Intronic Polymorphisms in the CDKN2B-AS1 Gene Are Strongly Associated with the Risk of Myocardial Infarction and Coronary Artery Disease in the Saudi Population

Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci

Coronary artery disease (CAD) is the leading cause of death worldwide. Recently, hundreds of genomic loci have been shown to increase CAD risk, however, the molecular mechanisms underlying signals from CAD risk loci remain largely unclear. We sought to pinpoint the candidate causal coding and non-coding genes of CAD risk loci in a cell type-specific fashion. We integrated the latest statistics of CAD genetics from over one million individuals with epigenetic data from 45 relevant cell types to identify genes whose regulation is affected by CAD-associated single nucleotide variants (SNVs) via epigenetic mechanisms. Applying two statistical approaches, we identified 1,580 genes likely involved in CAD, about half of which have not been associated with the disease so far. Enrichment analysis and phenome-wide association studies linked the novel candidate genes to disease-specific pathways and CAD risk factors, corroborating their disease relevance. We showed that CAD-SNVs are enriched to regulate gene expression by affecting the binding of transcription factors (TFs) with cellular specificity. Of all the candidate genes, 23.5% represented non-coding RNAs (ncRNA), which likewise showed strong cell type specificity. We conducted a proof-of-concept biological validation for the novel CAD ncRNA gene IQCH-AS1 . CRISPR/Cas9-based gene knockout of IQCH-AS1 , in a human preadipocyte strain, resulted in reduced preadipocyte proliferation, less adipocyte lipid accumulation, and atherogenic cytokine profile. The cellular data are in line with the reduction of IQCH-AS1 in adipose tissues of CAD patients and the negative impact of risk alleles on its expression, suggesting IQCH-AS1 to be protective for CAD. Our study not only pinpoints CAD candidate genes in a cell type-specific fashion but also spotlights the roles of the understudied ncRNA genes in CAD genetics.

The association between the single-nucleotide polymorphism of site rs1333040 in region 9p21 and the risk of coronary heart disease in Chinese population

BACKGROUND

Rs1333040 is the single-nucleotide polymorphisms (SNP) related with coronary heart disease (CHD). The aim of the present study is to examine the association between rs1333040 polymorphism genotypes and CHD and to further explore the molecular mechanism in Chinese population.

METHODS

A case-control study was used in this study, including 500 CHD patients and 500 control subjects. CHD patients and controls were distinguished by coronary angiography. Genotypes of rs1333040 were determined on the Agena MassARRAY system. Statistical analysis was conducted by SPSS (Ver 16.0) and plink (Ver. 1.07, Shaun Purcell).

RESULTS

Fisher's exact test by plink indicated a significant difference in the allele distribution between cases and controls, the allele T may be associated with a higher risk of CHD (p = 0.012, odds ratio (OR) = 1.258). The serum levels of low-density lipoprotein cholesterol (LDL-C) (p = 0.029) and Gensini score (p = 0.008) distributed differently in patients with various alleles. In the recessive model, the levels of high-density lipoprotein (HDL) and apolipoprotein A (ApoA) were higher in the TC + CC genotype than in the TT genotype. The TC + TT genotype was found to be risk factors against CHD in a dominant model (OR = 1.278, p = 0.014). The TC + TT genotype along with multiple risk factors significantly positively correlated with the risk of CHD.

CONCLUSIONS

The present study investigates the association between the rs1333040 polymorphism genotypes and CHD. The T allele of rs1333040 is the susceptibility site of CHD. The interaction between SNP and various risk factors plays an important role in the development of CHD.

Genetic variants of ANRIL and coronary artery disease: Insights from a Turkish study population

BACKGROUND AND AIM

Coronary artery disease (CAD) remains a leading cause of morbidity and mortality globally despite advancements in treatment. Long non-coding RNAs (lncRNAs) play crucial roles in the atherosclerotic process, with ANRIL being one such lncRNA. This study explored the association between ANRIL polymorphisms (rs1333049:C > G, rs564398:T > C, and rs10757274:A > G) and CAD along with CAD risk factors in a Turkish patient group.

METHODS

The study included 1285 participants, consisting of 736 patients diagnosed with CAD (mean age = 63.3 ± 10.5 years) and 549 non-CAD controls (mean age = 57.52 ± 11.01 years). Genotypes for rs1333049, rs564398, and rs10757274 were determined using qRT-PCR.

RESULTS

G allele carriage of both rs1333049 and rs10757274 polymorphisms were associated with higher Gensini score, SYNTAX score, total cholesterol, and triglyceride levels in female CAD patients and non-CAD males. Females with rs564398 CC genotype were more susceptible to CAD (p = 0.02) and severe CAD (p = 0.05). Moreover, the G and T alleles of rs10757274 and rs564398 were more prevalent among hypertensive males. Also, carrying the C allele for rs564398 was associated with a decreased risk for type 2 diabetes mellitus (T2DM) (p = 0.02). Besides, carriers of the rs1333049 C allele for decreased risk for T2DM (p = 0.03) and CAD complexed with T2DM (p = 0.04) in logistic regression analyses.

CONCLUSIONS

In conclusion, selected ANRIL polymorphisms were associated with CAD presence/severity and CAD risk factors, T2DM, and hypertension. Notably, this study, the largest sample-sized study examining the effects of selected polymorphisms on CAD and its risk factors among Turkish individuals, supported the findings of previous studies conducted on different ethnicities.

Abdominal aortic aneurysm and cardiometabolic traits share strong genetic susceptibility to lipid metabolism and inflammation

Abdominal aortic aneurysm has a high heritability and often co-occurs with other cardiometabolic disorders, suggesting shared genetic susceptibility. We investigate this commonality leveraging recent GWAS studies of abdominal aortic aneurysm and 32 cardiometabolic traits. We find significant genetic correlations between abdominal aortic aneurysm and 21 of the cardiometabolic traits investigated, including causal relationships with coronary artery disease, hypertension, lipid traits, and blood pressure. For each trait pair, we identify shared causal variants, genes, and pathways, revealing that cholesterol metabolism and inflammation are shared most prominently. Additionally, we show the tissue and cell type specificity in the shared signals, with strong enrichment across traits in the liver, arteries, adipose tissues, macrophages, adipocytes, and fibroblasts. Finally, we leverage drug-gene databases to identify several lipid-lowering drugs and antioxidants with high potential to treat abdominal aortic aneurysm with comorbidities. Our study provides insight into the shared genetic mechanism between abdominal aortic aneurysm and cardiometabolic traits, and identifies potential targets for pharmacological intervention.

Two missense variants of the epidermal growth factor receptor gene are associated with non small cell lung carcinoma in the subjects from Iraq

BACKGROUND

Lung carcinoma is a foremost cause of cancer-related mortality worldwide. Variable genetic factors are associated with the development of lung cancer. This study was performed to evaluate the possible association of epidermal growth factor receptor (EGFR) gene polymorphisms with non small cell lung carcinoma (NSCLC) in Iraqi population.

