Interaction between SNPs in the RXRA and near ANGPTL3 gene region inhibits apoB reduction after statin-fenofibric acid therapy in individuals with mixed dyslipidemia

The mixed dyslipidemia phenotype is characterized by elevated triglycerides (TG), low HDL cholesterol (HDL-C), increased ApoB levels, and premature coronary atherosclerosis. Fibrate-statin combination therapy reduces ApoB levels and coronary events in the mixed dyslipidemia population. We sought to identify gene-gene interactions that affect ApoB response to statin-fenofibric acid therapy in the mixed dyslipidemia population. Using a predefined subset of single-nucleotide polymorphisms (SNPs) that were previously associated with TG, VLDL, or HDL-C, we applied gene-gene interaction testing in a randomized, double-blind, clinical trial examining the response to fenofibric acid (FNA) and its combination with statin in 1,865 individuals with mixed dyslipidemia. Of 11,783 possible SNP pairs examined, we detected a single significant interaction between rs12130333, located within the ANGPTL3 gene region, and rs4240705, within the RXRA gene, on ApoB reduction after statin-FNA therapy (P = 4.0 × 10−6). ApoB response to therapy gradually reduced with the increasing number of T alleles in the rs12130333 but only in the presence of the GG genotype of rs4240705. Individuals doubly homozygous for the minor alleles at rs12130333 and rs4240705 showed a paradoxical increase of 1.8% in ApoB levels after FNA-statin combination therapy. No gene-gene interaction was identified other than an interaction between SNPs in the ANGPTL3 and RXRA regions, which results in the inhibition of ApoB reduction in response to statin-FNA therapy. Further study is required to examine the clinical applicability of this genetic interaction and its effect on coronary events. The mixed dyslipidemia phenotype is characterized by elevated triglycerides (TG), low HDL cholesterol (HDL-C), increased ApoB levels, and premature coronary atherosclerosis. Fibrate-statin combination therapy reduces ApoB levels and coronary events in the mixed dyslipidemia population. We sought to identify gene-gene interactions that affect ApoB response to statin-fenofibric acid therapy in the mixed dyslipidemia population. Using a predefined subset of single-nucleotide polymorphisms (SNPs) that were previously associated with TG, VLDL, or HDL-C, we applied gene-gene interaction testing in a randomized, double-blind, clinical trial examining the response to fenofibric acid (FNA) and its combination with statin in 1,865 individuals with mixed dyslipidemia. Of 11,783 possible SNP pairs examined, we detected a single significant interaction between rs12130333, located within the ANGPTL3 gene region, and rs4240705, within the RXRA gene, on ApoB reduction after statin-FNA therapy (P = 4.0 × 10−6). ApoB response to therapy gradually reduced with the increasing number of T alleles in the rs12130333 but only in the presence of the GG genotype of rs4240705. Individuals doubly homozygous for the minor alleles at rs12130333 and rs4240705 showed a paradoxical increase of 1.8% in ApoB levels after FNA-statin combination therapy. No gene-gene interaction was identified other than an interaction between SNPs in the ANGPTL3 and RXRA regions, which results in the inhibition of ApoB reduction in response to statin-FNA therapy. Further study is required to examine the clinical applicability of this genetic interaction and its effect on coronary events. The mixed dyslipidemia phenotype comprised of elevated triglycerides (TG), reduced HDL cholesterol (HDL-C), and increased ApoB is associated with diabetes and increased risk of coronary artery disease. One of the commonly used agents to treat individuals with mixed dyslipidemia are fibrates, including fenofibric acid (FNA), which are peroxisome proliferator-activated receptor-α (PPAR-α) agonists. FNA decreases TG, ApoB containing VLDL particles, and APOC-III while increasing HDL-C (1van Raalte D.H. Li M. Pritchard P.H. Wasan K.M. Peroxisome proliferator-activated receptor (PPAR)-α: a pharmacological target with a promising future.Pharm. Res. 2004; 21: 1531-1538Crossref PubMed Scopus (206) Google Scholar). Among the factors that determine the individual response to FNA and its combination with statins are single nucleotide polymorphisms (SNPs), which were previously shown to affect HDL-C, TG, and APOC-III levels in response to fibrates and statins (2Brautbar A. Covarrubias D. Belmont J. Lara-Garduno F. Virani S.S. Jones P.H. Leal S.M. Ballantyne C.M. Variants in the APOA5 gene region and the response to combination therapy with statins and fenofibric acid in a randomized clinical trial of individuals with mixed dyslipidemia.Atherosclerosis. 