Int J Clin Exp Pathol 2017;10(1):804-810 www.ijcep.com /ISSN:1936-2625/IJCEP0039729 Original Article CDKN2BAS polymorphisms are associated with coronary artery disease in Chinese Han population Xiaoli Li1*, Huijun Ma2*, Fei Li1, Yizhou Li3, Zhilan Xie4,5, Huaisheng Bai1, Bo Gao1, Qian Liang1, Feng Gao1, Tianbo Jin4,5 1Department of The Cardiology, Yan’an University Affiliated Hospital, Yan’an, China; 2Department of Cardiology, The First Hospital of Xi’an, Xi’an, China; 3Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; 4Key Laboratory of Resource Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi’an, Shaanxi, China; 5Xi’an Tiangen Precision Medical Institute, Xi’an, Shaanxi, China. *Equal contributors and co-first authors. Received September 9, 2016; Accepted November 1, 2016; Epub January 1, 2017; Published January 15, 2017 Abstract: Background: Previous studies have identified various SNPs in CDKN2BAS gene that influence the risk of developing coronary artery disease (CAD). In our study, we evaluated the association between CDKN2BAS poly- morphisms and CAD risk in the Chinese Han population. Methods: In our study, among 1,141 participants (456 CAD patients, and 685 normal individuals), eight single nucleotide polymorphisms within the CDKN2BAS loci were genotyped and examined for their correlation with the risk of CAD and treatment response using Pearson’s χ2 test and unconditional logistic regression analysis. Results: Overall, the strongest associations were found between rs10757274 in CDKN2BAS gene with the risk of CAD in the allele model (P=0.013). Moreover, we discovered a no- table association between SNP rs10757274 and CAD in co-dominant, dominant and log-additive models (P=0.027, P=0.008, P=0.013 respectively). The results, adjusted by confounding factors, were also significant in co-dominant, dominant models (P=0.015, P=0.045 respectively). Moreover, the haplotypes “AA” and “AG” exhibited a protective factors for the risk of CAD after adjusted for age and gender (P=0.013, P=0.034 respectively). Conclusion: We found a remarkable association between rs10757274 and CAD in the Chinese Han population. Keywords: Coronary artery disease (CAD), CDKN2BAS, polymorphism Introduction CDKN2BAS gene is a large antisense non-cod- ing RNA, which is differentially expressed in a Coronary artery disease (CAD) is the most variety of tissues such as vascular endothelial cause of human death in the European coun- cells and smooth coronary muscle cells [7, 8]. tries and Asian countries especially containing Non-coding RNAs are involved in the regulation China [1]. CAD comes to be a complex disease of gene expression through transcriptional and caused by a combination of genetic and envi- translational control. CDKN2BAS expression is ronmental factors [2]. Over the past years, shown to be associated with multiple pheno- much progress has been made in the pharma- cotherapy of major risk factors like dyslipid- types comprising the risk of coronary disease emias, diabetes mellitus and hypertension [3]. [9]. Interestingly, CDKN2BAS expression has Clinical observation has found that all of the been shown to be regulated by a CAD-ass- risk factors result in the induction of athero- ociated genetic variant. Regulation of cardiac sclerosis, which is one of the major pathophysi- CDKN2BAS expression has been found to play ological mechanisms of CAD [4]. Recently, a pivotal role in the development of CAD by genome-wide association studies of the rela- altering the dynamics of vascular cell prolifera- tions between single nucleotide polymorphisms tion [10]. Moreover, evidence has shown that (SNPs) and CAD risk have been focused to iden- CDKN2BAS gene variants are associated with tify the cause of the CAD [5], and also found a CAD [11]. CDKN2BAS may serve as a biomark- relationship between CDKN2BAS gene and er for the risk of myocardial infarction and hem- CAD risk [6]. orrhagic stroke, and their recurrence [12-14]. The association between CDKN2BAS and CAD risk Table 1. The characteristic of controls and cases in this Selection of SNPs and methods of study genotyping Characteristic Case (n=456) Control (n=685) P According to the previous reports, we Sex, N (%) 0.01a selected eight SNPs for this study Female 165 (36.2%) 300 (43.8%) and they were rs7865618, rs117- Male 291 (63.8%) 385 (56.2%) 90231, rs1412832, rs6475606, rs- b Age (Mean Age ± SD ) 61.17±11.86 48.59±9.556 <0.001 1333040, rs1537370, rs10757274 a b P value was calculated by Pearson’s Chi-square test. P value was calcu- and rs1333042. The minor allele fre- lated by Welch’s t test. P<0.05 indicates statistical significance. quencies of these SNPs were >5% in the Hap Map of the Chinese Han And common variants of CDKN2BAS are shown Beijing (CHB) population. The procedure includ- to be associated with