Browsing by Author "Özkan, Didem"

Now showing 1 - 12 of 12

Citation Count: 0
AKUT MİYELOİD LÖSEMİDE SWITCH/SUKROZ FERMENTE EDILEMEZ KROMATİN YENİDEN ŞEKİLLENDİRME KOMPLEKSİNİN GENOMİK GÖRÜNÜMÜ
(2024) Ozkan, Didem Torun; Akın, Dilara Fatma; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
SWI/SNF kromatin yeniden modelleme kompleksi, hematopoietik kök hücrelerde hücre bakımı ve farklılaşma gibi süreçler için gerekli olan gen ekspresyonunun düzenlenmesinde görev alır. Hematolojik süreçlerin homeostazında yer alan SWI/SNF kompleksi alt birimlerindeki değişiklikler hematolojik malignitelerin başlamasına veya ilerlemesine katkıda bulunmaktadır, ancak bu fenotipin arkasındaki mekanizmalar tam olarak açıklanmamıştır. Çalışmada, SWI/SNF kompleksini oluşturan genlerde mutasyonların ve ekspresyon profilinin biyoinformatik araçları kullanılarak kapsamlı belirlenmesi amaçlanmıştır. AML kohortuna (n:872) ait genom dizileri ve ifade profillerine biyoinformatik araçlar aracılığı ile elde edilmiş ve analiz edilmiştir. Kompleksin alt ünitelerini kodlayan 9 gende ARID1A, ARID1B, SMARCA2, SMARCA4, SMARCE1, SMARCB1, DPF2, PMBR1 ve BCL7A belirlenen mutasyonların AML patogenezinde onkojenik/patojenik etkilerinin tahmini PolyPhen-2, SIFT ve Mutation Assessor araçları kullanılmıştır. Mutasyona uğrayan proteinlerinin fonksiyenel etkilerini anlamak için STRING aracı ile analiz gerçekleştirilmiştir. Mutasyon profili değil aynı zamanda mutasyon varlığının gen ifadesi ve sağ kalım üzerine etkileride değerlendirilmiştir. 9 gende 9 yanlış anlam, 6 çerçeve kayması mutasyon, 1 splize bölge ve 1 füzyon mutasyonu olmak üzere toplam 17 genetik anormallik belirlenmiştir. AML kohortunda ARID1A, ARID1B, SMARCA2 ve PMBR1 ekspresyon seviyelerin hasta grubunda sağlıklı gruba yüksek ve istatistiksel olarak anlamlıdır (p<0.01). Düşük ve yüksek gen ekspresyon profillerine göre yapılan sağ kalım analizi sonuçlarımızda bir farklılık görülmemiştir. STRING analizinde, hedef genlerimizin, hücre döngüsü kontrolünde görev alan PHF10 ile fonksiyonel ilişkileri bulunduğu belirlenmiştir. Sonuç olarak, sonuçlarımız, ARID1A, ARID1B, SMARCA2, SMARCA4 ve PBRM1’de tespit ettiğimiz mutasyonlarının, SWI/SNF kromatin yeniden modelleme komplekslerinin fonksiyonunu bozarak AML patogenezi sırasında farklı kromatin ortamlarını içeren farklı hücresel yolları indükleyebileceği/inaktive edebileceğini düşündürmektedir.
Citation Count: 0
Beta-lactam antibiotic-induced thrombocytopenia: MYH9 & TUBB1 genes
(Bayrakol Medical Publisher, 2022) Ozkan, Didem; Akisin, Yasemin Ardicoglu; Bali, Dilara Fatma Akin; Akar, Nejat; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Aim: Macrothrombocytopenia is a congenital autosomal-dominant blood disorder characterized by increased platelet size and a decreased number of circulating platelets. In this study, it was aimed to show the MYH9 and TUBB1 gene changes, which are the genes associated with the disease, in a patient with thrombocytopenia receiving beta-lactam antibiotic therapy. Material and Methods: In this study, coagulation parameters and platelet aggregation tests were performed after ingestion of a beta-lactam antibiotic in an 8-year-old boy with thrombocytopenia, the MYH9 and TUBB1 genes were scanned by PCR and DNA sequencing, and the results were subsequently analyzed using bioinformatics tools. Results: We found previously described TUBB1 polymorphisms, p.R307H , p.Q43P, p.T178T and the novel mutation p.K64A in the MYH9 gene in a boy and his mother. Changes in genes important for thrombocytopenia in a boy after taking beta-lactam antibiotics prompted us to study the same genes in the mother, since her mother had macrothrombocytopenia, and we found a new mutation in her mother Discussion: Determination of gene changes after beta-lactam antibiotic use in bleeding patients is important in terms of helping the clinic in the treatment.
