HotSpots
Beneficial metabolic phenotypes caused by loss-of-function APOC3 mutations References 1. Gagné SE, Larson MG, Pimstone SN et al. A common truncation variant of lipoprotein lipase (Ser447X) confers protection against coronary heart disease: the Framingham Offspring Study. Clin Genet 1999: 55 (6): 450–454. 2. Cohen JC, Boerwinkle E, Mosley TH Jr, Hobbs HH. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med 2006: 354 (12): 1264–1272. 3. Nierman MC, Rip J, Kuivenhoven JA et al. Carriers of the frequent lipoprotein lipase S447X variant exhibit enhanced postprandial apoprotein B-48 clearance. Metabolism 2005: 54 (11): 1499–1503.
Loss-of-function mutations in APOC3, triglycerides, and coronary disease. TG & HDL Working Group of the NHLBI Exome Sequencing Project (2014) N Engl J Med 371:22–31 Loss-of-function mutations in APOC3 and risk of ischemic vascular disease. Jørgensen et al. (2014) N Engl J Med 371:32–41 Studies of extreme phenotypes have borne interesting fruit this year, with the publication of rare variants in major lipid genes that reduce risk for common disease.
Two independent groups have recently identified loss-of-function (LOF) mutations in APOC3 in people with low levels of circulating triglycerides (TGs). These rare alleles turn out to be antipathogenic because they are antiatherogenic. Jørgensen et al. preselected APOC3 as a candidate gene in a city-based cohort study among ethnically Danish individuals. By contrast, the Exome Sequencing Project (ESP) investigators cast their net more broadly, sequencing 18,666 genes to an average of 89-fold coverage in their n = 3734 discovery set, and following up with targeted genotyping in a replication cohort that was almost 111,000 strong. Both groups report that rare variants in APOC3 reduce triglyceride levels and significantly affect health outcomes. They also report comparable effect sizes, with different loss-of-function alleles in APOC3 each lowering TGs by 40% and also, on average, reducing vascular disease by 40% among heterozygotes. Jørgensen et al. report that carriers have a 16% reduction in ApoB, a 24% increase in ApoA1 and a 9% increase in high-density lipoprotein (HDL) cholesterol, and the ESP team reported a 16% reduction in low-density lipoprotein (LDL) cholesterol and a 22% increase in HDL. All of the ESP team’s signals held up in their European replication cohort, though the LDL signal was much weaker in their combined European–African replication set (Fig. 2). The observation of biologically and clinically significant lifelong cardioprotection from loss-of-function mutations in APOC3 is the latest in a group of ‘hyperhealthy’ genotype–phenotype correlations, a group that includes the lipoprotein lipase rs328 (p.Ser474Ter) allele (1) and certain rare variants in PCSK9 (2). From the perspective of personalized medicine, then, ‘third-generation’ algorithms that attempt to deliver predictive risk scores may improve their accuracy by moving beyond common single-nucleotide polymorphism (SNP) panels and incorporating targeted genotyping for rare variants in a manageable subset of known genes. In these studies, cardioprotective APOC3 variants were seen in 1 in 150 to 1 in 300 individuals, depending on the source populations. Because the number of genes harbouring rare variants of large effect on metabolic syndrome is likely to be in the dozens or more, the collective importance of rare variants may rival or surpass that of SNPs for prediction of genotype-specific risk. However, these studies were not designed to assess risk prediction of genotype-based algorithms compared to algorithms based on circulating lipids and family history.
Fig. 2. General schematic of research approach. Cohort sizes are not to scale. Cardiovascular risk is represented by a colour gradient from low (green) to high (red).
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HotSpots So how, exactly, do these loss-of-function variants promote resilience? Genetic epidemiology studies are designed to detect and quantify the strength of protective effects, not answer the molecular mechanisms behind such effects. Nonetheless, ApoC3 is known to inhibit lipoprotein lipase (LPL), so a lowering of ApoC3 levels would be expected to disinhibit LPL, and thereby increase hydrolysis of TG-rich lipoproteins [such as chylomicrons and very-low-density lipoproteins (VLDL)]. In this way, ApoC3 loss-of-function variants might lower risk by mechanisms similar to the LPL p.Ser474Ter allele, which increases the mass of available LPL and enhances ApoB48 clearance (3). ApoC3 also reduces the liver’s uptake of TG-rich lipoproteins and promotes TG and VLDL synthesis and secretion by the liver. A reduction in any or all of these activities would be expected to reduce circulating lipid levels and have metabolic benefit. Thus, multiple mechanisms are plausible and more than one is likely to be operating in carriers of cardioprotective APOC3 mutations. These reports show the value of large wellcharacterized prospective cohorts, whether they be cohorts of heterogeneous ancestry such as in the ESP, or national cohorts of intermediate heterogeneity. The findings are relevant for anyone with a biobank or cohort study. Successful studies pre-consent participants for linking clinical phenotyping to banked samples, or have mechanisms in place to recontact participants if new assays become available. Critical value is added by marrying high-throughput genotyping to high-resolution phenotyping to identify both extreme good health and disease. Although the power of next-generation sequencing for finding rare variants that cause extreme phenotypes is now well accepted, a welcome surprise is that clever selection of candidate genes coupled with Sanger validation (the strategy used by the Danish group) can still assign medically relevant phenotypes to genes of major physiological importance such as APOC3. Now that medically relevant outcomes at the population level are proven to be affected by rare variants in these genes, we have the strongest evidence yet that these genes are viable therapeutic targets. W. T. Gibson Department of Medical Genetics, University of British Columbia (UBC), Vancouver, British Columbia, Canada e-mail: [email protected]
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Beneficial metabolic phenotypes caused by loss-of-function APOC3 mutations References 1. Gagné SE, Larson MG, Pimstone SN et al. A common truncation variant of lipoprotein lipase (Ser447X) confers protection against coronary heart disease: the Framingham Offspring Study. Clin Genet 1999: 55 (6): 450–454. 2. Cohen JC, Boerwinkle E, Mosley TH Jr, Hobbs HH. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med 2006: 354 (12): 1264–1272. 3. Nierman MC, Rip J, Kuivenhoven JA et al. Carriers of the frequent lipoprotein lipase S447X variant exhibit enhanced postprandial apoprotein B-48 clearance. Metabolism 2005: 54 (11): 1499–1503.
