Nevin Karakus

P53 Codon 72 and HER2 Codon 655 Polymorphisms in Turkish Breast Cancer Patients

The polymorphisms in codon 72 of the tumor suppressor protein p53 (P53) gene and codon 655 of the human epidermal growth factor receptor 2 (HER2) gene have been suggested to play roles in most cancers. The purpose of this study was to investigate the association between common variants of HER-2 and P53 genes with breast cancer risk. Blood samples collected from 204 women with primary breast carcinoma and 192 healthy female controls were analyzed through polymerase chain reaction-restriction fragment length polymorphism methods. The frequencies of Arg/Arg, Arg/Pro, and Pro/Pro genotypes for P53 codon 72 were 51.7%, 41.4%, and 6.9% in patients and 42.6%, 47.3%, and 10.1% in controls, respectively. The frequencies of Ile/Ile, Ile/Val, and Val/Val genotypes for HER2 codon 655 were 75.0%, 22.5%, and 2.5% in patients and 73.4%, 25.0%, and 1.6% in controls, respectively. The genotype and allele frequencies between patient and control groups for P53 gene polymorphism were not significantly different (p = 0.177 and p = 0.07, respectively). Similarly, the genotype and allele frequencies between patient and control groups for HER2 gene polymorphism were not significantly different (p = 0.716 and p = 0.891, respectively). With the exception of association between the P53 codon 72 polymorphism and tumor stages (p = 0.026), there was no significant association between the studied polymorphisms and clinicopathological characteristics. The P53 gene codon 72 Arg/Pro and Her2 gene Ile655Val polymorphisms were not associated with the risk of breast cancer in Turkish women. However, significant associations between the P53 codon 72 and the homozygote and heterozygote Pro genotypes with tumor stages were found.

Significance of MEFV gene R202Q polymorphism in Turkish familial Mediterranean fever patients

OBJECTIVE Familial Mediterranean fever (FMF) is an autosomal recessive disorder characterized by recurrent attacks of fever and inflammation in the peritoneum, synovium, or pleura, accompanied by pain. The disease is associated with mutations in the Mediterranean fever (MEFV) gene, which encodes for the pyrin protein. The aim of this study was to explore the frequency and clinical significance of the R202Q (c.605G>A) polymorphism in exon 2 of the MEFV gene in a cohort of Turkish patients with FMF. METHODS The study included 191 patients with FMF and 150 healthy controls. Genomic DNA was isolated and genotyped using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) assay for the MEFV gene R202Q polymorphism. RESULTS The genotype and allele frequencies of R202Q polymorphism showed a statistically significant difference between FMF patients and controls (p<0.0001 and p=0.0004, respectively) and especially the homozygous AA genotype was significantly higher in FMF patients than healthy controls (p=0.0002; odds ratio=6.27; 95% CI=2.1-18.3). However no significant association was observed between clinical and demographic features of FMF patients and R202Qpolymorphism. CONCLUSION The results of this study showed that there was a high association between MEFV gene R202Q polymorphism and FMF. R202Q polymorphism should be included in routine molecular diagnosis of FMF patients.

Tumor necrosis factor alpha and beta and interferon gamma gene polymorphisms in Turkish breast cancer patients.

Cytokine genes are important for researching cancer predisposition to cancers that elicit anti-tumor immune response. In this study, we investigated the association between breast cancer and tumor necrosis factor alpha (TNF-α) -308 (G>A), TNF-β +252 (A>G), and interferon gamma (IFN-γ) +874 (T>A) gene polymorphisms in a Turkish population. This study involved 204 female breast cancer patients and 204 healthy female controls. Genomic DNA was extracted from EDTA-preserved peripheral venous blood of patients and controls by a salting-out method and analyzed by polymerase chain reaction, allele-specific oligonucleotide polymerase chain reaction, and restriction fragment length polymorphism. TNF-α -308 genotype was found to have no effect on breast cancer susceptibility. However, there were statistically significant differences between the genotype frequencies of patients and controls for TNF-β polymorphism (p = 0.016) and the allele and genotype frequencies for the IFN-γ polymorphism (p = 0.0312 and p = 0.001, respectively). In the composite genotype analysis, the TNF-α/β GAAG composite genotype (p = 0.0424), the TNF-α/IFN-γ GGTT and GATT composite genotypes (p = 0.0296 and p = 0.0129, respectively), the TNF-β/IFN-γ AGTT composite genotype (p = 0.0003), and the TNF-α/β/IFN-γ GGAGTT and GAAGTT composite genotypes (p = 0.0437 and p = 0.0038, respectively) were estimated to have a protective effect against breast cancer. However, the TNF-α/IFN-γ GGTA composite genotype is a risk factor for breast cancer (p = 0.0156). In conclusion, TNF-β +252GG genotype was found more frequent in Turkish breast cancer patients than controls and IFN-γ TA+AA genotypes were estimated to increase breast cancer risk significantly in Turkish population.

