CAV1-A Susceptibility Gene for Atrial Fibrillation: The Impact of Coding and Noncoding Variants.

Uncovering an Intermediate Phenotype Associated With rs2200733 at 4q25 in Lone Atrial Fibrillation

Introduction: Atrial fibrillation (AF) is the most common sustained arrhythmia and is associated with substantial morbidity and mortality. AF is known to have a heritable component, with >100 associated common variant loci. Rare variant studies have yielded limited robust associations for AF. We aimed to utilize large genome and exome sequencing data to discover rare genetic variants conferring large effects on AF risk. Methods: We meta-analyzed genome and exome sequencing data from 36 studies, including TOPMed, CCDG, UK Biobank and FOURIER. We performed exome-wide gene burden testing of rare (MAF<0.1%) loss-of-function and deleterious missense variants, and single variant testing of low-frequency and rare (MAF<1%) coding variants. Within genome sequenced samples, we performed gene burden testing of rare structural variants. Novel signals were replicated in MyCode. Finally, we functionally validated a novel gene by siRNA knockdown in pluripotent-induced atrial cardiomyocytes. Results: We included 52,416 AF cases and 277,762 controls, of which 49.6% were female, 83.4% were of European ancestry, and the mean baseline age was 56 years. In analysis of rare coding variation, we identified 4 novel genes associated with AF, including MYBPC3 (OR 3.5, P =2.1x10 -15 ), LMNA (OR 5.7, P =8.8x10 -11 ), PKP2 (OR 1.9, P =5.2x10 -8 ) and KDM5B (OR 2.3, P =3.0x10 -6 ). These signals were robust to removal of heart failure and cardiomyopathy cases and were replicated in independent datasets. Single variant analysis identified 2 novel signals in FAM189A2 (OR 3.9, P =7.86x10 -8 ) and ZFC3H1 (OR 5.9, P =9.7x10 -8 ). Rare deletions in CTNNA3 (OR 4.5, P =7.0x10 -9 ) were associated with increased AF risk and were supported by independent coding variant analyses, while duplications of GATA4 (OR 0.24, P =2.1x10 -5 ) were associated with reduced AF risk. In functional studies, knockdown of KDM5B resulted in shortening of the atrial action potential duration. Conclusions: Our analyses show the contribution of rare coding and structural variants to AF risk, highlight the shared genetic pathways underlying cardiomyopathy and AF, and implicate the histone demethylase gene KDM5B in AF susceptibility. In sum, we expanded our understanding of the rare variant architecture of this common arrhythmia.

Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma

The prevalence of adult congenital heart disease (ACHD) has risen markedly over the past 2 decades, with the number of adults now rivaling the number of children with severe defects.1 This is, perhaps, not surprising given that current care allows nearly 90% of infants born with heart defects to thrive into their adult years.1,2 This remarkable triumph is tempered, however, by the realization that early interventions were reparative and not curative. Numerous complications may surface years after uneventful childhood courses, justifying vigilant clinical follow-up throughout adulthood. The 12-lead ECG remains an invaluable cornerstone in the clinical appraisal of adults with congenital heart disease that, in certain circumstances, provides diagnostic and/or prognostic information. The present review imparts a clinical perspective to ECG interpretation in ACHD, emphasizing practical and pathogenomonic findings in the more frequently encountered congenital defects in adults. Anatomic features of the conduction system relevant to ECG findings in ACHD are summarized, including variations in the location of the sinus node, atrioventricular (AV) node, and His-Purkinje system. Thereafter, pertinent ECG features are highlighted for common subtypes of ACHD (Table). Examples are provided throughout for illustration. View this table: Table. Typical ECG Features in Common Forms of ACHD ### Sinus Node In the morphologically normal heart, a crescent-shaped sinus node is characteristically located epicardially along the lateral aspect of the superior cavoatrial junction. It generates a P-wave axis typically between 15° and 75°. Most patients with ACHD have normally positioned atrial chambers, called atrial situs solitus, with normal sinus node location. The position of the sinus node may, however, vary with the atrial chambers and their appendages. #### Juxtaposition of the Atrial Appendages In juxtaposition of the atrial appendages, both appendages are on the same side of the arterial pedicle rather than each being ipsilateral to its respective atrium. Left juxtaposition, with left-sided atrial appendages, frequently accompanies tricuspid atresia and has …

