Nurten Kara

Vitamin D receptor gene polymorphisms in patients with urolithiasis

Urolithiasis is a multifactorial disease, the onset and severity of which is influenced by both genetic and environmental factors. This study represents an investigation of the role of vitamin D receptor (VDR) gene polymorphisms (ApaI, BsmI, and TaqI) and combined genotypes in urolithiasis in a Turkish population. We studied 110 patients with urinary stones and 150 control subjects. The polymorphic regions were amplified using polymerase chain reaction, followed by digestion with restriction enzymes BsmI, ApaI, and TaqI, and analyzed electrophoretically. Genotype and allele frequencies were calculated, and the association with urolithiasis, family history, and recurrence of stone was investigated. Our data provide no evidence for an association between urolithiasis and VDR ApaI, BsmI, and TaqI genotypes. We also analyzed the effects of VDR ApaI, BsmI, and TaqI genotypes in combination; the “GTT” VDR haplotype, constructed from three adjacent restriction fragment length polymorphisms was overrepresented among the urolithiasis patients. However, no significant differences between heterozygous carriers (OR 1.302; 95% CI 0.527–3.215) and homozygous carriers (OR 3.39; 95% CI 0.719–15.985) were observed in our study population. A significant association was found only between the ApaI polymorphism and family history (P=0.017; χ2=5.657). Our data indicate that the VDR ApaI, BsmI, and TaqI polymorphisms do not confer a significant risk for urolithiasis.

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.

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.

Lack of evidence for association between endothelial nitric oxide synthase gene polymorphism (glu298asp) with Behçet’s disease in the Turkish population

Endothelial nitric oxide synthase (eNOS) could be a candidate gene for Behçet’s disease (BD). This study investigated the relationship of the eNOS Glu298→Asp polymorphism with the presence and severity of BD in the Turkish population. Ninety-two patients with BD and 100 controls were studied. Analyses of Glu298Asp polymorphism in exon 7 of the eNOS gene were made by the polymerase chain reaction (PCR)-restriction fragment length polymorphism technique. The frequencies of the eNOS genotypes were similar for BD patients (GG:GT:TT=58.7%:38%:3.3%) and controls (59.2%:33.7%:7.1 %), P=0.335. No evidence of difference was found in the frequency of the T allele between BD patients (22.3%) and controls (24%), [OR=0.91, 95% CI (0.55–1.50), P=0.690]. Glu298→Asp polymorphism of the eNOS gene does not appear to be associated with the presence of BD in the Turkish population.

Association between osteoporosis and polymorphisms of the bone Gla protein, estrogen receptor 1, collagen 1-A1 and calcitonin receptor genes in Turkish postmenopausal women.

In this study, we have investigated the association between osteoporosis and osteocalcin (BGLAP) -298 C>T, estrogen receptor 1 (ER1) 397 T>C, collagen type1 alpha 1 (Col1A1) 2046 G>T and calcitonin receptor (CALCR) 1340 T>C polymorphisms. Genomic DNA was obtained from 266 persons (158 osteoporotic and 108 healthy controls). Genomic DNA was extracted from EDTA-preserved peripheral venous blood of patients and controls by a salting-out method and analyzed by PCR-RFLP. As a result, there was no statistically significant difference in the genotype and allele frequencies of patients and controls for BGLAP -298 C>T, Col1A1 2046 G>T, ER1 397 T>C and CALCR 1340 T>C polymorphisms. However, ER1 CC genotype compared with TT+TC genotypes was found to increase the two fold the risk of osteoporosis [p=0.039, OR=2.156, 95% CI (1.083-4.293)] and CALCR CC genotype compared with TT+TC genotypes was found to have protective effect against osteoporosis [p=0.045, OR=0.471, 95% CI (0.237-0.9372)]. In the combined genotype analysis, ER1/CALCR TCCC combined genotype was estimated to have protective effect against osteoporosis [p=0.0125, OR=0.323, 95% CI (0.1383-0.755)] whereas BGLAP/Col1A1 CCTT and ER1/CALCR CCTT combined genotypes were estimated as risk factors for osteoporosis in Turkish population (p=0.027, p=0.009 respectively).

