Fakülteler / Faculties
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Item Frequency of IL-1B Gene Polymorphisms in Patients with Gastroesophageal Cancer in the Hakkari Region(2023) Yaman, Derya; Akad Dincer, Selin; Karaka, Yusuf; Unsoy, Gozde; Terzi, Yunus Kasim; Sahin, Feride IffetObjective: Gastric cancer is a complex malignant tumor associated with chronic inflammation. In the present study, we aimed to investigate the frequency of interleukin 18 (IL-18) gene polymorphisms affecting gene expression in patients with gastroesophageal cancer (GC) diagnosed in the Hakkari region. Methods: Blood samples of 17 patients with GC (group 1) and 59 healthy controls (group 2) were enrolled in the study. The single-nucleotide polymorphisms (SNPs) rs1143627 c.-118C>T, rs16944 c.-598C>T, and rs1143634 c.315C>T polymorphisms in the IL-18 gene were studied among groups via polymerase chain reaction and restriction fragment length polymorphism. Results were analyzed by descriptive statistics and the x(2) test. The association between SNPs and GC risk was evaluated by odd ratios (ORs) and 95% confidence intervals. Results: The frequencies of the three genotypes in the SNP rs1143627, rs16944, and rs1143634 were similar between the groups, and C>T transition was not found to be significant [(p=0.69, OR: 1.16 95%, confidence interval (CI): 0.54-2.51; p= 0.16, OR: 0.58 95%, CI: 0.26-1.25; p=0.7, OR: 0.83 95%, CI: 0.32-2.11, respectively]. Conclusion: Our results did not reveal any significant association between IL-18 gene SNPs and gastroesophageal cancer in the Hakkari region.Item Biochemical, Radiologic, Ultrastructural, and Genetic Evaluation of Iron Overload in Acute Leukemia and Iron-chelation Therapy(2014) Olcay, Lale; Hazirolan, Tuncay; Yildirmak, Yildiz; Erdemli, Esra; Terzi, Yunus Kasim; Arda, Kemal; Ozturkmen, Seda; Akyay, Arzu; Kaymak-Cihan, Meric; Bicakci, Zafer; Bal, Ceylan; https://orcid.org/0000-0001-5612-9696; https://orcid.org/0000-0002-4480-7784; 23887025; B-4372-2018; ABI-7551-2020Iron overload in hereditary hemochromatosis and hematologic malignancy has unfavorable effects on morbidity. Herein, 53 children (age 108.4 +/- 58.3 mo, 25 girls and 28 boys) with acute myeloblastic and lymphoblastic leukemia, who received 4 different chemotherapy protocols, were evaluated for iron overload throughout chemotherapy. Iron overload arose: (1) before chemotherapy, which was dependent on neither chemotherapy nor packed red blood cell transfusions and (2) after chemotherapy, which was dependent on the duration and nature of chemotherapy and partially on transfusion of packed red blood cells. Iron overload was documented in 75% of patients with a ferritin level >1000 ng/mL, by liver and heart magnetic resonance imaging, and they were administered iron-chelation therapy with success. Three of 10 radiologically iron-overloaded patients were heterozygous for H63D mutation. Aminolevulinic acid and porphobilinogen levels were normal. Light microscopic examination of the bone marrow revealed increased iron granules in erythroblasts, platelets, and megakaryocytes, iron-laden macrophages, free iron in the matrix, dyshematopoiesis, and apoptotic cells. Electron microscopic examination revealed iron-laden secondary lysosomes and autolysosomes in normoblasts and iron-laden primary granules in promyelocytes, irrelevant to the ferritin level, implying autophagia due to chemotherapy as a source of the excess iron. We think that iron overload, which is an important complication of acute leukemia, should be evaluated separately from transfusion overload, and the management principles specific to leukemia should be implemented.Item Chronic Tonsillitis Is Not Associated with Beta Defensin 1 Gene Polymorphisms in Turkish Population(2015) Arslan, Fatih; Babakurban, Seda Turkoglu; Erbek, Selim S.; Sahin, Feride I.; Terzi, Yunus Kasim; 0000-0001-7308-9673; 0000-0001-5612-9696; 0000-0003-4825-3499; 0000-0001-5067-4044; 25683590; AAC-7232-2020; B-4372-2018; B-7604-2019; AAI-8856-2021Background: Defensins are antimicrobial peptides expressed on mucosal surfaces. They function as part of the innate immune system. Palatine tonsils play important roles in innate immune system. However, our knowledge on the pathophysiology of chronic tonsils is limited. Objective: The aim of this study was to investigate the association between beta defensin 1 gene single nucleotide polymorphisms and chronic tonsillitis. Study design: Prospective, non-randomized, controlled clinical study. Setting: Tertiary referral center. Subjects and methods: Eighty six patients with chronic tonsillitis and eighty controls without history of chronic tonsillitis were enrolled in this study. Genotypes were determined by restriction fragment length polymorphism analyses after polymerase chain reaction. Results: Genotype and allele frequencies of the -20G/A (rs11362), -44C/G (rs1800972) and -52G/A (rs1799946) single nucleotide polymorphisms were not statistically different between patients and control groups (p > 0.05). Conclusion: In this study, we found that DEFB1 gene -20G/A, -44C/G and -52G/A single nucleotide polymorphisms were not associated with chronic tonsillitis. Studies, which analyse other polymorphism of the beta defensin 1 gene in large case series, should be conducted to understand the role of DEFB1 gene on chronic tonsillitis. (C) 2015 Elsevier Ireland Ltd. All rights reserved.Item Fractalkine Receptor Polymorphism and Chronic Tonsillitis(2014) Babakurban, Seda Turkoglu; Erbek, Selim S.; Terzi, Yunus Kasim; Arslan, Fatih; Sahin, Feride I.; https://orcid.org/0000-0001-5067-4044; https://orcid.org/0000-0003-4825-3499; https://orcid.org/0000-0001-5612-9696; https://orcid.org/0000-0001-7308-9673; 24496565; AAI-8856-2021; B-7604-2019; B-4372-2018; AAC-7232-2020The objective of this study is to examine whether there is an association of fractalkine gene receptor polymorphisms with chronic tonsillitis. This is a cross-sectional study in the setting of a tertiary referral center. The study group included 79 patients with chronic tonsillitis and 76 controls without history of chronic tonsillitis. Genotypes were identified by restriction fragment length polymorphism analyses after polymerase chain reaction. c.745G > A (V249I) single nucleotide polymorphism and the frequencies of the G and A alleles did not differ in the patient and control groups (p = 0.363; p = 0.743, respectively). c.839C > T (T280M) single nucleotide polymorphism was found to be higher in controls than in the patients with chronic tonsillitis (p < 0.001). Consistent with this result, T allele frequency was higher in controls than in the patients with chronic tonsillitis (p < 0.001). In this study, we suggested that fractalkine gene receptor c.839C > T (T280M) single nucleotide polymorphism could be associated with a reduced risk of chronic tonsillitis.Item Retrieving Relevant Experiments: The Case of MicroRNA Microarrays(2015) Acici, Koray; Terzi, Yunus Kasim; Ogul, Hasan; 0000-0001-5612-9696; 0000-0002-3821-6419; 26116091; B-4372-2018; HDM-9910-2022Content-based retrieval of biological experiments in large public repositories is a recent challenge in computational biology and bioinformatics. The task is, in general, to search in a database using a query-by-example without any experimental meta-data annotation. Here, we consider a more specific problem that seeks a solution for retrieving relevant microRNA experiments from microarray repositories. A computational framework is proposed with this objective. The framework adapts a normal-uniform mixture model for identifying differentially expressed microRNAs in microanay profiling experiments. A rank-based thresholding scheme is offered to binarize real-valued experiment fingerprints based on differential expression. An effective similarity metric is introduced to compare categorical fingerprints, which in turn infers the relevance between two experiments. Two different views of experimental relevance are evaluated, one for disease association and another for embryonic germ layer, to discern the retrieval ability of the proposed model. To the best of our knowledge, the experiment retrieval task is investigated for the first time in the context of microRNA microarrays. (C) 2015 Elsevier Ireland Ltd. All rights reserved.Item The Notch Signaling System Is Involved in the Regulation of Reparative Angiogenesis in the Zone of Stasis(2017) Abbas, Ozan Luay; Ozatik, Orhan; Terzi, Yunus Kasim; Ozatik, Fikriye Yasemin; Nar, Rukiye; Turna, Gamze; https://orcid.org/0000-0001-5612-9696; 28319529; B-4372-2018The Notch pathway ligand Delta-like 4 (Dll4) functions as an antiangiogenic factor, inhibiting vascular endothelial growth factor (VEGF)-induced angiogenesis. This function is documented in tumor and embryonic vasculature. However, its implication in burn wounds remains unexplored. Our objective was to explore the involvement of the Notch in the healing of zone of stasis burns. We hypothesized that anti-Dll4 therapy would prevent progressive necrosis in the stasis zone by promoting angiogenesis. Burns were created in 21 rats using the comb burn model. The Notch inhibitor N-[N-(3,5-difluorophenacetyl)1- alanyl]-S-phenylglycine-t-butyl-ester was administered in the treatment group. Controls were given the same amount of solvent. Seven days after the burn, skin samples were evaluated for VEGF and Dll4 gene expressions. Immunohistochemical analysis was used for the assessment of vascular density, endothelial Dll4 expression, and apoptosis count. Histologic grading of tissue damage was performed. Circulating levels of VEGF and Dll4 were determined. VEGF and Dll4 mRNA levels were found to be simultaneously induced after the burn. In the treatment group, a significant increase in the number