Theses supervised by Prof. Dr. Turgay İsbir
32 theses · Yeditepe University
KLK1 gene polymorphism effect on the development of coronaryartery disease and diabetes mellitus type 2
Coronary artery disease is the most common cause of death worldwide. According to the statistics of the World Health Organization, 15 million patients were diagnosed with coronary artery disease in 2015. Diabetes disease is a metabolic chronic disease and is classified into three groups; type 1, type 2 and gestational. Type 2 diabetes is responsible for more than 90% of all diabetes cases. Both environmental and genetic factors play a role in the formation of these two diseases. The positive effects of the Klk1 gene on glucose balance, insulin synthesis and cardiovascular system have been shown in studies. In this study, the role of klk1 genetic polymorphism in these two diseases was investigated. This study included 4 groups of 174 people in total, the control group (n = 50), the coronary artery disease group (n = 48), the type 2 diabetes group (n = 50), and the coronary artery disease and type 2 diabetes group (n=26). There was no significant difference between these four groups in terms of gender and age criteria. When the body mass index values were examined, a significant difference was found (p< 0,00001). There was a significant difference in terms of HDL in the lipid profiles examination (P< 0,00001) but no significant difference was found in terms of cholesterol, LDL, VDL and TG. When the Klk1 genotypes were compared, the GG genotype differed significantly between the control and patient groups (P=0.010). Coronary artery disease was not significant in terms of Klk1 genotypes. When the genotypes of diabetic and nondiabetic individuals were compared, the AA genotype showed a significant difference (P=0.029). In terms of allele, the A allele showed a significant difference between people with and without diabetes (P=0.029). High body mass index poses a risk for these two diseases, and HDL is protective against coronary artery disease. These findings also revealed the protective effects of a healthy diet and physical activity against these diseases. The incidence of these 2 diseases is lower in people with the GG genotype. People with the AA genotype are at risk for type 2 diabetes. In these findings, mutations in the klk1 gene cause impairment of normal glucose metabolism and pose a risk for diabetes.
İnsan inflamator sitokinleri (IL-1β ve IL-6) kardiovasküler hastalıklara etkisinin araştırılması
Although deaths due to cardiovascular diseases have decreased in the last 30 years worldwide, they are still among the most common causes of death in North America and Europe. The Turkish Society of Cardiology (TEKHARF) pioneered since 1990, has conducted according to a study data that, two million cases of coronary heart disease were recorded and about 160,000 people are dying from coronary heart disease every year in Turkey. Cytokines are biological mediators that regulate immunological, local, or systemic inflammatory and restorative host responses and act as signals between cells. IL-1β is a type of cytokine that can have multiple effects, such as growth and differentiation, on many cell types simultaneously. In our study, we evaluated a comparison between a patient group (n=39) with cardiovascular diseases and a healthy, who were not previously diagnosed with this disease a control group (n=30) about several risk factors including diabetes, obesity, smoking, and hyperlipidemia and their correlation between Interleukin-1 beta (IL-1β), and cardiovascular diseases. A statistically significant relationship was found between triglycerides and the expression of IL-1β in the study groups (p=0.012). However, the complete statistical analysis of the absence of clear significant differences between the pathological and non-pathological states in most of the studied traits except for triglycerides, and the variables used such as gender, age, weight, BMI have no significant effects, except in very few replications. The relationship of cytokines, which are biological response modifying molecules that can show activity even at very low concentrations, with cardiovascular events is still being investigated.
Investigation of p53 gene polymorphisms in colorectal cancer
Globally, colorectal cancer ranks third in incidence, and it's also the leading cause of cancer-related death. When colorectal polyps form, they are benign and do not cause cancer. However, they can evolve into advanced adenomas with high-grade dysplastic lesions and distant organ metastases. Oncogenes and tumor suppressor genes are believed to play a role in colorectal tumor progression. Genome-wide studies have identified APC, KRAS, SMAD4, and TP53 as genes that are often mutated in human colorectal tumors in 10 to 80 percent of non-hypermutated cases. The TP53 gene has been related to a poor prognosis in a range of malignancies, including colorectal tumors, according to new research. People with advanced colorectal cancer who had metastasized were found to have an 80 percent increase in TP53 mutations. However, This mutation is uncommon in benign colonic polyps, and the conversion rate to malignant polyps is 15-30 percent. It is believed that DNA damage and telomere erosion as well as hypoxia and malnutrition as well as oncogenic signals trigger the activation of p53. This results in cell cycle arrest and death, depending on the level and content of cellular stress During our research, we included six individuals with colorectal cancer in the study. Genotyping and polymorphism areas were determined when the patients' blood was isolated and DNA sequenced. Other than frequent polymorphisms, only three unusual polymorphic areas were found in Patient 3.