Citation Count: 0
Computational Analysis of Cohesin Complex Genes and their Role in the Pathogenesis of AML
(2024) Akın, Dilara Fatma; Özkan, Didem; Bourouba, Romyla; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Objective: Anomalies in the cohesion complex contribute to the pathogenesis of myeloid malignancies by affecting the self-renewal capacity of hematopoietic and progenitor stem cells, but the underlying mechanisms of this phenotype are not fully understood. Therefore, this study aims to shed light on the relationship between AML pathogenesis and the cohesion complex by comprehensively determining the mutations and expression profiles in the genes constituting the cohesion complex and investigating the effect of expression on survival using bioinformatics databases and tools. Methods: A total of 96 different mutations were identified in 13 genes. Out of these 96 mutations, 26 were classified as pathogenic/oncogenic. The expression levels of STAG1, REC8, MAU2, CDCA5, and PDS5B were significantly higher in the patient group compared to the healthy group (p< .01). Survival analysis based on low and high gene expression profiles revealed that increased REC8 expression was significantly associated with survival (p= .024), which is considered a prognostic marker. In STRING analysis, it was determined that hub proteins interact with acetyltransferases ESCO1 and ESCO2 involved in sister chromatid cohesion, with TERF1, a component of the telomere nucleoprotein complex, and with PDS5A and BRCA2, which are functionally related to genetic stability and genetic recombination, respectively. Results: An increase in language outcomes, particularly in repetition, was observed following the treatments. It was also found that therapy gains were more robust following bihemispheric stimulation of the posterior temporal sites compared to the inferior frontal targets. Conclusion: Overall, none of the target genes except the mutated REC8 showed a significant and independent effect on the clinical outcome defined as overall survival. However, we have identified the diversity of genetic alterations in individual cohesin subunits through comprehensive molecular analysis. The results may be beneficial in the development of targeted drug therapies and personalized medicine approaches.
Citation Count: 0
FIRST OBSERVATION OF TUBB1 GENE MUTATIONS IN TURKISH PATIENTS WITH MACROTHROMBOCYTOPENIA
(Ferrata Storti Foundation, 2016) Ozkan, D.; Waheed, A. A.; Kandilci, A.; Akar, N.; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
[No Abstract Available]
Citation Count: 1
Genetic Analysis of Afibrinogenemia and Hypofibrinogenemia: Novel Mutations in the FGB Gene in the Turkish Population
(Karger, 2020) Ozkan, Didem Torun; Sarper, Nazan; Akar, Nejat; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Introduction: Congenital afibrinogenemia is a rare autosomal recessive disorder characterized by bleeding that varies from mild to severe and by complete absence or extremely low levels of plasma and platelet fibrinogen. Hypofibrinogenemia is characterized by fibrinogen levels Objective: In this study, we analyzed fibrinogen beta chain gene mutations in Turkish afibrinogenemia and hypofibrinogenemia patients. Methods: We evaluated 20 afibrinogenemia and hypofibrinogenemia patients and 80 healthy controls. We have sequenced all exons of the FGB gene using the DNA isolated from the peripheral blood samples of patients and controls. Results and Conclusion: We found a nonsense mutation in exon 4 at nucleotide 630 that encoded serine amino acid, and in the same exon a missense mutation of T to C at nucleotide 647, resulting in a transition from leucine to proline (p.L198P) in a child with hypofibrinogenemia. These mutations have been shown for the first time in the same patient of Turkish descent. Furthermore, there was a novel heterozygous guanine-to-adenine nucleotide change in exon 3. This caused the change of arginine amino acid to threonine amino acid at position 136 (p.A136T) in a protein, which has not been described in the literature before.
