Ugur Ozbek | Istanbul University (original) (raw)

Papers by Ugur Ozbek

Leukemia, 2003

Most anticancer strategies mediate apoptosis in tumor cells. Therefore, deregulation in apoptosis... more Most anticancer strategies mediate apoptosis in tumor cells. Therefore, deregulation in apoptosis signalling pathways may contribute to therapy resistance and apoptosis regulating molecules represent novel targets for future therapeutic approaches. Activation of apoptosis pathways include triggering of death ligand/receptor interaction such as the CD95 or TRAIL system, "activation" of mitochondrial apoptogenic function with subsequent release of apoptosis inducing molecules such as cytochrome c and Smac Diablo, activation of the cellular stress pathway and ultimately, activation of caspases as effectors of the cell death machinery. Although, in vitro, the contribution of apoptosis signalling to cell death e.g. by antileukemia agents has been described in many different experimental settings, most in vivo studies in leukemia have failed to directly correlate e.g. the deregulated expression of apoptosis inducing regulating molecules to treatment response or outcome. In search for molecular parameters of apoptosis sensitivity we identified downregulation of caspase-8 expression as a novel mechanism of drug resistance in a variety of human tumors. Treatment with demethylating agents such as 5-Aza-2-Deoxycidin reversed hypermethylation of the caspase-8 gene, resulting in reexpression of caspase-8 and sensitisation for TRAIL or drug-reduced apoptosis. Also, treatment with Interferon in neuroectodermal tumor cells lead to re-expression of caspase-8 through a Stat1/IRF-1 dependent pathway. Further strategies to increase apoptosis sensitivity in constitutively resistant tumor cells may include modulation of thresholds for caspase activation. We found that Smac gene transfer or cell permeable Smac peptides sensitized various tumor cell lines in vitro including leukemia cells and malignant glioma cells in vivo for apoptosis induced by TRAIL or cytotoxic drugs. Complete eradication of established glioma xenografts in nude mice was established by combination of locally delivered Smac peptides and TRAIL without acute or delayed neurotoxicity. In addition to the development of novel strategies to overcome intrinsic apoptosis resistance, we have analysed activation of apoptosis pathways during antileukemia treatment in vivo. Interestingly, in ALL and AML, significant activation of apoptosis pathways and apoptosis induction was predominantly found in CD34+ leukemic cells suggesting that induction of apoptosis is confined to the elimination of the putative leukomogenic stem cells. Further detailed analysis of caspase-3 activation in cytochrome c release in individual leukemic cells from patients undergoing chemotherapy in vivo, deficient cytochrome c release was identified as the most important parameter for treatment response in vivo. Taken together, molecular insights into the apoptosis regulation will direct our understanding of therapy response in conventional treatment strategies, may help to device molecule based rational treatment approaches and provides novel targets for future therapeutic intervention.

Bezmialem Science, 2019

Introduction Colorectal cancer (CRC) is the third most common cancer type and cause of death in t... more Introduction Colorectal cancer (CRC) is the third most common cancer type and cause of death in the world and it is estimated that more than 1.3 million new diagnosed individuals are present in the world and CRC may cause more than 700 000 deaths a year (1). The incidence varies all over the world. It was reported that India had the lowest incidence rate. On the other hand, highest incidence rates are present in developed countries (2,3). Data from immigrants show that there are also international differences. Incidence of CRC has changed very quickly in Italy, Japan, poor regions of China, and Polynesianmales in Hawaii. Furthermore, it was highly sensitive to environment, suggesting that colon cancer is, in part, highly susceptible to environmental changes (2,3). The incidence of migrants and their descendants quickly reached to the rates in countries (4,5). The internationally stated rate of 20 times more frequent observation can be explained by diet habits and environmental differences in large section (2). However, it has been known that CRC is common in some families (6-8). As a result, CRC is considered as a disease associated with genetic and environmental factors. Despite the rapid and major advances in human cancer biology, no significant increase has been observed in the overall life span and survival rates of these patients over the past three decades.

Frontiers in Public Health

Rare disease patients constitute a significant part of the healthcare system of all countries. Ho... more Rare disease patients constitute a significant part of the healthcare system of all countries. However, the information on the experiences during disease processes and daily life of rare disease patients is still limited. So far, there is a small number of studies conducted in Türkiye, and they mainly cover specific issues like education or anxiety. Here we present a comprehensive survey analysis conducted among the patients and their families within the scope of the Istanbul Solution Platform for Undiagnosed and Rare Diseases-ISTisNA project. A total of 498 individuals responded to the survey, and 58% of the participants answered all questions. The majority of the patients were in the age range of 1–10 years (44.7%), and 91% of all the patients had a precise diagnosis. The diagnosis rate in the first 6 months was 69%, and almost 10% of the patients remained undiagnosed. The mothers were the primary caregivers (72%). Nearly 30% of the caregivers had to quit their jobs and 25% of the...

Clinical and experimental rheumatology, 2009

BACKGROUND Behçet's disease (BD) is a multisystem inflammatory disorder characterized by recu... more BACKGROUND Behçet's disease (BD) is a multisystem inflammatory disorder characterized by recurrent oral ulcers, genital ulcers and ocular inflammation, as well as skin, joint, vascular, pulmonary, central nervous system (CNS) and gastrointestinal tract manifestations. The etiopathogenesis of BD has not yet been identified; but it has generally been accepted that several environmental factors may induce an inflammatory attack in genetically susceptible individuals. In this study, we aimed to identify antigens that could elicit high-titer IgG responses by the serological analysis of recombinant expression of cDNA libraries method (SEREX). METHODS We screened a human testis cDNA library with pooled sera obtained from 4 BD patients by SEREX. Antigens that were identified with the initial analysis were selected for seroreactivity analysis of a larger group of BD patients (n=78) and controls (n=66) by serological immunoscreening. RESULTS We observed seroreactivity against 6 antigens u...

