Genomics in sudden cardiac death

Discovering disease-genes by topological features in human protein-protein interaction network

MOTIVATION

Mining the hereditary disease-genes from human genome is one of the most important tasks in bioinformatics research. A variety of sequence features and functional similarities between known human hereditary disease-genes and those not known to be involved in disease have been systematically examined and efficient classifiers have been constructed based on the identified common patterns. The availability of human genome-wide protein-protein interactions (PPIs) provides us with new opportunity for discovering hereditary disease-genes by topological features in PPIs network.

RESULTS

This analysis reveals that the hereditary disease-genes ascertained from OMIM in the literature-curated (LC) PPIs network are characterized by a larger degree, tendency to interact with other disease-genes, more common neighbors and quick communication to each other whereas those properties could not be detected from the network identified from high-throughput yeast two-hybrid mapping approach (EXP) and predicted interactions (PDT) PPIs network. KNN classifier based on those features was created and on average gained overall prediction accuracy of 0.76 in cross-validation test. Then the classifier was applied to 5262 genes on human genome and predicted 178 novel disease-genes. Some of the predictions have been validated by biological experiments.

Incidence of sudden cardiac arrest is higher in areas of low socioeconomic status: A prospective two year study in a large United States community

BACKGROUND

A potential effect of socioeconomic status on occurrence of sudden cardiac arrest in the community is likely, but has not been evaluated fully.

METHODS

All cases of sudden cardiac arrest in Multnomah County Oregon (population 660,486; February 2002-January 2004) were identified prospectively and categorized by census tract based on the address of residence and specific geographic location of occurrence of cardiac arrest. Each census tract was assigned to quartiles of median income, poverty level, median home value, and educational attainment.

RESULTS

Of 714 cases (annual incidence 54 per 100,000), 697 (98%) had residential addresses that matched a county census tract successfully. For each socioeconomic status measure, the incidence of cardiac arrest was 30-80% higher in the lowest compared to the highest socioeconomic status census tracts. Annual incidence in census tracts in the lowest compared to the highest quartiles of median home value was 60.5 versus 35.1 per 100,000 (RR 1.7, 95% CI 1.4-2.2). This gradient was exaggerated significantly for age<65 years (34.5 versus 15.1 per 100,000, RR 2.3, 95% CI 1.6-3.3). Identical trends were observed for sudden cardiac arrest based on location, with 60% of all cases and 66% of cases age<65 years occurring in the two quartiles with lowest socioeconomic status.

CONCLUSIONS

Low neighborhood socioeconomic status was associated with a significantly higher incidence of sudden cardiac arrest based on address of residence as well as location of cardiac arrest. For effective deployment of strategies for community-based prevention such as the automated external defibrillator, neighborhood socioeconomic status is likely to be an important consideration.

Cumulative Experience of Azimilide-Associated Torsades de Pointes Ventricular Tachycardia in the 19 Clinical Studies Comprising the Azimilide Database

OBJECTIVES

The purpose of this study was to assess the incidence, temporal characteristics, and risk factors associated with azimilide-associated torsades de pointes (TdP) ventricular tachycardia.

BACKGROUND

Azimilide dihydrochloride is a class III antiarrhythmic drug possessing Ikr and Iks channel-blocking properties.

METHODS

Oral azimilide (75 to 125 mg/day) was taken by 5,375 patients in 19 clinical trials conducted at 775 international centers. Of 3,964 patients in double-blind studies, 1,427 had a history of atrial fibrillation or other supraventricular arrhythmia, 510 had an implantable cardioverter-defibrillator, and 2,027 were post-myocardial infarction patients with a left ventricular ejection fraction < or =35%.

RESULTS

The TdP occurred in 56 patients assigned to azimilide, was dose-related, and tended to occur earlier with an azimilide-loading regimen. Forty-three percent of TdP patients had a QT interval corrected by Bazett's formula, for heart rate, (QTc) > or =500 ms at the time of or before the TdP occurrence. Significant risk factors using logistic regression were increasing age, female gender, diuretic use, and lack of aspirin use.

CONCLUSIONS

Azimilide-associated TdP has characteristics and risk factors similar to other Ikr blockers. However, there is a distinctive temporal profile. The TdP events are not concentrated in the first week. The azimilide-associated TdP rate is 1% (95% confidence interval 0.78 to 1.35) and is not increased in patients with low left ventricular ejection fraction, even in women.

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets

We present the first analysis of the human proteome with regard to interactions between proteins. We also compare the human interactome with the available interaction datasets from yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans) and fly (Drosophila melanogaster). Of >70,000 binary interactions, only 42 were common to human, worm and fly, and only 16 were common to all four datasets. An additional 36 interactions were common to fly and worm but were not observed in humans, although a coimmunoprecipitation assay showed that 9 of the interactions do occur in humans. A re-examination of the connectivity of essential genes in yeast and humans indicated that the available data do not support the presumption that the number of interaction partners can accurately predict whether a gene is essential. Finally, we found that proteins encoded by genes mutated in inherited genetic disorders are likely to interact with proteins known to cause similar disorders, suggesting the existence of disease subnetworks. The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states.