Association of the polymorphisms in promoter and intron regions of the interleukin-4 gene with chronic periodontitis in a Turkish population.

Objectives. The etiology of periodontitis is related to the interaction between micro-organisms and host responses. Host modifying factors, such as genetic predisposition, may increase the severity of periodontitis. Recent works have shown that the levels of cytokine expression are regulated by genetic polymorphisms, and that these variations can interfere with progression of the disease. This study therefore aimed to evaluate whether interleukin (IL) 4 gene polymorphisms are associated with severe generalized chronic periodontitis. Material and Methods. Seventy-five severe generalized chronic periodontitis patients and 73 healthy subjects were examined. Blood samples were taken and genomic DNA was amplified by polymerase chain reaction (PCR). Identification of 70 base-pair repeat polymorphisms in intron 2 and C→T polymorphisms at −590 position of the promoter region was performed through PCR-restriction fragment length polymorphism (RFLP). Results. No significant differences were found in the allele and genotype frequencies between the control and periodontitis group. Conclusion. The IL-4 polymorphisms were not related to severe generalized chronic periodontitis in a Turkish population.

Association between osteoporosis and polymorphisms of the IL-10 and TGF-beta genes in Turkish postmenopausal women.

Osteoporosis is a multifactorial disease in which genetic determinants are modulated by hormonal, environmental and nutritional factors. The balance between bone resorption and bone formation seems to be regulated by a variety of growth factors and cytokines. An important clinical risk factor in the pathogenesis of osteoporosis is the presence of genetic polymorphisms in susceptibility genes. In this study, we investigated the association between osteoporosis and interleukin 10 (IL-10) -597 C > A and transforming growth factor β1 (TGF-β1) T869C (also named Leu10 > Pro) polymorphisms in Turkish postmenopausal women. Genomic DNA obtained from 255 individuals (152 osteoporotic and 103 healthy controls). The DNA sample was isolated from peripheral bloods by salting-out method and analyzed by the techniques of PCR-RFLP. Genotype and allele frequencies were calculated and data were analyzed using the χ(2) test. We found a statistically significant difference between the groups with respect to IL-10 genotype distribution (p = 0.001) and allele frequencies (p < 0.0002). However, we did not found any difference between the groups with regarding TGF-β1 genotype distribution and allele frequencies (p > 0.05). In the combined genotype analysis, IL-10/TGF-β1 CCCC combine genotype was also estimated risk factor for osteoporosis in Turkish postmenopausal women (p = 0.026). To our knowledge, this is the first report to examine IL-10 gene -597 C > A polymorphism and osteoporosis in Turkish population.

Lack of association between the G-2548A polymorphism of the leptin gene and psoriasis in a Turkish population

Background   Psoriasis is a multifactorial disease in which genetic and inflammatory factors play important roles. Leptin is classified as a cytokine and plays an important role in the regulation of the T‐helper response. A common polymorphism in the promoter of the human leptin gene (G‐2548A) may have a role in the pathogenesis of psoriasis.

Association of transforming growth factor β1 gene polymorphism with rheumatoid arthritis in a Turkish population

OBJECTIVE Cytokine genes play important roles in the pathogenesis of rheumatoid arthritis (RA). In RA, the plasma and synovial fluid levels of transforming growth factor beta1 (TGFbeta1) have been shown to be raised. The aim of this study was to investigate the relationship between the TGFbeta1 T869C polymorphism and RA in a Turkish population. METHODS One hundred and thirty-one patients with a clinical diagnosis of RA and 133 healthy controls were enrolled in this study. Analyses of TGFbeta1 T869C gene were made by the polymerase chain reaction-restriction fragment length polymorphism technique. RESULTS There was no significant difference in genotypic frequency of TGFbeta1 T869C polymorphism between the patients with RA (TT:TC:CC=42.7%:41.2%:16%) and controls (TT:TC:CC=36.1%:48.1%:15.8%) (p=0.48). The age at first occurrence of clinical symptoms of RA did not differ significantly in relation to TGFbeta1 T869C genotypes (p=0.07). Furthermore, there was no significant association between TGFbeta1 T869C genotypes and the presence or absence of radiographic erosions in the patient group (p=0.67). But presence of T allele was associated with 1.92-fold increased risk for RF positivity (p=0.02, OR=1.92, 95% CI=1.08-3.40). CONCLUSION The allele frequencies for TGFbeta1 T869C polymorphism in RA patients were similar to those in the control group. However, the T allele carriers had 1.92-fold increased risk for RF positivity. Further studies on larger numbers of cases and on the other polymorphic regions of this gene are needed before definite conclusions can be drawn about the role of TGFbeta1 in the etiology of RA.

