Dataset Information

Lack of association of SNP rs4236601 near CAV1 and CAV2 with POAG in a Saudi cohort.

ABSTRACT: PURPOSE: To determine the role of the recently discovered primary open angle glaucoma (POAG) single nucleotide polymorphism (SNP) rs4236601 near the caveolin-1 (CAV1) and CAV2 among patients and controls from Saudi Arabia. METHODS: A cohort of 220 POAG patients and 405 control subjects from Saudi Arabia were genotyped for a SNP (rs4236601;g.2891 G>A) in the chromosome 7q31 locus near CAV1 and CAV2 using a standard polymerase chain reaction (PCR) and sequencing method. RESULTS: The minor allele frequency (MAF) of rs4236601 was 0.3 in controls and 0.31 in POAG patients. We detected no statistical difference when we compared the allele frequencies between POAG patients and control subjects (p=0.699). Similarly, we detected no statistical difference in the frequency of the three possible rs4236601 genotypes between patients and controls. The p-values were 0.928 and 0.683 for heterozygous genotype (G/A) and homozygous mutant genotype (A/A), respectively. We found no statistically significant difference among patients with any of the three possible genotypes and various clinical indices important for glaucoma. Among patients with homozygous (A/A), the mean IOP was higher (21.4) compared to patients with G/G wildtype (20.4) and to patients with G/A genotype (18.5). However, this apparent difference did not reach the statistical significance threshold (p=0.062). CONCLUSIONS: We were unable to detect this association in our POAG-patients from Saudi Arabia, suggesting that this risk factor may not have a strong effect in all populations. A founder effect may play a role in certain populations where the link was established.

SUBMITTER: Abu-Amero KK

PROVIDER: S-EPMC3413415 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Lack of association of SNP rs4236601 near CAV1 and CAV2 with POAG in a Saudi cohort.

Abu-Amero Khaled K KK Kondkar Altaf A AA Mousa Ahmed A Osman Essam A EA Al-Obeidan Saleh A SA

Molecular vision 20120718

<h4>Purpose</h4>To determine the role of the recently discovered primary open angle glaucoma (POAG) single nucleotide polymorphism (SNP) rs4236601 near the caveolin-1 (CAV1) and CAV2 among patients and controls from Saudi Arabia.<h4>Methods</h4>A cohort of 220 POAG patients and 405 control subjects from Saudi Arabia were genotyped for a SNP (rs4236601;g.2891 G>A) in the chromosome 7q31 locus near CAV1 and CAV2 using a standard polymerase chain reaction (PCR) and sequencing method.<h4>Results</h4 ...[more]

PMID: 22876122

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Project description:BackgroundThe CAV family, especially CAV1 and CAV2, is significantly associated with tumor development. In this study, we aimed to explore the pathogenic and prognostic roles of CAV1 and CAV2 in head and neck squamous cell carcinoma (HNSCC) through bioinformatic analysis and verified in human tissue.MethodsWe analyzed expression profiles of CAV1 and CAV2 in HNSCC and in normal tissues via data from The Cancer Genome Altas. Prognostic significance was examined by Kaplan-Meier survival curve obtained from the Xena browser together with Cox regression analysis. Co-expressed genes were uploaded to GeneMANIA and applied to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, showing interaction networks. Signaling pathways of CAV1 and CAV2 in HNSCC were analyzed by Gene Set Enrichment Analysis to elucidate potential regulatory mechanisms. Gene-drug interaction network was explored via Comparative Toxicogenomics Database. Immunohistochemistry was performed to verify theoretical results.ResultsCompared with normal tissues, expression levels of CAV1 and CAV2 were remarkably higher in HNSCC (p < 0.0001), which independently implies poor OS (CAV1: HR: 1.146, p = 0.027; CAV2: HR: 1.408, p = 0.002). Co-expressed genes (PXN, ITGA3, TES, and MET) were identified and analyzed by FunRich with CAV1 and CAV2, revealing a significant correlation with focal adhesion (p < 0.001), which has a vital influence on cancer progression. GSEA also showed cellular protein catabolic process (ES = 0.42) and proteasome complex (ES = 0.72), which is a key degradation system for proteins involved in oxidatively damaging and cell cycle and transcription, closely correlated with high expression of CAV2 in HNSCC. More importantly, we found the relationship between different immune cell infiltration degrees in the immune micro-environment in HNSCC and expression levels of CAV1/CAV2 (p < 0.0001). Gene-drug interaction network was checked via CTD. Moreover, tissue microarrays verified higher expression levels of CAV1/CAV2 in HNSCC (p < 0.0001), and the high expression subgroup indicated significantly poorer clinical outcomes (p < 0.05).ConclusionsThe results revealed that CAV1 and CAV2 are typically upregulated in HNSCC and might predict poor prognosis.

Dataset Information

Lack of association of SNP rs4236601 near CAV1 and CAV2 with POAG in a Saudi cohort.

Publications

Lack of association of SNP rs4236601 near CAV1 and CAV2 with POAG in a Saudi cohort.

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