The association between Interleukin (IL)-4 gene intron 3 VNTR polymorphism and alopecia areata (AA) in Turkish population.

OBJECTIVE Alopecia areata (AA) is hypothesized to be an organ-specific autoimmune disease of hair follicles mediated by T cells. As immunological and genetic factors have been implicated in the pathogenesis of AA, the purpose of the present study was to investigate possible associations between the functional Interleukin (IL)-4 gene intron 3 VNTR polymorphism and AA susceptibility and disease progression in Turkish population. METHODS The study group consisted of 116 unrelated patients with AA and 125 unrelated healthy controls. Genomic DNA was isolated and IL-4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers. RESULTS No association was observed between AA patients and controls according to genotype distribution (p=0.051). The allele distribution of IL-4 gene intron 3 VNTR polymorphism was statistically different between AA patients and control group (p=0.026). The frequency of P1 allele in patients was significantly higher than that in the control group. When the P2P2 genotype was compared with P1P2+P1P1 genotypes, a statistically significant difference was observed between patients and controls (p=0.036). Intron 3 VNTR polymorphism in the IL-4 gene was found to be associated with AA susceptibility in Turkish population. CONCLUSION The results suggest that IL-4 VNTR polymorphism in the intron 3 region may be a risk factor for the development of AA among Turkish population. This is the first to report that intron 3 VNTR polymorphism in the IL-4 gene is associated with AA susceptibility.

The importance of association between angiotensin-converting enzyme (ACE) Gene I/D polymorphism and diabetic peripheral neuropathy.

BACKGROUND Diabetic peripheral neuropathy (DPN) is a microvascular complication of diabetes mellitus (DM) due to decreasing quality of life. In the present study, it is aimed to evaluate angiotensin-converting enzyme (ACE) Gene I/D polymorphism in Turkish population. MATERIALS AND METHODS Two hundred and thirty-five DPN patients and two hundred and eighty-one controls were enrolled in this study. Genomic DNA was isolated and genotyped using polymerase chain reaction (PCR) analyses for the ACE gene I/D polymorphism. RESULTS Baseline characteristics of the DPN patients according to ACE genotypes were similar, except for history of hypertension. The frequency of II genotype was significantly higher in patients with positive history of hypertension than the patients with negative history of hypertension (p=0.013). DD genotype of I/D polymorphism was found to be a susceptibility factor for DPN in homozygous form (p=0.032). According to allele frequencies, D allele of I/D polymorphism was found to be a susceptibility factor for DPN (p=0.031). CONCLUSION ACE gene I/D polymorphism may research in DM patients to determine genetic predisposition for DPN. It can be useful for taking early measures and avoiding DPN in a Turkish population.

High Association of IL-4 Gene Intron 3 VNTR Polymorphism with Diabetic Peripheral Neuropathy

Diabetic peripheral neuropathy (DPN) is a common disease. It is one of the late complications of diabetes mellitus. DPN can lower the quality of life by causing severe painful clinic symptoms. The aim of this study is to evaluate interleukin (IL)-4 gene variable number of tandem repeat (VNTR) polymorphism on DPN in Turkish population. Two hundred and twenty-seven DPN patients and 241 controls were enrolled in this study. Genomic DNA was isolated and genotyped using polymerase chain reaction analyses for the IL-4 gene intron 3 VNTR polymorphism. The distribution of genotype frequencies of IL-4 gene intron 3 VNTR polymorphism was statistically different between DPN patients and control group (p = 0.001). The frequency of P1 and P2 alleles was statistically different between DPN patients and control group (p = 0.00009). The results of this study suggested that intron 3 VNTR polymorphism of the IL-4 gene plays an important role in the occurrence of DPN in the Turkish population.

Association between interleukin 4 gene intron 3 VNTR polymorphism and recurrent aphthous stomatitis in a cohort of Turkish patients.

OBJECTIVE Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal diseases, with a multifactorial etiopathogenesis, an interaction between predisposing factors and/or systemic conditions and immunological components in genetically predisposed subjects. Although there is no clear genetic mode of inheritance, there is evidence that inheritance of specific gene polymorphisms may predispose individuals to RAS. The purpose of the present study was to investigate a possible association between the functional interleukin 4 (IL4) VNTR genetic polymorphism and RAS in a sample of Turkish patients. METHODS The study included 145 unrelated patients with a clinical diagnosis of RAS and 150 unrelated healthy controls. Genomic DNA was isolated and IL4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers. RESULTS The distribution of genotype and allele frequencies of IL4 gene intron 3 VNTR polymorphism was statistically different between RAS patients and control group (p<0.0001 and p<0.0001, respectively) P2P2 genotype and P2 allele were also found to be protective with a lower risk for susceptibility to RAS (p<0.0001). CONCLUSION The results of this study suggest that intron 3 VNTR polymorphism in the IL4 gene is associated with RAS susceptibility in Turkish population.

