Theses supervised by Prof. Dr. Turgay İsbir
32 theses · Yeditepe University
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
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.
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.
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.
Association of tumor necrosis factor (TNF) alpha and beta polymorphism in coronary artery disease
Coronary Artery Disease or Atherosclerosis is a dynamic and progressive inflammatory pathology and is the major cause of death and disability worldwide. The purpose of this study is to bring together the current information concerning the role of pro- and anti-inflammatory cytokines in the development, progression, and complications of atherosclerosis. The aim of the study was to assess whether these Tumor Necrosis Factor (TNF) Alpha and Beta polymorphisms were related to the risk of CAD or not Genotyping was performed with techniques based on Real Time-Polymerase Chain Reaction. In our study we compared patient group (n:50) which have coronary artery disease and control group (n:50) about risk factors such as hyperlipidemia, smoking, obesity and diabetes and their association between Tumor Necrosis Factor (TNF) Alpha and Beta polymorphisms and Coronary Artery Disease. In the comparison of the patient and control groups, male gender (p=0.0860) and cigarette consumption (p=0.110) and diabetes (p=0.026) were assumed to be the risk factors . Total cholesterol (p=0.102) and LDL (p=0.178) levels were high, HDL (p=0,040) levels were found to be lower in patients group. Tumor Necrosis Factor Alpha (TNFα) genotype was significantly higher in patients group compared to control group. The frequency of the Hemozygote Mutant Genotype was found to be significantly higher in patients compared to controls (p=0.004). The cardiovascular risk for Homozygote Mutant Genotype was 12.2-times increased in patients compared with the control group (OR=12.250, 95% CI=1.504-99.798; p=0.004). No association was found about those Tumor Necrosis Factor (TNF) Beta polymorphisms and CAD between the groups. Genetic predisposition of individuals can be determined with new approaches in the early life stages and thus disease formation can be prevented with new measures taken against Coronary Artery Disease .
Tip 2 diabette SCARB1 gen polimorfizminin araştırılması
Diabetus Mellitus (DM), kısaca Diabet, tüm dünya çapında sıklıkla görülmeye başlayan , ve her geçen yıl epidemiyolojisi artmakta olan kompleks bir hastalıktır. Bir grup metabolik hastalık olan diabet kan şekerinin ya da kan glukozunun çok yüksek olmasıyla karaterize olmuştur. Bundan dolayı kandaki şeker oranına bakılarak hastaya tanı konulabilir. Pankreastan üretilen insülin, yiyeceklerden alınan glukozun hücreler içinde enerji olarak kullanılmasına yardım eder. Bazı bozukluklar sonucu üretilemeyen ya da yeteri kadar üretilmeyen insülin yetmezliği sonucu diabet ortaya çıkar. Tip -1 ve Tip-2 Diyabet, kardiyovasküler ve bir çok hastalıkla ilişkili olup ölümcül olabilir. Diabet, dünya çapında günden güne artan bir yaygınlık göstermektedir. 1980'li yıllarda tüm dünyada yaklaşık olarak 108 milyon diabet hastası varken bu rakam 2016'da 422 milyona kadar çıkmıştır. 2040 yıllarında ise bu değerlerin 642 milyonlara ulaşması beklenmektedir. İnsülin, pankreasta bulunan Beta hücrelerinden (β –hücreleri) salınan glukozun vücut içerisinde taşınımını kontrol eden bir hormondur. Kanda glukozun (yani şekerin) yüksek olması durumunda insülin salınımı artar ve glukoz üretimini durdurur. Kanda şekerin düşük olduğu durumlarda ise glukagon göreve başlar. Glukagon ise yine pankreasta bulunan Alpha hücrelerinden (α –hücrelerinden ) salgılanan ve şeker üretimini sağlayan bir hormondur. Çöpçü Reseptör Sınıf B Tip 1 (SCARB1,SR-BI) çok ligandlı hücre yüzey reseptörü olup Çöpçü Reseptör Sınıf B gen ailesinin bir üyesidir. İnsanlarda SCARB1 geni 12. Kromozomda bulunur ve genin tam lokasyonu 12q24.31'dir. 13 ekzona sahip olan SCARB1 geni yaklaşık olarak 75 kb'lık bir alanı kapsar. Bu genin proteini olan SCARB1 (SR-BI) 509 amino asitten oluşur ve molekül ağırlığı yaklaşık olarak 8 kDA'dur . SCARB1 ağırlıklı olarak karaciğerde ve küçük oranlarda diğer hücre tiplerinde ifade edilir. Çalışmamızda hasta grubundaki vücut kitle indeksi ortalaması ve HDL seviyelerinde istatistiksel olarak anlamlı bir artış gözlemlenmiştir. LDL kolesterol seviyeleri ise kontrol grubunda daha yüksek miktarda saptanmıştır. Tip 2 Diabet ve SCARB1 G>A polimorfizmi incelendiğinde ise herhangi bir anlamlılık elde edilememiştir. Daha güvenilir sonuçlar elde etmek için çalışılan örnek sayısının artırılmasının faydalı olacağını düşünmekteyiz.