Turkish Journal of Medical Sciences, 2003

In this study, quantification levels were investigated to define alterations in the expression of... more In this study, quantification levels were investigated to define alterations in the expression of the FLI1 gene on acute promyelocytic leukemia (APL), which is characterized by a reciprocal t(15,17) translocation of fusing the PML gene to the retinoic acid receptor alpha (RAR alpha) gene. The FLI1 gene plays an important role in several signal transduction pathways, and is involved in the normal regulation of myeloid hematopoiesis and leukomogenesis. We used the real-time quantitative RT-PCR (LightCycler) with SYBR Green I dye method for the labeling and analysis of the quantification of FLI1 gene RT-PCR products. Ribosomal protein S9 (RPS9) was used as an internal control for the normalization of the results. FLI1 gene levels were found up- regulated in two PMLRARA fusion gene positive APL patients compared to bone marrow samples from four healthy donors. To our knowledge, this study is the first attempt to quantify the FLI1 gene in APL patients by real-time RT-PCR. SYBR Green I dy...

Leukemia Research, 2015

The MN1 (Meningioma 1) gene is overexpressed in certain subtypes of acute myeloid leukemia (AML) ... more The MN1 (Meningioma 1) gene is overexpressed in certain subtypes of acute myeloid leukemia (AML) and high levels of MN1 expression in mouse bone marrow cells results in myeloid leukemia. We showed that compared with control bone marrow (BM) MN1 expression was increased (2-fold or more) in 29 out of 73 (40%) pediatric B-cell acute lymphoblastic leukemia (B-ALL) patient BM.

Aims and background. The SET gene is a target of chromosomal translocations in acute leukemia and... more Aims and background. The SET gene is a target of chromosomal translocations in acute leukemia and encodes a widely expressed multifunctional phosphoprotein. It has been shown that SET is upregulated in BCR-ABL1-positive cell lines, patient-derived chronic myeloid leukemia CD34-positive cells, and some solid tumors. Methods and study design. We determined the expression level of SET in 59 pediatric acute lymphoblastic leukemia patients who were BCR-ABL-negative using quantitative real-time reverse-transcriptase-polymerase chain reaction. Results. We showed that SET expression was significantly upregulated in 96.5% of Bacute lymphoblastic leukemia (28 of 29; 16.6 fold) and 93% of T-acute lymphoblastic leukemia (28 of 30; 47.6 fold) patients. This upregulation was not associated with any clinical features or overall and relapse-free survival. Conclusions. Our results showed that SET is significantly overexpressed in pediatric acute lymphoblastic leukemia samples, and an increased level of SET might contribute to leukemic process.

Pituitary, 2007

Aromatase (P450AROM) converts testosterone to estrogen. This conversion could be important in nor... more Aromatase (P450AROM) converts testosterone to estrogen. This conversion could be important in normal physiology and estradiol-induced tumorigenesis in human pituitary. The objective of this study was to examine the expression of P450AROM in normal human pituitary and determine the gender difference. We examined aromatase expression in 19 normal human pituitary glands [13 males, 6 females, median age: 30 years (interquartile ranges, IQR: 23-63)] obtained from autopsy. We demonstrated aromatase gene expression levels by quantitative RT-PCR and aromatase protein with immunohistochemical staining in normal male and female human pituitary. Although median relative expression level of aromatase mRNA of male individuals [median DCt = 42.6 (IQR: 7.6-93.9)] was higher than the female individuals [median DCt = 3.9 (IQR:0-44.8)], we could not determine a significant gender difference in aromatase mRNA levels (p = 0.2). The difference between the aromatase protein density by immunohistochemistry was not significant between genders (p = 0.78). The aromatase levels were also not correlated with the age of the study subjects (p = 0.42 r = À0.21). The results indicate that aromatase enzyme is present in human pituitary. The amount and the density of the enzyme show a large variance among different individuals. Although higher mRNA expression was observed in male pituitary compared to female pituitary, there was no statistically significant difference for gender or age.

Journal of Biotechnology, 2014

Turkish Journal of Hematology, 2014

Objective: The prominent functions of the local renin-angiotensin system (RAS) in primitive hemat... more Objective: The prominent functions of the local renin-angiotensin system (RAS) in primitive hematopoiesis further support the hypothesis that local autocrine bone marrow RAS could also be active in neoplastic hematopoiesis. The aim of this study is to examine critical RAS elements in normal CD34+ hematopoietic stem cells and multiple myeloma (MM)-related progenitor cells. Materials and Methods: The study group comprised the total bone marrow cells (CBM) of 10 hematologically normal people, the CD34+ stem cell samples (CD34+CBM) of 9 healthy donors for allogeneic peripheral stem cell transplantation, and the CD34+ stem cell samples (CD34+MM) of 9 MM patients undergoing autologous peripheral stem cell transplantation. We searched for the gene expression of the major RAS components in healthy hematopoietic cells and myeloma cells by quantitative real-time polymerase chain reaction analysis. Results: RENIN, angiotensinogen (ANGTS), and angiotensin converting enzyme-I (ACE I) mRNA expression levels of CBM were significantly higher than those in myeloma patients (p=0.03, p=0.002, and p=0.0008, respectively). Moreover, RENIN and ANGTS mRNA expression levels were significantly higher in CD34+ stem cell samples of healthy allogeneic donors compared to those in myeloma patients (p=0.001 and p=0.01). However, ACE I expression levels were similar in CD34+CBM and CD34+MM hematopoietic cells (p=0.89). Conclusion: Although found to be lower than in the CBM and CD34+CBM hematopoietic cells, the local RAS components were also expressed in CD34+MM hematopoietic cells. This point should be kept in mind while focusing on the immunobiology of MM and the processing of autologous cells during the formation of transplantation treatment protocols.