of vessels was observed. However, gross evaluation documented an expansion of necrosis to the zone of stasis with marked activation of apoptosis. Histologic assessment showed that the resultant vascular overgrowth was accompanied by extensive edema and abundant infiltration of leukocytes. We provide evidence for the involvement of Notch in the regulation of angiogenesis in zone of stasis burns.Item Enhancement of Vascular Endothelial Growth Factor's Angiogenic Capacity by the Therapeutic Modulation of Notch Signalling Improves Tram Flap Survival in Rats Submitted to Nicotine(2017) Abbas, Ozan Luay; Terzi, Yunus Kasim; Ozatik, Orhan; Ozatik, Fikriye Yasemin; Turna, Gamze; Nar, Rukiye; Musmul, Ahmet; 0000-0001-5612-9696; 0000-0002-4662-6493; 0000-0002-8422-2975; 28277073; B-4372-2018; GXA-2381-2022; HOH-8201-2023Background: Smoke of cigarettes, and specifically nicotine, has been shown to diminish pedicled transverse rectus abdominis musculocutaneous (TRAM) flap survival. Considering that Notch signalling through its ligand Delta-like 4 (Dll4) functions as anti-angiogenic factor by inhibiting the pro-angiogenic effects of vascular endothelial growth factor (VEGF), it is hypothesised that inhibition of the Notch would promote angiogenesis and increase TRAM flap survival in rats submitted to nicotine. Methods: Twenty rats were treated with nicotine for 28 days preoperatively. Thereafter, a pedicled TRAM flap was created in all animals. The Notch inhibitor N-[N-(3,5-difluorophenacetyl)-1-alanyl]-S-phenylglycine-t-butyl-ester was administered in animals of the treatment group. Animals in the control group were given the same amount of solvent. Five days after the surgery, viable flap areas were determined. Skin samples were evaluated for VEGF and Dll4 mRNA levels. Immunohistochemical analysis was used for the assessment of endothelial Dll4 expression. Vascular density was determined histologically. Plasma levels of VEGF and Dll4 were measured. Results: A significant improvement in TRAM flap surviving area was observed in the treatment group (53.5014.25%) compared with the controls (32.20 +/- 9.15%). Immunohistochemical analysis revealed a significant increase in the number of Dll4 stained vessels in animals of the treatment group (9.2 +/- 1.6) in comparison with the controls (5.7 +/- 1.9). VEGF mRNA levels (0.22 +/- 0.08) in the treatment group were significantly lower than those in the control group (0.36 +/- 0.09). Conclusion: Notch inhibition significantly improved TRAM flap survival in animals exposed to nicotine by promoting VEGF-induced angiogenesis.Item Clinical Findings and Mutation Analysis of NF1 Patients in Turkey(2018) Terzi, Yunus Kasim; Oguzkan-Balci, Sibel; Anlar, Banu; Varan, Ali; Ersoy-Evanse, Sibel; Sharafif, Parisa; Ayter, Sukriye; https://orcid.org/0000-0001-5612-9696; B-4372-2018Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that is caused by mutations of the NF1 gene. NF1 is clinically characterized by neurofibromas, pigmentation anomalies, and an increased risk of malignant tumors. The mutation rate of NF1 is one of the highest known for human disorders: approximately 50% of all affected individuals are sporadic cases and carry de novo mutations Therefore mutation analysis of NF1 may be an important tool in early diagnosis and genetic counseling. This is the first large NF1 study performed in Turkey. The data collected in this study enabled us to overview the genetic and clinical aspects of NF1 molecular diagnostics. The patients, who were clinically diagnosed for NF1, were included in this study. These patients were clinically evaluated, and subgroup of them genotyped or DNA sequenced for mutations in NF1, either to confirm the clinical diagnosis or to identify pathogenic mutations. The mutation detection rate was 52%, based on analysis of only genomic DNA. We observed that frameshift mutations were the largest proportion of the identified mutations (38.5%). The frequency of microdeletions was 26.9% and the splice site and nonsense mutations were 11.5% in this cohort. Turkish NF1 patients have similar NF1 germline mutations compared to other populations. Considering that some of these detected mutations belonged to the patients who did not fulfill the NIH criteria for NF1 diagnosis, mutation analysis of NF1 is an important tool in early diagnosis and genetic counseling.Item Immune and inflammatory genes possibly involved in the pathogenesis of severe COVID-19(2021) Beksac, Burcu; Dincer, Selin Akad; Avdullahi, Egzon; Yaman, Derya; Terzi, Yunus Kasim; Babakurban, Seda Turkoglu; Celik, Zerrin Yilmaz; Tasci, Canturk; Sahin, Feride IffetItem Investigation of Toll Like Receptor-7 Gene (TLR-7) Mutations in COVID-19 Patients(2021) Dincer, Selin Akad; Beksac, Burcu; Avdullahi, Egzon; Yaman, Derya; Terzi, Yunus Kasim; Babakurban, Seda Turkoglu; Celik, Zerrin Yilmaz; Tasci, Canturk; Sahin, Feride Iffet