Determination of IDH 1, IDH2, MGMT, TERT, ATRX and H3F3A gene mutations in glial tumors
OBJECTIVE: Glial tumors make up almost half of all malignant brain tumors. The most popular and dangerous kind of primary brain tumor is Glioblastoma Multiforme(GBM). The survival rates of GBM are very short and it could be predictable with molecular markers. The aim of our study is to evaluate IDH1, IDH2, TERT, MGMT and ATRX genes with next-generation sequencing to find potential pathological mutations and their effect on survival. MATERIALS AND METHODS: Thirty patients who had a craniotomy and diagnosed with high-grade glioma were evaluated for this study. Peripheral blood samples were obtained from all participants. IDH1, IDH2, TERT, MGMT and ATRX genes were evaluated with next-generation sequencing from the samples. To evaluate the effects of all these mutations on survival we made survival analysis by SPSS. RESULTS: The median age of the patients was 58.5 (11-74), and 56.7% (n=17) were under 60 years of age. According to gender, the rate of male patients was 66.7% and the rate of female patients was 33.3%. Eighty percent of the patients had IDH, 83.3% MGMT, and 70% had EGFR positivity. After the targeted gene sequencing performed on the patients, 21 mutations were detected. Three of these mutations were found in IDH 1, 2 in IDH2, 6 in TERT, 7 in MGMT, and 3 in ATRX. When female gender status was taken as reference, the overall survival of female gender status was 4.63 times, and when more than three chromosome anomaly was accepted as a reference, it was determined from the available data that anomaly in three or less chromosomes negatively affected overall survival 2.83 times. CONCLUSIONS: Targeted NGS enables glial tumor categorization that is both accurate and therapeutically meaningful, providing better prognostic information than conventional histology. There is evidence to suggest that these cancers should be reclassified using molecular markers, although how this should be done in clinical practice is still up for debate. However, it's obvious that incorporating molecular diagnostics into our standard-of-care routine will help us better understand our patients' outcomes. Key Words: Next Generation Sequencing, Glioblastoma, Molecular Biology, IDH1/2, MGMT, TERT, ATRX
Kistik fibrozisli çocuklarda glukagonun glukoz regülasyonundaki rolü ve etkisi
Post-oral glucose tolerance test-related hypoglycemia is common and important issue in Cystic Fibrosis (CF). The underlying mechanisms of hypoglycemia are still controversial. The current mice studies show that CFTR gene is identified in alpha cells and regulates glucagon secretion. The aim of the study is to determine of the role and effect of glucagon in CF patients with hypoglycemia. A 3-hour OGTT was performed in 45 non-diabetic children with CF and 9 age-matched healthy controls. The subjects were classified based on OGTT as isolated hypoglycemia, hypoglycemia with abnormal glucose intolerance (AGT), AGT, CF related diabetes (CFRD) and normal glucose tolerance (NGT). After CFRD subjects were excluded, the demographic characteristics and plasma glucose, insulin and glucagon levels obtained at 0,60,120,150 and 180.min during OGTT were assessed. Isolated hypoglycemia group did not differ from NGT and controls in terms of age, sex, BMI and genetics. The frequency of isolated hypoglycemia, hypoglycemia + AGT, AGT and NGT were 31%(n=14), 18%(n=8), 11%(n=5) and 35.5%(n=16), respectively. Level 2 hypoglycemia (<54 mg/dL) was observed in 15% of the subjects. Basal glucagon level in NGT was significantly lower than the controls (p<0.05) and glucose-stimulated glucagon response were not observed in NGT. The glucagon levels at 60, 120 and 150.min in isolated hypoglycemia were significantly higher than controls (p<0.01, p<0.01, p<0.05, respectively). However, the statistically significant difference did not observe at 180.min (p=0.17) despite of higher insulin levels. These findings can be interpreted as the glucagon secretion is still sensitive to glycemic changing in isolated hypoglycemia group but not properly, whereas it was blunted in NGT. It might be suggested that NGT is more pathologic state than isolated hypoglycemia in terms of glucagon secretion.
Türk popülasyonunda over kanseri hastalarinda TERT geninin yeni nesil dizileme yöntemiyle mutasyon analizi
Ovarian cancer is the most common gynecological cancer after uterine cancer in our country. Although the frequency of the disease varies among different racial and ethnic groups, it is higher in developed countries than in developing countries. It affects women of all ages. Epithelial tumors constitute the majority of malignant ovarian tumors. Various risk factors are known to be associated with an increased risk of ovarian cancer. Among these risk factors, especially genetic factors, are responsible for the increased risk of developing ovarian cancer. Mutations are inherited changes in genetic material and are important because they can cause cancer. Most of the mutations in TERT, ATRX, MGMT, and IDH genes are associated with the risk of multiple cancer types. The Next Generation Sequencing approach is used in cancer studies, including ovarian cancer, facilitating the identification of existing mutations as well as new discoveries. In our study, 33 female patients between the ages of 18 and 76 who were diagnosed with ovarian cancer at Yeditepe University hospital and had demographically identical characteristics were included. With their consent, DNA was isolated from the blood samples collected from the patients, and significant and nonsense mutations in the IDH1, IDH2, TERT, MGMT, and ATRX genes were detected using the Next Generation Sequencing method. A bioinformatics analysis study was carried out with the Illumina Data Analysis Program. 7 different variants of the TERT gene were observed in 24 to 33 patients. Mutations were seen in both exonic and intronic regions. In our study, in the TERT gene, heterozygous in 7 patients and homozygous in 1 patient, c.2850-3039C>T; (p.H950H, p.H1013H) mutation, heterozygous in 2 patients c.2517G>A;(p.T839T) mutation, heterozygous in 1 patient, c.2031C>T; (p.G677G) mutation, heterozygous in 3 patients c.835G>A (p.A279T) mutation, heterozygous in 1 patient c.1392C>T; (p.F464F) mutation, heterozygous in 1 patient c.2995-3184G>A; (p.A1062T, p.A999T) mutation and heterozygous in 16 patients and homozygous in 3 patients c.915G>A; (p.A305A) mutations have been detected. Among the 7 different variants seen in the study, variants of unknown clinical significance were detected. For the other genes included in our study, 5 variants in the ATRX gene, 3 variants in the IDH1 gene, 1 variant in the IDH2 gene, and 6 variants in the MGMT gene were detected. A c.699-3delC deletion was observed in one patient in the intronic region of the IDH1 gene, and the c.532G > A (p.V178I) mutation seen in 3 patients was evaluated as possibly harmful. In addition, novel variant c.881A > G ; c.995A > G was detected in the ATRX gene. The heterozygous novel variant detected in the ATRX gene was confirmed to be heterozygous by Sanger sequencing.The variants of TERT, IDH1, IDH2, MGMT, and ATRX genes we found in our study were evaluated by comparing them with existing databases and literature. The variants we found were not previously associated with ovarian cancer and were evaluated as a new marker candidate for ovarian cancer susceptibility. If our results are confirmed by future studies with larger cohorts or functional studies, our findings will contribute significantly to elucidating the molecular mechanisms of ovarian cancer. Key Words: Over cancer, Tert, polymorphisms
The relationship between leptin, miRNA221 and the coronar yartery disease and the severity of the disease