myocardial infarction (MI) ed DNA extraction and genotyping. Extraction in European whites and Hispanic population of DNA from whole blood samples was per- [15, 16]. formed using the Gold Mag-Mini Whole Blood Genomic DNA Purification Kits (Gold Mag Co., In Chinese population, CDKN2BAS gene vari- Ltd.; Hainan City, China), and the DNA concen- ants are related to Type 2 diabetes risk [17]. tration was measured using a Nano Drop 2000 However, there is a lack of investigation for spectrophotometer. the association between polymorphism of CDKN2BAS gene and CAD risk in Han Chinese. Genotyping steps include PCR and single base The purpose of the present case-control extension. Firstly, we designed primers for study was to identify the association between amplification and extension reactions using eight high frequency SNPs CDKN2BAS of and Sequenom Mass ARRAY Assay Design 3.0 CAD risk in Han Chinese. Software (Sequenom Inc., San Diego, CA, USA) (Table 1). Then, Genotyping was performed Materials and methods using the Sequenom Mass ARRAY RS1000 sys- tem and the standard protocol recommended Study population by the manufacturer. After the experimentation progress mentioned above, data management All of the cases and control individuals were the and analysis was conducted using Sequenom members of the Chinese Han population. The Typer4.0 software [18, 19]. control participants and CAD cases were Statistical analysis recruited between 2013 and 2015 from Yan’an University Affiliated Hospital and the First We used Microsoft Excel and SPSS 18.0 sta- Hospital of Xi’an. This case-control study strict- tistical package (SPSS, Chicago, IL, USA) to ly obeyed the principles of the Declaration on perform statistical analyses. In our study, all Helsinki of the World Medical Association and P-values were based on two-sided tests and got the permission from the Ethics Committ- we achieved P≤0.05 among all the p values as ee of Yan’an University Affiliated Hospital, the the threshold of statistical significance. The First Hospital of Xi’an, Inner Mongolia Medical validation of each SNP frequency in control University and Northwest University. All of the subjects was tested for departure from Hardy- participants were informed the case-control Weinberg Equilibrium (HWE) using an exact study and their consent were obtained. test. In order to clearly evaluated the associa- tion between the polymorphism of eight SNPs Demographic information and CAD risk, the method of the chi-square test was used to calculate the difference in geno- We used a standard epidemiological question- type frequencies between case and control naire and in-person interview to collect person- [20]. Furthermore, five genetic models (allele, al data, including the residential regions; age; co-dominant, dominant, recessive and log- gender; histories of medication use. The case additive model) were used to test the associa- information was collected through a consulta- tion of certain SNPs with the risk of CAD. tion with the treating physicians or from a medi- cal chart review. All of the participants signed Finally, the SHEsis software platform (http:// an informed consent agreement. www.nhgg.org/analysis) and Haploview soft- 805 Int J Clin Exp Pathol 2017;10(1):804-810 The association between CDKN2BAS and CAD risk Table 2. The basic information of SNPs in CDKN2BAS gene MAF in MAF in Gene SNP No. Chromosome Location Allele HWE pa Pb-value O (HET) case group control group CDKN2BAS rs7865618 9p21.3 Intron G/A 0.124 0.120 1 0.789 0.212 rs11790231 9p21.3 Intron A/G 0.148 0.150 0.369 0.882 0.265 rs1412832 9p21.3 Intron C/T 0.264 0.285 0.707 0.264 0.415 rs6475606 9p21.3 Intron C/T 0.285 0.300 0.318 0.431 0.437 rs1333040 9p21.3 Intron C/T 0.281 0.294 0.41 0.507 0.429 rs1537370 9p21.3 Intron C/T 0.284 0.298 0.236 0.477 0.438 rs10757274 9p21.3 Intron G/A 0.474 0.421 0.696 0.013* 0.480 rs1333042 9p21.3 Intron A/G 0.315 0.347 0.735 0.117 0.447 SNPs: Single nucleotide polymorphisms; A: Miner alleles, B: Major alleles; MAF: Minor allele frequency; HWE: Hardy-Weinberg equilibrium; OR: Odds ratio. CI: Confidence interval; pa: p value was calculated using exact test; pb: p value was calculated us- ing Chi-square test; *P<0.05 indicates statistical significance. ware package (version 4.2) were used to ana- associations between SNPs and CAD risks lyze the association between haplotypes and using the logistic test. We discovered an asso- risk of CAD [21, 22]. Control samples were used ciation regarding increased risks between SNP to the haplotype construction. The linkage dis- rs11790231 and CAD in Recessive model equilibrium degree of the Two SNPs is mea- (OR=2.16, 95% CI=1.02-4.57, P=0.042 for sured by D’ value, and D’ confidence interval is A/A), however, the results mentioned about used to divide haplotype block.