METHODS

DNA samples were extracted from 100 patients and 100 controls. Four PCR fragments were designed to amplify four high-frequency variants within EGFR, namely rs1050171, rs2072454, rs2227984, and rs2227983. The PCR fragments were genotyped by single-strand conformation polymorphism (SSCP) method, and each genotype was subjected to direct sequencing.

RESULTS

Genotyping experiments confirmed the variability of three targeted variants, and logistic regression analysis showed that two of these variants (rs1050171 and rs2227983) tend to exhibit a significant association with NSCLC. Individuals with rs1050171:GA genotype showed a possible association with the increased risk of NSCLC (P = 0.0110; OD 5.2636; Cl_95% 1.4630 to 18.9371). Individuals with rs2227983:GG genotype exhibited a potential association with NSCLC (P = 0.0037; OD 5.2683; Cl_95% 1.7141 to 16.1919). Linkage disequilibrium analysis showed that the effects of the investigated variants seem to take independent actions, and no haplotype was found to be associated with the high prevalence of NSCLC.

CONCLUSIONS

Our collective data indicated that EGFR-rs1050171G/A and EGFR-rs2227983G/G SNPs tend to exert significant and separate associations with the increased risk of NSCLC. However, this study recommends using a broader spectrum of the investigated samples to get further details of both SNPs in terms of their association with the susceptibility to NSCLC.

Inflammasome Genetic Variants Are Associated with Protection to Clinical Severity of COVID-19 among Patients from Rio de Janeiro, Brazil

COVID-19 has a broad spectrum of clinical manifestations, from asymptomatic or mild/moderate symptoms to severe symptoms and death. The mechanisms underlying its clinical evolution are still unclear. Upon SARS-CoV-2 infection, host factors, such as the inflammasome system, are activated by the presence of the virus inside host cells. The search for COVID-19 risk factors is of relevance for clinical management. In this study, we investigated the impact of inflammasome single-nucleotide polymorphisms (SNPs) in SARS-CoV-2-infected individuals with distinct severity profiles at clinical presentation. Patients were divided into two groups according to disease severity at clinical presentation based on the WHO Clinical Progression Scale. Group 1 included patients with mild/moderate disease (WHO < 6; n = 76), and group 2 included patients with severe/critical COVID-19 (WHO ≥ 6; n = 357). Inpatients with moderate to severe/critical profiles were recruited and followed-up at Hospital Center for COVID-19 Pandemic – National Institute of Infectology (INI)/FIOCRUZ, RJ, Brazil, from June 2020 to March 2021. Patients with mild disease were recruited at Oswaldo Cruz Institute (IOC)/FIOCRUZ, RJ, Brazil, in August 2020. Genotyping of 11 inflammasome SNPs was determined by real-time PCR. Protection and risk estimation were performed using unconditional logistic regression models. Significant differences in NLRP3 rs1539019 and CARD8 rs2043211 were observed between the two groups. Protection against disease severity was associated with the A/A genotype (OR_adj = 0.36; P = 0.032), allele A (OR_adj = 0.93; P = 0.010), or carrier-A (OR_adj = 0.45; P = 0.027) in the NLRP3 rs1539019 polymorphism; A/T genotype (OR_adj = 0.5; P = 0.045), allele T (OR_adj = 0.93; P = 0.018), or carrier-T (OR_adj = 0.48; P = 0.029) in the CARD8 rs2043211 polymorphism; and the A-C-G-C-C (OR_adj = 0.11; P = 0.018), A-C-G-C-G (OR_adj = 0.23; P = 0.003), C-C-G-C-C (OR_adj = 0.37; P = 0.021), and C-T-G-A-C (OR_adj = 0.04; P = 0.0473) in NLRP3 genetic haplotype variants. No significant associations were observed for the other polymorphisms. To the best of our knowledge, this is the first study demonstrating an association between CARD8 and NLRP3 inflammasome genetic variants and protection against COVID-19 severity, contributing to the discussion of the impact of inflammasomes on COVID-19 outcomes.

Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma

Background

Primary open‐angle glaucoma (POAG) is the commonest form of glaucoma which is estimated to cause bilaterally blind within 11.1 million people by 2020. Therefore, the primary objectives of this study were to investigate the clinical significance of single‐nucleotide polymorphisms (SNPs) in the lncRNAs MALAT1 and ANRIL in a Chinese Han POAG cohort.

Methods

Three hundred and forty‐six glaucoma patients and 263 healthy controls were recruited, and totally 14 SNPs in MALAT1 and ANRIL were genotyped between the two populations.

Results

The MALAT1 SNPs rs619586 (A>G), rs3200401 (C>T), and rs664589 (C>G) were associated with POAG risk, and the ANRIL SNPs rs2383207 (A>G), rs564398 (A>G), rs2157719 (A>G), rs7865618 (G>A), and rs4977574 (A>G) were associated with POAG (p < 0.05). The MALAT1 haplotypes ACG and ATC, comprised rs619586, rs3200401, and rs664589, increased POAG risk, and the ANRIL haplotype AAGAA, made up of rs2383207, rs7865618, rs4977574, rs564398, and rs2157719, show a significantly increased risk of POAG. In addition, rs619586 (A>G) of MALAT1 and rs564398/rs2157719 of ANRIL were associated with a smaller vertical cup‐to‐disc ratio, while rs619586 of MALAT1 and rs2383207/rs4977574 of ANRIL were associated with higher intraocular pressure in the POAG population.

Conclusion

Single‐nucleotide polymorphisms and haplotypes in ANRIL and MALAT1 were associated with POAG onset in our study population, which provide more possibilities to POAG diagnosis and treatment.

MiR-146a and miR-155 polymorphisms in Egyptian patients with Behcet's disease

INTRODUCTION

The current study was designed to analyze whether polymorphisms of miR-146a and miR-155 are related to Behçet's disease (BD) in the Egyptian population.

MATERIAL AND METHODS

A total of 96 unrelated BD patients and 100 healthy subjects were genotyped for miR-146a (rs2910164) and miR-155 (rs767649) using real-time polymerase chain reaction.

RESULTS

The results showed significant elevation in the frequency of rs2910164 GG and CC genotypes in BD patients compared with controls (adjusted OR = 22.156, 95% CI: 4.728-103.818; p < 0.001 and adjusted OR = 40.358, 95% CI: 8.928-182.440; p < 0.001, respectively). Also, the rs2910164 G allele conferred a higher risk of developing BD (adjusted OR = 3.665, 95% CI: 2.013-6.671; p < 0.001). MiR-146a (rs2910164) polymorphism was a risk factor for susceptibility to BD in dominant, recessive and additive models of inheritance (all p < 0.001), while the miR-155 (rs767649) polymorphism was a risk factor in the recessive model only (p = 0.021). GG and CG genotypes of rs2910164 were associated with higher Behcet's disease current activity index (BDCAI) and ocular involvement compared with CC genotype (p = 0.005 and p = 0.004, respectively). Genotype AT of rs767649 was related to higher BDCAI (p = 0.026) compared with TT and AA genotypes.