Journal of Medical Microbiology, 2003

Constantly expressed genes are used as internal controls in relative quantification studies. Suit... more Constantly expressed genes are used as internal controls in relative quantification studies. Suitable internal controls for such studies have not yet been defined for Pseudomonas aeruginosa. In this study, the genes ampC, fabD, proC, pbp-2, rpoD and rpoS of P. aeruginosa were compared in terms of expression stability by real-time quantitative RT-PCR. A total of 23 strains with diverse resistance phenotypes were studied. Stability of expression among the housekeeping genes was assessed on the basis of correlation coefficients, with the best-correlated pair accepted as being the most stable one. Eventually, proC and rpoD formed the most stable pair (r ¼ 0•958; P , 0•001). Next, in four ciprofloxacin-selected nfxC-like mutants, levels of oprD, oprM and oprN mRNA were compared with those of their wild-type counterparts. The comparison was made after correcting the raw values by the geometric mean of the internal control genes proC and rpoD. The level of oprN mRNA was significantly up-regulated, while the oprD gene was down-regulated (although this difference was statistically insignificant), in the mutants. This expression pattern was consistent with that of the expected expression profile of nfxC-type mutants; this experiment therefore lends further support to the use of proC and rpoD genes simultaneously as internal controls for such studies.

Medical oncology (Northwood, London, England), 2008

Small cell lung cancer (SCLC) has a rapid growth rate and is characterized by early metastases. T... more Small cell lung cancer (SCLC) has a rapid growth rate and is characterized by early metastases. Tumor growth is dependent on angiogenesis. Vascular endothelial growth factor (VEGF) is an important regulator of angiogenesis. Whether surveillance of pre- and post-treatment serum VEGF and especially its receptors VEGF-1 and VEGF-2 levels in SCLC patients have impact on clinical outcome is unknown.

Genetic Testing and Molecular Biomarkers, 2012

Polymorphisms of the x-ray repair cross-complementing group 1 (XRCC1) gene have been reported to ... more Polymorphisms of the x-ray repair cross-complementing group 1 (XRCC1) gene have been reported to be associated with various forms of cancer. We evaluated the possible effects of the Arg194Trp and the Arg399Gln polymorphisms on the risk for chronic lymphocytic leukemia (CLL) in 73 patients and 50 controls. We also analyzed their relation to frequency of sister chromatid exchange (SCE). With respect to codon 194, the allelic frequency of the Arg194Trp polymorphism did not significantly differ between the 2 groups. The proportion of individuals carrying the Arg194Trp polymorphism was not different in the 2 groups. With respect to codon 399, the proportion of the individuals carrying the Arg399Gln allele (90% vs 62%; p = 0.000; odds ratio [OR], 5.779; 95% confidence interval [CI], 2.2-15.183) and the allelic frequency of the Arg399Gln polymorphism (56% vs 36%; p = 0.002; OR, 2.278; 95% CI, 1.350-3.843) was significantly higher in the patient group. The frequency of the Arg/Gln genotype was significantly higher in the patient group (68.50% vs 52%; p = 0.049; OR, 2.007; 95% CI, 0.955-4.217). The mean SCE frequency in the patient group was significantly higher (9.2-4 vs 7.5-2; p = 0.02). When different compound genotypes were compared, the coexistence of Arg/Arg genotype in codon 194 with Arg/Arg genotype in codon 399 was significantly more frequent in the control group (30% vs 9%; p = 0.004; OR, 0.247; 95% CI, 0.092-0.664). Within the patient group, SCE frequency did not differ between patients with various genotypes. The Arg399Gln polymorphism may be etiologically associated with CLL; however, it does not seem to increase SCE frequency.

British Journal of Haematology, 2012

TRIB2 is a potent oncogene, elevated in a subset of human acute myeloid leukaemias (AML) with a m... more TRIB2 is a potent oncogene, elevated in a subset of human acute myeloid leukaemias (AML) with a mixed myeloid/lymphoid phenotype and NOTCH1 mutations. Although rare in AML, activating NOTCH1 mutations occur in 50% of all T-acute lymphoblastic leukaemias (T-ALL). TRIB2 is a NOTCH1 target gene that functions in the degradation of key proteins and modulation of MAPK signaling pathways, implicated in haematopoietic cell survival and proliferation. We show that TRIB2 expression level is highest in the lymphoid compartment of normal haematopoietic cells, specifically in T cells. Analysis of TRIB2 expression across 16 different subtypes of human leukaemia demonstrated that TRIB2 expression was higher in ALL phenotypes versus all other phenotypes including AML, CLL, MDS and CML. A T cell profile was distinguished by high TRIB2 expression in normal and malignant haematopoiesis. High TRIB2 expression was seen in TALL with normal karyotype and correlated with NOTCH signalling pathways. In a pediatric patient TALL cohort high TRIB2 expression correlated with NOTCH1/FBXW7 mutations, strongly linking NOTCH1 activation and high TRIB2 expression in paediatric TALL. The relationship between TRIB2 and T cell signaling pathways uniquely identifies leukaemia subtypes and will be useful in the advancement of our understanding of T cell and ALL biology.

Arthritis & Rheumatism, 2006

Familial Mediterranean fever (FMF) is associated with more than 70 missense mutations in the MEFV... more Familial Mediterranean fever (FMF) is associated with more than 70 missense mutations in the MEFV gene. The purpose of this study was to investigate the relative expression of messenger RNA (mRNA) for the MEFV gene in peripheral blood leukocytes (PBLs) obtained from patients with FMF during attacks of acute abdominal inflammation as well as during asymptomatic periods. We studied 16 patients with FMF during an attack of acute peritonitis and 17 otherwise healthy individuals who were undergoing surgery because of acute appendicitis. Blood samples were collected from both groups of patients during both acute inflammatory and asymptomatic periods. Relative levels of MEFV mRNA in PBLs were detected with real-time reverse transcriptase-polymerase chain reaction using LightCycler, with 2 sets of primers for the MEFV gene (exons 7-10 and exons 2-3) and with primers for CIAS1 and PSTPIP1 genes. Expression levels were compared with beta(2)-microglobulin as an internal control. MEFV expression was reduced in FMF patients during asymptomatic periods as compared with the non-FMF controls (P < 0.001). We observed a further decrease in MEFV expression in FMF patients during periods of inflammation (P = 0.01). Reduced levels of MEFV mRNA were also noted during the preoperative period as compared with asymptomatic periods in control patients with acute appendicitis (P = 0.01). CIAS1 expression in PBLs from patients with FMF was also found to be lower than that in the control patients. However, CIAS1 expression did not change with acute inflammation. This study confirmed that reduced expression of the MEFV gene is associated with inflammation and that it may be one of the pathogenic mechanisms of the attacks of inflammation in FMF patients, along with disease-associated variations in pyrin.