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
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 GSTP1 promotor region methylation in peripheral bloods of prostate cancer
In this project, it was investigated whether it is possible to analyse the promoter region methylation of GSTP1 gene in peripheral blood. For this purpose, DNA was isolated from peripheral blood of prostate cancer patients and the promoter region methylation of GSTP1 gene was examined by using the obtained isolate. After bisulfite modification of the isolated DNAs, Methylation Sensitive High-Resolution Melting (MS-HRM) was performed using primer pairs designed for methylated and unmethylated DNA sequences. As a result, when MS-HRM method applied to the peripheral blood DNA isolates, GSTP1 promoter methylation could not detected due to due to the presence of excessive amount of unmethylated leukocyte gDNA. The same DNA isolates were examined by ddPCR, which is known to be one of the most accurate and reliable tools due to its high sensitivity and specificity and 2 of 65 samples were detected as GSTP1 methylated. In this study, the third method used to detect GSTP1 promoter methylation was Nested MS-PCR method which consists of Nested PCR and MS-HRM. The purpose of this method is to increase the number of copies of methylated GSTP1 fragments released from the tumour cells which has very low concentration compared to unmethylated GSTP1 fragments of leukocyte gDNA and to increase the sensitivity and specificity of the MS-HRM to be performed to detect methylation. With this method, methylation was detected in the promoter region of GSTP1 gene in 9 of 65 samples.As a result of this study, although the sample could not be collected in accordance with ctDNA studies, it was shown that it is possible to detect promoter region methylation using appropriate methods.Bu yöntem ile toplamda 65 örnekten 9 tanesinde GSTP1 geni promotor bölgesinde metilasyon varlığı saptanmıştır. Bu çalışmanın sonucunda ctDNA çalışmalarına uygun olarak örnek toplanamamış olsa da uygun yöntemler kullanılarak promotor bölge metilasyonunun saptanabileceği gösterilmiştir.
Glial tümörlerde microrna-221 ekspresyon seviyelerinin analizi
MicroRNAs (miRNAs) consist of 18–25 nucleotides which a group of endogenous regulatory Ribonucleic Acid (RNA) partipicates as an epigentic mechanism that regulate gene expression by using RNA interference (RNAi) metabolism. miRNAs are found in relationship with pathological processes and begun to be used as biomarker in some diseases. Glial tumors are consisiting 80% of primary brain tumors. The aim of our study is to examine miRNA-221 as a biomarker candidate to define prognosis and/or classification for glial tumors. The hospital-based prospective case-control study consisted of 39 patients with glial tumor surgery and a 40 healthy individuals as control group. The peripheral blood samples were drawn from patients and control group after getting their "informed consent" were collected into EDTA-tubes. miRNA221 expression is evaluated from all blood samples. Of the 39 patients we evaluated, 23 were male (59%) and 16 were female (41%). As for the control group which consist of 40 healty individuals, 25 were male (62,5%) and 15 were female (37,5%). The levels of miRNA221 expression were determined by comparing the ΔCT values of miRNAs and the internal control. When the expression levels of miRNA221was compared according to the ΔCT factor, it was determined that the mean expression value of the patient group was 2,98 ± 2,11 while control group had 0,82 ± 2,27, there was statistically significant difference between the groups (p<0.0001). The expression levels of both miRNA221 was found to be significantly increased in the patient group than the control group. In conclusion, we found that miRNA221 expression could be a biomarker for glial tumors. But further researches must be made to make clear for its sensitivity and specifity to use for prognosis of glial tumors.
Investigation of the effects of MIRNA133, MIRNA26 AND MIRNA378 expression levels in left ventricular hypertrophy
Left ventricular hypertrophy (LVH) is characterized by the growth in muscular mass of left ventricule due to increased cardiomyocyte size. The microRNAs, a class of endogenously small non-coding RNAs which have approximately 22-nucleotide, play important roles in numerous biological processesare as mediation of cardiac hypertrophy. In present study we aimed to determine roles of miRNA-133, miRNA26, miRNA378 expression levels in left ventricular hypertrophy. In this study we compared left ventricle hypertrophy patient group (n= 70) and control group (n=16) were obtained from the Yeditepe University Hospital Cardiology Clinic. miRNA expression levels determined by realtime polymerase chain reaction (RT-PCR). The analysis of Receiver operating characteristic (ROC) curve was performed to determine the diagnostic capability of miRNAs. The miRNA expression analysis showed that the mean miRNA378 CT (p= 0.029) and ∆CT (p= 0.020) were significantly higher in patients than controls. By the ROC analysis, high expression of miRNA-378 expression maybe highly associated with the left ventricular hypertrophy. The threshold value in which miRNA-133 CT expression level can be evaluated as a diagnosis in patient group has not been demonstrated. According to teh CT values, miRNA was found to be AUC=0.484, 98.6° CI =0.329-0.641, P= 0.860.The mean CT values of miRNA-26 of the control group had highest expression levels (23.12 ± 3.10), it was followed by hypertrophic and eccentric group were 22.43 ± 2.36 and 22.06 ± 3.68 respectively (p=0.782). In conclusion, while there was no statistically significant relationship was found miRNA-133 and miRNA-26 expression levels there was statically significant relationship was found between miRNA-378 expresion levels in LVH group.