The Mayer-Rokitansky-Kuster-Hauser and gonadal dysgenesis anomaly in a girl with 45,X/46,X,del(X)(p11.21).

The Mayer–Rokitansky–Kuster–Hauser (MRKH) anomaly is characterized by uterine aplasia or hypoplasia associated with normal ovaries [Morcel et al., 2007]. The co-occurrence of gonadal dysgenesis and mullerian agenesis has been previously described as a rare event [Alper et al., 1985; Mohapatra et al., 1992; Guitron-Cantu et al., 1999]. Structural or numerical abnormalities of X chromosome can cause gonadal dysgenesis as absent or streak gonads [Goldman et al., 1982]. Although gonadal dysgenesis has been reported with structural abnormalities in X chromosome such as 46Xi(Xq),45,X and 45X/46XX, neither structural nor numerical abnormalities of X chromosome have been associated with the MRKH anomaly [Gardo et al., 1971; De Leon et al., 1984; Gray et al., 2001]. Associated skeletal abnormalities including spine, face and limb such as asymmetric or fused vertebra, ectrodactly, radial agenesis and facial asymmetry have been reported in patients with MRKH [Behera et al., 2005; Morcel et al., 2007]. The etiology of this condition is still unknown. Here, we report on a girl whohas 45,X/46,X,del(X)(p11.21!pter)withMRKH and gonadal dysgenesis. A 17-year-old girl with complaints short stature, primary amenorrhea, hypertrophy of both second toes was admitted to the hospital. She was attending high school, and her school performance was good. She had two sisters and two brothers who were chromosomal and physically normal. There was no consanguinity in her parents who were also normal. Physical examination showed that her height was 129.9 cm (<3rd centile); weight 28.8 kg (<3rd centile). Height SDS was – 4.5, bone age was 12. She had downslanting palpebral features, a webbed neck, low posterior hairline, cubitus valgus, and short 4th metacarpals. She also had long and hyperplastic second toes in both feet (Fig. 1) and a grade 1/6 systolic murmur. Development of breast was Tanner phase I, pubic hair Tanner phase II. Axillary hair was absent. Serum gonadotropin levels were high (LH: 14.43 ml U/ml, FSH: 86.59 ml U/ml) and estradiol level were low (10.44 pg/ml). Thyroid function test was normal. Serum fasting glucose, lipids and insulin levels were within normal range. Bone mineral density (BMD) obtained from lumbar vertebral and femoral neck was osteopenic (Z score: 1.93 and 1.21, respectively). Echocardiographic and abdominal ultrasonographic examinations were normal. Ultrasonographic examination and magnetic resonance imaging of the pelvis revealed absence of uterus and ovaries and hypoplastic vagina. Cytogenetic analysis was performed on peripheral blood lymphocytes. A 100 GTG banded metaphases were analyzed utilizing the following DNA probe sequences: CEP X (DXZ1) SpectrumAquaTM; TelVysion Xp/Yp SpectrumGreenTM TelVysion Xq/Yq SpectrumOrangeTM (Vysis). Of 100 metaphase cells examined from PHA-stimulated blood cultures by conventional G-banding techniques, 30 were characterized as missing a sex chromosome (45,X) while the remaining 70 were characterized as containing number of chromosomes with deletion