Neurological Sciences, 2017

SYNE1 related autosomal recessive cerebellar ataxia type 1 (ARCA1) is a late-onset cerebellar ata... more SYNE1 related autosomal recessive cerebellar ataxia type 1 (ARCA1) is a late-onset cerebellar ataxia with slow progression originally demonstrated in French-Canadian populations of Quebec, Canada. Nevertheless, recent studies on SYNE1 ataxia have conveyed the condition from a geographically limited pure cerebellar recessive ataxia to a complex multisystem phenotype that is relatively common on the global scale. To determine the underlying genetic cause of the ataxia phenotype in a consanguineous family from Turkey presenting with very slow progressive cerebellar symptoms including dysarthria, dysmetria, and gait ataxia, we performed SNP-based linkage analysis in the family along with whole exome sequencing (WES) in two affected siblings. We identified a homozygous variant in SYNE1 (NM_033071.3: c.13086delC; p.His4362GlnfsX2) in all four affected siblings. This variant presented herein has originally been associated with only pure ataxia in a single case. We thus present segregation and phenotypic manifestations of this variant in four affected family members and further extend the pure ataxia phenotype with upper motor neuron involvement and peripheral neuropathy. Our findings in turn established a precise molecular diagnosis in this family, demonstrating the use of WES combined with linkage analysis in families as a powerful tool for establishing a quick and precise genetic diagnosis of complex neurological phenotypes.

The presence of the t(12,21) is associated with good response to therapy in acute lymphoblastic l... more The presence of the t(12,21) is associated with good response to therapy in acute lymphoblastic leukemia (ALL) but molecular background of this pathology is not clear. FLI1 gene plays important roles in normal regulation of myeloid hematopoiesis and leukemogenesis. The chemokine receptor CXCR4 gene may play a role in the homing of hematopoietic stem cells. Our aim was to investigate possible relationships between t(12,21) existence and expression changes of these two genes (FLI1, CXCR4) in ALL. Thirty-one ALL patients were investigated. Twenty-one of these patients were t(12,21) carriers. We used the Quantitative Real-Time RT-PCR. Obtained results were compared to normal bone marrow samples of five healthy subjects. Expression differences were not found significant in both groups. Our study was the first attempt to quantify these genes in t(12,21) patients. We conclude that Quantitative RT-PCR is a reliable method for the monitoring of these gene expressions and similar studies shou...

Objective: Monitoring minimal residual disease has become increasingly important in clinical prac... more Objective: Monitoring minimal residual disease has become increasingly important in clinical practice of ALL management. Break-point fusion regions of leukaemia related chromosomal aberrations and rearranged immunoglobulin (Ig) and T cell-receptor (TCR) genes are used as leukaemia specific markers in genetic studies of MRD. Material and Methods: A total of 31 consecutive patients with newly diagnosed ALL were screened for eligibility criteria. Of those 26 were included in the study. One patient with partial response following induction therapy and four patients who were lost to follow-up after induction were excluded from the study; thus 21 patients were evaluated for MRD by using polymerase chain reaction (PCR), heteroduplex analysis, sequencing and quantitative real time PCR techniques. Results: Chromosomal aberrations were detected in 5 (24%) of the patients and were used for MRD monitoring. Three patients had t(9;22) translocation, the other 2 had t(4;11) and t(1;19). MRD-based ...

CXCR4 is the receptor of CXC chemokine SDF-1 and may play a role in the homing of hematopoietic s... more CXCR4 is the receptor of CXC chemokine SDF-1 and may play a role in the homing of hematopoietic stem cells. We have investigated the CXCR4 gene expression during ATRA treatment in acute promyelocytic leukaemia (APL) patients. APL is a characteristic disorder with a specific translocation between PML and RAR alpha genes on chromosome 15 and 17. ATRA-induced differentiation of APL cells is strictly dependent on the presence of PML-RAR alpha. In our study, five APL patiens were involved. Two samples from each patient were compared to each other: Primary diagnostic sample and a sample taken at remission. Quantitative real-time PCR (LightCycler) has been used for quantification, which is a recently developed method for rapid and sensitive detection of gene expression. CXCR4 gene ratios were found under-expressed in cases 1 and 6 with blast counts at diagnosis 18%, and 20% but only moderately under-expressed in cases two and four where the blast count was at diagnosis 50%, and 80%. It was...