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.
HSP90 gen polimorfizmi ile over ve endometriyum kanseri arasındaki ilişkinin belirlenmesi
Over kanserleri kadınlarda görülen genital kanserlerinin %25'ini oluşturmaktadır. Gelişmiş ülkelerde görülen en sık ikinci jinekolojik kanser olarak belirtilmektedir. Ülkemizde ise Sağlık Bakanlığının 2002 yılındaki verilerine göre over kanseri jinekolojik kanserler içersinde en öldürücü olanı, kadın kanserleri içersinde de dördüncü öldürücü olan olarak tespit edilmiştir. Endometrium kanseri, gelişmiş ülkelerde, kadın genital sisteminin en sık malign tümörü olarak belirlenmiş ve olguların %75'i menopoz sonrası, genellikle evre 1'de semptomların varlığı ile başvuran kadınlardır. Etkin bir tarama testi olmamasına karşın, semptom vermesi nedeniyle % 75 olguda erken evrede teşhis edilebilmektedir. Isı şok proteinleri, ısı şoku, fiziksel stres ve çeşitli ajanlarla güçlü olarak uyarılan protein kümesi olarak tanımlanmaştır. Bu özelliklerin dışında da ısı şok proteinleri diğer temas ettiği proteinlerin yapısını düzenleyen ve modifiye eden moleküler şaperon olarak tarif edilmiştir. Isı şok protein gen transkripsiyonu, ısı şok faktör (HSF) denilen transkripsiyon faktörü ile düzenlenir, söz konusu faktör, stress durumlarında transkripsiyon aktivasyonunu başlatıcı etki yapar. HSP90'nın; Hsp90α (indüklenebilir/ major form), Hsp90β yapıcı/minor form) olmak üzere iki ana sitoplazmik isoform şekli mevcuttur. Hsp90α stres koşullarında uyarılırken, Hsp90β yapıcı protein olarak aktiftir. Kanserde rol oynayan mutant genlerin prtoeinlerini hücre içersinde stabilize etiğinden dolayı HSP90'nın moleküler seviyesi veya moleküler kapasitesi modifiye edilebilir kemoterapik ilaçlar geliştirilmiştir. Bu çalışmayla HSP90'nın HSP90AA1, HSP90AB1 ve HSP90B1 genlerindeki polimorfizmlerinin belirlenmesi sonucu over ve endometriyum kanser oluşumunda olası etkilerinin araştırılması, özellikle tedaviye yönelik biyobelirteçlerin erken dönemde belirlenmesi amaçlanmıştır. Çalışmamızda 77 over kanseri, 13 endometriyum kanseri ve 44 sağlıklı kontrol örneğinden elde edilen DNA'lar da Hakiki zamanlı PZR ile HSP90AA1 (rs4947), HSP90AB1 (rs13296) ve HSP90B1 (rs2070908) genlerinde polimirfizmlere bakılmıştır. Çalışmanın sonuçlarına göre; HSp90AA1 ve HSP90B1 genleri açısından over ve endometriyum kanserleri arasında istatistiksel olarak anlamlılık bulunamamıştır. HSP90AB1 geni açısından over kanseri ve kontrol grupları kıyaslandığında istatistiksel olarak anlamlı farklılık bulunamazken, endometriyum kanserinde CC genotipi taşıma sıklığı kontrol grubuna göre daha yüksek bulunmuştur. Buda bize HSP90AB1 genotipinin endometriyum kanseri riskini artırabileceğini düşündürmektedir. Bu çalışmadan elde edilen sonuçlar literatürdeki HSP90AA1, HSP90AB1 ve HSP90B1 geni açısından over kanseri ve endometriyum kanserlerini inceleyen ilk çalışma niteliğindedir.