2011; 219: 737-742Abstract Full Text Full Text PDF PubMed Scopus (37) Google Scholar–3Lai C-Q. Arnett D.K. Corella D. Straka R.J. Tsai M.Y. Peacock J.M. Adiconis X. Parnell L.D. Hixson J.E. Province M.A. et al.Fenofibrate effect on triglyceride and postprandial response of apolipoprotein A5 variants: the GOLDN study.Arterioscler. Thromb. Vasc. Biol. 2007; 27: 1417-1425Crossref PubMed Scopus (108) Google Scholar, 4Brautbar A. Virani S.S. Belmont J. Nambi V. Jones P.H. Ballantyne C.M. LPL gene variants affect apoC-III response to combination therapy of statins and fenofibric acid in a randomized clinical trial of individuals with mixed dyslipidemia.J. Lipid Res. 2012; 53: 556-560Abstract Full Text Full Text PDF PubMed Scopus (12) Google Scholar). Going beyond the individual, additive effect of single loci, gene-gene interaction, or epistasis, is an important mechanism in determining an individual response to FNA therapy (5Ma L. Brautbar A. Boerwinkle E. Sing C.F. Clark A.G. Keinan A. Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations.PLoS Genet. 2012; (In press)Google Scholar, 6Ma L. Yang J. Runesha H.B. Tanaka T. Ferrucci L. Bandinelli S. Da Y. Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data.BMC Med. Genet. 2010; 11: 55Crossref PubMed Scopus (69) Google Scholar). In this study, we sought to identify gene-gene interactions affecting the response of ApoB to therapy with FNA. To improve statistical power, we focused on a small set of SNPs that we identified as known to be highly relevant to the mixed dyslipidemia phenotype. Our study population included DNA from 1,865 participants from three concurrent prospective, randomized, clinical trials examining the response to FNA, all of which had the same design. The study received Institutional Review Board approval from Baylor College of Medicine, and informed consent was obtained by Abbott Laboratories. Only individuals with mixed dyslipidemia were included, defined as TG ≥150 mg/dl, HDL-C <40 mg/dl for men or <50 mg/dl for women, and LDL cholesterol (LDL-C) ≥130 mg/dl. Exclusion criteria included active or recent ulcer, type 1 diabetes (type 2 diabetes was included unless uncontrolled), unstable cardiovascular disease, severe heart failure, renal failure, and elevated liver or muscle enzymes at baseline. Participants were randomized into groups receiving FNA monotherapy, statin monotherapy, or statin-FNA combination. After a washout period of 6 weeks, participants received the assigned treatment for 12 weeks. ApoB levels were measured before and after the 12 weeks of therapy (7Jones P.H. Davidson M.H. Kashyap M.L. Kelly M.T. Buttler S.M. Setze C.M. Sleep D.J. Stolzenbach J.C. Efficacy and safety of ABT-335 (fenofibric acid) in combination with rosuvastatin in patients with mixed dyslipidemia: a phase 3 study.Atherosclerosis. 2009; 204: 208-215Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar, 8Jones P.H. Bays H.E. Davidson M.H. Kelly M.T. Buttler S.M. Setze C.M. Sleep D.J. Stolzenbach J.C. Evaluation of a new formulation of fenofibric acid, ABT-335, co-administered with statins: study design and rationale of a phase III clinical programme.Clin. Drug Investig. 2008; 28: 625-634Crossref PubMed Scopus (36) Google Scholar). The statin that was used in each clinical trial was different and was either simvastatin, rosuvastatin, or atorvastatin. Baseline characteristics for the three clinical studies separately and combined are presented in supplementary Tables I–IV. Genes that are involved in TG, VLDL, and HDL-C pathways were selected (1van Raalte D.H. Li M. Pritchard P.H. Wasan K.M. Peroxisome proliferator-activated receptor (PPAR)-α: a pharmacological target with a promising future.Pharm. Res. 2004; 21: 1531-1538Crossref PubMed Scopus (206) Google Scholar, 9Kane J.P. Havel R.J. Disorders of the biogenesis and secretion of lipoproteins containing the B-apolipoproteins.in: Scriver C.R. Beaudet A.L. Valle D. Sly W.S. The Metabolic Basis of Inherited Disease. McGraw-Hill, New York2001: 2717-2752Google Scholar). Common (>5%) and uncommon (1–5%) tag SNPs within up to 10 Kb upstream and downstream of these gene boundaries were selected using the Genome Variation Server (http://gvs.gs.washington.edu/GVS/). Criteria for tag SNP selection included minor allele frequency (MAF) ≥1% in the HapMap-CEU dataset and tagging with linkage disequilibrium of r2≥0.8 for of any SNP in the target genes. Additional SNPs that were previously identified in a genome-wide association study as associated with TG and HDL-C levels were added (10Kathiresan S. Willer C.J. Peloso G.M. Demissie S. Musunuru K. Schadt E.E. Kaplan L. Bennett D. Li Y. Tanaka T. et al.Common variants at 30 loci contribute to polygenic dyslipidemia.Nat. Genet. 