CONCLUSIONS

miR-146a (rs2910164) and miR-155 (rs767649) are likely to play an important role in the Egyptian population in development of BD and also influence disease severity.

LncRNA functional annotation with improved false discovery rate achieved by disease associations

The long non‐coding RNAs (lncRNAs) play critical roles in various biological processes and are associated with many diseases. Functional annotation of lncRNAs in diseases attracts great attention in understanding their etiology. However, the traditional co-expression-based analysis usually produces a significant number of false positive function assignments. It is thus crucial to develop a new approach to obtain lower false discovery rate for functional annotation of lncRNAs. Here, a novel strategy termed DAnet which combining disease associations with cis-regulatory network between lncRNAs and neighboring protein-coding genes was developed, and the performance of DAnet was systematically compared with that of the traditional differential expression-based approach. Based on a gold standard analysis of the experimentally validated lncRNAs, the proposed strategy was found to perform better in identifying the experimentally validated lncRNAs compared with the other method. Moreover, the majority of biological pathways (40%∼100%) identified by DAnet were reported to be associated with the studied diseases. In sum, the DAnet is expected to be used to identify the function of specific lncRNAs in a particular disease or multiple diseases.

Genetic association between CDKN2B-AS1 polymorphisms and the susceptibility of primary open-angle glaucoma (POAG): a meta-analysis from 21,775 subjects

Background

Primary open-angle glaucoma (POAG) is affected by both genetics and environmental factors. CDKN2B-AS1 polymorphisms have been reported to be involved in the pathogenesis of POAG. However, the results of the genetic associations between the CDKN2B-AS1 polymorphisms and POAG risk were inconclusive.

Aims

This study aimed to evaluate the correlation of CDKN2B-AS1 polymorphisms and POAG susceptibility using a meta-analysis.

Methods

Meta-analysis was performed by searching PubMed, Web of science, the Cochrane database of system reviews, CNKI, and Embase databases. The relationship of CDKN2B-AS1 rs4977756, rs10120688, rs2157719, and rs7049105 polymorphisms and POAG risk was evaluated by the odds ratios (ORs) and 95% confidence intervals (CIs).

Results

Eleven studies with 8290 cases and 13,485 controls were included in the present meta-analysis. The alleles of rs4977756 and rs10120688 significantly increased the risk of POAG (rs4977756: OR = 1.20, 95%CI = 1.03–1.39, p = 0.02; rs10120688: OR = 1.36, 95%CI = 1.29–1.44, p < 0.00001). As for ethnicity, rs4977756 polymorphism significantly increased POAG risk in Caucasians (OR = 1.33, 95%CI = 1.12–1.57, p = 0.0009), but not in Asians. In addition, the rs2157719 allele was significantly associated with POAG risk in Asians (OR = 0.66, 95%CI = 0.55–0.80, p < 0.0001), but not in Caucasians (p > 0.05).

Conclusions

The CDKN2B-AS1 rs4977756 might increase the POAG risk in Caucasian population, and rs2157719 might decrease the POAG risk in Asian population, while rs10120688 might increase the risk of POAG.

Genetic and epigenetic associations of ANRIL with coronary artery disease and risk factors

BACKGROUND

Both DNA genotype and methylation of antisense non-coding RNA in the INK4 locus (ANRIL) have been robustly associated with coronary artery disease (CAD), but the interdependent mechanisms of genotype and methylation remain unclear.

METHODS

Eighteen tag single nucleotide polymorphisms (SNPs) of ANRIL were genotyped in a matched case-control study (cases 503 and controls 503). DNA methylation of ANRIL and the INK4/ARF locus (p14^ARF, p15^INK4b and p16^INK4a) was measured using pyrosequencing in the same set of samples (cases 100 and controls 100).

RESULTS

Polymorphisms of ANRIL (rs1004638, rs1333048 and rs1333050) were significantly associated with CAD (p < 0.05). The incidence of CAD, multi-vessel disease, and modified Gensini scores demonstrated a strong, direct association with ANRIL gene dosage (p < 0.05). There was no significant association between ANRIL polymorphisms and myocardial infarction/acute coronary syndrome (MI/ACS) (p > 0.05). Methylation levels of ANRIL were similar between the two studied groups (p > 0.05), but were different in the rs1004638 genotype, with AA and AT genotype having a higher level of ANRIL methylation (pos4, p = 0.006; pos8, p = 0.019). Further Spearman analyses indicated that methylation levels of ANRIL were positively associated with systolic blood pressure (pos6, r = 0.248, p = 0.013), diastolic blood pressure (pos3, r = 0.213, p = 0.034; pos6, r = 0.220, p = 0.028), and triglyceride (pos4, r = 0.253, p = 0.013), and negatively associated with high-density lipoprotein cholesterol (pos2, r = - 0.243, p = 0.017). Additionally, we identified 12 transcription factor binding sites (TFBS) within the methylated ANRIL region, and functional annotation indicated these TFBS were associated with basal transcription. Methylation at the INK4/ARF locus was not associated with ANRIL genotype.

CONCLUSIONS

These results indicate that ANRIL genotype (tag SNPs rs1004638, rs1333048 and rs1333050) mainly affects coronary atherosclerosis, but not MI/ACS. There may be allele-related DNA methylation and allele-related binding of transcription factors within the ANRIL promoter.

CDKN2B-AS1 gene rs4977574 A/G polymorphism and coronary heart disease: A meta-analysis of 40,979 subjects

It has been implied that there is a possible relationship between cyclin‐dependent protein kinase inhibitors antisense RNA 1 (CDKN2B‐AS1) gene rs4977574 A/G polymorphism and coronary heart disease (CHD) susceptibility. However, as the research results are discrepant, no distinct consensus on this issue has been reached so far. In order to further elaborate the latent association of the CDKN2B‐AS1 gene rs4977574 A/G polymorphism and CHD, this present meta‐analysis was conducted. There were 40,979 subjects of 17 individual studies in the present meta‐analysis. The pooled odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were estimated to determine the association strength. Considering the significant heterogeneity among the individual studies, the random‐effect models were used. In the current meta‐analysis, a significant association between CDKN2B‐AS1 gene rs4977574 A/G polymorphism and CHD was found under allelic (OR: 1.18, 95% CI: 1.08–1.29, p = 4.83×10⁻⁴), recessive (OR: 1.36, 95% CI: 1.11–1.67, p = 0.003), dominant (OR: 0.71, 95% CI: 0.58–0.86, p = 6.26×10⁻⁴), heterozygous (OR:1.210, 95% CI: 1.076–1.360, p = 0.001), homozygous (OR: 1.394, 95% CI: 1.163–1.671, p = 3.31×10⁻⁴) and additive (OR: 1.180, 95% CI: 1.075–1.295, p = 4.83×10⁻⁴) genetic models. A more significant association between them was found in the Asian population than that in the whole population under these genetic models (p < 0.05). However, no significant association between them was found in the Caucasian population (p > 0.05). CDKN2B‐AS1 gene rs4977574 A/G polymorphism was associated with CHD susceptibility, especially in the Asian population. G allele of CDKN2B‐AS1 gene rs4977574 A/G polymorphism is the risk allele for CHD.