Immunologic Research, 2021

Leukemia, 2003

Most anticancer strategies mediate apoptosis in tumor cells. Therefore, deregulation in apoptosis... more Most anticancer strategies mediate apoptosis in tumor cells. Therefore, deregulation in apoptosis signalling pathways may contribute to therapy resistance and apoptosis regulating molecules represent novel targets for future therapeutic approaches. Activation of apoptosis pathways include triggering of death ligand/receptor interaction such as the CD95 or TRAIL system, "activation" of mitochondrial apoptogenic function with subsequent release of apoptosis inducing molecules such as cytochrome c and Smac Diablo, activation of the cellular stress pathway and ultimately, activation of caspases as effectors of the cell death machinery. Although, in vitro, the contribution of apoptosis signalling to cell death e.g. by antileukemia agents has been described in many different experimental settings, most in vivo studies in leukemia have failed to directly correlate e.g. the deregulated expression of apoptosis inducing regulating molecules to treatment response or outcome. In search for molecular parameters of apoptosis sensitivity we identified downregulation of caspase-8 expression as a novel mechanism of drug resistance in a variety of human tumors. Treatment with demethylating agents such as 5-Aza-2-Deoxycidin reversed hypermethylation of the caspase-8 gene, resulting in reexpression of caspase-8 and sensitisation for TRAIL or drug-reduced apoptosis. Also, treatment with Interferon in neuroectodermal tumor cells lead to re-expression of caspase-8 through a Stat1/IRF-1 dependent pathway. Further strategies to increase apoptosis sensitivity in constitutively resistant tumor cells may include modulation of thresholds for caspase activation. We found that Smac gene transfer or cell permeable Smac peptides sensitized various tumor cell lines in vitro including leukemia cells and malignant glioma cells in vivo for apoptosis induced by TRAIL or cytotoxic drugs. Complete eradication of established glioma xenografts in nude mice was established by combination of locally delivered Smac peptides and TRAIL without acute or delayed neurotoxicity. In addition to the development of novel strategies to overcome intrinsic apoptosis resistance, we have analysed activation of apoptosis pathways during antileukemia treatment in vivo. Interestingly, in ALL and AML, significant activation of apoptosis pathways and apoptosis induction was predominantly found in CD34+ leukemic cells suggesting that induction of apoptosis is confined to the elimination of the putative leukomogenic stem cells. Further detailed analysis of caspase-3 activation in cytochrome c release in individual leukemic cells from patients undergoing chemotherapy in vivo, deficient cytochrome c release was identified as the most important parameter for treatment response in vivo. Taken together, molecular insights into the apoptosis regulation will direct our understanding of therapy response in conventional treatment strategies, may help to device molecule based rational treatment approaches and provides novel targets for future therapeutic intervention.

Bezmialem Science, 2019

Introduction Colorectal cancer (CRC) is the third most common cancer type and cause of death in t... more Introduction Colorectal cancer (CRC) is the third most common cancer type and cause of death in the world and it is estimated that more than 1.3 million new diagnosed individuals are present in the world and CRC may cause more than 700 000 deaths a year (1). The incidence varies all over the world. It was reported that India had the lowest incidence rate. On the other hand, highest incidence rates are present in developed countries (2,3). Data from immigrants show that there are also international differences. Incidence of CRC has changed very quickly in Italy, Japan, poor regions of China, and Polynesianmales in Hawaii. Furthermore, it was highly sensitive to environment, suggesting that colon cancer is, in part, highly susceptible to environmental changes (2,3). The incidence of migrants and their descendants quickly reached to the rates in countries (4,5). The internationally stated rate of 20 times more frequent observation can be explained by diet habits and environmental differences in large section (2). However, it has been known that CRC is common in some families (6-8). As a result, CRC is considered as a disease associated with genetic and environmental factors. Despite the rapid and major advances in human cancer biology, no significant increase has been observed in the overall life span and survival rates of these patients over the past three decades.

Frontiers in Public Health

Rare disease patients constitute a significant part of the healthcare system of all countries. Ho... more Rare disease patients constitute a significant part of the healthcare system of all countries. However, the information on the experiences during disease processes and daily life of rare disease patients is still limited. So far, there is a small number of studies conducted in Türkiye, and they mainly cover specific issues like education or anxiety. Here we present a comprehensive survey analysis conducted among the patients and their families within the scope of the Istanbul Solution Platform for Undiagnosed and Rare Diseases-ISTisNA project. A total of 498 individuals responded to the survey, and 58% of the participants answered all questions. The majority of the patients were in the age range of 1–10 years (44.7%), and 91% of all the patients had a precise diagnosis. The diagnosis rate in the first 6 months was 69%, and almost 10% of the patients remained undiagnosed. The mothers were the primary caregivers (72%). Nearly 30% of the caregivers had to quit their jobs and 25% of the...

Clinical and experimental rheumatology, 2009

BACKGROUND Behçet's disease (BD) is a multisystem inflammatory disorder characterized by recu... more BACKGROUND Behçet's disease (BD) is a multisystem inflammatory disorder characterized by recurrent oral ulcers, genital ulcers and ocular inflammation, as well as skin, joint, vascular, pulmonary, central nervous system (CNS) and gastrointestinal tract manifestations. The etiopathogenesis of BD has not yet been identified; but it has generally been accepted that several environmental factors may induce an inflammatory attack in genetically susceptible individuals. In this study, we aimed to identify antigens that could elicit high-titer IgG responses by the serological analysis of recombinant expression of cDNA libraries method (SEREX). METHODS We screened a human testis cDNA library with pooled sera obtained from 4 BD patients by SEREX. Antigens that were identified with the initial analysis were selected for seroreactivity analysis of a larger group of BD patients (n=78) and controls (n=66) by serological immunoscreening. RESULTS We observed seroreactivity against 6 antigens u...

Turkish Journal of Medical Sciences, 2003

In this study, quantification levels were investigated to define alterations in the expression of... more In this study, quantification levels were investigated to define alterations in the expression of the FLI1 gene on acute promyelocytic leukemia (APL), which is characterized by a reciprocal t(15,17) translocation of fusing the PML gene to the retinoic acid receptor alpha (RAR alpha) gene. The FLI1 gene plays an important role in several signal transduction pathways, and is involved in the normal regulation of myeloid hematopoiesis and leukomogenesis. We used the real-time quantitative RT-PCR (LightCycler) with SYBR Green I dye method for the labeling and analysis of the quantification of FLI1 gene RT-PCR products. Ribosomal protein S9 (RPS9) was used as an internal control for the normalization of the results. FLI1 gene levels were found up- regulated in two PMLRARA fusion gene positive APL patients compared to bone marrow samples from four healthy donors. To our knowledge, this study is the first attempt to quantify the FLI1 gene in APL patients by real-time RT-PCR. SYBR Green I dy...