Coronary artery disease (CAD) has probably the most critical and most widespread type of cardiovascular disease (CVD) threatening people's health, worldwidely. High leptin levels in obese individuals participate to low-graded systemic inflammation, which makes this patients more sensitive for CVDs. The soluble leptin receptor (sOB-R) is the primary protein for leptin binding, so it is able to pivotally modifying its bioavailability. The degree of leptin's decrease may be a gauge for remaining leptin sensitivity. The status of leptin resistance and action has a biomarker called the free leptin index (FLI) and it is one of a fraction of total leptin and the sOB-R concentrations. In cardiovascular biology, micro ribonucleic acids (miRNAs) regulate many diverse processes including the maintenance of cardiac function and development of the heart. Also miRNAs are found in relationship with pathological processes and begun to be used as biomarker in some diseases. Within the scope of the study, it was aimed to search the relationship between leptin, sOB-R, FLI and miRNA221 and the CAD and the severity of the CAD. The prospective case-control study consisted of 78 individuals who had an indication for coronary angiography except acute coronary syndrome. 40 patients whose coronary lesion needed invasive treatment and 38 individuals who had normal coronary artery as the control group. The peripheral blood samples were drawn from patients and control group after performing coronary angiography. Coronary angiograms also were evaluated by quantification of the lesions according to the SYNTAX score. sOB-R and leptin levels in serum samples were determined by an enzyme immunoassay method, a two-site sandwich Enzyme Linked Immunosorbent Assay (ELISA) to quantitate sOB-R and leptin in samples. miRNA-221 expression levels determined by realtime polymerase chain reaction (PCR). The analysis of Receiver operating characteristic (ROC) curve was performed to determine the diagnostic capability of miRNA-221. We evaluated a total of 40 patients that 23 were male (57,5%) and 17 were female (42,5%). Control group included 38 individuals and 17 were male (44,7%) and 21 were female (55,3%). The results indicate that sOB-R levels were statistically higher (p<0,001*) and FLI results were significantly lower (p<0,001*) in patients than the control group. In addition, leptin level differences were not found significant between groups. As a result of the subgroup analyzes performed, the relationship between CAD and sOB-R levels and also with FLI results were independent from obesity. Also we found a significant positive correlation between l sOB-R and SYNTAX score (p<0,001*) and significant negative correlation between FLI and SYNTAX score (p<0,001*). Beside these findings miRNA-221 levels was found significantly three-folds higher in the patient group than the controls (P= 0,024). Furthermore, there was a statistically significant correlation between miRNA-221 and sOB-R (p=0,029) but no correlation with leptin, FLI and SYNTAX score. In conclusion, the results showed that sOB-R level is statistically higher and FLI is statistically lower in CAD group than the normal coronary artery group. miRNA-221 levels statistically higher in CAD group than the normal coronary artery group. Also sOB-R levels and FLI are correlated with the severity of CAD. Further, if these results are confirmed in other studies, sOB-R levels, FLI and miRNA-221 may be useful to detect significant CAD before performing coronary angiography. Key words: miRNA221, Leptin, Soluble Leptin Receptor, Coronary Artery Disease
CCR2 C64I polimorfizmi ve CCR5 delta 32 delesyonu ile koroner arter hastalığı arasındaki ilişki
Inflammation plays an important role in the development and progress of atherosclerosis. Chemokines are small proteins secreted by certain cells to attract inflammatory cells such as macrophages, neutrophiles and lymphocytes to the inflammation site via their corresponding receptors. Ccr2 V64I polymorphism was shown to be involved in atherosclerosis in mice models. The human studies, however, found conflicting results. Ccr5 Delta 32 deletion results in a truncated protein that doesn't reach the surface and function as a receptor. This deletion was associated with coronary artery disease in animal and human studies. In this study we aimed to investigate the relationship between Ccr2 V64I polymorphism, Ccr5 Delta 32 deletion and significant coronary artery disease. Blood samples were collected before coronary angiography. Ccr2 V64I polymorphism and Ccr5 Delta 32 deletion was studied by PCR and then gel electrophoresis. Significance of coronary artery disease was evaluated by SYNTAX score. The patients were grouped into patient group ( with significant coronary artery disease) and control group (without significant coronary artery disease). Median age was 61 and majority of subjects were male (54.5%). Patient group had significantly more hypertension, diabetes, and hyperlipidemia. Prevalence of Ccr2 V64I allele was 30.7% in overall population and did not differ between patient and control groups. Prevalence of Ccr5 Delta 32 mutation was low (5.9%) and no statistical comparison could be made between groups. Subjects with Ccr2 V64I polymorphism had significantly higher diabetes whereas subjects with Ccr5 Delta deletion had significantly higher body mass index. Linear regression analysis revealed male gender, hypertension, obesity and low HDL as independent predictors of significant coronary artery disease. Our study adds valuable information about the role of chemokine system in atherosclerosis. Inflammatory pathways should be thoroughly investigated to unravel potential therapeutic targets and preventive measures.
Investigation of the use of miRNA223 as a biomarker in glioma tumors
The purpose of this study is to determine of the use of miRNA223 as a biomarker in glioma tumors. The expression of several microRNAs in glioma tumors has been studied. miRNA223 has been studied in several forms of cancer. This is the first study in literature to investigate the expression level of miRNA223 in patients having glioma at the Turkish population. This study demonstrates the role of possible biomarkers in the expression analysis of miRNA223 in glioma tumors. The blood samples used in this thesis study are previously taken samples and present at the Molecular Medicine Laboratory of Yeditepe University. Yeditepe University Non-Interventional Clinical Research Ethics Committee approval is obtained prior to the study. Blood samples are obtained from the laboratory freezer which were priorly obtained from 35 patients who have referred to Yeditepe University Hospital having glial tumors. Blood samples from 30 healthy subjects are used as a control group. Depending on the location of the tumor, 3 different serum chambers were constructed from patient sera. A serum pool was created from the control structures. Qiagen's miRNeasy Serum/Plasma Kit (Cat. No. / ID: 217184) is used to practice miRNA isolation. Subsequently the cDNA is converted by conventional PCR, using the miRCURY LNA RNA miRCURY LNA RT Kit (Cat. No./ID: 339340 - Qiagen). A fluorometer is used to measure cDNA levels. Dilutions of the samples were made. To detect miRNA expression levels, expression analysis was performed by PCR method in Rotor Gene (Rotor-Gene Q –Qiagen) using miRCURY LNA SYBR Green PCR Kit (Cat. No. / ID: 339346). Real-Time Polymerase Chain Reaction is used to detect miRNA expression levels (RT-PCR). SPSS ver. 23.0 is used for statistical analysis (SPSS Inc, Chicago, IL, USA). ROC curve analysis has been done. The p value is set to 0.05 for statistically significant results.
