Fakülteler / Faculties
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Item Evaluation of the Genetic Analysis Results in Infertile Patients with Non-Obstructive Azoospermia(2023) Sen, Erhan; Kizilkan, Yalcin; Duran, Mesut Berkan; Turunc, Tahsin; Sahin, Feride Iffet; Ozkardes, Hakan; 0000-0001-7308-9673; 0000-0002-7277-449X; AAC-7232-2020; AAH-1052-2020Objective: To evaluate the genetic analysis results of patients who referred to our clinic infertility and whom semen analysis revealed non -obstructive azoospermia (NOA).Materials and Methods: Among 994 patients who underwent a microscopic testicular sperm extraction (micro-TESE) operation for NOA, 497 patients who were tested for karyotype analysis and 450 patients who were tested for chromosome Y microdeletion were included in our study. The rates of Klinefelter syndrome (KS) and Y chromosome microdeletion, sperm retrieval rates (SRR) in these genetic anomalies and the factors affecting them were investigated. Additionally, the association between the age, duration of infertility, testicular size, serum follicle stimulant hormone (FSH) and testosterone levels of patients and sperm extraction rates of micro-TESE operations were also evaluated.Results: The overall SRR of NOA patients who underwent micro-TESE was 47.5%. Among 104 patients with KS, sperm was successfully found after micro-TESE in 22 (21.2%). Fourteen patients were diagnosed with the Y chromosome microdeletion and sperm was successfully found in 4 (28.6%) of them; while the duration of infertility did not affect the SRR after micro-TESE (p=0.712); age, testicular volume serum FSH and testosterone levels had a significant effect on the SRR (p<0.005).Conclusion: In this study, the SRR of patients who have chromosome Y microdeletion or KS, was found to be lower than other studies in the literature. This difference could be derived from the genetically tested population's structure, variance in the gene areas used for scanning and different demographic characteristics of different regions.Item Reclassification of Clinical Exome Data Leads To Significant Clinical Assessment Changes in Almost Half of the Patients(2023) Bayraktar, Umut Arda; Sahin, Feride Iffet; Polat, Mert; Terzi, Yunus KastmPurpose: With the global accumulation of genetic/clinical data, we are understanding the clinical significance of the reclassification of pathogenicity for gene variants. We hypothesized that this evolution in classification(s) may cause clinically-relevant discrepancies in the genetic risk assessment of subjects. In this study, we sought to reclassify the clinical exome sequence (CES) data of our patients to assess whether these changes would have clinical significance.Materials and Methods: The study included CES data of 23 cases diagnosed with cancer or familial cancer predisposition. The variants were first classified in 2020 and then reclassified a year after based on the ACMG database. Chart reviews were performed to record clinical history and interventions.Results: In the first classification of CES data, a total of 80 variants were identified as being not benign (26 likely pathogenic/pathogenic and 54 variants of undetermined significance (VUS)). The clinical significance of fifteen variants (19%) changed after reclassification in 10 patients (43%). The only upgraded variant was the c.9097 dup in exon 23 of BRCA2 gene (likely pathogenic to pathogenic). Fourteen variants were downgraded at reanalysis in 9 patients: from pathogenic to likely pathogenic (2 variants), pathogenic to VUS (2), likely pathogenic to VUS (4), and VUS to benign (6).Conclusion: Considering that the clinical significance of CES data changed due to reclassification in almost half of the studied patients, we believe genetic variant-related data should be assessed at regular intervals, regardless of follow-up status in the clinic.Item Corchorus olitorius L. (Jute) leaf and seed extracts exerted high antibacterial activity against food and plant pathogenic bacteria(2022) Iseri, Ozlem Darcansoy; Korpe, Didem Aksoy; Sahin, Feride Iffet; Cabi, Evren; Haberal, Mehmet; 0000-0002-3462-7632; AAJ-8097-2021Aim of this study was to comparatively evaluate antibacterial activities of methanol (MetOH), acetone (Ace), petroleum ether (PE) and aqueous (dw) leaf (L), root (R), and seed (S) extracts of Corchorus olitorius L. on both food- and plant-borne pathogens, with DPPH radical scavenging activities (DRSA), and quantitative and qualitative constituent analysis. Leaf PE has the highest strain susceptibility on both food- and plant-borne pathogens. Clavibacter michiganensis, Pseudomonas tomato, and Erwinia caratovora were susceptible to nearly all the leaf and seed extracts. Very low minimum inhibitory concentration (8-128 mL(-1)) and minimum bactericidal concentration (32-2048 mu g mL(-1)) were determined for both leaf and seed extracts against C. michiganensis. Total phenolic contents were correlated to DRSA. The phenolic compounds tested were higher in the leaf MetOH, cholorogenic acid being the most abundant one. Palmitic acid was determined in leaf PE and seed PE extracts. Results presented here demonstrate high antibacterial activity of C. olitorius leaf seed extracts against phytopathogens for the first time, and provide the most comprehensive data on the antibacterial activity screening against food-borne pathogens. Considering limitations in plant disease control, antibacterial activities of these extracts would be important in plant disease control.Item MLPA Method does not Always Confirm the Results of aCGH: A Study of KANSL1 Gene Deletion Patients(2022) Dincer, Selin Akad; Celik, Zerrin Yilmaz; Erol, Ilknur; Sahin, Feride Iffet; AAC-8356-2020Background: Microdeletion and microduplications are detected on chromosomes as a pathological subgroup of copy number variants of DNA. It has become easierto identify such chromosomal syndromes after use of array-based comparative genomic hybridization technology. One of them is the 17q21.31 microdeletion and microduplication syndrome. A 500-650 kb sized copy loss on 17q21.31 results in a phenotype which was described as Koolen-de Vries Syndrome including mental retardation, epilepsia, hypotonia and characteristic facial features. Today, we know that haplo-insufficiency of KANSL1 gene located in this region is responsible for these findings. A total of 30 patients with KANSL1 deletion detected during aCGH analyses were enrolled in the current study. All patients were analyzed by Multiplex Ligation-Dependent Probe Amplication (MLPA) method in order to confirm the results. Results: Three of the 30 patients had KANSL1 gene deletion detected by both methods and duplication was found in one patient. Conclusion: As a result of the study, we concluded that although new generation molecular methods enable us to obtain big and valuable data, each method has its own limitations and confirming the reults with another method increases test reliability. Using together of these methods are useful for the geneticists during diagnosis, clinical assessment and genetic counseling of patients.Item Comparison Of Diagnostic Criteria For Children With Familial Mediterranean Fever(2022) Onder, Esra Nagehan Akyol; Ozcan, Kudret Ebru; Sahin, Feride Iffet; Gulleroglu, Kaan Savas; Baskin, Esra; 35006379Familial Mediterranean fever (FMF) is an autoinflammatory disease characterized by recurrent attacks of fever and serositis. Diagnosis is made according to clinical findings and supported by genetic analysis. The most commonly used adult diagnostic criteria are the Tel-Hashomer criteria. Pediatric criteria for FMF diagnosis were described in 2009, but their reliability should be supported by additional reports. In this study, we aimed to compare the pediatric criteria and the Tel-Hashomer and 2019 Eurofever/PRINTO classification criteria using our FMF cohort. A total of 113 patients diagnosed with FMF were included. Demographic features and laboratory findings were retrospectively collected from the patients' files. The patients were evaluated with the Tel-Hashomer, pediatric and Eurofever/PRINTO classification criteria. At least two of five new pediatric criteria were as sensitive (89%) and specific (85%) as the Tel-Hashomer criteria (sensitivity 70%, specificity 96%). We also evaluated the Eurofever/PRINTO classification criteria using our cohort and found a sensitivity of 94% and specificity of 91%. Conclusion: Using pediatric criteria for the diagnosis of FMF in children is a feasible and simple approach