Citation Count: 1
Identification of novel TUBB1 variants in patients with macrothrombocytopenia
(Tubitak Scientific & Technological Research Council Turkey, 2021) Caliskaner, Zihni Onur; Waheed, Abdullah Abdul; Ozturk, Merve Tuzlakoglu; Oymak, Yesim; Tazebay, Uygar Halis; Akar, Nejat; Ozkan, Didem Torun; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Background/aim: Macrothrombocytopenia is an autosomal-dominant disorder characterized by increased platelet size and a decreased number of circulating platelets. The membrane skeleton and the link between actin filaments of the skeleton and microtubules, which consist of alpha and beta tubulin [including the tubulin beta-1 chain (TUBB1)] heterodimers, are important for normal platelet morphology, and defects in these systems are associated with macrothrombocytopenia. Materials and methods: In this study, we sequenced the exons of the TUBB1 gene using DNA isolated from the peripheral blood samples of healthy controls (n = 47) and patients with macrothrombocytopenia (n = 37) from Turkey. The TUBB1 expression levels in fractioned blood samples from patients and healthy controls were analyzed by RT-qPCR and Western blot. Microtubule organization of the platelets in the peripheral blood smears of patients, and in mutant TUBB1-transfected HeLa cells, were analyzed by immunofluorescence staining. Results: A new TUBB1 c.803G > T (p.T178T) variant was detected in all of the control and patient samples. Importantly, we found 3 new heterozygous TUBB1 variants predicting amino acid substitutions: G146R (in 1 patient), E123Q (in 1 patient), and T274M (in 4 patients); the latter variant was associated with milder thrombocytopenia in cancer patients treated with paclitaxel. Ectopic expression of TUBB1 T274M/R307H variant in HeLa cells resulted in irregular microtubule organization. Conclusion: Further clinical and functional studies of the newly identified TUBB1 variants may offer important insights into their pathogenicity in macrothrombocytopenia.
Koroner aterosklerozis tanısı alan hastalara nutrigenetik yaklaşımlar ve Apo E gen incelemesi
(2018) Yücelli, Esra; Özkan, Didem; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Ateroskleroz, tüm dünyada en yaygın damar tıkanıklığı nedeni olup, kardiyovasküler hastalıkların altında yatan temel bir faktördür. Lipitler ile doldurulmuş arterlerin multifokal, immuno-inflamatuvar hastalığı olarak tanımlanan bu hastalıkta; arter duvarları bu yumuşak çökeltilerle kaplanır ve bunun sonucunda zamanla sertleşerek damarları darlaştırıp kan akımının engellenmesine neden olur. Ateroskleroz'da temel risk faktörleri genetik (kalıtımsal) ve çevresel olarak tanımlanmaktadır. Çevresel faktörler için de beslenme önemli bir yer tutmaktadır. Çalışmanın amacı; Türk popülasyonunda klinik olarak aterosklerozis tanısı alan hastalarda beslenme alışkanlıklarını belirlemek ve bunun doğrultusunda hastalıkla ilişkili gen olan Apolipoprotein E gen değişimlerini ilgili hastalarda saptayarak konuyla ilişkili ilk kez Türk popülasyonunda nutrigenetik yaklaşımları saptayabilmek olarak belirlenmiştir. İlgili tez çalışması, literatürde konuyla ilişkili yapılacak ilk çalışma olması açısından önem arz etmektedir. Bu çalışma iki basamaklı olarak planlanmıştır. Çalışma 30 hasta gönüllü ile yapılmıştır. İlk aşamada klinik olarak aterosklerozis tanısı alan hastalarda beslenme alışkanlıklarının belirlenmesi amaçlanmıştır. İkinci aşamada ise tanı alan hastalarda aterosklerozis ile ilişkili en önemli gen olan Apolipoprotein E (ApoE) geninin taraması yapılarak genetik değişimlerin ortaya konulması planlanmıştır. Çalışmanın sonucunda 30 gönüllü katılımcıya yapılan Apolipoprotein E geninin taraması sonucu 7 kişide mutasyon/polimorfizm görülmüştür. Çalışmaya katılan gönüllü hasta katılımcıların beslenme ile ilgili veri sonuçları SPSS 15.0 programı ile elde edilmiştir. Katılımcıların ortalama yaş değeri 61,5 yıl bulunurken, ortalama beden kütle indeksi (BKİ) değeri ise 28,72 kg/m2 bulunmuştur. Çalışmanın beslenme ile ilgili bulguları Türkiye Beslenme Rehberi (TÜBER) 2015 verileri ile karşılaştırılarak yazılmıştır. Mutasyon/polimorfizm görülen hastaların beslenme durumu incelendiğinde beslenme ile mutasyon/polimorfizm arasında bireysel olarak ilişki bulunmaktadır, ancak genele bakıldığı zaman anlamlı ilişkiler bulunamamıştır. Bu nedenle bu konu hakkında örneklerin sayısı artırılarak çalışmaya ihtiyaç duyulmaktadır. Anahtar Kelimeler: Nutrigenetik, Aterosklerozis, Apo E geni, Akdeniz diyeti