Leukemia Research, 2015

The MN1 (Meningioma 1) gene is overexpressed in certain subtypes of acute myeloid leukemia (AML) ... more The MN1 (Meningioma 1) gene is overexpressed in certain subtypes of acute myeloid leukemia (AML) and high levels of MN1 expression in mouse bone marrow cells results in myeloid leukemia. We showed that compared with control bone marrow (BM) MN1 expression was increased (2-fold or more) in 29 out of 73 (40%) pediatric B-cell acute lymphoblastic leukemia (B-ALL) patient BM.

Aims and background. The SET gene is a target of chromosomal translocations in acute leukemia and... more Aims and background. The SET gene is a target of chromosomal translocations in acute leukemia and encodes a widely expressed multifunctional phosphoprotein. It has been shown that SET is upregulated in BCR-ABL1-positive cell lines, patient-derived chronic myeloid leukemia CD34-positive cells, and some solid tumors. Methods and study design. We determined the expression level of SET in 59 pediatric acute lymphoblastic leukemia patients who were BCR-ABL-negative using quantitative real-time reverse-transcriptase-polymerase chain reaction. Results. We showed that SET expression was significantly upregulated in 96.5% of Bacute lymphoblastic leukemia (28 of 29; 16.6 fold) and 93% of T-acute lymphoblastic leukemia (28 of 30; 47.6 fold) patients. This upregulation was not associated with any clinical features or overall and relapse-free survival. Conclusions. Our results showed that SET is significantly overexpressed in pediatric acute lymphoblastic leukemia samples, and an increased level of SET might contribute to leukemic process.

Pituitary, 2007

Aromatase (P450AROM) converts testosterone to estrogen. This conversion could be important in nor... more Aromatase (P450AROM) converts testosterone to estrogen. This conversion could be important in normal physiology and estradiol-induced tumorigenesis in human pituitary. The objective of this study was to examine the expression of P450AROM in normal human pituitary and determine the gender difference. We examined aromatase expression in 19 normal human pituitary glands [13 males, 6 females, median age: 30 years (interquartile ranges, IQR: 23-63)] obtained from autopsy. We demonstrated aromatase gene expression levels by quantitative RT-PCR and aromatase protein with immunohistochemical staining in normal male and female human pituitary. Although median relative expression level of aromatase mRNA of male individuals [median DCt = 42.6 (IQR: 7.6-93.9)] was higher than the female individuals [median DCt = 3.9 (IQR:0-44.8)], we could not determine a significant gender difference in aromatase mRNA levels (p = 0.2). The difference between the aromatase protein density by immunohistochemistry was not significant between genders (p = 0.78). The aromatase levels were also not correlated with the age of the study subjects (p = 0.42 r = À0.21). The results indicate that aromatase enzyme is present in human pituitary. The amount and the density of the enzyme show a large variance among different individuals. Although higher mRNA expression was observed in male pituitary compared to female pituitary, there was no statistically significant difference for gender or age.

Journal of Biotechnology, 2014

Turkish Journal of Hematology, 2014

Objective: The prominent functions of the local renin-angiotensin system (RAS) in primitive hemat... more Objective: The prominent functions of the local renin-angiotensin system (RAS) in primitive hematopoiesis further support the hypothesis that local autocrine bone marrow RAS could also be active in neoplastic hematopoiesis. The aim of this study is to examine critical RAS elements in normal CD34+ hematopoietic stem cells and multiple myeloma (MM)-related progenitor cells. Materials and Methods: The study group comprised the total bone marrow cells (CBM) of 10 hematologically normal people, the CD34+ stem cell samples (CD34+CBM) of 9 healthy donors for allogeneic peripheral stem cell transplantation, and the CD34+ stem cell samples (CD34+MM) of 9 MM patients undergoing autologous peripheral stem cell transplantation. We searched for the gene expression of the major RAS components in healthy hematopoietic cells and myeloma cells by quantitative real-time polymerase chain reaction analysis. Results: RENIN, angiotensinogen (ANGTS), and angiotensin converting enzyme-I (ACE I) mRNA expression levels of CBM were significantly higher than those in myeloma patients (p=0.03, p=0.002, and p=0.0008, respectively). Moreover, RENIN and ANGTS mRNA expression levels were significantly higher in CD34+ stem cell samples of healthy allogeneic donors compared to those in myeloma patients (p=0.001 and p=0.01). However, ACE I expression levels were similar in CD34+CBM and CD34+MM hematopoietic cells (p=0.89). Conclusion: Although found to be lower than in the CBM and CD34+CBM hematopoietic cells, the local RAS components were also expressed in CD34+MM hematopoietic cells. This point should be kept in mind while focusing on the immunobiology of MM and the processing of autologous cells during the formation of transplantation treatment protocols.

Journal of Medical Microbiology, 2003

Constantly expressed genes are used as internal controls in relative quantification studies. Suit... more Constantly expressed genes are used as internal controls in relative quantification studies. Suitable internal controls for such studies have not yet been defined for Pseudomonas aeruginosa. In this study, the genes ampC, fabD, proC, pbp-2, rpoD and rpoS of P. aeruginosa were compared in terms of expression stability by real-time quantitative RT-PCR. A total of 23 strains with diverse resistance phenotypes were studied. Stability of expression among the housekeeping genes was assessed on the basis of correlation coefficients, with the best-correlated pair accepted as being the most stable one. Eventually, proC and rpoD formed the most stable pair (r ¼ 0•958; P , 0•001). Next, in four ciprofloxacin-selected nfxC-like mutants, levels of oprD, oprM and oprN mRNA were compared with those of their wild-type counterparts. The comparison was made after correcting the raw values by the geometric mean of the internal control genes proC and rpoD. The level of oprN mRNA was significantly up-regulated, while the oprD gene was down-regulated (although this difference was statistically insignificant), in the mutants. This expression pattern was consistent with that of the expected expression profile of nfxC-type mutants; this experiment therefore lends further support to the use of proC and rpoD genes simultaneously as internal controls for such studies.