Coronary Artery Disease: Association Study of 5 Loci with Angiographic Indices of Disease Severity

Background

Different common gene variants were related to coronary artery disease (CAD) in many studies. Yet, the relation of these loci to the severity of CAD is not completely elucidated.

Methods

We enrolled 520 subjects (315 CAD cases and 205 controls). CAD presence and extension were assessed by coronary angiography (CAG). Genotyping of five SNPs (namely, rs2230806 (1051G > A) in ABCA1 on chromosome 9, rs2075291 (553G > T) in ApoA5 on chromosome 11, rs320 in LPL on chromosome 8 intron (T → G at position 481), rs10757278 (c.22114477A > G), and rs2383206 (c.22115026 A > G) on chromosome 9p21 locus) was performed by allele-specific PCR. The degree and site of arterial lesions were used to classify patients, tested for association with CAD severity, and related to allele dosage.

Results

The polymorphisms rs2383206 and rs10757278 showed significant associations with 2- and 3-vessel coronary disease (p =0.003 and 0.006, respectively). The homozygous GG genotypes of rs10757278 was associated with higher frequency of left anterior descending (LAD), right coronary artery (RCA) and left circumflex (LCX) diseases (p =0.002, 0.016 and 0.002, respectively). The GG genotypes of rs2383206 were found in higher percentage in patients with left main (LM) trunk and left circumflex (LCX) diseases (p = 0.013 and 0.002, respectively).

Conclusion

SNPs rs10757278 and rs2383206 allele dosage could predict CAD severity in the Saudi Arab population.

Influence of the FCGR2A rs1801274 and FCGR3A rs396991 Polymorphisms on Response to Abatacept in Patients with Rheumatoid Arthritis

Abatacept (ABA) is an immunosuppressant indicated for treatment of rheumatoid arthritis (RA). Effectiveness might be influenced by clinical RA variants and single-nucleotide polymorphisms (SNPs) in genes encoding protein FCGR2A (His131Arg) and FCGR3A (Phe158Val) involved in pharmacokinetics of ABA. An observational cohort study was conducted in 120 RA Caucasian patients treated with ABA for 6 and 12 months. Patients with the FCGR2A rs1801274-AA genotype (FCGR2A-p.131His) showed a better EULAR response (OR = 2.43; 95% CI = 1.01-5.92) at 12 months and low disease activity (LDA) at 6 months (OR = 3.16; 95% CI = 1.19-8.66) and 12 months (OR = 6.62; 95% CI = 1.25-46.89) of treatment with ABA. A tendency was observed towards an association between the FCGR3A rs396991-A allele (FCGR3A-p.158Phe) and better therapeutic response to ABA after 12 months of treatment (p = 0.078). Moreover, we found a significant association between the low-affinity FCGR2A/FCGR3A haplotypes variable and LDA after 12 months of ABA treatment (OR = 1.59; 95% CI = 1.01-2.58). The clinical variables associated with better response to ABA were lower age at starting ABA (OR = 1.06; 95% CI = 1.02-1.11) and greater duration of ABA treatment (OR = 1.02; 95% CI = 1.01-1.04), lower duration of previous biological therapies (OR = 0.99; 95% CI = 0.98-0.99), non-administration of concomitant disease-modifying antirheumatic drugs (DMARDs) (OR = 24.53; 95% CI = 3.46-523.80), non-use of concomitant glucocorticoids (OR = 0.12; 95% CI = 0.02-0.47), monotherapy (OR = 19.22; 95% CI = 2.05-343.00), lower initial patient's visual analogue scale (PVAS) value (OR = 0.95; 95% CI = 0.92-0.97), and lower baseline ESR (OR = 0.92; 95% CI = 0.87-0.97). This study showed that high-affinity FCGR2A-p.131His variant, low-affinity FCGR3A-p.158Phe variant, and combined use of FCGR2A/FCGR3A genetic variations could affect ABA effectiveness. Further studies will be required to confirm these results.

A Study of Associations Between rs9349379 (PHACTR1), rs2891168 (CDKN2B-AS), rs11838776 (COL4A2) and rs4880 (SOD2) Polymorphic Variants and Coronary Artery Disease in Iranian Population

Recent genome-wide association studies reported the association of polymorphic alleles of PHACTR1 (rs9349379 (G)), CDDKN2B-AS1 (rs2891168 (G)), COL4A2 (rs11838776 (A)) and SOD2 (rs4880 (T)) with increased risk of coronary artery disease (CAD). The aim of our study was to assess the association of genetic variants with risk of CAD and its severity and in Southeast Iranian population. This study was examined in 250 CAD-suspected patients (mean age 53.49 ± 6.9 years) and 250 healthy individuals (mean age 52.96 ± 5.9 years). The Taqman SNP genotyping assay was used for genotyping of rs9349379 and rs2891168 variants. Tetra-primer Amplified refractory mutation system-PCR (Tetra-primer ARMS-PCR) was employed for rs11838776 and rs4880. Multivariate logistic regression analyses indicated that the G allele of rs9349379 and rs2891168 were associated with increased risk of CAD. The GG homozygous genotype of rs9349379 and rs2891168 had also been associated with risk of CAD. Additionally, the AG genotype of rs2891168 was associated with CAD. The significance of association of rs2891168 (G, GG, AG) increases with severity of CAD; but the rs9349379 (G, GG) have shown reverse association with severity of CAD. The genetic variants of COL4A2 (rs11838776) and SOD2 (rs4880) reflected no association with CAD in Southeast Iranian population. The findings of this study revealed that the PHACTR1 (rs9349379) and CDKN2B-AS1 (rs2891168) genetic variants might serve as genetic risk factor in CAD.

Genetic Association of rs10757278 on Chromosome 9p21 and Coronary Artery Disease in a Saudi Population

Purpose

Coronary artery disease (CAD) is one of the most important leading causes of morbidity and mortality worldwide. Few studies have been carried out in the Saudi population regarding the association of rs10757278 polymorphism with CAD. This study aimed to investigate the association of the rs10757278 polymorphism with CAD in Saudi population.

Materials and Methods

In this case-control study, we recruited 437 patients with CAD and 251 cross-matched healthy controls and performed polymorphism genotyping for rs10757278 using a polymerase chain reaction followed by a restriction fragment length polymorphism analysis.

Results

The G allele (OR-1.44; 95% CI: 1.15–1.80; p=0.001), as GG (OR-2.13; 95% CI: 1.35–3.36; p=0.0009), in the dominant (OR-1.47; 95% CI: 1.03–2.10; p=0.03) and recessive mode (OR-1.84; 95% CI: 1.26–2.70; p=0.001) of inheritance showed a high-risk association. A disease stratified risk analysis was conducted and comparisons were made using an ANOVA analysis. Diabetes showed a risk association (p=0.001). However, a regression analysis confirmed that for the CAD cases, there was an association between the GG genotype and diabetes (p=0.005).