Significant association of interleukin-4 gene intron 3 VNTR polymorphism with susceptibility to knee osteoarthritis.

OBJECTIVE Interleukin-4 (IL-4) is a strong chondroprotective cytokine and polymorphisms within this gene may be a risk factor for osteoarthritis (OA). We aimed to investigate genotype and allele frequencies of IL-4 gene intron 3 variable number of tandem repeats (VNTR) polymorphism in patients with knee OA in a Turkish population. METHODS The study included 202 patients with knee OA and 180 healthy controls. Genomic DNA was isolated and IL-4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers followed by restriction fragment length polymorphism (RFLP) analysis. RESULTS Our result show that there was statistically significant difference between knee OA patients and control group with respect to IL-4 genotype distribution and allele frequencies (p=0.000, OR: 0.20, 95% CI: 0.10-0.41, OR: 0.22, 95% CI: 0.12-0.42, respectively). CONCLUSIONS Our findings suggest that there is an association of IL-4 gene intron 3 VNTR polymorphism with susceptibility of a person for development of knee OA. As a result, IL-4 gene intron 3 VNTR polymorphism could be a genetic marker in OA in a Turkish study population. This is the first association study that evaluates the associations between IL-4 gene VNTR polymorphism and knee OA.

Genetic association of 5-HT1A and 5-HT1B gene polymorphisms with migraine in a Turkish population

Migraine, a very common headache disorder, is regarded as a polygenic disease and serotonergic pathways appear to play a major role in its pathogenesis. The present study was designed to explore the associations of polymorphisms of 5-hydroxytryptamine (serotonin) receptor 1A (5-HT1A) and 5-hydroxytryptamine receptor 1B (5-HT1B) genes in Turkish migraine patients. 5-HT1A C-1019G (rs6295) promoter and 5-HT1B G861C (rs6296) exon polymorphisms in 203 migraine patients and 202 healthy subjects were analyzed by using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Allele and genotype frequencies were not significantly different between migraine patients and healthy subjects for both the 5-HT1A C-1019G promoter and 5-HT1B G861C exon polymorphisms. Our data do not support the hypothesis that 5-HT1A C-1019G and 5-HT1B G861C polymorphisms have effects on migraine.

Association between sequence variations of the Mediterranean fever gene and fibromyalgia syndrome in a cohort of Turkish patients

OBJECTIVE Fibromyalgia syndrome (FMS) is a common chronic widespread pain syndrome mainly affecting women. Genetic risk factors are known to contribute to the etiology of the syndrome. Clinical features show that FMS and familial Mediterranean fever (FMF) have some overlapping symptoms. Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF. The aim of this study was to explore the frequency and clinical significance of missense mutations and a common polymorphism of MEFV gene in a cohort of Turkish patients with FMS. METHODS The study included 187 patients with FMS and 190 healthy controls. Genomic DNA was isolated and genotyped using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses for the five MEFV gene mutations (M694V, M680I, V726A, E148Q and P369S) and one polymorphism (R202Q). RESULTS There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between FMS patients and healthy controls (p=0.002, OR: 2.3, 95% CI: 1.35-4.16 and p=0.003, OR: 2.2, 95% CI: 1.28-3.75, respectively). There was also a significant difference between MEFV mutation carriers and non-carriers with respect to the clinical characteristic of morning fatigue (p=0.045). The genotype and allele frequencies of R202Q polymorphism of MEFV gene showed statistically significant differences between FMS patients and healthy controls (p<0.0001 and p<0.0001, respectively) and especially the homozygous AA genotype was significantly higher in FMS patients than in healthy controls (p=0.0003; OR: 7.43, 95% CI: 2.14-39.75). While 13 of the 44 FMS patients with MEFV mutation had R202Q polymorphism, none of the 22 controls with MEFV mutation had R202Q polymorphism. Stratification analysis according to clinical features for this disease reveals that morning fatigue and irritable bowel syndrome had associations with R202Q polymorphism (p=0.022 and p=0.031 respectively). CONCLUSION The results of this study suggest that MEFV gene mutations and polymorphism are positively associated with predisposition to develop FMS. Further studies with larger populations will be required to confirm these findings.