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• Lower mRNA levels of CDKN2A and CDKN2B, as well as higher mRNA level of MTAP may be related to CHD. • Rs2383207 may affect the occurrence of CHD by influencing the patients'CDKN2A mRNA expression level. • ANRIL may not be related to the occurrence of CHD in Chinese Han population. [ABSTRACT FROM AUTHOR]

Background Several studies have demonstrated that variants on chromosome 9p21 confer susceptibility to ischemic stroke (IS) disease. But, the results of variants' roles in Chinese IS population are blank or inconsistent. Methods We performed a case–control analysis in 116 patients with IS and 118 non-IS controls of Han background to determine whether 4 single nucleotide polymorphisms were associated with IS. DNA was extracted from saliva using a magnetic nanoparticles–based method. Results After we adjusted for clinical parameters, we found that the rs10757278-GG genotype conveyed 1.88-fold (95% confidence interval [CI], 1.1-3.1; P = .015), the rs1537378-C allele conveyed 2.0-fold (95% CI, 1.2-3.5; P = .008), and the rs1333047-TT genotype conveyed 1.64-fold (95% CI, 1.02-2.6; P = .041) increased risk of IS, respectively. In addition, there is a significant difference of the lipids level between GG genotype compared with that of AA genotype in rs10757278 ( P < .05). Conclusions This study is the first one to demonstrate that the rs10757278-GG genotype, the rs1537378-C allele, and rs1333047-TT genotype are associated with IS in Chinese Han populations. More importantly, the variant of rs10757278 may have different degrees of influence on lipids level. [ABSTRACT FROM AUTHOR]

Abstract: Purpose: A number of studies reported on associations of single nucleotide polymorphisms (SNPs) present in chromosome 9p21 with early-onset coronary artery disease (CAD). The present study was then undertaken to perform a meta-analysis of all the results published to date. Methods: All studies of the 9p21 association with early-onset CAD that were published between 2007 and 2012 were retrieved from the PubMed database. RevMan 5.0 software was used to perform meta-analysis of the data that fulfilled the criteria for our meta-analysis. The effect size of four SNPs in the 9p21 region on early-onset CAD risk was assessed based on the odds ratios (ORs) with calculation of 95% confidence interval (CI). Results: A total of 7123 subjects from 7 case–control studies were genotyped. Meta-analysis demonstrated disease association for rs2383207 (OR=0.79, 95% CI 0.71–0.88, P <0.0001), rs2383206 (OR=1.17, 95% CI 1.10–1.25, P <0.00001), rs10757278 (OR=1.28, 95% CI 1.15–1.42, P <0.00001), and rs10757274 (OR=1.17, 95% CI 1.08–1.33, P =0.02). Conclusion: Genetic variation in the chromosome 9p21 region may contribute to the etiology of early-onset CAD although their effect size is rather small. [Copyright &y& Elsevier]

Abstract: Background and aims: Genome-Wide Association Studies found some variants on chromosome 9p21 associated with type 2 diabetes (T2D). We performed a meta-analysis to estimate strength, accuracy and feature of the association of polymorphisms in 9p21 with T2D. Methods and results: Articles were retrieved screening electronic databases and cross references. Twenty-two publications were identified, for a total of 38,455 T2D patients and 60,516 controls. Twenty-one studies investigated the role of the SNP rs10811661; in some studies three additional SNPs (rs564398, rs10757278, rs1333040) were genotyped. Population attributable risk (PAR) was computed as: risk allele frequency∗(OR-1)/OR, using the per-allele odds ratio (OR). The risk allele (T) of rs10811661 was associated with T2D in most of the studies. In meta-analysis the overall per-allele OR was 1.24 (95% CI: 1.21–1.27; P < 10−15), with no difference according to ethnicity (P = 0.45), and low heterogeneity (P = 0.040) across studies partly explained by sample size. Modeling of inheritance suggested an additive effect of the T allele. PAR of T2D related to this polymorphism was 15% for Caucasians and 13% for Asians. The overall odds ratio for the T allele of the SNP rs564398 was 1.08 (95% CI: 1.05–1.12; PAR = 6%). The other SNPs showed negligible associations. Conclusions: This meta-analysis provides accurate and comprehensive estimates of the association of some genetic variants at chromosome 9p21 and T2D. A relatively small but significant role of the T allele of the rs10811661 SNP in increasing by 21–27% the risk of T2D in an additive way was apparent. [Copyright &y& Elsevier]