Atopik dermatitli çocuklarda KIF3A gen polimorfizminin etkisinin belirlenmesi
Atopic dermatitis (AD) is the most common chronic, pruritic, recurrent inflammatory skin disease in childhood. Disruption of the skin barrier and exaggeration of the immune response (especially the Th2 response) seem to be associated with the development, severity and persistence of atopic diseases. Skin barrier/epidermal regulation genes and genes involved in immune response/host defense play key roles. However, the mechanism of these relationships is not clear yet. In recent years, studies indicating that KIF3A may have an important role in skin barrier homeostasis and inflammation have been increasing. The literature has begun to reveal the relationship between the KIF3A gene (rs2897442) polymorphism and AD. To date, the relationship between atopic dermatitis and genetic mutation has not been demonstrated in Turkish population. It is aimed to investigate the KIF3A mutation and the inflammatory changes that occur in Turkish children with atopic dermatitis and their relationship with each other. The KIF3A gene (rs2897442) polymorphism was performed in 48 with atopic dermatitis and 46 healthy children aged 2 months to 16 years. Clinical data including age, gender, atopy status, SCORAD, presence of other concomitant allergic diseases, family history, and eosinophil count, percentage, total Ig E, skin prick test results were recorded. DNA isolation was performed using the DNA Isolation Robot. Real-Time PCR (RT-PCR) was then performed using the KIF3A detection kit. Allelic discrimination was then obtained from both the patient and control groups. Then, statistical analyzes were made using Fisher's Exact Tests and Chi-square tests in SPSS 26.0 program, and also student's t-test, Mann-Whitney U-test and Kruskal-Wallis test were used for numerical values. P values less than or equal to 0.05 are considered statistically significant. The KIF3A region of 48 patients with atopic dermatitis ( M: 25, F: 23 with a mean age of 4.89 ± 3.67 years) and 46 healthy children in the control group (M: 27, F: 19 with a mean age of 3.76 ± 2.83) years was genotyped. Total IgE, absolute eosinophil count and eosinophil percentage are higher in individuals with atopic dermatitis than in healthy individuals. There was no significant difference between KIF3A genotype and atopic dermatitis and control groups (p=0.08). Carrying the CC genotype increased the risk of atopic dermatitis disease 4 fold compared to the control group (p=0.043, χ2 =4.610, OR=4.053, 95%). CI=1.051-15.631). Carrying the T allele protects against atopic dermatitis (p=0.040, OR=0.235, 95%. CI=0.061-0.905). TT genotype had lower absolute eosinophil counts (p=0.023), and those with C allele had higher values (p=0.023). No statistically significant relationship was found between the KIF3A gene polymorphism and the severity of atopic dermatitis. In conclusion, It is the first pilot study showing the risk of KIF3A gene polymorphism in the development of atopic dermatitis for the Turkish population. Carrying a homozygous C (CCgenotype) increases the risk of developing AD, and carrying the T allele decreases the risk of AD. TT genotype had lower absolute eosinophil counts, and those with C allele had higher values In this regard, it is recommended to perform gene polymorphism in a larger study group and to conduct more analysis on the genotype-phenotype relationship and its effect on treatment.
Mutation analysis of IDH1 gene in prostate cancer patients by next generation sequencing method
The second most common type of cancer among men is prostate cancer. The aim of our study was to evaluate MGMT and ATRX genes, especially IDH1, with next-generation sequencing, to detect potential mutations and their relationship with risk classes of the disease. Analyses were performed using peripheral blood samples from 27 patients diagnosed with prostate cancer. IDH1, MGMT and ATRX genes were evaluated by next generation sequencing. In addition, analysis was performed to evaluate the effects of detected mutations in D'Amico intermediate-risk and high-risk groups. The mean age of the study group was 68 years (53-83); 88.89% of the patients were aged 60 years or older, and 11.11% were under 60 years of age. The prostate volume, PSA level, cT1c, Gleason score, and Tm % of the patient group's clinical data were significantly different between the intermediate-risk and high-risk patient groups (p=0.003, p=0.048, p=0.000, and p=0.001, respectively). The target genes were sequenced, and as a result, 11 mutations were found in total: 3 in IDH1, 6 in MGMT, and 2 in ATRX genes. The majority of the detected mutations in prostate cancer were identified for the first time. According to D'Amico risk groups, it was found that the c.159C>T (rs1803965) and c.250C>T (rs12917) MGMT gene mutations varied significantly from one another (p=0.017). The heterozygous mutant genotypes of the patient with the IDH1 c.548 A>G (rs34599179) missense mutation, the five patients with the MGMT gene c.159C>T synonymous mutation, and the five prostate cancer patients with the MGMT gene c.250C>T missense mutation were confirmed by Sanger sequencing. These identified mutations should undoubtedly be included in the classification of prostate cancer. Whether or not they can be assessed in clinical applications is debatable. However, integrating molecular parameters with standard evaluation criteria will contribute to the application of personalized treatment methods by evaluating the clinical data of prostate cancer patients with a higher accuracy rate.