Interpreting the mechanism of genetic variants is one of the greatest challenges impeding the analysis of the rapidly increasing volume of patients' genomic data, particularly for rare variants that do not reach GWAS significance due to low population frequencies. There are 153 GWAS hits for altered kidney function due to commonly inherited genetic variants, yet minimal knowledge of the mechanism of these variations is known at the current time. Utilizing a computational strategy to filter 3,921 genetic variants that are found within linkage disequilibrium of the GWAS hits we have nominated 4 damaging protein coding variants and more importantly 30 noncoding variants predicted to alter transcription factor based gene regulation. One of these noncoding variants, rs17319721 associated with risk of chronic kidney disease (CKD), is found near the SHROOM3 gene and is thought to play a functional role in podocytes of the kidney. In this study we show this variant falls upstream of a novel transcriptional start site that results in a shorter SHROOM3 isoform lacking the PDZ domain. This variant disrupts binding of TCF7L2 in podocytes and the single variant (rs17319721) alters transcription levels of SHROOM3 as determined by variant mutation into the genome using CRISPR/Cas9 technology.To begin deciphering the role of rare variants within human genomes we performed a full assessment of the ExAC database for >60,000 sequenced human exomes, revealing several coding variants in SHROOM3 that are likely to alter function, including a coding variant (P1244L) we show to have association to CKD in humans. We determined that P1244L attenuates the interaction of SHROOM3 with 14‐3‐3 binding and alters signaling through the Hippo pathway, a known mediator of CKD. Animal studies show a loss of function in zebrafish kidney due to the variant, resulting in increased glomerular permeability. These data demonstrate multiple new SHROOM3‐dependent genetic and molecular mechanisms that regulate CKD and demonstrate a novel analytical pipeline with broad application to systematically characterizing risk mechanisms of CKD and other complex diseases.Support or Funding InformationSupport for this study was from NIH‐K01ES025435 (to JWP), NIH‐R01HL069321 (to HJJ), NIH‐R01EY014167 (to BL), the Collaborative Research Centre 1093 through the Deutsche Forschungsgemeinschaft (DFG, to CO), and HudsonAlpha Institute for Biotechnology.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5′ UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5′ UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci.