that can diagnose the disease based on at least two criteria. Therefore, our study supports the use of pediatric criteria in FMF diagnosis of children. Our results also confirm that the Eurofever/PRINTO classification criteria can be successfully applied for the diagnosis of FMF due to their high sensitivity (94%) and specificity (91%). What is Known: center dot The FMF diagnosis is made according clinical findings and supported by genetic analysis. center dot The use of adult diagnostic criteria in pediatric FMF patients is controversial since classical clinical presentation is often absent in children. What is New: center dot Our study supports both the use of pediatric criteria and Eurofever/PRINTO classification criteria in clinical practice.Item The Influence of Sex on Brain Development Genetics and the Possible Relationship with Sex-Dependent Differences in Psychiatric Disorders(2021) Bagcaz, Arda; Terzi, Yunus Kasim; Sahin, Feride Iffet; 0000-0001-5947-0179; 0000-0001-7308-9673; AAK-2321-2021; AAC-7232-2020There are sex-dependent differences in the prevalence, age of onset, and course of psychiatric disorders and cognitive abilities. Although it has been assumed that the direct effect of gonadal hormones in sensitive periods leads to sexually dimorphic brain development, current evidence suggests that another possible factor may be sex-specific regulations at the gene level. Understanding the sex differences at the gene level can be promising to identify the mechanisms that predispose or trigger psychiatric disorders, and may provide new prevention or treatment strategies. This paper aims to review the findings on the mechanisms that affect the sex-specific differences in brain development at the gene level and to discuss the relationship of these findings with different cognitive characteristics of the sexes and psychiatric disorders.Item The Role of Heredity and the Prevalence of Strabismus in Families with Accommodative, Partial Accommodative, and Infantile Esotropia(2020) Eroglu, Fatma Corak; Oto, Sibel; Sahin, Feride Iffet; Terzi, Yunus; Kaya, Ozge Ozer; Tekindal, Mustafa Agah; 0000-0003-0171-4200; 0000-0001-7308-9673; 0000-0001-5612-9696; 32631000; AAJ-4668-2021; AAC-7232-2020; B-4372-2018Objectives: To investigate the prevalence of strabismus in families of a proband with accommodative, partial accommodative, or infantile esotropia, and to evaluate the mode of inheritance and the role of consanguineous marriages in this prevalence. Materials and Methods: Families of probands with comitant strabismus were invited to participate in the study. The family members of 139 subjects with accommodative, 55 with partial accommodative, and 21 with infantile esotropia agreed to participate. Detailed family trees were constructed. The first- and second-degree relatives were invited for a complete ophthalmological examination, and 518 individuals from 168 families were evaluated. The role of consanguinity, the presence of tropia, phoria (>= 8 PD), microtropia, and hypermetropia (>= 3.00 D) among first- and second-degree relatives were analyzed. Results: A non-Mendelian pattern was found in 49 families (23%), an autosomal dominant pattern in 39 families (18%), and an autosomal recessive pattern in 6 families (3%). The prevalence of consanguineous marriages among parents of probands was 18.1%, 22.6%, and 14.3% in the accommodative, partial accommodative, and infantile esotropia groups, respectively (p=0.652). The prevalence of strabismus in first-degree relatives was 58.9%, 45.5%, and 38.1%, respectively (p=0.07). The prevalence of microtropia in probands' siblings was significantly higher in the accommodative esotropia group (p=0.034). Conclusion: Sporadic cases and non-Mendelian inheritance were more frequent than autosomal recessive inheritance. Autosomal recessive inheritance was found not to be frequent in consanguineous marriages. The prevalence of strabismus and microtropia was significantly higher in families of esotropia cases than in the general population.Item Investigation of ARHGEF12 Single Nucleotide Polymorphism in Hypercholesterolemia and Primary Open Angle Glaucoma(2020) Yaman, Derya; Takmaz, Tamer; Dincer, Selin Akad; Sahin, Feride Iffet; 0000-0001-7308-9673; AAK-2511-2021; AAC-7232-2020Objective:To