Medical oncology (Northwood, London, England), 2008

Small cell lung cancer (SCLC) has a rapid growth rate and is characterized by early metastases. T... more Small cell lung cancer (SCLC) has a rapid growth rate and is characterized by early metastases. Tumor growth is dependent on angiogenesis. Vascular endothelial growth factor (VEGF) is an important regulator of angiogenesis. Whether surveillance of pre- and post-treatment serum VEGF and especially its receptors VEGF-1 and VEGF-2 levels in SCLC patients have impact on clinical outcome is unknown.

Genetic Testing and Molecular Biomarkers, 2012

Polymorphisms of the x-ray repair cross-complementing group 1 (XRCC1) gene have been reported to ... more Polymorphisms of the x-ray repair cross-complementing group 1 (XRCC1) gene have been reported to be associated with various forms of cancer. We evaluated the possible effects of the Arg194Trp and the Arg399Gln polymorphisms on the risk for chronic lymphocytic leukemia (CLL) in 73 patients and 50 controls. We also analyzed their relation to frequency of sister chromatid exchange (SCE). With respect to codon 194, the allelic frequency of the Arg194Trp polymorphism did not significantly differ between the 2 groups. The proportion of individuals carrying the Arg194Trp polymorphism was not different in the 2 groups. With respect to codon 399, the proportion of the individuals carrying the Arg399Gln allele (90% vs 62%; p = 0.000; odds ratio [OR], 5.779; 95% confidence interval [CI], 2.2-15.183) and the allelic frequency of the Arg399Gln polymorphism (56% vs 36%; p = 0.002; OR, 2.278; 95% CI, 1.350-3.843) was significantly higher in the patient group. The frequency of the Arg/Gln genotype was significantly higher in the patient group (68.50% vs 52%; p = 0.049; OR, 2.007; 95% CI, 0.955-4.217). The mean SCE frequency in the patient group was significantly higher (9.2-4 vs 7.5-2; p = 0.02). When different compound genotypes were compared, the coexistence of Arg/Arg genotype in codon 194 with Arg/Arg genotype in codon 399 was significantly more frequent in the control group (30% vs 9%; p = 0.004; OR, 0.247; 95% CI, 0.092-0.664). Within the patient group, SCE frequency did not differ between patients with various genotypes. The Arg399Gln polymorphism may be etiologically associated with CLL; however, it does not seem to increase SCE frequency.

British Journal of Haematology, 2012

TRIB2 is a potent oncogene, elevated in a subset of human acute myeloid leukaemias (AML) with a m... more TRIB2 is a potent oncogene, elevated in a subset of human acute myeloid leukaemias (AML) with a mixed myeloid/lymphoid phenotype and NOTCH1 mutations. Although rare in AML, activating NOTCH1 mutations occur in 50% of all T-acute lymphoblastic leukaemias (T-ALL). TRIB2 is a NOTCH1 target gene that functions in the degradation of key proteins and modulation of MAPK signaling pathways, implicated in haematopoietic cell survival and proliferation. We show that TRIB2 expression level is highest in the lymphoid compartment of normal haematopoietic cells, specifically in T cells. Analysis of TRIB2 expression across 16 different subtypes of human leukaemia demonstrated that TRIB2 expression was higher in ALL phenotypes versus all other phenotypes including AML, CLL, MDS and CML. A T cell profile was distinguished by high TRIB2 expression in normal and malignant haematopoiesis. High TRIB2 expression was seen in TALL with normal karyotype and correlated with NOTCH signalling pathways. In a pediatric patient TALL cohort high TRIB2 expression correlated with NOTCH1/FBXW7 mutations, strongly linking NOTCH1 activation and high TRIB2 expression in paediatric TALL. The relationship between TRIB2 and T cell signaling pathways uniquely identifies leukaemia subtypes and will be useful in the advancement of our understanding of T cell and ALL biology.

Arthritis & Rheumatism, 2006

Familial Mediterranean fever (FMF) is associated with more than 70 missense mutations in the MEFV... more Familial Mediterranean fever (FMF) is associated with more than 70 missense mutations in the MEFV gene. The purpose of this study was to investigate the relative expression of messenger RNA (mRNA) for the MEFV gene in peripheral blood leukocytes (PBLs) obtained from patients with FMF during attacks of acute abdominal inflammation as well as during asymptomatic periods. We studied 16 patients with FMF during an attack of acute peritonitis and 17 otherwise healthy individuals who were undergoing surgery because of acute appendicitis. Blood samples were collected from both groups of patients during both acute inflammatory and asymptomatic periods. Relative levels of MEFV mRNA in PBLs were detected with real-time reverse transcriptase-polymerase chain reaction using LightCycler, with 2 sets of primers for the MEFV gene (exons 7-10 and exons 2-3) and with primers for CIAS1 and PSTPIP1 genes. Expression levels were compared with beta(2)-microglobulin as an internal control. MEFV expression was reduced in FMF patients during asymptomatic periods as compared with the non-FMF controls (P < 0.001). We observed a further decrease in MEFV expression in FMF patients during periods of inflammation (P = 0.01). Reduced levels of MEFV mRNA were also noted during the preoperative period as compared with asymptomatic periods in control patients with acute appendicitis (P = 0.01). CIAS1 expression in PBLs from patients with FMF was also found to be lower than that in the control patients. However, CIAS1 expression did not change with acute inflammation. This study confirmed that reduced expression of the MEFV gene is associated with inflammation and that it may be one of the pathogenic mechanisms of the attacks of inflammation in FMF patients, along with disease-associated variations in pyrin.

