient :
                Funded by: KCNQ2 Cure Alliance;
                Award Recipient :
                Funded by: Miles Family Fund;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: K08 NS110924
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Genetics and Genomics
                Neuroscience
                Custom metadata
                A single amino acid change in a neuronal ion channel called KCNQ2 blocks ion flow, prevents protein localization on axons, and results in severe epilepsy and slowed neurological development.
                prc

                Life sciences
                channelopathy,axon initial segment,brain development,epilepsy,precision medicine,human,mouse
                Life sciences
                channelopathy, axon initial segment, brain development, epilepsy, precision medicine, human, mouse

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