The effect of idh2 gene variation and tert gene variation in prostate cancer
Worldwide, prostate cancer is the leading cause of death from cancer in males. It is still a chemotherapy-resistant disease with a highly metastatic potential, despite its pathological classification and the availability of numerous treatments because its molecular foundation has not yet been completely understood. The primary objective of this research was to use next-generation sequencing technology to identify variations in the IDH2 and TERT target genes in prostate cancer. For the study, blood samples from 27 patients at Yeditepe University Hospital who had been identified with prostate cancer were used. The mean age of the study population was 68 years of age; 88.89% of them were 60 years and older, and 11.11% were individuals under 60 years of age. The mean prostate volume and PSA level for the patient with prostate cancer were 43.59 cc and 31.28 ng/mL, respectively, according to clinical data. It was determined that there were fourteen patients with a Gleason score of less than seven and thirteen patients with a Gleason score of seven or higher. The IDH2 and TERT genes were examined using next-generation sequencing and five mutations were identified. One of these mutations was discovered in the IDH2 gene and four others within the TERT gene. One variant detected in IDH2 was seen in 2 heterozygous patients. Four variants located in the exonic region of the TERT gene have been identified. Of these, c.3039C>T mutation was heterozygous in 6 patients, c.1392 C>T heterozygous in 1 patient, c.915G>A in 18 patients, 4 of which were homozygous and 14 heterozygous, and c.261G> T was heterozygous in one prostate cancer patient. Among these five variants, TERT c.261G>T was identified as potentially harmful. It was confirmed by Sanger sequencing that the patient carrying the potentially harmful variant was heterozygous mutant. The five variations we found in our study hold a potential to serve as new prostate cancer biomarkers, and great majority of the mutations have not been associated with this cancer type. It will help to rearrange pathological categorization by explaining the molecularly inexplicable characteristics of prostate cancer in accordance with further validation of our findings with studies to be conducted with a larger sample size. Key Words: Next Generation Sequencing, Prostate Cancer, IDH2, TERT
Lu-177 prostat spesifik membran antijeni (PSMA) ligantlari ile tedavi edilen prostat kanserli hastalarda DNA tamir genlerindeki varyasyonlarin tedavi cevabinin üzerine etkisinin incelenmesi
Lu-177 PSMA has the potential to be a very effective treatment for advanced prostate cancer. The main objectives of this study were to determine whether there is a connection between ERCC2 gene variants, Lu-177 PSMA treatment and the expression levels of miRNA-182 and miRNA-187. This study was conducted on 57 patients. 50 patients were grouped according to whether they received treatment or not, and 7 patients were grouped to examine the changes before and after Lu-177 PSMA treatment. It was found that the expression levels of miRNA-182 (p <0.001) and miRNA-187 were significantly higher in patients who received treatment, including Lu-177 PSMA, than in patients who did not receive any treatment (p = 0.000). The doses that resulted in PSA response as a result of treatment were determined to be 150 mCi and 200 mCi. A significant relationship was found between the post-treatment expression level of miRNA-182 and the change in posttreatment DNA concentration (p = 0.028). The relationship between Lu-177 PSMA treatment and ERCC2 gene variants was investigated in the study groups. It was found that the rs13181 variant was present in both heterozygote mutant and wild type genotypes in patients who received treatment and did not receive treatment. For the rs1799793 variant, it was determined that patients who received treatment had wild-type and homozygous mutant genotypes, while patients who did not receive treatment had homozygous mutant and heterozygous mutant genotypes. When looking at the pre-treatment and post-treatment, it was determined that 50% of the patients with PSA response after treatment had heterozygous mutant for ERCC2 rs13181 variant; 66.66% of the patients who did not have PSA response had wild-type genotype. For ERCC2 rs1799793, it was determined that 100% of those with PSA response were heterozygous mutant, while 50% of those without PSA response had wild-type and 50% had homozygous mutant genotype. In addition, it was found that patients with high post-treatment miRNA-182 levels were more likely to have heterozygous mutant genotype for ERCC2 rs13181 (p = 0.028). In conclusion, it was found that miRNA expressions showed a bimodal feature and that they could vary depending on the dose of treatment, the stage and course of the disease. Monitoring of miRNA-182 expression and analysis of ERCC2 rs13181 and rs1799793 variants can help in the correct planning of personalized Lu-177 PSMA treatment strategies. Key Words: Lu-77 PSMA, Prostate Cancer, miRNA-182, miRNA-187, ERCC2
Genetic variation in the EGFR gene and the relation with glioma in Turkish population
While glioma constitutes approximately 30% of brain and central nervous system carcinomas, it covers 80% of all brain carcinomas. [1]. The gene that encodes 170 KD transmembrane receptor tyrosine kinase, located on chromosome 7p12-13 and enounced on the facial of epithelial cells, is the EGFR gene. In most prior works, single nucleotide polymorphisms (SNPs) within the EGFR gene are evaluated to correlate cancer risks like carcinoma, carcinoma, prostatic adenocarcinoma, and esophageal cancer. How EGFR contributes to glioma susceptibility variants in the gene and in order to examine that, in a case-control study from Turkey (35 cases, 36 controls) genotyping both groups determined by real-time PCR and was carried out using statistical analysis SPSS data. According to our results, CC genotype (homozygous wild type) 19 (52.8%), CT genotype (heterozygous type) 16 (44.4%), TT genotype (homozygous variant type) 1 (2.8%) were found in the control group. Genotype distribution in the patient group was 8 (23.5%), 22 (64.7%) and 4 (11.8%), respectively. Significant relationship was found between the patient and control groups compared to genotypes (p = 0.028). This study can provide a new approach to the clinical treatment of glioma patients.
Role of microRNA in chronic rhinosinusitis
The pathogenesis of chronic rhinosinusitis (CRS) shows strong connections with microRNA-155 (miR-155) through its inflammatory pathways. Research has concentrated on determining miR-155 expression levels in patients who receive montelukast treatment as a leukotriene receptor antagonist for asthma and allergic conditions. The immune system depends on miR-155 for its regulation through its effects on T cells and macrophages. The elevated levels of miR-155 promote Th2-mediated inflammation through increased eosinophilic activity and elevated IL-4 and IL-13 pro-inflammatory cytokines. Research on patients with asthma and allergies who take montelukast shows that the medication may adjust miR-155 expression levels, thus enabling the immune system to achieve better balance through microRNA downregulation. This study examined 30 patients diagnosed with CRS who did not respond to medical treatment and therefore underwent surgery. Blood samples were taken from the patients before the operation to measure IL-1β and miR-155 levels. They were asked to answer the Sino-Nasal Outcome Test (SNOT-22) to evaluate sinonasal symptoms. After the operation, these patients were given a standard treatment and nasal irrigation with montelukast and saline for one month. One month later, IL-1β and miR-155 levels were measured in serum samples taken from the patients. The SNOT-22 questionnaire was repeated. When the SNOT-22, miRNA155 and IL-1β values obtained after the operation were compared with the values before the operation, it was seen that they decreased and this difference was found to be statistically significant (p=0.0001, p=0.0030, p=0.0001; respectively). The disease severity and inflammatory status of patients could be monitored through elevated serum miR-155 levels. The significance of miR-155 in chronic rhinosinusitis makes it both a therapeutic target and a biomarker for disease management.