Loss-of-function mutations in APOC3, triglycerides, and coronary disease. TG & HDL Working Group of the NHLBI Exome Sequencing Project (2014) N Engl J Med 371:22–31 Loss-of-function mutations in APOC3 and risk of ischemic vascular disease. Jørgensen et al. (2014) N Engl J Med 371:32–41 Studies of extreme phenotypes have borne interesting fruit this year, with the publication of rare variants in major lipid genes that reduce risk for common disease.
Two independent groups have recently identified loss-of-function (LOF) mutations in APOC3 in people with low levels of circulating triglycerides (TGs). These rare alleles turn out to be antipathogenic because they are antiatherogenic. Jørgensen et al. preselected APOC3 as a candidate gene in a city-based cohort study among ethnically Danish individuals. By contrast, the Exome Sequencing Project (ESP) investigators cast their net more broadly, sequencing 18,666 genes to an average of 89-fold coverage in their n = 3734 discovery set, and following up with targeted genotyping in a replication cohort that was almost 111,000 strong. Both groups report that rare variants in APOC3 reduce triglyceride levels and significantly affect health outcomes. They also report comparable effect sizes, with different loss-of-function alleles in APOC3 each lowering TGs by 40% and also, on average, reducing vascular disease by 40% among heterozygotes. Jørgensen et al. report that carriers have a 16% reduction in ApoB, a 24% increase in ApoA1 and a 9% increase in high-density lipoprotein (HDL) cholesterol, and the ESP team reported a 16% reduction in low-density lipoprotein (LDL) cholesterol and a 22% increase in HDL. All of the ESP team’s signals held up in their European replication cohort, though the LDL signal was much weaker in their combined European–African replication set (Fig. 2). The observation of biologically and clinically significant lifelong cardioprotection from loss-of-function mutations in APOC3 is the latest in a group of ‘hyperhealthy’ genotype–phenotype correlations, a group that includes the lipoprotein lipase rs328 (p.Ser474Ter) allele (1) and certain rare variants in PCSK9 (2). From the perspective of personalized medicine, then, ‘third-generation’ algorithms that attempt to deliver predictive risk scores may improve their accuracy by moving beyond common single-nucleotide polymorphism (SNP) panels and incorporating targeted genotyping for rare variants in a manageable subset of known genes. In these studies, cardioprotective APOC3 variants were seen in 1 in 150 to 1 in 300 individuals, depending on the source populations. Because the number of genes harbouring rare variants of large effect on metabolic syndrome is likely to be in the dozens or more, the collective importance of rare variants may rival or surpass that of SNPs for prediction of genotype-specific risk. However, these studies were not designed to assess risk prediction of genotype-based algorithms compared to algorithms based on circulating lipids and family history.
Fig. 2. General schematic of research approach. Cohort sizes are not to scale. Cardiovascular risk is represented by a colour gradient from low (green) to high (red).
31
HotSpots So how, exactly, do these loss-of-function variants promote resilience? Genetic epidemiology studies are designed to detect and quantify the strength of protective effects, not answer the molecular mechanisms behind such effects. Nonetheless, ApoC3 is known to inhibit lipoprotein lipase (LPL), so a lowering of ApoC3 levels would be expected to disinhibit LPL, and thereby increase hydrolysis of TG-rich lipoproteins [such as chylomicrons and very-low-density lipoproteins (VLDL)]. In this way, ApoC3 loss-of-function variants might lower risk by mechanisms similar to the LPL p.Ser474Ter allele, which increases the mass of available LPL and enhances ApoB48 clearance (3). ApoC3 also reduces the liver’s uptake of TG-rich lipoproteins and promotes TG and VLDL synthesis and secretion by the liver. A reduction in any or all of these activities would be expected to reduce circulating lipid levels and have metabolic benefit. Thus, multiple mechanisms are plausible and more than one is likely to be operating in carriers of cardioprotective APOC3 mutations. These reports show the value of large wellcharacterized prospective cohorts, whether they be cohorts of heterogeneous ancestry such as in the ESP, or national cohorts of intermediate heterogeneity. The findings are relevant for anyone with a biobank or cohort study. Successful studies pre-consent participants for linking clinical phenotyping to banked samples, or have mechanisms in place to recontact participants if new assays become available. Critical value is added by marrying high-throughput genotyping to high-resolution phenotyping to identify both extreme good health and disease. Although the power of next-generation sequencing for finding rare variants that cause extreme phenotypes is now well accepted, a welcome surprise is that clever selection of candidate genes coupled with Sanger validation (the strategy used by the Danish group) can still assign medically relevant phenotypes to genes of major physiological importance such as APOC3. Now that medically relevant outcomes at the population level are proven to be affected by rare variants in these genes, we have the strongest evidence yet that these genes are viable therapeutic targets. W. T. Gibson Department of Medical Genetics, University of British Columbia (UBC), Vancouver, British Columbia, Canada e-mail: [email protected]
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