Protein-altering germline mutations implicate novel genes related to lung cancer development

Few germline mutations are known to affect lung cancer risk. We performed analyses of rare variants from 39,146 individuals of European ancestry and investigated gene expression levels in 7,773 samples. We find a large-effect association with an ATM L2307F (rs56009889) mutation in adenocarcinoma for discovery (adjusted Odds Ratio = 8.82, P = 1.18 × 10-15) and replication (adjusted OR = 2.93, P = 2.22 × 10-3) that is more pronounced in females (adjusted OR = 6.81 and 3.19 and for discovery and replication). We observe an excess loss of heterozygosity in lung tumors among ATM L2307F allele carriers. L2307F is more frequent (4%) among Ashkenazi Jewish populations. We also observe an association in discovery (adjusted OR = 2.61, P = 7.98 × 10-22) and replication datasets (adjusted OR = 1.55, P = 0.06) with a loss-of-function mutation, Q4X (rs150665432) of an uncharacterized gene, KIAA0930. Our findings implicate germline genetic variants in ATM with lung cancer susceptibility and suggest KIAA0930 as a novel candidate gene for lung cancer risk.

P4667Loss of function in PCSK9, atherogenic lipoprotein concentrations, and calcific aortic valve stenosis

Background

Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition reduces plasma concentrations of most atherogenic lipoproteins such as low-density lipoprotein cholesterol (LDL-C), apolipoprotein B (apoB) and lipoprotein(a) [Lp(a)]. Atherogenic lipoprotein concentrations have also been linked with calcific aortic valve stenosis (CAVS).

Purpose

1) To determine the association between genetic variants in PCSK9 and lipoprotein-lipid levels, 2) to determine whether loss of function (LOF) in PCSK9 is associated with CAVS and 3) to evaluate if PCSK9 could be implicated in aortic valve interstitial cells (VICs) calcification.

Methods

We built a weighted genetic risk score (wGRS) using 10 single nucleotide polymorphisms at the PCSK9 locus associated with LDL-C in the Global Lipids Genetics Consortium. We determined the association between the wGRS and LDL-C, apoB and Lp(a)] in 9692 participants of the EPIC-Norfolk study using linear regression. We investigated the association between the LOF PCSK9 R46L variant and CAVS risk in a meta-analysis of published (three Copenhagen studies, 1463 cases and 101,620 controls) and unpublished studies (UK Biobank, 1350 cases and 349,043 controls, Malmö Diet and Cancer study, 682 cases and 5963 controls and EPIC-Norfolk, 508 cases and 20,421 controls) prospective, population-based studies using logistic regression adjusted for age and sex. We evaluated PCSK9 expression and localization in explanted aortic valves by capillary Western blot and immunohistochemistry in patients with and without CAVS. Von Kossa staining was used to visualize aortic leaflet calcium deposits. We also assessed VICs calcification potential under oxidative stress condition.

Results

In EPIC-Norfolk, the wGRS was significantly associated with TC, LDL-C, and apoB (all p<0.0001), but not with VLDL-C, HDL-C, triglycerides apoA-I, or Lp(a). Carriers of the R46L variant were at lower CAVS risk (odds ratio=0.71 (95% CI, 0.57–0.88, p<0.001)). Aortic valves of patients with aortic sclerosis (n=12) and CAVS (n=8) presented elevated PCSK9 levels (log2 fold change [FC]=+28.6±5.1, p=0.008 and FC=+39.3±15.2, p=0.02, respectively) compared to controls (n=4).In calcified leaflets, PCSK9 expression co-localized with calcium deposits. PCSK9 expression in VICs was induced by oxidative stress (FC=+2.3±0.4, p=0.02), and subsequent increment in calcification potential was observed.

Conclusion

PCSK9LOF variants are associated with lifelong reductions in non-Lp(a) apoB-containing lipoprotein levels and a lower risk of coronary artery disease and CAVS. PCSK9 is abundant in fibrotic and calcified aortic leaflets. Oxidative stress increases PCSK9 expression in VICs. These results support randomized clinical trials of PCSK9 inhibition in the prevention of CAVS.

Deleterious variants in DCHS1 are prevalent in sporadic cases of mitral valve prolapse

Background

A recent study identified DCHS1 as a causal gene for mitral valve prolapse. The goal of this study is to investigate the presence and frequency of known and novel variants in this gene in 100 asymptomatic patients with moderate to severe organic mitral regurgitation.

Methods

DNA sequencing assays were developed for two previously identified functional missense variants, namely p.R2330C and p.R2513H, and all 21 exons of DCHS1. Pathogenicity of variants was evaluated in silico.

