Enhancers implicate new genes in QT interval below GWAS detection threshold
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE53567 | GEO | 2014/10/10
SECONDARY ACCESSION(S): PRJNA232387
REPOSITORIES: GEO
Similar Datasets
Project description:Our goal is to identify high-confidence candidate genes associated with sub-threshold QT interval loci. We predicted enhancer-promoter targets using two different methods. 1) We used the correlation in activity between enhancers and transcribed genes across 59 human cell lines and tissues to identify significantly correlated enhancer-promoter pairs that represent potential regulatory interactions. 2) We used chromosome conformation capture followed by high-throughput sequencing (4C-seq) to probe physical enhancer-promoter interactions.
2014-10-10 | E-GEOD-53567 | biostudies-arrayexpress
Project description:Genome-wide association studies (GWAS) have suggested that sequence variation in cis-regulatory elements (CREs) modulate common disease risk and trait variation. However, identification of the majority of these causal variants and their mechanism of action have remained significant challenges. We used reporter assays for all common variants at the QT interval associated SCN5A GWAS locus with the goal of identifying causal variants for the association. A target region of ~500kb containing SCN5A was defined based on recombination hotspots (rate>10cM/Mb; estimated from HapMap) flanking the 5 independent QT interval GWAS hits. Within this region, all common variants (minor allele frequency >5%), from the 1000 Genomes European ancestry populations, in moderate linkage disequilibrium (LD; r2>0.3) with any of the 5 sentinel hits, were selected for analyses. Of a total 121 variants selected, 112 variants in 104 amplicons passed primer design (amplicon size 256-617bp; median 397bp), with both alleles of 106 variants successfully cloned along with flanking sequences into 98 amplicons upstream of a minimal promoter-driven firefly luciferase gene in pGL4.23. Cardiomyocyte cells, AC16 (human) and HL1 (mouse), were transfected with test constructs and Renilla luciferase vector (for transfection normalization) in triplicate; luciferase assays were performed 24h later. All cloning and reporter assays were performed in 96- and 24-well plates. In reporter assays across the two cell lines, compared to empty vector, 37 amplicons showed enhancer activity (z-score>99 %tile), with a concordance rate of ~70%. Of these 37 enhancer CREs, 9 overlapped open chromatin regions (DNase-seq peaks) observed in adult human heart tissue, largest among all human tissues evaluated by the RoadMap Epigenomics project. Of these 37 enhancer CREs, 12 showed allelic difference in reporter activity (P<0.05), thus identifying at least one enhancer CRE variant in high-to-moderate LD with each of the 5 sentinel hits. Using GTEx heart left ventricle (n=190) gene expression data, we showed correlation between SCN5A expression and the number of QT interval prolonging alleles across the 5 index SNPs. We are currently assessing the binding of cardiac nuclear factors at the 12 enhancer CRE variants by gel-shift assays and the effect of CRISPR-Cas9 mediated CRE deletion on SCN5A expression in AC16 and HL1 cells, an analyses helped by evaluation of AC16 and HL1 cells by RNA-seq, ATAC-seq and karyotyping. Thus, independent of the publicly available epigenomic data, which are of limited cell-type relevance, an unbiased in vitro reporter screen for CREs overlapping all common variants associated with QT interval at the SCN5A GWAS locus identified 12 common cis-regulatory variants that map to cardiac open chromatin regions and correlate with SCN5A cardiac expression.