Citation Count: 2
Molecular profiling of TAM tyrosine kinase receptors and ligands in endometrial carcinoma: An in silico-study
(Elsevier Taiwan, 2023) Akin, Dilara Fatma; Ozkan, Didem; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Objectives: TAM Receptors (TYRO3, AXL, and MerTK) and their ligands on tumor-associated macrophages are promising therapeutic targets for most solid cancers. However, in endometrial cancer, the most common invasive gynecologic malignancy, the TAM receptor-mediated activation pathway, its molecular mechanisms, and its pathophysiology are unknown. The goal of this research; to uncover the comprehensive genetic profile of TAM receptors and ligands in endometrial cancer.Material and methods: Mutation and expression profiles of the Uterine Corpus Endometrial Carcinoma (UCEC) cohort (n 1/4 509) were obtained using bioinformatics tools providing data from The Cancer Genome Atlas (TCGA). PolyPhen-2 and SNAP tools were used to predict the oncogenic/pathogenic properties of the identified mutations for UCEC. STRING network analysis was performed to better understand the functional relationships of the mutant proteins in cellular processes. Furthermore to the mutation profile, gene expression and survival profiles were also determined. Finally, the correlation between target genes and macrophage infiltration was investigated using the tool TIMER.Results: A total of 229 mutations were detected in 6 genes, and 81 missense mutations are pathogenic. In the UCEC cohort, the expression level of MerTK, AXL, GAS6, and PROS1 was statistically significantly lower in the patient group, while the expression level of CD47 was higher in the patient group than in the healthy group (p < 0.01). Protein-protein interaction analysis identified target genes, SRC protein responsible for important cellular mechanisms such as cell proliferation, adhesion and migration, ITGB3, ITGAV and THSB1 proteins involved in endothelial mesenchymal transition and tumor metabolism reprogramming, and FOLR1 involved in DNA replication and damage repair.Conclusion: We believe that TAM receptors and their ligands may be attractive molecular targets for the treatment of endometrial carcinoma because they act as pleiotropic inhibitors of immune cells, effectively regulate phagocytic clearance of apoptotic cells, and make the tumor microenvironment a more suitable niche for the tumour.(c) 2023 Taiwan Association of Obstetrics & Gynecology. Publishing services by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Citation Count: 8
Novel mutations of integrin αIIb and β3 genes in Turkish children with Glanzmann's thrombasthenia
(Taylor & Francis inc, 2015) Tokgoz, Huseyin; Ozkan, Didem Torun; Caliskan, Umran; Akar, Nejat; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Glanzmann's thrombasthenia (GT) is an inherited disorder of platelet aggregation, characterized by qualitative and quantitative defect on platelet alpha IIb beta 3 integrin (GpIIb/IIIa), resulting in lifelong bleeding tendency due to defective platelet plug formation. The alpha IIb gene (ITGA2B) and beta 3 gene (ITGB3) are closely located at chromosome 17q21.31-32. ITGA2B consist of 30 exons and encoding alpha chain, whereas ITGB3 has 15 exons and encoding beta chain. Until now, according to the Human Gene Mutation Database (HGMD), 138 mutations at ITGA2B gene and 101 mutations at ITGB3 gene have been identified. We aimed to determine whether there