Population-based analysis of sudden cardiac death with and without left ventricular systolic dysfunction: two-year findings from the Oregon Sudden Unexpected Death Study

OBJECTIVES

We sought to evaluate the contribution of left ventricular (LV) dysfunction toward occurrence of sudden cardiac death (SCD) in the general population, and to identify distinguishing characteristics of SCD in the absence of LV dysfunction.

BACKGROUND

Patients who manifest warning symptoms and signs are more likely to undergo evaluation before SCD. Although prevalence of LV dysfunction in this subgroup may overestimate the prevalence in overall SCD, this is the only means of assessment in the general population.

METHODS

All cases of SCD in Multnomah County, Oregon (population 660,486; 2002 to 2004) were prospectively ascertained in the ongoing Oregon Sudden Unexpected Death Study. We retrospectively assessed LV ejection fraction (LVEF) among subjects who underwent evaluation of LV function before SCD (normal: > or =55%; mildly to moderately reduced: 36% to 54%; and severely reduced: < or =35%). Of a total of 714 SCD cases (annual incidence 54 per 100,000), LV function was assessed in 121 (17%).

RESULTS

The LVEF was severely reduced in 36 patients (30%), mildly to moderately reduced in 27 (22%), and normal in 58 (48%). Patients with normal LVEF were distinguishable by younger age (66 +/- 15 years vs. 74 +/- 10 years; p = 0.001), higher proportion of females (47% vs. 27%; p = 0.025), higher prevalence of seizure disorder (14% vs. 0%; p = 0.002), and lower prevalence of established coronary artery disease (50% vs. 81%; p < 0.001).

CONCLUSIONS

In this community-wide study, only one-third of the evaluated SCD cases had severe LV dysfunction meeting current criteria for prophylactic cardioverter-defibrillator implantation. The SCD cases with normal LV function had several distinguishing clinical characteristics. These findings support the aggressive development of alternative screening methods to enhance identification of patients at risk.

Elimination of allosteric modulation of myocardial KATP channels by ATP and protons in two Kir6.2 polymorphisms found in sudden cardiac death

The major cause of sudden cardiac death (SCD) is ventricular arrhythmias due to unstable myocardial electrical activity in which the ATP-sensitive K+ (KATP) channels play a role. Genetic disruption of these channels predisposes the myocardium to arrhythmias. Two point mutations in the Kir6.2 subunit are found in SCD with acute myocardial infarction. Here we show evidence for the functional consequences of the P266T and R371H variants. Baseline single-channel properties, expression density, and channel modulations were studied in patch clamp. We focused on channel modulations by intracellular ATP and protons, as the concentration of these two important KATP channel regulators changes widely with hypoxic ischemia. We found that both variants expressed functional currents even though they occur at two highly conserved regions. The open state probability of P266T was twice as high as the wild-type (WT) channel, whereas its channel density was only approximately 20% of the WT channel. Although the outward current was not affected by these two mutations at neutral pH, it was approximately 20% lower at acidic pH in the P266T than in the WT channel. Both P266T and R371H mutations significantly reduced ATP sensitivity and increased pH sensitivity. More dramatically, allosteric regulation by intracellular ATP and protons was almost completely eliminated in the polymorphic P266T and R371H channels. Such an abnormality was seen in both inward and outward currents. Given the importance and beneficial effects of allosteric regulation in cellular responses to metabolic stress, the loss of such a regulatory mechanism in the P266T and R371H variants appears consistent with the adverse consequences occurring during acute myocardial infarction in patients.

Genomics and cardiac arrhythmias

Sudden cardiac death in patients younger than 35 years of age is primarily due to genetic causes. Familial hypertrophic cardiomyopathy accounting for 30% to 40% is associated with structural heart disease while the Brugada syndrome and the long QT syndrome (LQTS) are associated with normal cardiac function. This is a review of the genetics of supraventricular and ventricular arrhythmias. Atrial fibrillation is mapped to nine chromosomal loci and four genes are identified. AMP-activated protein kinase is one gene responsible for Wolff-Parkinson-White syndrome. The LQTS and the Brugada syndromes are due to defects primarily in cardiac sodium and potassium ion channels. The role of single nucleotide polymorphisms in predisposing to arrhythmias in acquired disorders such as hypertrophy is discussed.

Mechanisms of sudden cardiac death

Despite recent advances in preventing sudden cardiac death (SCD) due to cardiac arrhythmia, its incidence in the population at large has remained unacceptably high. Better understanding of the interaction among various functional, structural, and genetic factors underlying the susceptibility to, and initiation of, fatal arrhythmias is a major goal and will provide new tools for the prediction, prevention, and therapy of SCD. Here, we review the role of aberrant intracellular Ca handling, ionic imbalances associated with acute myocardial ischemia, neurohumoral changes, and genetic predisposition in the pathogenesis of SCD due to cardiac arrhythmia. Therapeutic measures to prevent SCD are also discussed.