2019-04-22 | GSE109716 | GEO
Project description:MULTIPLE SCN5A ENHANCERS MODULATE CARDIAC GENE EXPRESSION AND QT INTERVAL VARIATION
| PRJNA431786 | ENA
Project description:To date, KCNH2 mutations identified in patients with long QT syndrome type 2 (LQT2) have been extensively studied using heterologous expression systems. While these systems allow for the evaluation of the pathogenicity of specific hERG mutations through the overexpression of mutant channels, they fail to recapitulate the full spectrum of electrophysiological alterations and ion channel remodeling that occur in cardiomyocytes under physiological conditions in LQT. Existing zebrafish and rodent models are also limited in their ability to faithfully model human QT interval abnormalities due to substantial differences in lifespan, size, anatomy, and physiology. For instance, rodents exhibit a much higher heart rate and significantly shorter action potential duration (APD) than humans. Moreover, IKr is the major repolarizing current in human ventricles, whereas its inhibition in rodents has minimal impact on ventricular repolarization, rendering genetic mouse models inadequate for the study of LQT2. Thus, there is a critical need to develop animal models that can more accurately mimic human inherited arrhythmias. To address this gap, we generated a miniature pig model of LQT2, capitalizing on the physiological similarities to humans, as well as advantages in breeding and genome editing compared to non-human primates. To investigate the mechanisms by which KCNH2 mutations lead to LQT, we performed single-nucleus RNA sequencing to compare the transcriptomes of ventricular tissues from KCNH2-mutant pigs and wild-type controls.
2025-09-11 | GSE307648 | GEO
Project description:To date, KCNH2 mutations identified in LQT2 patients have been heavily studied by heterologous expression systems, allowing for pathogenicity evaluation of a certain hERG mutation by overexpressing mutant channels. However, they fall short in mimicking the full spectrum of electrophysiological changes and ion channel remodeling that occur in cardiomyocytes under physiological conditions in the context of LQT. Due to the marked differences in the lifespan, size, anatomy and physiology from humans, current zebrafish and rodent models cannot fully mimic the abnormal QT interval diseases 2. For instance, rodents exhibit an extremely higher heart rate and a much shorter action potential duration (APD) compared to humans. IKr is the predominant repolarizing current in human ventricles while inhibition of IKr in rodents has no significant effect on ventricular repolarization, making it infeasible to study LQT2 by genetic mouse model 3. Hence, there is a crucial need to construct an animal model capable of mimicking human inherited arrhythmia conditions. To address the above scientific question, we chose to create a miniature pig model. Given many physiological similarities with humans, and breeding and genome editing advantages (when compared to non-human primates), To explore the mechanism underlying mutation of KCNH2 caused LQT, we compared the transcriptomes of KCNH2-mut pigs and WT controls
2025-02-03 | GSE288082 | GEO
Project description:Peribacillus frigoritolerans QT-140 TE12474 genome sequencing
| PRJNA1115250 | ENA
Project description:Prolonged electrocardiographic indices reflecting myocardial impulse conduction and repolarization are risk factors for sudden cardiac death and drug-induced arrhythmia. The PR-interval, QRS-duration and QT-interval are heritable traits influenced by multiple genetic and environmental factors. The genetic underpinnings of these traits are still largely unknown. In this study, we leveraged the variability in cardiac gene expression and the variation in PR-, QRS- and QT-intervals among F2 mice harboring the cardiac sodium ion-channel mutation Scn5a-1798insD/+ derived from the 129P2-Scn5a1798insD/+ and FVB/NJ-Scn5a1798insD/+ cross, to isolate novel genes and biological pathways impacting on cardiac conduction and repolarization.