Kronik yaralarda miRNA'larin rolü
Chronic wounds, especially diabetic foot wounds, cause significant loss of workforce and impose a significant financial strain on the medical system in all countries. Diabetic foot ulcers are a primary contributor to leg amputations globally. Small, non-coding RNA molecules known as miRNAs control post-transcriptional levels of gene expression and are becoming more and more significant in the control of wound healing processes. This study examined the function of the miRNA-29 family in the pathophysiology of diabetic foot wounds, which are classified as chronic wounds. The study included a total of 16 individuals, comprising eight with diabetic foot wounds and eight control individuals with acute surgical wounds. RNA was isolated from tissue biopsies taken from the patients, and then the levels of miRNA-29a-5p, miRNA-29b-1-5p, and miRNA-29c-5p were evaluated using the real-time PCR method. The data were statistically analyzed using non-parametric tests and ROC curve analysis, and expression levels were normalized with the RNU6 reference gene. The results indicated that the expression of miR-29a in diabetic foot wounds was substantially reduced in comparison to the control group (p=0.0087) and that the AUC value in the ROC analysis was 0.89, indicating a highly discriminatory potential. In contrast, it was determined that miR-29b and miR-29c did not show significant differences in tissue. It is widely recognized that miR-29a is involved in numerous critical biological processes, including immune regulation, angiogenesis, and fibrosis. In conclusion, this thesis emphasizes the fundamental role of the miRNA-29 family, particularly miR-29a, in the pathogenesis of chronic wounds, specifically diabetic foot wounds. The results indicate that miR-29a has the potential to serve as a tissue-based biomarker and that it may be a targetable therapeutic agent in the future.
Determination of serum miRNA-124 expression levels before and after sedation in patients receiving intravenous ketamine
This thesis aimed to show the effects of intravenous ketamine on miRNA-124 and SOCS3 protein expression in subjects undergoing surgical procedures under sedoanalgesia. Ketamine modulates inflammation by reducing inflammatory cytokines, including in the central nervous system. By suppressing the effects of pro-inflammatory cytokines, SOCS3 helps prevent the excessive response to inflammation, therefore maintaining immune homeostasis. Ketamine's ability to reduce inflammation may be partly linked to SOCS3 expression. Blood samples were collected from 20 patients before and after ketamine administration, therefore 40 serum samples analysed. Although no difference was found between the SOCS3 values before and after ketamine administration, the average SOCS3 increased by 2.18 times after ketamine application. On the other hand, a significant difference was found between the miRNA-124 (2^(-ΔΔCT)) values before and after the ketamine (p=0.0172), with the average miRNA-124 increasing by 9.2 times after the ketamine treatment. Sensitivity and specificity calculations for various cut-off values of miRNA-124 expression(2^(-ΔΔCT)) for predicting before and after ketamine treatment status, and the optimum cutoff value for miRNA-124 are presented in Table 4. An empirical ROC curve corresponding to these findings yielding an AUC of 0.71 (95% CI: 0.541-0.879; p<0.001) was generated (figure 16). ROC curve for miRNA-124 indicates that the ROC data possesses an excellent predictive ability in distinguishing before and after ketamine treatment. A ROC curve corresponding to the SOCS3 values yielding an AUC of 0.604 (95%CI of 0.393-0.165) was generated, as well (figure 17). The AUC value of 0.604 for SOCS3 protein indicates a mild predictive capacity to distinguish patients from before and after ketamine treatment. Our study has shown that subanesthetic doses of ketamine increased SOCS3 protein levels by 2.18-fold compared to baseline. Furthermore, ketamine increased both blood miRNA¬-124 expression (2^(-ΔΔCT)) and SOCS3 protein levels significantly from baseline values; their sensitivity and specificity to predict ketamine's effect was prominent, with a ROC value of 0.71 and 0.60.
Yapay zeka kullanarak primeri bilinmeyen kanserlerde primer sistemin tahmini
Sümerkent, K. (2025). Using Artificial Intelligence to Predict the Primary System for Cancers of the Unknown Primary. Yeditepe University, Institute of Health Sciences, Department of Molecular Medicine. Doctorate Thesis. İstanbul. This dissertation presents an AI computational methodology using Whole Slide Images (WSIs) to determine the primary site of Cancers of Unknown Primary (CUP). Addressing CUP's diagnostic challenges where origin is elusive, it builds upon deep learning advancements in medical imaging. The project utilized over 1000 histopathological images from TCGA and ICGC databases representing diverse malignancies. Pre-processing included colour normalisation and patch extraction. A custom convolutional neural network (CNN), optimised via hyperparameter tuning, achieved >90% accuracy, outperforming baseline and transfer learning models in analysing morphological patterns. Validation on 300 cases from Yeditepe University Hospitals confirmed high sensitivity and specificity, particularly for breast and prostate cancers. Error analysis linked diagnostic challenges primarily to ambiguous tissue features or suboptimal image quality. While effective, integrating supplementary molecular and clinical data could further enhance diagnostic precision for CUP management. Implementing this AI-driven analysis in clinical workflows shows promise for improving patient care by facilitating more accurate identification of cancer origins.