The present study is to generate a mouse model of a p53 noncoding germline polymorphism that predisposes human carriers to multiple types of cancer. p53, encoded by TP53, is recognized as the guardian of the human genome. Three distinct sets of alterations occur at the TP53 locus, which spans ∼20kb in the human genome: tumor-associated somatic mutations, germline mutations causing Li-Fraumeni syndrome, and germline polymorphisms. The first two types of TP53 mutations occur in the coding sequence (CDS) and produce mutant p53 proteins that lack most or all of the normal tumor suppressive functions and often confer oncogenic properties. By contrast, only a few of the >200 naturally occurring germline variants of TP53 in human populations cause measurable perturbation of p53 function. More than 90% of TP53 germline variants occur in 10 introns alleged to have no cancer-related biological consequences. None of the 20 variants in the TP53 CDS have been reproducibly linked to cancer predisposition. Genome-wide association studies (GWAS) reported no significant association between any germline TP53 polymorphism and any cancer with a P value ≤ 10-7 (a threshold for genome-wide significance) until a single nucleotide polymorphism (SNP) rs78378222 was found to be associated strongly with skin basal cell carcinoma. rs78378222 is located in the fifth nucleotide of the TP53 polyadenylation signal (PAS) that is required for polyadenylation machinery recognition and subsequent cleavage and polyadenylation of mRNA. The risk-associated minor allele is a “C”, resulting in an alternative PAS (AATACA) instead of the canonical PAS (AATAAA). This variant is also associated with an increased risk of colorectal adenoma, prostate cancer, glioma, and esophageal squamous cell carcinoma. It is notable that cancer susceptibility of this p53 noncoding variant does not mirror that of p53 coding germline mutations (patients with Li-Fraumeni syndrome develop predominantly breast cancer, brain tumors, acute leukemia, sarcoma, and adrenal cortical carcinoma). Specifically, carriers with the p53 PAS variant are not predisposed to breast cancer. The p53 PAS variant is uniquely positioned among cancer-susceptibility alleles: (i) low frequency (∼2% in the general populations), (ii) intermediate cancer risk (odds ratio 1.39-3.54), and (iii) predisposing carriers to multiple types of cancer. To mimic this naturally occurring human variant, we have generated a mouse line with a p53 gene carrying the alternative PAS (AATACA) using zinc-finger nuclease technology. The resultant mutant p53 allele is termed p531755C as the 1755th nucleotide of mouse p53 reference mRNA is the ortholog of human rs78378222. We demonstrate that heterozygote p53+/1755C and homozygote p531755C/1755C mice treated with azoxymethane (AOM) and dextran sodium sulfate (DSS) developed more colon tumors than the p53+/+ controls and homozygous mice developed more advanced tumors than heterozygous mice. With data from murine tumorigenesis and human epidemiology, we propose that this p53 noncoding germline variant is a cancer susceptibility allele associated with Lynch syndrome rather than Li-Fraumeni syndrome. Citation Format: Qipan Deng, Yong Li. TP53 coding and noncoding variants in cancer susceptibility: From Li-Fraumeni syndrome to Lynch syndrome. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 37. doi:10.1158/1538-7445.CANSUSC14-37

Extending Rare-Variant Testing Strategies: Analysis of Noncoding Sequence and Imputed Genotypes

Ethnic variation has been reported in age-related macular degeneration (AMD)-associated Y402H polymorphism in complement factor H (CFH). This variation is evident in the Japanese population. Recently a strong association between a novel single-nucleotide polymorphism (SNP; rs1410996) in the CFH gene and AMD has been identified in Caucasian patients. The present study was undertaken to investigate whether four coding and noncoding variants of the CFH gene, including rs1410996, are associated with AMD in native, unrelated Japanese patients. A total of 188 patients with AMD and 139 control subjects without AMD were recruited for the study. Four SNPs (rs800292, rs1061170, rs1410996, and rs2274700) in the CFH gene were assessed by genotyping assay. The information regarding systemic conditions and lifestyle including smoking were documented in each subject by standardized questionnaire. The intronic SNP (rs1410996) and the synonymous SNP (rs2274700) were associated with a significant risk of AMD (P = 2.37 x 10(-5) and 3.52 x 10(-5), respectively). A significant association was also noted between a coding variant (rs800292, I62V) and AMD (P = 8.63 x 10(-6)). In contrast, the Y402H variant showed no significant association with AMD (P = 0.101). Two common haplotypes also demonstrated significant association with AMD (P = 1.08 x 10(-3) and 2.00 x 10(-5)). Among the environmental factors, smoking alone had a significant association with AMD (P = 1.17 x 10(-4)). Although the Y402H variant was not significantly associated with AMD, other coding and noncoding variants in the CFH gene including rs1410996 and smoking moderately influenced the risk of AMD in a Japanese population.

The funny and not-so-funny effects of dronedarone

PO-629-03 IN-DEPTH ANALYSIS OF THE SCN5A LOCUS HIGHLIGHTS DISTINCT GENETIC ARCHITECTURES FOR BRUGADA SYNDROME IN DIFFERENT ANCESTRIES AND IDENTIFIES A NOVEL RARE ENHANCER VARIANT ASSOCIATED WITH DISEASE IN SOUTHEAST ASIAN PATIENTS