2012-12-01 | GSE27236 | GEO
Project description:BackgroundApple watch-derived electrocardiogram (awECG) may help identify prolongation of corrected QT (QTc) interval. This study aimed to determine its usefulness for assessment of prolongation of QTc interval in children and adolescents with long QT syndrome (LQTS).MethodsChildren and adolescents with and without LQTS were recruited for measurement of QTc intervals based on standard 12-lead (sECG) and awECG lead I, II and V5 tracings. Bland-Altman analysis of reproducibility, concordance assessment of T wave morphologies, and receiver operating characteristic (ROC) analysis of sensitivity and specificity of awECG-derived QTc interval for detecting QTc prolongation were performed.ResultsForty-nine patients, 19 with and 30 without LQTS, aged 3-22 years were studied. The intraclass correlation coefficient was 1.00 for both intra- and inter-observer variability in the measurement of QTc interval. The awECG- and sECG-derived QTc intervals correlated strongly in all three leads (r = 0.90-0.93, all p < 0.001). Concordance between awECG and sECG in assessing T wave morphologies was 84% (16/19). For detection of QTc prolongation, awECG lead V5 had the best specificity (94.4% and 87.5%, respectively) and positive predictive value (87.5% and 80.0%, respectively), and for identification of patients with LQTS, awECG leads II and V5 had the greatest specificity (92.3%-94.1%) and positive predictive value (85.7% to 91.7%) in both males and females.ConclusionsApple Watch leads II and V5 tracings can be used for reproducible and accurate measurement of QTc interval, ascertainment of abnormal T wave morphologies, and detection of prolonged QTc interval in children and adolescents with LQTS.
| S-EPMC10279543 | biostudies-literature
Project description:QT interval prolongation is a heritable risk factor for ventricular arrhythmias and can predispose to sudden death. Most genome-wide association studies (GWAS) of QT were performed in European ancestral populations, leaving other groups uncharacterized. Herein we present the first QT GWAS of Hispanic/Latinos using data on 15,997 participants from four studies. Study-specific summary results of the association between 1000 Genomes Project (1000G) imputed SNPs and electrocardiographically measured QT were combined using fixed-effects meta-analysis. We identified 41 genome-wide significant SNPs that mapped to 13 previously identified QT loci. Conditional analyses distinguished six secondary signals at NOS1AP (n = 2), ATP1B1 (n = 2), SCN5A (n = 1), and KCNQ1 (n = 1). Comparison of linkage disequilibrium patterns between the 13 lead SNPs and six secondary signals with previously reported index SNPs in 1000G super populations suggested that the SCN5A and KCNE1 lead SNPs were potentially novel and population-specific. Finally, of the 42 suggestively associated loci, AJAP1 was suggestively associated with QT in a prior East Asian GWAS; in contrast BVES and CAP2 murine knockouts caused cardiac conduction defects. Our results indicate that whereas the same loci influence QT across populations, population-specific variation exists, motivating future trans-ethnic and ancestrally diverse QT GWAS.
| S-EPMC5719082 | biostudies-literature
Project description:Objective. Motor-evoked potentials (MEPs) are among the most prominent responses to brain stimulation, such as supra-threshold transcranial magnetic stimulation and electrical stimulation. Understanding of the neurophysiology and the determination of the lowest stimulation strength that evokes responses requires the detection of even smaller responses, e.g. from single motor units. However, available detection and quantization methods suffer from a large noise floor. This paper develops a detection method that extracts MEPs hidden below the noise floor. With this method, we aim to estimate excitatory activations of the corticospinal pathways well below the conventional detection level.Approach. The presented MEP detection method presents a self-learning matched-filter approach for improved robustness against noise. The filter is adaptively generated per subject through iterative learning. For responses that are reliably detected by conventional detection, the new approach is fully compatible with established peak-to-peak readings and provides the same results but extends the dynamic range below the conventional noise floor.Main results. In contrast to the conventional peak-to-peak measure, the proposed method increases the signal-to-noise ratio by more than a factor of 5. The first detectable responses appear to be substantially lower than the conventional threshold definition of 50µV median peak-to-peak amplitude.Significance. The proposed method shows that stimuli well below the conventional 50µV threshold definition can consistently and repeatably evoke muscular responses and thus activate excitable neuron populations in the brain. As a consequence, the input-output (IO) curve is extended at the lower end, and the noise cut-off is shifted. Importantly, the IO curve extends so far that the 50µV point turns out to be closer to the center of the logarithmic sigmoid curve rather than close to the first detectable responses. The underlying method is applicable to a wide range of evoked potentials and other biosignals, such as in electroencephalography.
| S-EPMC10155352 | biostudies-literature