RNA Editing Genes Associated with Extreme Old Age in Humans and with Lifespan in C. elegans

The strong familiality of living to extreme ages suggests that human longevity is genetically regulated. The majority of genes found thus far to be associated with longevity primarily function in lipoprotein metabolism and insulin/IGF-1 signaling. There are likely many more genetic modifiers of human longevity that remain to be discovered.Here, we first show that 18 single nucleotide polymorphisms (SNPs) in the RNA editing genes ADARB1 and ADARB2 are associated with extreme old age in a U.S. based study of centenarians, the New England Centenarian Study. We describe replications of these findings in three independently conducted centenarian studies with different genetic backgrounds (Italian, Ashkenazi Jewish and Japanese) that collectively support an association of ADARB1 and ADARB2 with longevity. Some SNPs in ADARB2 replicate consistently in the four populations and suggest a strong effect that is independent of the different genetic backgrounds and environments. To evaluate the functional association of these genes with lifespan, we demonstrate that inactivation of their orthologues adr-1 and adr-2 in C. elegans reduces median survival by 50%. We further demonstrate that inactivation of the argonaute gene, rde-1, a critical regulator of RNA interference, completely restores lifespan to normal levels in the context of adr-1 and adr-2 loss of function.Our results suggest that RNA editors may be an important regulator of aging in humans and that, when evaluated in C. elegans, this pathway may interact with the RNA interference machinery to regulate lifespan

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

[Background] One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. [Results] We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. [Conclusion] Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects.Supported by NHLBI grants R21 HL080463 (PS); R01 HL68970 (MHS); K-24, AG025727 (TP); K23 AG026754 (D.T.)

Genetic Polymorphisms in NEDD4L Are Associated with Pulmonary Hypertension of Sickle Cell Anemia.

Abstract Abstract 2562 Poster Board II-539 Pulmonary hypertension (PH) is present in up to 43% of adults with sickle cell anemia (SCA; homozygosity for HBB, glu6val) when defined by echocardiography. The relatively mild cardiopulmonary hemodynamics, as well as the co-existence of proteinuria, relative systemic hypertension, diastolic dysfunction and an increased hemolytic rate in this population suggests that this echocardiographic finding may be reflective of a more diffuse vasculopathy, the etiology of which, while unclear, may in part result from reduced nitric oxide bioavailability. Importantly, despite mild hemodynamic findings compared with idiopathic pulmonary arterial hypertension, an elevated tricuspid regurgitant jet velocity (TRV) carries with it a 6-10-fold increased mortality risk. We undertook the unbiased approach of a genome-wide association analysis (GWAS) to investigate the hypothesis that single nucleotide polymorphisms (SNPs) in genes affecting the vasculature might be associated with TRV and could play a role in the pathogenesis of PH in SCA. Based upon the associated increased mortality risk, PH cases were defined by a TRV of ≥ 2.5 m/sec. Controls were SCA patients with normal echocardiograms. 166 DNA samples were genotyped (59 PH cases and 107 SCA controls) on the Illumina Human 610-Quad SNP array and the data was analyzed using the software PLINK. Among the genes most significantly associated with a TRV ≥ 2.5 m/sec was NEDD4L where two SNPs were identified (rs559046, p=7.3 × 10−5, rs1624292, p=2.1 × 10−4). NEDD4L, on chromosome 18, is an E3 ubiquitin ligase localized to the renal and pulmonary alveolar epithelium. In the kidney, this gene is thought to be important in epithelial sodium channel surface expression and sodium reabsorption. Functional SNPs in this gene have been associated with systemic hypertension and salt sensitivity. Although expressed within the alveolar epithelium, its functional significance in the lung is less well understood. The SNPs we identified in NEDD4L are located within intron 1 similarly to other SNPs associated with systemic hypertension particularly in African Americans. To provide support for our findings, we undertook a candidate gene-focused approach using a phenotype related to but not identical to TRV. We analyzed 121 SNPs in NEDD4L in 139 adult subjects that participated in the Cooperative Study of Sickle Cell Disease (CSSCD). Given the lack of routine echocardiography in this cohort, cases were defined by the presence of an N-terminal pro-brain natriuretic peptide (NT-pro-BNP) level ≥ 160 pg/ml, that was previously associated with increased TRV and mortality in SCA and was therefore suggestive of pulmonary vasculopathy. In the CSSCD population, NT-pro-BNP levels ≥ 160 pg/ml were significantly associated with increased LDH concentrations, one measure of increased intravascular hemolysis (p&lt;0.004). Using a case control approach, we found 4 SNPs in intron 1 of NEDD4L associated with an elevated NT-pro-BNP level (p&lt;0.05) lending credence to the associations we found by GWAS. Although a larger sample size with a similarly ascertained phenotype is necessary to confirm our initial GWAS findings, based on the association of NEDD4L with systemic hypertension and NT-pro-BNP levels, this gene may have a role in the pathogenesis of PH of SCA. Disclosures: No relevant conflicts of interest to declare. </jats:sec

Distribution of the logBayes factor in 1,114 false positive associations generated in approximately 10association tests with an estimated false positive rate 5 10

<p><b>Copyright information:</b></p><p>Taken from "A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples"</p><p>http://www.biomedcentral.com/1471-2156/9/6</p><p>BMC Genetics 2008;9():6-6.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2248205.</p><p></p> The analysis shows that the chance to observe a very large Bayes factor has an exponential decay, and the probability of observing a Bayes factor greater than 10 by chance is 6 10, the probability of observing a Bayes factor greater than 100 is 3 10, greater than 1000 is 2 10

The reproducibility of the allele frequency estimates is shown by the scatter plot of repeated estimates of allele frequency inferred from pooled DNA samples (left)

<p><b>Copyright information:</b></p><p>Taken from "A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples"</p><p>http://www.biomedcentral.com/1471-2156/9/6</p><p>BMC Genetics 2008;9():6-6.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2248205.</p><p></p> The labels "run 1" and "run 2" in the x- and y-axis specify each replication. The accuracy of the allele frequency estimates is shown by the scatter plot of the estimates of allele frequency inferred from pooled DNA samples (y-axis in the right plots) and those computed from individually genotyped samples (x-axis). The analysis of the other chromosomes shows similar results

Relation between the pattern of LD (x-axis) and the global measure of association (y-axis) in the regional filter

<p><b>Copyright information:</b></p><p>Taken from "A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples"</p><p>http://www.biomedcentral.com/1471-2156/9/6</p><p>BMC Genetics 2008;9():6-6.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2248205.</p><p></p> The pattern of LD is measured by the average of the Bayes D' between consecutive SNPs in the region, and the global measure of association is the joint probability of association in the region. The two figures in the top half show the relation using data from the study of fetal hemoglobin in the sickle cell anemia subjects. The two figure in the bottom half show the relation using data from the longevity study. The different extent of LD reflect the fact that sickle cell anemia subjects are all African American while centenarians in the longevity study are all Caucasians The correlations in the four sets are 0.03, 0.18, 0.018, -0.10