investigate the effect of single nucleotide polymorphism rs58073046 A>G within the ARHGEF12 gene in patients with hypercholesterolemia and primary open angle glaucoma. Methods: Blood samples of 20 patients with high serum cholesterol and primary open angle glaucoma (Group 1), 20 sex and age matched healthy subjects (Group 2) as controls were enrolled to the study. The ARHGEF12 gene polymorphism was determined by polymerase chain reaction and DNA sequence analysis. The data were assessed by descriptive statics and Fisher exact x(2) test. Results: The homozygous wild type genotype (AA) was identified in 95 % of Group 1 versus 100 % of Group 2. The homozygous mutant genotype (GG), presented the highest prevelance in Group 1 (5%), although the difference was not statistically significant between groups (p=0.5). Conclusion: This is the first study to identify the role of ARHGEF12 gene variant in the risk of hypercholesterolemia and POAG. Our results showed that there is no association between rs58073046 A>G polymorphism and disease development.Item beta-Adrenoreceptor antagonists reduce cancer cell proliferation, invasion, and migration(2014) Iseri, Ozlem Darcansoy; Sahin, Feride Iffet; Terzi, Yunus Kasim; Yurtcu, Erkan; Erdem, S. Remzi; Sarialioglu, Faik; 25026350Context: Propranolol, atenolol, and ICI118,551 are non-selective beta-adrenergic receptor (AR), beta(1)-AR, and beta(2)-AR antagonists, respectively. Objective: We investigated the efficacy of propranolol, atenolol, and ICI118,551 on proliferation, migration, and invasion of non-stimulated breast (MCF7), colon (HT-29), and hepatocellular (HepG2) cancer cells. Materials and methods: beta-AR expression profiling of cells was performed by real time PCR. Cell proliferation was determined by MTT. Boyden chamber and scratch assays were performed to evaluate invasion and migration. Results and discussion: All cell lines expressed beta-ARs. ICI118,551 was the most cytotoxic, whereas atenolol was the least effective beta-AR antagonist for 24, 48, and 72 h. Cell invasion was inhibited by ICI118,551 (45, 46, and 50% for MCF7, HT29, and HepG2, respectively) and propranolol (72, 65, and 90% for MCF7, HT29, and HepG2, respectively). Propranolol, atenolol, and ICI118,551 reduced migration of MCF7, HT-29, and HepG2 cells to varying extents depending on the application concentration and duration. Propranolol and atenolol reduced migration of MCF7 and HT-29 in a concentration-dependent manner, whereas migration of these cells decreased after 48 and 72 h of ICI118,551 applications. Conclusion: Beta(2)-AR antagonist seemed to be the most cytotoxic beta-blocker on non-stimulated cancer cells. Propranolol and ICI118,551 were more effective than atenolol in inhibiting invasion and migration of non-stimulated MCF7 and HT-29 cells; ICI118,551 being the most potent. Concordantly, beta(2)-selective blockage seemed to be more effective for non-stimulated cells. Effect of the selective beta-AR antagonists showed variation depending on the concentration, incubation time, and histological origin of cells.Item Epigallocatechin 3-gallate applications on HT-29 and MCF-7 cell lines and evaluation of tumor suppressor gene methylation(2015) Terzi, Yunus Kasim; Kaya, Ozge Ozer; Iseri, Ozlem Darcansoy; Celik, Zerrin; Sahin, Feride IffetEpigallocatechin 3-gallate (EGCG) is an antitumor molecule and shows this activity by binding to the active center of a methyltransferase enzyme (DNMT1). The methylation of DNA sequences of tumor suppressor and DNA repair genes is observed in different stages of carcinogenesis. In this study, we analyzed the effect of EGCG on the methylation status of 25 tumor suppressor genes in cancer cell lines HT-29 and MCF-7. HT-29 and MCF-7 cells were incubated with 10 mu M, 20 mu M, and 50 mu M and 1 mu M, 5 mu M, and 10 mu M EGCG for 48 h, respectively. We found promoter hypermethylation of (1) CDH13, GATA5, and RAR beta genes in MCF-7 cell line and (2) RAR beta, ESR1, PAX6, WT1, CADM1, CHFR, CDH13, and GATA5 genes in HT-29 cell line. However, (3) after EGCG application, no changes in methylation status were detected in our samples. Our results suggest that methylation status of tumor suppressor genes did not change with different EGCG doses.