Conclusion

The results of this study suggest that the polymorphism rs10757278 is related to a high risk of CAD in a Saudi population.

Association of vitamin D receptor gene polymorphisms with rheumatoid arthritis

Introduction

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease of unknown etiology which causes progressive deterioration of the joints, leading to severe pain and functional disability. Vitamin D and its receptor (VDR) play a significant part in the onset of autoimmune diseases such as RA. The purpose of this study was to evaluate the association between VDR gene polymorphisms and risk of developing RA.

Material and methods

A retrospective study was performed, including 214 RA cases and 748 controls of Caucasian origin. FokI (rs2228570), BsmI (rs1544410), TaqI (rs731236), ApaI (rs7975232) and Cdx2 (rs11568820) gene polymorphisms were analyzed by TaqMan.

Results

The recessive logistic regression model showed that the VDR FokI-AA genotype was associated with lower risk of RA (p = 0.0255; OR = 0.58; 95% CI: 0.35-0.92). No other genetic polymorphism showed any association with RA in any of the models tested. Haplotype analysis revealed that the haplotypes ACGAG (p = 0.033; OR = 1.62; 95% CI: 1.04-2.53) and GTGCA (p < 0.01; OR = 2.77; 95% CI: 1.53-4.98) for BsmI, Cdx2, FokI, ApaI and TaqI were associated with higher risk of RA.

Conclusions

VDR FokI gene polymorphism showed a trend for risk of RA, taking into account the variables of gender, age and tobacco use, and preventing false positives. Among our patients we found no influence of VDR BsmI, TaqI, ApaI and Cdx2 on the risk of developing RA. However, haplotype analysis indicated that the haplotypes ACGAG and GTGCA were associated with higher risk of RA.

The Emerging Role of Long Non-coding RNAs and Circular RNAs in Coronary Artery Disease

Coronary artery disease (CAD) is a common disorder caused by atherosclerotic processes in the coronary arteries. This condition results from abnormal interactions between numerous cell types in the artery walls. The main participating factors in this process are accumulation of lipid deposits, endothelial cell dysfunction, macrophage induction, and changes in smooth muscle cells. Several lines of evidence underscore participation of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in the pathogenesis of CAD. Several lncRNAs such as H19, ANRIL, MIAT, lnc-DC, IFNG-AS1, and LEF1-AS1 have been shown to be up-regulated in the biological materials obtained from CAD patients. On the other hand, Gas5, Chast, HULC, DICER1-AS1, and MEG3 have been down-regulated in CAD patients. Meanwhile, a number of circRNAs have been demonstrated to influence function of endothelial cells or vascular smooth muscle cells, thus contributing to the pathogenesis of CAD. In the current review, we summarize the function of lncRNAs and circRNAs in the development and progression of CAD.

Impact of Single-Nucleotide Polymorphisms of CTLA-4, CD80 and CD86 on the Effectiveness of Abatacept in Patients with Rheumatoid Arthritis

Abatacept (ABA) is used as a first-line treatment in patients diagnosed with moderate and severe rheumatoid arthritis (RA). The interindividual response to ABA therapy is very variable in these patients. The objective of our study was therefore to investigate the role of polymorphisms of the CTLA-4, CD80 and CD86 genes, as well as that of clinical factors of the disease, in the response to ABA in patients with RA. A retrospective cohort study was carried out in 109 patients receiving treatment with ABA and diagnosed with RA. The genetic variables were analyzed using real-time PCR with TaqMan^® probes. The patients were classified according to the European League Against Rheumatism (EULAR) criteria at 6 and 12 months from start of treatment. The independent variables associated with higher EULAR response were lower duration of previous biologic disease-modifying anti-rheumatic drugs and lower baseline values of the disease activity score 28 after 6 months of ABA treatment; and lower baseline patient’s visual analogue scale (PVAS) after 12 months. In addition, a significant association was found between duration of ABA treatment, non-administration of concomitant glucocorticoids and lower baseline values of the number of inflamed joints and erythrocyte sedimentation rate clinical variables, with remission of the disease after 6 months’ treatment with ABA. Finally, remission of the disease after 12 months’ treatment with ABA was associated with earlier age at start of ABA therapy and lower number of previous biologic therapies (BTs). The CTLA-4rs5742909-T allele and the CTLA-4rs231775-G allele were found to be associated with satisfactory EULAR response and low disease activity (LDA) after 12 months’ treatment with ABA (CTLA-4rs5742909 T vs. CC; OR = 5.88; CI_95% = 1.48–23.29 and OR = 4.75; CI_95% = 1.35–17.94, respectively, and CTLA-4rs231775 G vs. AA, OR = 3.48; CI_95% = 1.20–10.09 and OR = 4.68; CI_95% = 1.49–17.94, respectively). In conclusion, patients with RA treated with ABA showed better EULAR response and LDA rate when they had the CTLA-4 rs5742909-T or CTLA-4 rs231775-G polymorphisms; furthermore, this remission rate increased in patients that began ABA treatment earlier, those with a lower number of previous BTs and those with a lower PVAS value.

Association of ANRIL polymorphisms with coronary artery disease: A systemic meta-analysis

BACKGROUND

The long noncoding RNAs have gradually been reported to be an important class of RNAs with pivotal roles in the development and progression of myocardial infarction (MI). In this study, we hypothesized that genetic variant of cyclin-dependent kinase inhibitor 2B antisense RNA (ANRIL) may affect the prognosis of MI patients.

METHODS

A systematic review and meta-analysis of studies including 11,269 cases and 10,707 controls on the association of 5 ANRIL single nucleotide polymorphism and the overall risk of MI or coronary artery disease (CAD) was performed.

RESULTS

In the meta-analysis, rs4977574 A > G, rs1333040 C > T, rs1333042 A > G and rs10757274 A > G ANRIL polymorphisms were correlated with overall MI or CAD risk. No significant associations were found between ANRIL rs1333049 G > C polymorphism and CAD risk.

CONCLUSIONS

The results indicated that ANRIL polymorphism (rs4977574, rs1333040, rs1333042, and rs10757274) were more generally associated with CAD or MI risk. Further experimental studies to evaluate the limits of this hypothesis are warranted, and future functional studies are required to clarify the possible mechanisms.

Relationship between Long Noncoding RNA H19 Polymorphisms and Risk of Coronary Artery Disease in a Chinese Population: A Case-Control Study

METHODS

We collected 732 samples from Liaoning Province, China, and three polymorphisms in long noncoding RNA H19 were genotyped using the KASP platform.