2009; 41: 56-65Crossref PubMed Scopus (1088) Google Scholar–11Willer C.J. Sanna S. Jackson A.U. Scuteri A. Bonnycastle L.L. Clarke R. Heath S.C. Timpson N.J. Najjar S.S. Stringham H.M. et al.Newly identified loci that influence lipid concentrations and risk of coronary artery disease.Nat. Genet. 2008; 40: 161-169Crossref PubMed Scopus (1324) Google Scholar, 12Spirin V. Schmidt S. Pertsemlidis A. Cooper R.S. Cohen J.C. Sunyaev S.R. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol.Am. J. Hum. Genet. 2007; 81: 1298-1303Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar, 13Thompson A. Di Angelantonio E. Sarwar N. Erqou S. Saleheen D. Dullaart R.P. Keavney B. Ye Z. Danesh J. Association of cholesteryl ester transfer protein genotypes with CETP mass and activity, lipid levels, and coronary risk.JAMA. 2008; 299: 2777-2788Crossref PubMed Scopus (425) Google Scholar), for a total of 338 SNPs used to examine possible epistatic effects in therapy response. Thirty-four additional known ancestry informative SNPs were used to correct for possible population stratification within the European-American population, with no significant substructure observed as previously shown (2Brautbar A. Covarrubias D. Belmont J. Lara-Garduno F. Virani S.S. Jones P.H. Leal S.M. Ballantyne C.M. Variants in the APOA5 gene region and the response to combination therapy with statins and fenofibric acid in a randomized clinical trial of individuals with mixed dyslipidemia.Atherosclerosis. 2011; 219: 737-742Abstract Full Text Full Text PDF PubMed Scopus (37) Google Scholar). SNPs, their relative location in relation to genes, and their frequency in our study population are detailed in supplementary Table V. SNPs were genotyped with the Golden Gate chemistry platform on an Illumina Bead Express system (Igenix, Seattle, WA). Individuals with >10% missing data were excluded, as well as subjects with SNPs with call rates <90%, MAF ≤1%, or subjects who departed from Hardy-Weinberg Equilibrium genotype proportions (P < 10−6). For the interaction test of each pair of SNPs, we also required a sample size of each of the nine possible genotype-combinations ≥3 and linkage disequilibrium of r2 < 0.1 between the two SNPs. The first requirement is a generalization of the MAF requirement in a single-marker analysis. We tested for the existence of gene-gene interaction between a pair of SNPs effects using an F-test with four degrees of freedom that compares two models with and without interaction (5Ma L. Brautbar A. Boerwinkle E. Sing C.F. Clark A.G. Keinan A. Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations.PLoS Genet. 2012; (In press)Google Scholar, 14Cordell H.J. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans.Hum. Mol. Genet. 2002; 11: 2463-2468Crossref PubMed Scopus (798) Google Scholar). This F-test does not assume a certain type of deviation from additive effects and allows for epistatic interaction of any type; hence, when little is known about the underlying epistatic effect, it tends to be more robust and powerful than tests that make such assumptions (14Cordell H.J. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans.Hum. Mol. Genet. 2002; 11: 2463-2468Crossref PubMed Scopus (798) Google Scholar). In total, we tested 11,783 pairwise interactions between 304 SNPs in their effect on percent change in levels of ApoB in each of the three treatment groups: FNA monotherapy, statin monotherapy, and statin-FNA combination. Gender, age, body mass index, and diabetes were included as covariates in the model. We estimated the effective number of tests out of the 11,783 interaction tests and used it to apply a Bonferroni correction on significance levels. First, by using the pairwise correlation of SNP genotypes, we estimated the effective number of SNPs from the original 304 markers to be 227 (15Moskvina V. Schmidt K.M. On multiple testing correction in genome wide association studies.Genet. Epidemiol. 