Abstract: Genome-wide association studies (GWAS) have identified genetic variants contributing to the risk of cardiovascular disease (CVD) at the chromosome 9p21 locus. The CVD-associated region is adjacent to the two cyclin dependent kinase inhibitors (CDKN)2A and 2B and the last exons of the non-coding RNA, ANRIL. It is still not clear which of or how these transcripts are involved in the pathogenesis of atherosclerosis. Objective: We assessed the hypothesis that 9p21 locus polymorphisms influence the expression of the transcripts in the region (ANRIL, CDKN2A/B) and that these transcripts contribute to atherogenesis through the modulation of proliferation in VSMC. Methods: We genotyped 18 SNPs (r 2 <0.8 and MAF>0.05) across the region of interest: CDKN2A/B and ANRIL, encompassing the CVD-associated region. RNA and DNA were extracted from the blood of 57 volunteers (69–72years old). Carotid ultrasound was performed in 56 subjects. CDKN2A/B and ANRIL (exons 1–2 and 17–18) expression was measured employing RT-PCR. Gene expression and cell growth were evaluated in cultured VSMC after the siRNA-mediated knock-down of ANRIL. Results: The risk alleles for atherosclerosis-related phenotypes were consistently associated with a lower expression of ANRIL when evaluating exons 1–2. Common carotid artery stenosis was associated with a significantly lower (P <0.01) expression of ANRIL (exons 1–2). ANRIL knock-down in VSMC caused significant variation in expression of CDKN2A/B (P <0.05) and reduction of cell growth (P <0.05) in vitro. Conclusion: Disease-associated SNPs at the 9p21 locus predominantly affect the expression of ANRIL. Overall, our results suggest that several CVD-associated SNPs in the 9p21 locus affect the expression of ANRIL, which, in turn modulate cell growth, possibly via CDKN2A/B regulation. [Copyright &y& Elsevier]

Abstract: Objective: Sequence variation at Ch9p21 is a predisposing genetic factor for a number of diseases, including myocardial infarction (MI) and diabetes. We determined the risk of MI associated with various alleles and haplotypes, established and compared the predictive values of risk alleles, tested for the independence of associations between different risk alleles and MI, and sought to provide evidence for dual association of alleles with MI and diabetes. Methods: With the use of 35 single nucleotide polymorphisms, together capturing common variation seen in the associated interval, we genotyped 3657 MI cases and 1211 controls prospectively sampled in a European population. Results: Polymorphisms rs10757278 and rs1333049 both exhibited the strongest individual risk signal (OR, 1.45; 95% CI, 1.32–1.59). Two haplotype blocks were established, each of which was mainly represented by a pair of a risk-conferring and a protective haplotype, but none of the risk-associated haplotypes exhibited stronger effects than rs10757278 or rs1333049 alone. Specific polymorphisms (rs7865618, rs1537378, rs7857345, rs1333049) were identified as independent predictors of MI in multivariable models adjusted for conventional cardiovascular risk factors. In specific instances, the presence of two or three polymorphisms in a model, instead of only one, improved the discriminating power. Finally, evidence was provided to suggest dual association of rs7865618 with MI and diabetes. Conclusion: In keeping with published results, this work was consistent with the association of alleles and haplotypes at Ch9p21 with MI and extended prior knowledge by also showing independence of associations among different risk alleles and an association of a specific polymorphism with both MI and diabetes. [Copyright &y& Elsevier]

Abstract: Objective: The pathophysiology underlying the chromosome (Chr) 9p21 locus of atherosclerosis susceptibility is presently unknown. Here, we sought to determine whether protein coding genes in the Chr9p21 region, i.e. cyclin-dependent kinase inhibitors CDKN2B (p15INK4b), CDKN2A (p16INK4a, p14ARF) and methylthioadenosine phosphorylase (MTAP) were expressed in human atherosclerotic lesions and whether expression was correlated with lesion composition. Methods and results: Protein expression of p15INK4b, p16INK4a, p14ARF and MTAP was demonstrated by immunostaining in normal and atherosclerotic coronary arteries and co-localized with CD68 and smooth muscle alpha-actin positive cells. Quantitative RT-PCR in human endarteryectomy specimens (n =57) revealed increased p16 INK4a and decreased MTAP expression in macrophage-rich lesions (P <0.001 and P =0.007, respectively). Functional studies suggest that decreased MTAP expression in macrophage-rich lesions might be mediated through down-regulation by TNF-alpha. No clear association of p15 INK4b , p16 INK4a , p14 ARF , and MTAP expression in plaque tissue with Chr9p21 haplotypes was found. The latter finding was corroborated by the lack of correlation of RNA expression of 9p21-regulated transcripts EU741058 and NR_003529 of antisense non-coding RNA in the INK4 locus (ANRIL) with mRNA expression of these genes. In contrast, ANRIL DQ485454 which is not genetically determined by the 9p21 genotype was significantly correlated with MTAP expression (P =0.01). Conclusion: CDKN2B (p15INK4b), CDKN2A (p16INK4a, p14ARF), and MTAP are abundantly expressed in atherosclerotic lesions. While expression levels showed no clear association with Chr9p21 genotype, association of high p16 INK4a and low MTAP expression with a less stable plaque phenotype suggests a more general role of these proteins in atherogenesis. [Copyright &y& Elsevier]