Solid tümörlü kanser hastalarında C-C motif kemokin ailesinden monosit kemotaktik protein-1 (MCP-1) ve kemokin reseptör-2 (ccr2) varyantlarının araştırılması
Tümörü oluşturan hücre gruplarına göre isimlendirilen solid tümörler, kanserlerin büyük bir kısmını oluşturmaktadır ve malign ile bening tümörler olarak ikiye ayrılmaktadır. Çalışmamızda ele aldığımız solid tümörler; akciğer kanseri, kolorektal kanser, meme kanseri, over kanseri ve tiroit kanseridir. Çalışmamızda toplamda 28 akciğer kanseri hastası (4 kadın, 24 erkek), 34 kolorektal kanser hastası (12 kadın, 22 erkek), 23 tiroit kanseri hastası (20 kadın, 3 erkek), 27 meme kanseri hastası (25 kadın, 2 erkek) ve 30 over kanseri hastası dahil edilmiştir. Çalışmamıza katılmayı kabul eden 66 sağlıklı gönüllünün 27si kadın ve geri kalan 39u erkektir. CCR2 V64I varyantının genotipinin belirlenmesi için, tek nükleotit değişimini içeren PZR amplikonları BsaB1 enzimi ile muamele edilmiştir. MCP-1 A2518G varyantının genotiplenmesi için bu tek nükleotit değişimini içeren PZR ürünleri PvuII enzimi ile muamele edilmiştir. Enzimler yabanıl tip PZR ürünlerini kesmezken değişimin olduğu PZR ürünlerini kesecek şekilde seçilmiştir. Elde edilen verilerin istatistiksel analizi IBM SPSS 20 paket programı ile yapılmıştır. Bu çalışmanın sonucunda kolorektal kanser ve akciğer kanseri ile CCR2 V64I varyantı arasında istatistiksel olarak ileri düzeyde anlamlı ilişki gözlenmiştir (p<0,0001). Ayrıca, MCP-1 A2518G varyantı AG ve AA genotipleri ve meme kanseri arasındaki ilişki istatistiksel anlamlı bulunmuştur (Sırasıyla AG genotipi için χ2=5,082; p<0,024, OR:2,843, %95CI: 1,129-7,160 ve AA için χ2=5,687; p<0,017, OR:0,319, %95CI: 0,122-0,833). Çalışmamız kolorektal kanserlerde, over kanserinde ve tiroit kanserinde CCR2 V64I ve MCP-1 A2518G ve ayrıca meme kanserinde MCP-1 A2518G tek nükleotit değişimlerinin incelendiği ilk çalışma olma niteliği taşımaktadır.
RRM1, RRM2, ERCCC2 gen polimorfizmleri ile ateroskleroz ve tip 2 diabet arasındaki ilişkinin belirlenmesi.
Ateroskleroz büyük, orta ve küçük arterlerde plak oluşumu şeklinde kendini gösteren mortalitesi yüksek bir hastalıktır. Miyokard Enfarktüsü, Anevrizma ve bu olgulara bağlı ölümlerin başlıca sebebi olan Ateroskleroz, yaş, cinsiyet, serum lipid düzeyi, beslenme bozukluğu, hipertansiyon, ailesel yatkınlık, sigara ve alkol tüketme gibi çevresel ve genetik faktörlere bağlı multifaktöriyel bir hastalıktır. Tip 2 Diabet erişkin dönemde insülin intoleransı yada yetersiz insülin sekresyonuna bağlı hiperglisemi şeklinde görülen metabolik bir hastalıktır. Tip 2 Diabet ilerleyen dönemde hiperglisemiye bağlı, kalp-damar hastalığı, nefropati, nöropati, retinopati ve geciken yara iyileşmesi olgularına sebep olmaktadır. Her iki olgunun toplumda görülme sıklıkları giderek artmakla beraber gelişimlerinde rol oynayan moleküler mekanizmalar tam olarak bilinmemektedir. Son dönemde yapılan çalışmalar doğrudan oksidatif stres yada oksidatif stres derivatiflerinin dolaylı olarak yol açtığı DNA hasarlarının Tip 2 Diabet ve Ateroskleroz gelişiminde rol oynayabileceğini göstermektedir. Bu bilgiler ışığında çalışmamızda, Tip 2 Diabet ve Ateroskleroza bağlı Koroner Arter Hastalarında, DNA Tamir mekanizmalarından Nukleotid Eksizyon Tamir yolağında bulunan XPD helikaz enzimini kodlayan ERCC2 geni ve DNA sentezinde kullanılmak üzere Ribonukleotidlerden Deoksiribonukleotid sentezinde görev alan Ribonukleotid Reduktaz enziminin alt birimlerini kodlayan RRM1 ve RRM2 gen varyasyonları incelenmiştir. Çalışma sonucunda Hasta ve Kontrol grupları arasında istatistiksel olarak anlamlı bir farklılık görülmemiştir. Anahtar Kelimeler: Ateroskleroz, Koroner Arter Hastalığı, Tip 2 Diabet, DNA Hasarı, DNA Tamiri, Nukleotid Ekzisyon Tamiri, RRM1, RRM2, ERCC2, Polimorfizm.
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.