RESULTS

Our data showed that H19 rs2735971 and rs3024270 variant genotypes were associated with a decreased risk of CAD (rs2735971, P = 0.003, odds ratio (OR) = 0.6195, 95% confidence interval = 0.44 - 0.84; rs3024270, P = 0.030, OR = 0.65, 95% confidence interval = 0.44 - 0.96). No significant association with the risk of CAD was found for H19 rs2839698 polymorphism (P > 0.05). In haplotype analysis, H19 polymorphisms of rs2735971-rs2839698-rs3024270 A-C-C haplotype reduced the risk of CAD by 0.61-fold (P = 0.004, OR = 0.61, 95% confidence interval = 0.43-0.86). In addition, we found that rs2839698 interacted with smoking (P interaction = 0.027), and according to multifactor dimensionality reduction analysis, the three-factor model including H19 rs2839698-smoking-drinking was the best model for the risk of CAD (testing balanced accuracy = 0.6979).

CONCLUSION

Our study demonstrated that some genotypes of H19 rs2735971 and rs3024270 polymorphisms, as well as rs2735971-rs2839698-rs3024270 A-C-C haplotype, were associated with the risk of CAD in a Chinese population, and these genotypes have the potential to be biomarkers for predicting CAD risk. We also found that rs2735971-rs2839698-rs3024270 A-C-C may have a significantly lower risk of CAD. The recessive genetic model of rs3024270 could predict the severity of CAD.

Rs10757274 gene polymorphisms in coronary artery disease: A systematic review and a meta-analysis

BACKGROUND

It has been reported the rs10757274 SNP (present on locus 9p21 in the gene for CDKN2BAS1) might be associated with susceptibility to coronary artery disease (CAD). Owing to mixed and inconclusive results, we conducted a meta-analysis to investigate the association between rs10757274 polymorphism and the risk of CAD.

OBJECTIVES

The present study aimed to investigate the relationship between rs10757274 polymorphism and the risk of CAD.

METHODS

All studies of the rs10757274 SNP with CAD that were published between 2007 and 2018 were retrieved from the PubMed database. Meta-analysis was performed with Stata 14.0 software. The effect size of the rs10757274 SNP with CAD risk was assessed based on the odds ratios (ORs) with calculation of 95% confidence interval (CI).

RESULTS

Eleven studies including 52,209 subjects (cases: 7990, controls: 44,219) were included in the final data combination. Pooled overall analyses showed that rs10757274 (allele model: P < .001; dominant model: P < .001; recessive model: P < .001; Heterozygote codominant: P = .002; Homozygote codominant: P < .001) polymorphisms were significantly associated with the likelihood of CAD. Significant heterogeneity between individual studies appears in all 5 models. Further subgroup analyses revealed that rs10757274 polymorphisms were all significantly correlated with the likelihood of CAD and no heterogeneity were observed in West Asians.

CONCLUSIONS

Our findings indicated that rs10757274 polymorphisms may serve as genetic biomarkers of CAD, especially in West Asians.

CDKN2B-AS1 Exerts Oncogenic Role in Osteosarcoma by Promoting Cell Proliferation and Epithelial to Mesenchymal Transition

Objective: Long non-coding RNAs (lncRNAs) are a new class of noncoding RNAs, which serve as crucial regulators in tumor progression, including osteosarcoma (OS). The objective of this study is to uncover the clinical significance and biological role of lncRNA CDKN2B antisense RNA 1 (CDKN2B-AS1) in OS. Methods: Quantitative real time PCR analysis was used to determine the expression of CDKN2B-AS1 in OS tissues and cell lines. The associations between CDKN2B-AS1 expression and clinicopathological characteristics of OS patients were assessed by Chi-squared test. CCK-8, colony formation, flow cytometry and transwell assay were utilized to evaluate the effects of CDKN2B-AS1 knockdown on cell proliferation, cell cycle, migration and invasion. The protein expression associated with cell cycle and epithelial-mesenchymal transition (EMT) was measured by western blotting. Results: CDKN2B-AS1 was found to be markedly up-regulated in OS tissues and cell lines. Clinical data further demonstrated highly expressed CDKN2B-AS1 tended to be strongly positively correlated with tumor size, distant metastasis and TNM stage. Loss-of-function of CDKN2B-AS1 leaded to inhibited cell proliferation and induced cell cycle G0/G1 phase arrest. In addition, CDKN2B-AS1 knockdown significantly suppressed OS cells migration and invasion. Mechanistically, CDKN2B-AS1 knockdown in OS cells suppressed the expression of CDK4 and Cyclin D1, as well as EMT, as demonstrated by elevated levels of epithelial markers (E-cadherin) and downregulation of mesenchymal markers (vimentin and N-cadherin). Conclusions: Taken together, our findings suggest that CDKN2B-AS1 represents a potential therapeutic target for OS.

The association between the chromosome 9p21 CDKN2B-AS1 gene variants and the lipid metabolism: A pre-diagnostic biomarker for coronary artery disease

Objective:

Recent genome-wide association studies have established that polymorphisms within CDKN2B-AS1 of chr9p21.3 locus increased susceptibility to coronary artery disease (CAD) or myocardial infarction. Common variants of CDKN2B-AS1 (including rs4977574 A>G and rs1333040 C>T) are determined to be directly associated with CADs in many populations worldwide and suggested biomarkers for the early detection of CAD. There is a lack of investigation for the association between CDKN2B-AS1 rs4977574 A>G and rs1333040 C>T genetic modifiers and CAD in a Turkish Cypriot population. The aim of the present study was to investigate the potential effects of these variants on susceptibility to developing CAD in a Turkish Cypriot population and their contribution to lipid metabolism.

Methods:

Seventy-one patients with angiography-confirmed CAD were recruited to the CAD group, whereas 153 voluntary subjects without CAD symptoms were enrolled to the control group. Genotyping for the CDKN2B-AS1 gene polymorphisms was performed by polymerase chain reaction, followed by restriction fragment length polymorphism analysis.

Results:

There is no statistical significant association observed between rs4977574 and rs1333040 single-nucleotide polymorphisms and two studied groups [odds ratio (OR): 0.763, p=0.185, 95% confidence interval (CI): 0.511–1.139 and OR: 1.060, p=0.802, 95% CI 0.672–1.671, respectively]. However, rs2977574 G and rs1333040 T alleles–the risk alleles–were found to be associated with higher level of serum total cholesterol and lower level of high-density lipoprotein-cholesterol in the CAD group (p=0.019, p=0.006 and p=0.022, p=0.031, respectively). To our knowledge, this is the first study that establishes the effect of rs1333040 on lipid metabolism.

Conclusion:

The presence of rs4977574 G and rs1333040 T alleles and interaction may exist as environmental factors associated with lipid metabolism and might be responsible for the development of CAD in a Turkish Cypriot population.

Long non-coding RNA CDKN2B-AS1 reduces inflammatory response and promotes cholesterol efflux in atherosclerosis by inhibiting ADAM10 expression

INTRODUCTION

Long non-coding RNAs (lncRNAs) play key roles in the development of atherosclerosis through the inflammatory pathway. This study aimed to investigate the role of lncRNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) in atherosclerosis via its function in A disintegrin and metalloprotease 10 (ADAM10).