Recent advances in understanding sex differences in cardiac repolarization

A number of gender differences exist in the human electrocardiogram (ECG): the P-wave and P-R intervals are slightly longer in men than in women, whilst women have higher resting heart rates than do men, but a longer rate-corrected QT (QT(C)) interval. Women with the LQT1 and LQT2 variants of congenital long-QT syndrome (LQTS) are at greater risk of adverse cardiac events. Similarly, many drugs associated with acquired LQTS have a greater risk of inducing torsades de pointes (TdP) arrhythmia in women than in men. There are also male:female differences in Brugada syndrome, early repolarisation syndrome and sudden cardiac death. The differences in the ECG between men and women, and in particular those relating to the QT interval, have been explored experimentally and provide evidence of differences in the processes underlying ventricular repolarization. The data available from rabbit, canine, rat, mouse and guinea pig models are reviewed and highlight involvement of male:female differences in Ca and K currents, although the possible involvement of rapid and persistent Na current and Na-Ca exchange currents cannot yet be excluded. The mechanisms underlying observed differences remain to be elucidated fully, but are likely to involve the influence of gonadal steroids. With respect to the QT interval and risk of TdP, a range of evidence implicates a protective role of testosterone in male hearts, possibly by both genomic and non-genomic pathways. Evidence regarding oestrogen and progesterone is less unequivocal, although the interplay between these two hormones may influence both repolarization and pro-arrhythmic risk.

Non-cardiac QTc-prolonging drugs and the risk of sudden cardiac death

AIMS

To assess the association between the use of non-cardiac QTc-prolonging drugs and the risk of sudden cardiac death.

METHODS AND RESULTS

A population-based case-control study was performed in the Integrated Primary Care Information (IPCI) project, a longitudinal observational database with complete medical records from more than 500,000 persons. All deaths between 1 January 1995 and 1 September 2003 were reviewed. Sudden cardiac death was classified based on the time between onset of cardiovascular symptoms and death. For each case, up to 10 random controls were matched for age, gender, date of sudden death, and general practice. The exposure of interest was the use of non-cardiac QTc-prolonging drugs. Exposure at the index date was categorized into three mutually exclusive groups of current use, past use, and non-use. The study population comprised 775 cases of sudden cardiac death and 6297 matched controls. Current use of any non-cardiac QTc-prolonging drug was associated with a significantly increased risk of sudden cardiac death (adjusted OR: 2.7; 95% CI: 1.6-4.7). The risk of death was highest in women and in recent starters.

CONCLUSION

The use of non-cardiac QTc-prolonging drugs in a general population is associated with an increased risk of sudden cardiac death.

What causes sudden death in heart failure?

Patients with heart failure experience a number of changes in the electrical function of the heart that predispose to potentially lethal cardiac arrhythmias. Action potential prolongation, the result of functional downregulation of K currents, and aberrant Ca2+ handling is a recurrent theme. Significant alterations in conduction and activation of a number of initially adaptive but ultimately maladaptive signaling cascades contribute to the generation of a highly arrhythmogenic substrate. We review the changes in active and passive membrane properties, neurohumoral signaling, and genetic determinants that predispose to sudden arrhythmic death in patients with heart failure and highlight the critical unanswered questions that are ripe for future investigation.

Current burden of sudden cardiac death: multiple source surveillance versus retrospective death certificate-based review in a large U.S. community

OBJECTIVES

We sought to determine the annual incidence of sudden cardiac death (SCD) in the general population using a prospective approach. To assess the validity of retrospective surveillance, a simultaneous comparison was made with a death certificate-based method of determining SCD incidence.

BACKGROUND

Accurate surveillance and characterization of SCD in the general population is likely to significantly facilitate current and future community-based preventive and therapeutic interventions.

METHODS

We performed a prospective evaluation of SCD among all residents of Multnomah County, Oregon (population 660,486) using multiple sources of surveillance. A comprehensive analysis of circumstances of death, medical records, and available autopsy data was performed. Comparisons were made with a retrospective, death certificate-based determination of SCD incidence using International Classification of Diseases-Version 10 codes and location of death.

RESULTS

Between February 1, 2002, and January 31, 2003, 353 residents suffered SCD (incidence 53 of 100,000; median age 69 years, 57% male) accounting for 5.6% of overall mortality. Of these, 75 cases (21%) were identified using sources other than first responders. Resuscitation was attempted in 237 cases (67%) and successful (survival to hospital discharge) in 28 (8%). The retrospective death certificate-based review yielded 1,007 cases (incidence 153 of 100,000; median age 81 years, 51% male), and the positive predictive value of this methodology was 19%.

CONCLUSIONS

Sudden cardiac death accounts for 5.6% of annual mortality, and prospective evaluation in the general population appears to be feasible. The use of multiple sources of ascertainment and information significantly enhances phenotyping of SCD cases. Retrospective death certificate-based surveillance results in significant overestimation of SCD incidence.