Neurological Sciences, 2017

SYNE1 related autosomal recessive cerebellar ataxia type 1 (ARCA1) is a late-onset cerebellar ata... more SYNE1 related autosomal recessive cerebellar ataxia type 1 (ARCA1) is a late-onset cerebellar ataxia with slow progression originally demonstrated in French-Canadian populations of Quebec, Canada. Nevertheless, recent studies on SYNE1 ataxia have conveyed the condition from a geographically limited pure cerebellar recessive ataxia to a complex multisystem phenotype that is relatively common on the global scale. To determine the underlying genetic cause of the ataxia phenotype in a consanguineous family from Turkey presenting with very slow progressive cerebellar symptoms including dysarthria, dysmetria, and gait ataxia, we performed SNP-based linkage analysis in the family along with whole exome sequencing (WES) in two affected siblings. We identified a homozygous variant in SYNE1 (NM_033071.3: c.13086delC; p.His4362GlnfsX2) in all four affected siblings. This variant presented herein has originally been associated with only pure ataxia in a single case. We thus present segregation and phenotypic manifestations of this variant in four affected family members and further extend the pure ataxia phenotype with upper motor neuron involvement and peripheral neuropathy. Our findings in turn established a precise molecular diagnosis in this family, demonstrating the use of WES combined with linkage analysis in families as a powerful tool for establishing a quick and precise genetic diagnosis of complex neurological phenotypes.

The presence of the t(12,21) is associated with good response to therapy in acute lymphoblastic l... more The presence of the t(12,21) is associated with good response to therapy in acute lymphoblastic leukemia (ALL) but molecular background of this pathology is not clear. FLI1 gene plays important roles in normal regulation of myeloid hematopoiesis and leukemogenesis. The chemokine receptor CXCR4 gene may play a role in the homing of hematopoietic stem cells. Our aim was to investigate possible relationships between t(12,21) existence and expression changes of these two genes (FLI1, CXCR4) in ALL. Thirty-one ALL patients were investigated. Twenty-one of these patients were t(12,21) carriers. We used the Quantitative Real-Time RT-PCR. Obtained results were compared to normal bone marrow samples of five healthy subjects. Expression differences were not found significant in both groups. Our study was the first attempt to quantify these genes in t(12,21) patients. We conclude that Quantitative RT-PCR is a reliable method for the monitoring of these gene expressions and similar studies shou...

Objective: Monitoring minimal residual disease has become increasingly important in clinical prac... more Objective: Monitoring minimal residual disease has become increasingly important in clinical practice of ALL management. Break-point fusion regions of leukaemia related chromosomal aberrations and rearranged immunoglobulin (Ig) and T cell-receptor (TCR) genes are used as leukaemia specific markers in genetic studies of MRD. Material and Methods: A total of 31 consecutive patients with newly diagnosed ALL were screened for eligibility criteria. Of those 26 were included in the study. One patient with partial response following induction therapy and four patients who were lost to follow-up after induction were excluded from the study; thus 21 patients were evaluated for MRD by using polymerase chain reaction (PCR), heteroduplex analysis, sequencing and quantitative real time PCR techniques. Results: Chromosomal aberrations were detected in 5 (24%) of the patients and were used for MRD monitoring. Three patients had t(9;22) translocation, the other 2 had t(4;11) and t(1;19). MRD-based ...

CXCR4 is the receptor of CXC chemokine SDF-1 and may play a role in the homing of hematopoietic s... more CXCR4 is the receptor of CXC chemokine SDF-1 and may play a role in the homing of hematopoietic stem cells. We have investigated the CXCR4 gene expression during ATRA treatment in acute promyelocytic leukaemia (APL) patients. APL is a characteristic disorder with a specific translocation between PML and RAR alpha genes on chromosome 15 and 17. ATRA-induced differentiation of APL cells is strictly dependent on the presence of PML-RAR alpha. In our study, five APL patiens were involved. Two samples from each patient were compared to each other: Primary diagnostic sample and a sample taken at remission. Quantitative real-time PCR (LightCycler) has been used for quantification, which is a recently developed method for rapid and sensitive detection of gene expression. CXCR4 gene ratios were found under-expressed in cases 1 and 6 with blast counts at diagnosis 18%, and 20% but only moderately under-expressed in cases two and four where the blast count was at diagnosis 50%, and 80%. It was...

Immunologic Research, 2021

BioRxiv , 2020

The COVID-19 outbreak caused by SARS-CoV-2 has created an unprecedented health crisis since there... more The COVID-19 outbreak caused by SARS-CoV-2 has created an unprecedented health crisis since there is no coronavirus vaccine in the market due to the novelty of this virus. Therefore, SARS-CoV-2 vaccines have become very important to reduce morbidity and mortality. At this point, inactivated vaccines are important because the straightforward process of existing infrastructure used for several licensed human vaccines can be used for SARS-CoV-2. Inactive vaccines provide an antigenic presentation similar to that when they encounter invasive virus particles of the immune system. In this study, in vitro and in vivo safety and efficacy analyzes of lyophilized vaccine candidates inactivated by gamma-irradiation were performed. Our candidate OZG-3861 version 1 (V1) is an inactivated SARS-CoV-2 virus vaccine, and SK-01 version 1 (V1) is the GM-CSF adjuvant added vaccine candidate. We applied the candidates intradermal to BALB/c mice to assess the toxicity and immunogenicity of the OZG-3861 V1 and SK-01 V1. Here, we report our preliminary results in vaccinated mice. When considered in terms of T and B cell responses, it was observed that especially the vaccine models containing GM-CSF as an adjuvant caused significant antibody production with neutralization capacity in absence of the antibody-dependent enhancement feature. Another finding showed that the presence of adjuvant is more important in T cell response rather than B cell. The vaccinated mice showed T cell response upon restimulation with whole inactivated SARS-CoV-2 or peptide pool. This study encouraged us to start the challenge test using infective SARS-CoV-2 viruses and our second version of gamma-irradiated inactivated vaccine candidates in humanized ACE2+ mice.