METHODS

Initially, the expression of CDKN2B-AS1 and ADAM10 in atherosclerotic plaque tissues and THP-1 macrophage-derived foam cells was determined, after which the cholesterol efflux rate of macrophages was calculated. Interaction between CDKN2B-AS1 and ADAM10 was analyzed, after which, expression of CDKN2B-AS1 and ADAM10 were altered to explore their effects on inflammatory response and cholesterol efflux. The aforementioned findings were further intended to be validated by the atherosclerosis mouse model experiments.

RESULTS

Atherosclerotic plaque tissue and THP-1 macrophage-derived foam cells exhibited downregulated CDKN2B-AS1 and upregulated ADAM10. Upon overexpressing CDKN2B-AS1 or silencing ADAM10, lipid accumulation was reduced and cholesterol efflux was increased. CDKN2B-AS1 located in the nucleus could bind to DNA methyltransferase 1 (DNMT1) to enhance methylation of ADAM10 promoter, leading to suppressed atherosclerotic inflammatory response and promoted cholesterol efflux.

CONCLUSION

Altogether, lncRNA CDKN2B-AS1 can inhibit the transcription of ADAM10 via DNMT1-mediated ADAM10 DNA methylation, consequently preventing inflammatory response of atherosclerosis and promoting cholesterol efflux.

Association of lncRNA polymorphisms with triglyceride and total cholesterol levels among myocardial infarction patients in Chinese population

AIM

The long noncoding RNAs (lncRNAs) have gradually been reported to be an important class of RNAs with pivotal roles in the development and progression of myocardial infarction (MI). In this study, we hypothesized that genetic variant of cyclin-dependent kinase inhibitor 2B antisense RNA (ANRIL) and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) may affect the prognosis of MI patients.

METHODS

The study included 401 Han Chinese MI patients and 409 controls. Four lncRNA tag single nucleotide polymorphisms (SNPs)-ANRIL rs9632884 and rs1537373, MALAT1 rs619586 and rs3200401-were selected. SNP genotyping was performed by an improved multiplex ligation detection reaction assay.

RESULTS

rs9632884 and rs3200401 SNPs were significantly associated with lipid levels in both controls and MI patients (P < 0.003-0.046). Several SNPs interacted with sex and age to modify total cholesterol, low-density lipoprotein cholesterol, and creatinine levels to modify the risk of MI. No association between the lncRNAs SNPs and susceptibility to MI was found (P > 0.05 for all).

CONCLUSIONS

Taken together, this study provides additional evidence that genetic variation of the ANRIL rs9632884 and MALAT1 rs3200401 can mediate lipid levels in MI patients.

The ANRIL Genetic Variants and Their Interactions with Environmental Risk Factors on Atherothrombotic Stroke in a Han Chinese Population

BACKGROUND

Ischemic stroke (IS) is considered to be a heterogeneous, multifactorial disease with a strong genetic background. This study aims to determine whether variants in the antisense noncoding RNA in the INK4 locus (ANRIL) gene are associated with IS in Han Chinese, as well as whether there is evidence of a gene-environment interactions.

MATERIALS AND METHODS

A case-controlled association study was conducted in which only patients with atherothrombotic stroke (ATS) were enrolled. Multifactor dimensionality reduction model was employed to screen the best interaction combinations among gene and environmental risk factors; RESULTS: A total of 405 subjects (200 cases and 205 controls) and 16 single nucleotide polymorphisms (SNPs) in ANRIL gene were included in this study. The 4 SNPs (rs1537378, rs2184061, rs7044859, and rs7865618) were found to be significantly related to ATS in Chinese Han nationality. In overall people or subjects aged 45 years or older, the GG genotype and G allele of rs1537378, the AA genotype and A allele of rs2184061 and rs7865618, and the AA genotype of rs7044859 increased the risk of ATS. In males, the GG genotype and G allele of rs1537378, the AA genotype and A allele of rs7865618, and the A allele of rs2184061 conferred a susceptibility to ATS. Additionally, the AAAGAGCAAAAAATAG haplotype exhibited an elevated risk of ATS, and a significant interaction was found in ATS susceptibility between ANRIL gene and dyslipidemia; CONCLUSIONS: The ANRIL gene was related to ATS susceptibility in a Han Chinese. Future studies should be performed with larger samples and among different ethnic populations.

ANRIL polymorphism rs4977574 is associated with increased risk of coronary artery disease in Asian populations: A meta-analysis of 12,005 subjects

BACKGROUND

Several studies have shown that ANRIL polymorphism may be associated with the risk of coronary artery disease (CAD). However, these studies do not provide a clear consensus in Asian population. Thus, this meta-analysis was aimed to evaluate the relationship between the common variant rs4977574 in ANRIL and CAD risk in Asian population.

METHODS

We conducted a systematic literature search of PubMed, Embase and the Cochrane Library and 2 Chinese databases. A total of 12,005 subjects from 6 independent studies were included. The pooled odds ratio (OR) and their corresponding 95% confidence intervals (CIs) were used to assess the association between rs4977574 and CAD using random effects model.

RESULTS

A significant association was observed between rs4977574 and CAD risk under the allelic (OR: 1.18, 95% CI: 1.04-1.34, P = .010), recessive (OR: 1.27, 95% CI: 1.01-1.60, P = .04), dominant (OR: 1.28, 95% CI: 1.13-1.44, P = .002), homozygous (OR: 1.46, 95% CI: 1.15-1.86, P = .002), and heterozygous model (OR: 1.17, 95% CI: 1.07-1.28, P = .0004), especially in the Chinese subgroup and the myocardial infarction (MI) subgroup (P < .05).

CONCLUSION

The ANRIL polymorphism rs4977574 is associated with CAD risk in Asian population. The rs4977574 with G allele may confer to a higher risk of CAD, especially MI.

The role of CDKN2B in cardiovascular risk in ethnic Saudi Arabs: A validation study

BACKGROUND

Genome-wide association studies (GWASs) have yielded a wealth of information furnishing support for the variability in genetic predisposition to disease. However, the actual impact of such findings on any particular ethnic population needs to be validated through replication studies. In the present study, we verified recent findings of a GWAS demonstrating a strong association for the cyclin-dependent kinase 4 inhibitor B (CDKN2B) genomic region with coronary artery disease (CAD)/myocardial infarction (MI) in ethnic Saudi Arabs.

METHODOLOGY

We genotyped 8 CDKN2B SNPs for cardiovascular risk in 4650 Saudi Arabs, comprising 2429 CAD cases (1860 males; 569 female) and 2221 controls (1189 male; 1032 female) by Taqman assay.

RESULTS

Four SNPs, rs4977574_A [0.56(0.50-0.63); p < 0.0001], rs10757274_A [0.87(0.77-0.97); p = 0.014], rs10738607_A [0.89(0.80-1.00); p = 0.043] and rs1333045_T [0.54(0.48-0.61); p < 0.0001] residing on the CDKN2B gene were significantly associated with CAD following multivariate adjustments for MI, HTN and DM, while four others were weakly associated with the disease. Likewise, three SNPs, rs1412829_G [0.84(0.72-0.97); p = 0.019], rs564398_C [0.81(0.70-0.94); p = 0.006], rs4977756_G [0.87(0.76-0.99); p = 0.036] were significantly associated with MI after multivariate adjustments for CAD, HTN and DM, while the other five displayed borderline associations.