See related article, pages 839–847 It is widely known that atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, with the problem magnified by the clinical sequelae; eg, thromboembolic events. It is pertinent that the incidence of AF is expected to increase in the future,1 especially in aging patients. Thus, finding preventive measures for this arrhythmia has become an increasingly important goal. In addition to considering clinical risk factors, focusing on prevention necessitates knowledge of the associated pathophysiology of AF,2 which involves the initiation of AF and the wavefront dynamics that sustain it. In recent years considerable new information has appeared concerning AF mechanisms that occur in different regions of the atria in different cardiac states.3 This point is highlighted by the report of Tanaka et al4 in this issue of Circulation Research . These authors used high-resolution electrophysiological and microstructural techniques, along with computer model simulations, to study wavefront dynamics during acetylcholine (ACh)-induced AF in heart failure sheep hearts. The heart failure hearts had developed prominent fibrotic patches in the posterior left atrium near the pulmonary veins, whereas in the control (normal) hearts patches of fibrosis were smaller, diffusely distributed, and more centrally located with respect to the 4 pulmonary vein ostia. In the heart failure hearts, during AF variable wavefront breakthroughs to the endocardium occurred in the area of fibrotic patches adjacent to the pulmonary veins. The authors concluded that scroll waves within the posterior left atrial wall produced a microreentry source for the endocardial breakthroughs in the region of the larger collagen patches, thus providing the underlying mechanism of AF.4 A myriad of reports provide varied information about substrates and mechanisms of AF as a background for the study of Tanaka et al …

Most sequence variants identified hitherto in genome-wide association studies (GWAS) of atrial fibrillation are common, non-coding variants associated with risk through unknown mechanisms. We performed a meta-analysis of GWAS of atrial fibrillation among 29,502 cases and 767,760 controls from Iceland and the UK Biobank with follow-up in samples from Norway and the US, focusing on low-frequency coding and splice variants aiming to identify causal genes. We observe associations with one missense (OR = 1.20) and one splice-donor variant (OR = 1.50) in RPL3L, the first ribosomal gene implicated in atrial fibrillation to our knowledge. Analysis of 167 RNA samples from the right atrium reveals that the splice-donor variant in RPL3L results in exon skipping. We also observe an association with a missense variant in MYZAP (OR = 1.38), encoding a component of the intercalated discs of cardiomyocytes. Both discoveries emphasize the close relationship between the mechanical and electrical function of the heart.

PREVALENCE OF UNREPORTED ATRIAL FIBRILLATION IN ELECTROCARDIOGRAMS WITH VENTRICULAR-PACED RHYTHM: A MULTICENTER EXPERIENCE

Sex differences have the potential to impact diagnostic and therapeutic interventions in a wide variety of medical conditions, and cardiac arrhythmias are no exception.1 Studies evaluating pathophysiology, disease course, and therapeutic options for cardiac arrhythmias have been performed predominantly in male patients. However, catheter and device-based therapies coupled with landmark clinical trials have contributed to an improved understanding of this important aspect. The objective of this review is to present the current state of knowledge on sex differences in cardiac arrhythmias with a focus on clinical management, while highlighting gaps in knowledge that would benefit from future investigation. ### Atrial Fibrillation and Atrial Flutter #### Disease Burden Atrial fibrillation (AF) and atrial flutter (AFL) are the most commonly encountered tachyarrhythmias in clinical practice, with significant implications for public health and healthcare costs. Stroke, hospitalization, and loss of productivity are the major consequences of AF.2 The incidence of AF (per 1000 person-years) is reported to be between 1.6 and 2.7 in women and between 3.8 and 4.7 in men.2 The age-adjusted incidence and prevalence of AF is lower in women compared with that in men, and accordingly, the lifetime risk of AF from the Framingham Heart Study at 40 years of age was higher in men (26.0% for men versus 23.0% for women).3 Another analysis from the Framingham Heart Study demonstrated no significant sex differences in the risk of developing AFL.4 The prevalence of AF continues to rise among both men and women. In a study investigating the global burden of disease from 1980 to 2010, there was not only an increase in overall burden, incidence, and prevalence of AF, but most importantly an increase in AF-associated mortality in both men and women (Figure 1).5 The age-adjusted mortality for women was consistently higher compared with that for men from 1990 to 2010 (Figure …