Determination of serum microRNA 339 expression levels in patients receiving propofol infusion
This study investigates the potential antioxidant effects of propofol, a commonly used anesthetic, in patients undergoing in vitro fertilization (IVF). The research focuses on measuring the levels of specific redox proteins, glutathione reductase and glutathione peroxidase, as well as the expression of a microRNA molecule called miRNA-339. These elements play crucial roles in the cellular response to oxidative stress, a condition characterized by an imbalance between free radicals and antioxidants. The study design employed two groups of 21 IVF patients each. One group received propofol infusion during the procedure, while the other served as a control group without propofol administration. This approach allowed researchers to compare the effects of propofol on the aforementioned biomarkers between the two groups. The levels of glutathione reductase (p=0.003) and glutathione peroxidase (p=0.006), enzymes responsible for neutralizing harmful free radicals, were significantly elevated in the group that received propofol infusion compared to the control group. This observation suggests that propofol may possess antioxidant properties, potentially aiding in mitigating oxidative stress during IVF procedures. However, the investigation into miRNA-339 expression presented a more complex picture. This miRNA molecule is known to regulate various cellular processes, and its involvement in oxidative stress response has also been implicated. The study noted a statistically significant decrease in miRNA-339 levels specifically within the propofol group after infusion (p=0.027). This finding suggests that propofol may have an effect on miRNA-339 expression. Interestingly, initial correlations between miRNA-339 and the antioxidant enzymes existed, but these correlations became non-significant after propofol use. When comparison was made between before and after, the area under ROC curve (AUC) was 0.6723 (95% confidence interval; CI = 0.5073–0.8373, P < 0.0001). Overall, this study suggests propofol may offer antioxidant benefits during IVF. However, the role of propofol on miRNA-339 remains unclear and requires further exploration with larger studies. These studies would help confirm propofol's influence on miRNA-339 and understand its implications for IVF procedures. By gaining a deeper understanding of these mechanisms, researchers can work towards optimizing patient care and potentially mitigating the negative effects of oxidative stress associated with IVF. Key Words: Propofol, miRNA-339, Redox Proteins, IVF
Investigation of serum MicroRNAs inpre-diabetes and newly diagnosedType 2 diabetes
Diabetes mellitus (DM) is a metabolic disease that threatens humanity and is spreading like an epidemic. The aim of our study was to identify and determine the biomarker candidacy of miRNA-30d, miRNA-124, and miRNA-29a and their relationship with the risk classes of the disease. A total of 90 people were included in the study, and the analyses were performed using serum samples from 60 diabetic patients and 30 healthy controls. The average age of the groups was 43, but women were more common in the control and prediabetes groups, while men were more common in the diabetes group (p = 0.030). Significant differences were observed between groups for glucose, HbA1c, insulin, HOMA-IR, and triglycerides among the 17 biochemical parameters analyzed. The analyses of the target miRNAs were performed using real-time PCR, and as a result, it was determined that the expression of miRNA-30d and miRNA-124 increased in prediabetes patients (group 2), while the expression of miRNA-29a decreased. In T2DM patients (group 3), miRNA-30d levels increased, while miRNA-124 and miRNA-29a levels decreased. These findings reveal potential changes in miRNA expression associated with different stages of DM. However, only miRNA-30d (p = 0.002) in prediabetics and miRNA-29a (p = 0.004) in T2DM were found to be significant. As expected, the ROC analysis confirmed that only miRNA-30d and miRNA-29a could be biomarker candidates. In addition to these findings, miRNA-30d, miRNA-124, and miRNA-29a expression levels were significantly higher in prediabetes patients than in T2DM patients (p values: 0.006, 0.032, and 0.011, respectively). This difference suggests the presence of potential miRNA changes associated with the transition from prediabetes to T2DM. Correlation analysis also suggested that miRNA-29a regulates insulin resistance, while miRNA-30d and miRNA-124 regulate disease progression. In conclusion, it is clear that miRNA-30d and miRNA-29a should be considered molecular biomarkers in diagnosing and developing treatment strategies for prediabetes and T2DM. Their inclusion in standard assessment criteria will contribute to the more effective application of personalized treatment methods by evaluating the clinical data of prediabetes and T2DM patients with a higher accuracy rate. Key Words: Diabetes Mellitus, miRNA-29, miRNA-30, miRNA-124
Glioblastoma multiforme tümörlerinde miRNA-582-5P ve miRNA-363 ekspresyon seviyelerinin kaspaz-9 üzerine etkisi
The aim of this thesis study is to investigate the expression levels of microRNA-582-5p and miRNA-363 as they relate to serum levels of caspase-9, which holds key roles in the initiation of apoptosis in glioblastoma multiforme (GBM) patients. For this purpose, a total of 71 individuals, were selected and divided into two groups: those who were diagnosed with GBM disease (n=35),and those who were not previously diagnosed with this disease (n=36).The expression levels of miRNA-582-5p, miRNA-363 and caspase-9 gene Ex5+32 G>A (rs1052576) polymorphism of the groups were analyzed using real-time polymerase chain reaction. The miRNA expression analysis showed that miRNA-582-5p and miRNA-363 expressions were significantly downregulated in the patient group (p=0.014* and p=0.010*). When the means of serum miRNA-582-5p, miRNA-363 and serum caspase-9 levels were compared, a statistically significant relationship between miRNA expression levels and caspase-9 level could not be determined (p=0.144 and p=0.050). Also, caspase-9 gene Ex5+32 G>A (rs1052576) polymorphism was investigated in GBM patients, as well as undiagnosed individuals in the Turkish population. Having GG genotype reduced the risk of GBM by 3.78 times (p=0.015*). According to the results of ROC analysis, which is the last assessment point for biomarker nomination, it was observed that miRNA-582-5p and miRNA-363 are candidate biomarkers for GBM (miRNA-582-5p ΔCт p=0.006*; fold change p= 0.0001* and miRNA-363 ΔCт p=0.0016*; fold change; p=0.0001*). In conclusion, while a statistically significant relationship was found between miRNA-582-5p, miRNA-363 expression levels and working groups, no statistically significant relationship was found between miRNA-582-5p and miRNA-363 expression levels regarding an effect on serum caspase-9 levels.