2008; 32: 567-573Crossref PubMed Scopus (184) Google Scholar). Assuming the number of independent interaction tests is equivalent to all possible pairs out of the 227 markers (227 × 226/2), it is equivalent to 56% of tests, which is slightly larger than the estimated 40% from Illumina HumanHap 550 data (16Becker T. Herold C. Meesters C. Mattheisen M. Baur M.P. Significance levels in genome-wide interaction analysis (GWIA).Ann. Hum. Genet. 2011; 75: 29-35Crossref PubMed Scopus (20) Google Scholar), presumably due to differences in the procedure of SNP selection. Thus, we estimated the effective number of interaction tests as 11,783 × 0.56 = 6,599, which is the number of hypotheses we corrected for in our multiple testing correction. In total, we tested 11,783 epistatic interactions on ApoB response to statin-FNA combination therapy. Of the interactions examined, two interactions were found significant after multiple testing correction. The two interactions are between rs12130333 and rs4240705 and between rs12130333 and rs3118571. rs4240705 and rs3118571 are in high linkage disequilibrium. The most significant interaction was observed between rs12130333 in the ANGPTL3 gene region and rs4240705 in the RXRA gene (P = 4.0 × 10−6; Pc= 0.026 after multiple-testing correction). Examining the ApoB response of each of the nine genotype combinations of the two SNPs suggests that the double homozygotes for the minor allele for each of the two SNPs is expected to exhibit an average increase in APOB, paradoxical to the expected drug response (Fig. 1). An additive effect was observed as a function of the number of T alleles in the rs12130333 but only in the presence of GG genotype for rs4240705. Conditioning on the latter, ApoB response to therapy was gradually reduced with the increasing number of T alleles in the rs12130333: −39.5% with CC, −29.99% with CT, and +1.8% with TT. All other genotype combinations predicted a considerable reduction in ApoB levels, although there was some attenuated response for the combination of the rs12130333 TT and the rs4240705 AA genotype (Table 1). Thus, the most prominent interaction was observed in individuals doubly homozygous for the minor alleles at rs12130333 and rs4240705 with a paradoxical increase of 1.8% in ApoB levels on average. A similar interaction was not observed for the FNA or statin monotherapy groups.TABLE 1Two-SNP (rs12130333 and rs4240705) joint-genotype frequencies, mean percent change of ApoB levels, and standard error in the combination therapy groupGenotypeCC:AACT:AATT:AACC:AGCT:AGTT:AGCC:GGCT:GGTT:GGFrequency191888208681762233Mean percent change−36.54−38.07−23.12−36.33−34.50−40.00−39.53−29.991.84Standard error1.181.828.711.142.203.271.844.4128.95 Open table in a new tab In this study, we examined multiple gene-gene interactions between multiple candidate genes associated with ApoB, HDL-C, and TG with identifying a single novel interaction between the alleles in the RXRA and ANGPTL3 gene regions. This interaction resulted in attenuation of the ApoB reduction in response to combination of FNA-statin therapy. PPAR-α is activated by FNA and to a minor degree by statins (17Inoue I. Itoh F. Aoyagi S. Tazawa S. Kusama H. Akahane M. Mastunaga T. Hayashi K. Awata T. Komoda T. et al.Fibrate and statin synergistically increase the transcriptional activities of PPARalpha/RXRalpha and decrease the transactivation of NFkappaB.Biochem. Biophys. Res. Commun. 2002; 290: 131-139Crossref PubMed Scopus (107) Google Scholar). Multiple downstream target genes with a PPAR-α response element (PPRE) are activated when PPAR-α forms a heterodimer with retinoid X receptor α (RXR-α), which is coded by the RXRA gene. Although PPAR-α alone can activate its PPRE targets, the PPAR-α/RXR-α heterodimer has a better ability to enhance gene transcription. The SNP rs4240705 is located in an RXRA intron and is not expected to affect RXR-α protein structure. However, this is a tag SNP that is possibly a marker of a coding variant. Another possibility is that the rs4240705 has an impact as a regulatory element on RXR-α expression. The rs12130333 is an intergenic SNP upstream of ANGPTL3 that was previously associated with reduced TG in a number of genome-wide association and other studies (18Kathiresan S. Melander O. Guiducci C. Surti A. Burtt N.P. Rieder M.J. Cooper G.M. Roos C. Voight B.F. Havulinna A.S. et al.Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.Nat. Genet. 2008; 40: 189-197Crossref PubMed Scopus (1130) Google Scholar–19Wang J. Ban M.R. Zou G.Y. Cao H. Lin T. Kennedy B.A. Anand S. Yusuf S. Huff M.W. Pollex R.L. et al.Polygenic determinants of severe hypertriglyceridemia.Hum. Mol. Genet. 2008; 17: 2894-2899Crossref PubMed Scopus (108) Google Scholar, 20Sabatti C. Service S.K. Hartikainen A.L. Pouta A. S. J. Jones T. M. et association analysis of in a from a Genet. 2009; 41: PubMed Scopus Google and with reduced J.E. D.J. et loci associated with plasma of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, apolipoprotein and in genome-wide analysis with Genet. 2008; PubMed Scopus (108) Google Scholar). in the ANGPTL3 gene previously shown in and of low ApoB and in D. V. F. E. M. R. S. et of ANGPTL3 and gene in subjects with combined Thromb. Vasc. Biol. 2012; 32: PubMed Scopus Google Scholar, K. J.P. R. Peloso G.M. Guiducci C. C. S. J. et ANGPTL3 and combined J. Med. 2010; PubMed Scopus Google Scholar). ANGPTL3 is an LPL and in ANGPTL3 in associated with low TG levels S. J. Boerwinkle E. Cohen J.C. in contribute to plasma triglyceride levels in 2009; Google Scholar). is an between ANGPTL3 and the PPAR-α PPAR-α such as FNA, the liver X receptor a PPRE in its S. V. B. E. A. M. N. et and cholesterol from of the Med. PubMed Scopus Google Scholar). The ANGPTL3 has a known and it has shown that ANGPTL3 is by T. M. M. N. N. Y. H. R. M. I. protein 3 by the liver X Biol. Full Text Full Text PDF PubMed Scopus Google R. T. M. of the protein 3 gene by Lipid Res. Full Text Full Text PDF PubMed Scopus Google Scholar, H. H. C. X. Li C. and of 3 and Lipid Res. Full Text Full Text PDF PubMed Scopus Google Scholar). Thus, FNA can possibly ANGPTL3 which is expected to increase ApoB levels. However, as observed in this study, the effect of FNA and statin was reduction in ApoB levels, reduction in TG and after the of the LPL with FNA. is possible that in the presence of FNA and the minor allele of the rs4240705 in RXRA in the of which in has a effect on ANGPTL3 due to the presence of the Thus, there is a larger ApoB increase that possibly the ApoB reduction effect of the statin-FNA combination. The attenuated ApoB in the mixed dyslipidemia phenotype in response to the FNA-statin combination with certain genotypes of the rs12130333 and rs4240705 possibly affect cardiovascular In the to in a combination of statin and not improve coronary in the study population J. F. R.P. of combination lipid therapy in type 2 diabetes J. Med. 2010; PubMed Scopus Google Scholar). However, were observed in participants with mixed dyslipidemia mg/dl and HDL-C Thus, therapy to more in individuals with mixed dyslipidemia. ApoB reduction to the from combination therapy in the individuals with mixed dyslipidemia who are of the minor alleles of rs4240705 and rs12130333 reduction in that their ApoB not be reduced as with individuals who are not of these minor However, we were not to examine coronary in this study the clinical trial was for a period of with no cardiovascular A possible of our study is the that three doubly homozygous individuals for the minor alleles for ANGPTL3 rs12130333 and GG for RXRA rs4240705) had a effect on the interaction However, the rs12130333 T allele in combination with the rs4240705 allele to the effect on the ApoB response. In after testing of multiple gene-gene we identified only a single interaction that has a effect on ApoB response to therapy. We shown that individuals with mixed dyslipidemia who are receiving a combination of FNA and statins an attenuated ApoB reduction are homozygous for the minor allele of SNPs in the ANGPTL3 and RXRA gene regions. This the cardiovascular risk reduction observed with the combination of FNA and statins with statins Further study is required to test the significance of this in a larger sample size and to examine the clinical of these and studies are to examine the effect of the interactions between ANGPTL3 and RXRA to influence ApoB response to therapy. with fenofibric acid HDL cholesterol LDL cholesterol liver X receptor minor allele frequency peroxisome proliferator-activated receptor PPAR-α response element retinoid X receptor single-nucleotide triglycerides