Results

p.R2330C and p.R2513H were not identified in this cohort. Sequencing all coding regions revealed eight missense variants including six considered deleterious. This includes one novel variant (p.A2464P) and two rare variants (p.R2770Q and p.R2462Q). These variants are predicted to be deleterious with combined annotation‐dependent depletion (CADD) scores greater than 25, which are in the same range as p.R2330C (CADD = 28.0) and p.R2513H (CADD = 24.3). More globally, 24 of 100 cases were carriers of at least one in silico‐predicted deleterious missense variant in DCHS1, suggesting that this single gene may account for a substantial portion of cases.

Conclusion

This study reveals an important contribution of germline variants in DCHS1 in unrelated patients with mitral valve prolapse and supports genetic testing of this gene to screen individuals at risk.

Genetic association analyses highlight biological pathways underlying mitral valve prolapse

Non-syndromic mitral valve prolapse (MVP) is a common degenerative cardiac valvulopathy of unknown aetiology that predisposes to mitral regurgitation, heart failure and sudden death¹. Previous family and pathophysiological studies suggest a complex pattern of inheritance^2–5. We performed a meta-analysis of two genome-wide association studies in 1,442 cases and 2,439 controls. We identified and replicated in 1,422 cases and 6,779 controls six loci and provide functional evidence for candidate genes. We highlight LMCD1 encoding a transcription factor⁶, for which morpholino knockdown in zebrafish results in atrioventricular (AV) valve regurgitation. A similar zebrafish phenotype was obtained for tensin1 (TNS1), a focal adhesion protein involved in cytoskeleton organization. We also show the expression of tensin1 during valve morphogenesis and describe enlarged posterior mitral leaflets in Tns1^−/− mice. This study identifies the first risk loci for MVP and suggests new mechanisms involved in mitral valve regurgitation, the most common indication for mitral valve repair⁷.

Analyses of associations with asthma in four asthma population samples from Canada and Australia

Asthma, atopy, and related phenotypes are heterogeneous complex traits, with both genetic and environmental risk factors. Extensive research has been conducted and over hundred genes have been associated with asthma and atopy phenotypes, but many of these findings have failed to replicate in subsequent studies. To separate true associations from false positives, candidate genes need to be examined in large well-characterized samples, using standardized designs (genotyping, phenotyping and analysis). In an attempt to replicate previous associations we amalgamated the power and resources of four studies and genotyped 5,565 individuals to conduct a genetic association study of 93 previously associated candidate genes for asthma and related phenotypes using the same set of 861 single-nucleotide polymorphisms (SNPs), a common genotyping platform, and relatively harmonized phenotypes. We tested for association between SNPs and the dichotomous outcomes of asthma, atopy, atopic asthma, and airway hyperresponsiveness using a general allelic likelihood ratio test. No SNP in any gene reached significance levels that survived correction for all tested SNPs, phenotypes, and genes. Even after relaxing the usual stringent multiple testing corrections by performing a gene-based analysis (one gene at a time as if no other genes were typed) and by stratifying SNPs based on their prior evidence of association, no genes gave strong evidence of replication. There was weak evidence to implicate the following: IL13, IFNGR2, EDN1, and VDR in asthma; IL18, TBXA2R, IFNGR2, and VDR in atopy; TLR9, TBXA2R, VDR, NOD2, and STAT6 in airway hyperresponsiveness; TLR10, IFNGR2, STAT6, VDR, and NPSR1 in atopic asthma. Additionally we found an excess of SNPs with small effect sizes (OR < 1.4). The low rate of replication may be due to small effect size, differences in phenotypic definition, differential environmental effects, and/or genetic heterogeneity. To aid in future replication studies of asthma genes a comprehensive database was compiled and is available to the scientific community at http://genapha.icapture.ubc.ca/.

The T111I mutation in the EL gene modulates the impact of dietary fat on the HDL profile in women

The objective of the present study was to examine the impact of the T111I missense mutation in exon 3 of the endothelial lipase (EL) gene on HDL and its potential interaction effect with dietary fat. The study sample included 281 women and 216 men aged between 17 and 76 years from the Québec Family Study. Plasma HDL3-C levels of I111I homozygote women were higher compared with those of women carrying the wild-type allele (P = 0.03). These differences were not attenuated when adjusted for levels of obesity and were not observed among men. Dietary PUFA interacted with the T111I mutation to modulate apolipoprotein A-I (apoA-I) and HDL3-C levels among women. Specifically, a diet rich in PUFA was associated with increased apoA-I levels among women carriers of the I111 allele and with decreased apoA-I among women homozygotes for the wild-type allele (P = 0.002). A similar interaction was observed with plasma HDL3-C levels (P = 0.003). These interactions were not observed among men. In conclusion, the EL T111I mutation appears to have a modest effect on plasma HDL levels. The gene-diet interaction among women, however, suggests that the T111I missense mutation may confer protection against the lowering effect of a high dietary PUFA intake on plasma apoA-I and HDL3-C levels.