Investigation of catechol-o-methyltransferase (COMT) gene VAL158MET polymorphism in ovarian cancer
Ovarian cancer is the seventh leading cause of death and is the eighth most common cancer among women. It has the highest mortality rate among all gynecological cancers. The prognosis of ovarian cancer is poor, especially when the disease is diagnosed at an advanced stage. The COMT enzyme synthesized from the Catechol-O-Methyltransferase (COMT) gene detoxifies the carcinogenic catechol estrogens. This enzyme catalyzes the methoxylation reaction to produce 2-methoxy estradiol. This metabolite induces apoptosis and suppresses carcinogenesis. In the COMT gene, the Val158Met polymorphism results in a decrease in the activity of this enzyme, resulting in the accumulation of carcinogenic catechol estrogens. This thesis study, it is aimed at examining the relationship of the disease with COMT Val158Met polymorphism which is thought to affect the risk of ovarian cancer. The two groups were seperated as a patient group with ovarian cancer (n = 47) and control group (n = 47). Genotyping of both groups was determined by Real-Time PCR, and the statistical analysis of the data was performed by SPSS program. According to our results, GG genotype (homozygote wild type) was found in 12 (25.5%), GA genotype (heterozygote type) in 22 (46.8%), AA genotype (homozygote variant type) in 13 (27.7%) in the control group statistically. In the patient group, genotype distributions were determined 17 (37.8%), 19 (42.2%) and 9 (20%) respectively. There was no significant relationship in comparison with genotypes between patient and control groups (p=0.413). This study could provide a novel approach for the clinical treatment of ovarian cancer. Key words: Polymorphism, Catechol-O-Methyltransferase, Catechol Estrogen, Ovarian Cancer
Ateroskleroz hastalığında apolipoprotein E (APOE) polimorfizmi ile mikrorna 221/222 arasındaki ilişkinin araştırılması
Bu çalışmada tüm dünyada önde gelen morbidite ve mortalite nedeni olan aterosklerozda ApoE gen varyasyonlarının etkilerinin araştırılması ve başta miRNA221/222 olmak üzere miRNAların hastalıkla olan ilişkisinin moleküler açıdan değerlendirilmesi amaçlanmıştır. 89 ateroskleroz tanısı almış hasta ve 93 sağlıklı kontrolden oluşan çalışma grubumuzun gerçek zamanlı pzr ile ApoE genotiplemesi, mikroRNA ifade düzeylerinin belirlenmiş ve lipid altgrup analizi yapılmıştır. Yapmış olduğumuz risk analizlerinde düşük HDL değerine sahip olmanın kardiyovasküler riskle ilişkili olduğu belirlenmiştir (p=0,011). ApoE genotip ve allel frekansları kontrol ve ateroskleroz hasta olguları ile karşılaştırıldığında E3/E4 genotipine sahip olguların hasta grubunda yüksek olduğu ve riskini artırdığı (p=0,029), E2/E3 genotipinin ise kontrol grubunda yüksek olduğu ve riski azalttığı gözlenmiştir (p=0,011). E2 alleli taşımanın ateroskleroz riskini 10 kat azalttığı gözlenmiştir (p=0,006). Lipid değerleri incelendiğinde E3/E3 genotipine sahip olguların sınır değerlerinin üstünde plazma kolesterol (p=0,012) ve LDL düzeylerine (p=0,039) sahip olduğu saptanılmıştır. Ayrıca [kolesterol]/[HDL] oranının da E3/E3 genotipinde yüksek olduğu belirlenmiştir (p=0,027). Allel düzeyindeki değerlendirmelerde E2 allelinin kolesterol değerleri üzerinde olumlu etki gösterdiği (p=0,036) E4 allelinin ise negatif etkilediği (p=0,038) gözlenmiştir. MiRNA ifade düzeyleri incelendiğinde miRNA221 ve miRNA221'nin hasta grubunda bu miRNAların daha az ifade edildiği belirlenmiştir. Ayrıca ROC analizi sonuçlarına göre miRNA221 ve miRNA221 ifade düzeylerinin eşik değeri olarak değerlendirilebileceği ve ateroskleroz tanısında biyobelirteç adayı olabileceği gösterilmiştir (p=0,004 ve p=0,003)). Ayrıca lipid düzeyleri ve miRNAlar üzerinde yapılan incelemelerimizde miRNA122a ifade düzeyinin azalmasının TG (p=0,046) ve VLDL (p=0,029) düzeyinde artışa neden olarak kardivasküler riski artırabileceği kanısına varılmıştır.
İnsan kallikrein 10 geni polimorfizminin over kanser gelişimi üzerine etkisinin araştırılması
Over kanseri dünya çapında ilerlemekte olan kadın hastalıklarının başında gelir. Over kanseri kadınlar arasında görülen kanser türleri arasında 5. sırada, genel olarak jinekolojik kanserler arasında ise 2. sırada yer alan ölüm oranı en yüksek olan jinekolojik kanser türüdür. TC. Sağlık Bakanlığı'nın 2009 yılında yayınladığı istatistiksel verilere göre over kanseri kadınlar arasında en sık görülen kanserler arasında 7. sırayı almaktadır. Kallikreinler yüksek substrat spesifitesine sahip serin proteaz ailesindendirler. Kallikrein (kininogen), arjinin ve lizin aminoasitleri arasından proteinleri kesen enzimlerdir. İnsan doku kallikrein-tipli peptidazlar fiziksel fonksiyonlar ile farklılaşmış 15 serin proteazdan oluşan bir ailedir. Kallikreinler; hücre büyümesinin düzenlenmesi ve farklılaşması, dokunun yeniden modellenmesi, anjiyogenez, deri dökülmesi, insan semen sıvılaşması, diş minesi oluşumu, nörodejenerasyon, inflamasyon, serviko-vajinal sıvı ve damarlanma gibi farklı fiziksel süreçlerde oldukça önemli rol oynar. Çalışmamıza over kanserli 50 kadın hasta ve 50 sağlıklı kontrol dahil edilmiş olup, gruplarda kallikrein 10 (KLK10) geni polimorfizmine bakılmıştır. Hasta ve kontrol grubu arasında genotip ve allel frekansları incelendiğinde istatistiksel açıdan anlamlılık gözlenmemiştir. Çalışma grupları arasında demografik veriler karşılaştırmalı olarak incelendiğinde açlık kan şekeri (AKŞ) ve kanser antijeni 125 (CA125) değerleri arasında anlamlılık gözlenmiştir. Saptanan bu değişikliklerin klinik tanıya yardımcı olması ve over kanserinde prognostik belirteç olarak kullanılabileceği düşünülmektedir. Anahtar Kelimeler: Over Kanseri, Kallikrein 10 (KLK10), Genotip, Allel, Polimorfizm.