Abstract: Objective: Recent large-scale genome-wide association studies have identified a novel susceptibility locus on chromosome 9p21.3 that contributes a significant attributable risk for myocardial infarction. The phenotypic significance of this locus in patients with established coronary artery disease is unknown. We sought to compare cardiovascular structure and function in carriers and non-carriers of the risk haplotype in a cross-sectional study. Methods: We genotyped the rs1333049 single-nucleotide polymorphism in 593 Caucasian individuals with stable coronary artery disease recruited in the Heart and Soul Study. All study subjects underwent resting and stress echocardiography. Linear and logistic regression models were used to examine the association between the rs1333049 polymorphism and echocardiographic parameters of cardiovascular structure and function. Results: There was no association between rs1333049 genotype and echocardiographic phenotype (left ventricular hypertrophy, systolic dysfunction, diastolic dysfunction, inducible ischemia, exercise capacity, mitral annular calcification, and aortic plaque). Conclusions: In a cross-sectional study of individuals with stable coronary artery disease, there was no association of chromosome 9p21.3 genotype with cardiovascular structure and function. [Copyright &y& Elsevier]

Summary: Cholangiocarcinoma in northeast Thailand is associated with liver fluke infection. Mechanisms of inactivation of the p15 INK4b , p16 INK4a , and p14 ARF have been reported in many human cancers but have not hitherto been studied in liver fluke–related cholangiocarcinoma, particularly genetic and epigenetic effects on protein expression. We investigated loss of heterozygosity and microsatellite instability and performed fine mapping of the chromosomal region 9p21-pter in 94 microdissected cholangiocarcinoma samples using polymerase chain reaction based–microsatellite markers. Methylation and protein expression of p14 ARF , p15 INK4b , and p16 INK4a was determined using methylation-specific polymerase chain reaction and immunohistochemistry, respectively. Genetic and epigenetic alterations, including loss of protein expression, were correlated with clinicopathological data. Fine mapping at 9p21-pter showed a distinctive region between D9S286 and D9S1752 of common loss. Methylation frequency was 40.2% for p14 ARF , 48.9% for p15 INK4b , and 28.3% for p16 INK4a . Loss of protein expression of p14ARF, p15INK4b, and p16INK4a was 30.9%, 58%, and 81.5%, respectively. Both p14 ARF methylation and allelic loss at 9p21 were associated with loss of p14ARF expression. Poor prognosis was associated with loss of p16INK4a expression. In conclusion, mechanisms of inactivation of p14 ARF , p15 INK4b , and p16 INK4a in liver fluke–related cholangiocarcinoma are preferentially different, by which epigenetic event being the main mechanism of p14 ARF , whereas p16 INK4a and p15 INK4b inactivation occurs through genetic and both genetic and epigenetic events, respectively. [Copyright &y& Elsevier]

Serous borderline tumors (SBT) are the most common subtype of ovarian borderline tumors with excellent clinical course. However, they can recur or progress to low-grade serous carcinoma (LGSC) in a small proportion of the cases. Beside BRAF and KRAS mutations, copy number alterations (CNA), particularly loss of chromosome 9p21 locus which results in deletion of genes CDKN2A and MTAP, have been suggested to be involved in disease progression. MTAP immunohistochemistry recently has been introduced for mesothelioma as a reliable surrogate marker for the homozygous deletion of chromosome 9p21 locus. Therefore, in the current study, we aimed to evaluate the MTAP loss of expression in serous borderline tumors and low-grade serous carcinomas to identify if it can be used as a marker for prognosis and progression. Eighty-four total cases of ovarian serous lesions, including 21 cases of serous cystadenomas, 21 cases of serous borderline tumors, 12 cases of low-grade serous carcinomas and 30 cases of high-grade serous carcinomas were selected. MTAP immunohistochemistry was performed on the representative blocks and cytoplasmic staining was used for interpretation. The cases were labeled as positive (retained) if MTAP showed cytoplasmic granular staining and negative (loss of expression) if negative cytoplasmic staining was observed in the presence of positive internal control. Ten of 21 cases of serous borderline tumors showed loss of MTAP expression (48%). Among those, 7 cases were bilateral, 2 cases had micropapillary features, one case had supraclavicular and cervical lymph node involvement by serous borderline tumor and 2 cases had progression to low-grade serous carcinoma, including one of micropapillary tumors. Also 8 out of 12 cases of LGSCs showed MTAP loss of expression (66%). Only 4 of 30 cases of high-grade serous carcinomas (13%) and none of the serous cystadenoma cases showed loss of expression of MTAP. To our knowledge, this is the first description of MTAP immunohistochemistry in serous borderline tumors and low-grade serous carcinomas. Our study was limited due to small sample size. However, it showed an association between MTAP loss of expression and adverse clinical behavior in ovarian serous borderline tumors. This supports the role for further investigations in larger series to evaluate the role of MTAP stain as a prognostic marker in these neoplasms. • Loss of chromosome 9p21 locus may play role in progression of ovarian serous borderline tumors (SBT) to low grade serous carcinoma. • Loss of MTAP expression can serve as a surrogate marker for homozygous deletions of chromosome 9p21. • MTAP immunohistochemistry may serve as a useful prognostic marker to identify SBTs with higher risk of recurrence and progression. [ABSTRACT FROM AUTHOR]