CONCLUSIONS

Our findings strongly support the notion of a critical role for the CDKN2B gene locus as a cardiovascular risk in ethnic Arabs. The study also demonstrates the importance of replication studies in ascertaining the role of a genomic sequence in disease.

Association of polymorphisms in MALAT1 with risk of coronary atherosclerotic heart disease in a Chinese population

Background

Metastasis associated lung adenocarcinoma transcript 1 (MALAT1) plays an important role in vascular remodeling. Down-regulation of MALAT1 can inhibit the proliferation of vascular endothelial cells and vascular smooth muscle cells, reduce cardiomyocyte apoptosis and improve left ventricular function, which is closely linked to numerous pathological processes such as coronary atherosclerotic heart disease (CAD). The aim of this study was to investigate whether polymorphisms in MALAT1 were associated with the susceptibility to CAD.

Methods

A total of 508 CAD patients and 562 age-, gender-, and ethnicity-matched controls were enrolled in this study. Four polymorphisms in MALAT1 (i.e., rs11227209, rs619586, rs664589, and rs3200401) were genotyped using a TaqMan allelic discrimination assay.

Results

The rs619586 AG/GG genotypes and G allele were associated with a reduced risk of CAD (AG/GG vs. AA: adjusted OR = 0.66, 95% CI: 0.48–0.91; G vs. A: adjusted OR = 0.68, 95% CI: 0.51–0.90). Stratification analyses showed that CAD patients with rs11227209 CG/GG, rs619586 AG/GG, and rs3200401 CT/TT genotypes exhibited lower levels of TCH (P = 0.02, 0.04, and 0.02, respectively). Moreover, CGCC haplotype was associated with a decreased risk of CAD (OR = 0.28, 95% CI: 0.16–0.48). Multivariate logistic regression analysis identified some independent risk factors for CAD, including rs619586 and rs664589. Subsequent combined analysis showed that the combined genotypes of rs619586AG/GG and rs664589CC were associated with a reduced risk of CAD (OR = 0.29; 95%CI, 0.16–0.53).

Conclusions

These findings indicate that rs619586AG/GG genotypes in MALAT1 may protect against the occurrence of CAD.

Electronic supplementary material

The online version of this article (10.1186/s12944-018-0728-2) contains supplementary material, which is available to authorized users.

CDKN2BAS polymorphisms are associated with coronary heart disease risk a Han Chinese population

The goal of our study was to determine whether CDKN2BAS polymorphisms are associated with coronary heart disease (CHD) risk in a Han Chinese population. Eight SNPs were genotyped in 676 men and 465 women. We used χ² tests and genetic model analyses to evaluate associations between the SNPs and CHD risk. We found that rs10757274 was associated with an increased risk of CHD in both men (allele G: Odds ratio [OR] = 1.30, 95% confidence interval [CI]: 1.05-1.61, P = 0.018; codominant model: P = 0.042; recessive model: OR = 1.70, 95% CI: 1.10-2.62, P = 0.016; log-additive model: OR = 1.34, 95% CI: 1.05-1.71, P = 0.019) and women (dominant model: OR = 2.26, 95% CI: 1.28-3.99, P = 0.004). In addition, rs7865618 was associated with an 8.10-fold increased risk of CHD in women under a recessive model (OR = 8.10, 95% CI: 1.74-37.68, P = 0.006). Interestingly, the haplotype AA (rs10757274 and rs1333042) of CDKN2BAS was associated with decreased the risk of CHD in men (OR = 0.72, 95% CI: 0.55 - 0.95, P = 0.022).

Haplotype-Contained PCR Products Analysis by Sequencing with Selective Restriction of Primer Extension

We develop a strategy for haplotype analysis of PCR products that contained two adjacent heterozygous loci using sequencing with specific primers, allele-specific primers, and ddNTP-blocked primers. To validate its feasibility, two sets of PCR products, including two adjacent heterozygous SNPs, UGT1A1⁎6 (rs4148323) and UGT1A1⁎28 (rs8175347), and two adjacent heterozygous SNPs, K1637K (rs11176013) and S1647T (rs11564148), were analyzed. Haplotypes of PCR products, including UGT1A1⁎6 and UGT1A1⁎28, were successfully analyzed by Sanger sequencing with allele-specific primers. Also, haplotypes of PCR products, including K1637K and S1647T, could not be determined by Sanger sequencing with allele-specific primers but were successfully analyzed by pyrosequencing with ddNTP-blocked primers. As a result, this method is able to effectively haplotype two adjacent heterozygous PCR products. It is simple, fast, and irrespective of short read length of pyrosequencing. Overall, we fully hope it will provide a new promising technology to identify haplotypes of conventional PCR products in clinical samples.

Chromosome 9p21 and ABCA1 Genetic Variants and Their Interactions on Coronary Heart Disease and Ischemic Stroke in a Chinese Han Population

The single nucleotide polymorphisms (SNPs) related to both coronary heart disease (CHD) and ischemic stroke (IS) in Chinese individuals have not been identified definitely. This study was developed to evaluate the genetic susceptibility to CHD and IS on the chromosome 9p21 and the adenosine triphosphate (ATP)-binding cassette transporter A1 genes (ABCA1) in a Chinese Han population. Genotypes of the rs1333040, rs1333042, rs4977574, rs2066715 and rs2740483 SNPs were determined in 1134 unrelated patients (CHD, 565 and IS, 569) and 541 controls. The frequencies of the rs4977574 genotypes and alleles between CHD and control groups, and the rs2740483 genotypes and alleles between IS and control groups were different (p = 0.006–0.001). The subjects with rs1333042GG genotype and the carriers of the rs4977574G allele were associated with increased risk of CHD. The carriers of the rs4977574G allele were associated with increased risk of IS. However, the carriers of the rs2740483C allele had lower risk of IS than the non-carriers of the rs2740483C allele after controlling for potential confounders. The rs4977574GG-age (>60 year) interaction increased the risk of CHD (p = 0.022), whereas the rs2740483CG/CC-body mass index (>24 kg/m²) interaction decreased the risk of IS (p = 0.035). The interactions of rs1333040-rs1333042 on the risk of CHD and IS were relatively strong, whereas the interactions of rs1333040-rs1333042-rs2066715 and rs1333040-rs1333042-rs2066715-rs2740483 on the risk of CHD, and rs1333040-rs1333042-rs4977574 and rs1333040-rs1333042-rs4977574-rs2740483 on the risk of IS were relatively weak. These findings suggest that some common variants on the chromosome 9p21 and ABCA1 and their interactions may significantly modify the risk of CHD and IS independent of effects on serum lipid levels.