Loss-of-function mutations in APOC3, triglycerides, and coronary disease

Abstract

Background: Plasma triglyceride levels are heritable and are correlated with the risk of coronary heart disease. Sequencing of the protein-coding regions of the human genome (the exome) has the potential to identify rare mutations that have a large effect on phenotype.

Methods: We sequenced the protein-coding regions of 18,666 genes in each of 3734 participants of European or African ancestry in the Exome Sequencing Project. We conducted tests to determine whether rare mutations in coding sequence, individually or in aggregate within a gene, were associated with plasma triglyceride levels. For mutations associated with triglyceride levels, we subsequently evaluated their association with the risk of coronary heart disease in 110,970 persons.

Results: An aggregate of rare mutations in the gene encoding apolipoprotein C3 (APOC3) was associated with lower plasma triglyceride levels. Among the four mutations that drove this result, three were loss-of-function mutations: a nonsense mutation (R19X) and two splice-site mutations (IVS2+1G→A and IVS3+1G→T). The fourth was a missense mutation (A43T). Approximately 1 in 150 persons in the study was a heterozygous carrier of at least one of these four mutations. Triglyceride levels in the carriers were 39% lower than levels in noncarriers (P<1×10(-20)), and circulating levels of APOC3 in carriers were 46% lower than levels in noncarriers (P=8×10(-10)). The risk of coronary heart disease among 498 carriers of any rare APOC3 mutation was 40% lower than the risk among 110,472 noncarriers (odds ratio, 0.60; 95% confidence interval, 0.47 to 0.75; P=4×10(-6)).

Conclusions: Rare mutations that disrupt APOC3 function were associated with lower levels of plasma triglycerides and APOC3. Carriers of these mutations were found to have a reduced risk of coronary heart disease. (Funded by the National Heart, Lung, and Blood Institute and others.).

Figure 1. Rare Mutations in APOC3 and Reductions in Plasma Triglyceride Levels

A schematic diagram of the gene encoding apolipoprotein C3 (APOC3) shows four exons and three introns, or intervening sequences (IVS). In the graph, each dot represents a single study participant who carried a specific mutation. Red dots denote persons of European ancestry (EA), and blue dots persons of African ancestry (AA). The mean level of triglycerides among all persons who did not carry any mutation in the coding sequence of APOC3 was 137 mg per deciliter (dashed line). To convert the values for triglycerides to millimoles per liter, multiply by 0.01129.

Figure 2. Association of APOC3 Loss-of-Function Mutations with Risk of Coronary Heart Disease among 110,970 Participants in 15 Studies

In each study, we tested the association of loss-of-function carrier status (heterozygous for any of four mutations: APOC3 R19X, IVS2+1G→A, IVS3+1G→T, or A43T) with the risk of coronary heart disease. We calculated P values for the association tests and confidence intervals for the odds ratios with the use of exact methods. We performed a meta-analysis with the use of the Cochran–Mantel–Haenszel statistics for stratified 2-by-2 tables. The Cochran–Mantel–Haenszel method combines score statistics rather than Wald statistics and is particularly useful when some observed odds ratios are zero. For each study, squares indicate the estimated odds ratios and the corresponding lines indicate the 95% confidence intervals. The diamond indicates the combined estimate of the odds ratio and the corresponding 95% confidence interval. HA denotes Hispanic ancestry. The full study names are as follows: ARIC Atherosclerosis Risk in Communities. ATVB Italian Atherosclerosis, Thrombosis, and Vascular Biology Study, EPIC European Prospective Study into Cancer and Nutrition, FHS Framingham Heart Study, FIA3 First Myocardial Infarction, in AC County 3, GoDARTS Genetics of Diabetes Audit and Research Tayside Study, HUNT Nord–Trøndelag Health Study, IPM Mt. Sinai Institute for Personalized Medicine Biobank, MDC–CVA Malmö Diet and Cancer Study Cardiovascular Cohort, OHS Ottawa Heart Study, PROCARDIS, Precocious Coronary Artery Disease Study, VHS Verona Heart Study, WHI Women’s Health Initiative, and WTCCC Wellcome Trust Case Control Consortium. All 15 studies are described in Table S3 in the Supplementary Appendix.

Figure 3. Cumulative Probability of Freedom from Coronary Heart Disease (CHD) According to Plasma Level of APOC3 at Baseline in the Framingham Heart Study

Plasma APOC3 levels were 14.2 mg per deciliter or less in the lowest third of the population, 14.3 to 17.9 mg per deciliter in the middle third, and 18.0 mg per deciliter or more in the highest third. Median follow-up was 14.4 years. The numbers in parentheses are the numbers of study participants who were undergoing follow-up at the specified time points.