was any mutation in the ITGA2B and ITGB3 genes, and a correlation between clinical phenotype and genotype in Turkish GT patients. We examined 20 patients with GT followed at the Department of Pediatric Hematology, Meram Faculty of Medicine, for Clinical and Laboratory Findings and Molecular Genetic Analysis. Peripheral blood was collected from patients, and a written informed consent for genetic analysis was obtained from parents. DNA was isolated from by proteinase K and phenol/chloroform extraction. ITGA2B and ITGB3 genes were screened by polymerase chain reaction. There were 12 females and 8 males with a median age of 15.25 years. Major clinical presentations of these patients were mucocutaneous bleedings. The most common bleeding type was epistaxis (85%). Life-threatening bleedings were seen in five patients. Seven (35%) patients showed various mutations in the ITGA2B or ITGB3 genes. We detected four novel mutations in three different regions and two mutations defined previously within the ITGA2B gene. These changes are at exon 4; c.570 T4G alteration, at exon 13 c.1277 T4A, c. 1291 T4G alterations, at exon 19 c.1921A4G alterations. And from the start point of exon 14, behind 107 bases, we detected a heterozygous alteration at Thymine to Guanine. According to PolyPhen Database Program and NCBI Multiple Alignment Tool Database, four transitions are conserved at evolutionary process, so we can say that these transitions are novel mutations. c. 468T4G alteration at exon 4 and c. 1378 T4A alteration at exon 13 were reported to HGMD previously. Screening the exons of the ITGB3 gene from the same patient groups, we reported a novel missense mutation at exon 5, at nucleotide 680. No correlation was found between clinical phenotype and genotype. These mutations were described for the first time in Turkish population, and all novel mutations are not defined previously. Furthermore, collaborative studies are needed for the population point of view.
Citation Count: 1
Pathogenic Ala303Val Mutation in the PROS1 Gene is Associated with the Pathogenesis of Deep Vein Thrombosis
(Erciyes Univ Sch Medicine, 2022) Bali, Dilara Fatma Akin; Eroglu, Tamer; Ozkan, Didem Torun; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Objective: The aim of this study was to predict the functional impact of pathogenic mutations and the mRNA expression profiles of the platelet endothelial aggregation receptor 1 (PEAR1), protein S (alpha) (PROS1), and adrenoceptor alpha 2A (ADRA2A) genes in deep vein thrombosis (DVT), as well as to examine the effects of these genes on the pathogenesis of DVT. Materials and Methods: Patients diagnosed with DVT were selected for the study and healthy individuals were used as controls. Mutations in the PEAR1, PROS1, and ADRA2A genes were determined by DNA sequencing analysis and gene expressions were determined using quantitative real-time polymerase chain reaction testing. Polymorphism Phenotyping v2 (Polyphen-2: http://genetics.bwh.harvard.edu/pph2/), SNAP2 (https://rostlab.org/services/snap2web/) and MutationTaster (https://www.mutationtaster.org/) software were used to define the pathogenic effects of mutations detected by sequencing the selected genes in hotspot regions. Mutation and gene expression analyses were noted in the results and clinical data. Results: A total of 27 patients with DVT and 10 healthy individuals were included in the study. Twenty-one mutations were detected in the 27 patients, most often in the PROS1 gene. A p.Ala303Val mutation is located on the human sex hormone-binding globulin (SHBG) domain of mutation PROS1 and is pathogenic. A p.A303V mutation is associated with premature termination in codon 303 of the SHBG domain. Examination of the effect on the mRNA expression level of wild-type versus mutant genotypes revealed that the mutant PROS1 p.A303V expression was significantly lower (p=0.041). Conclusion: A p.A303V mutation in PROS1 might be an independent risk factor for DVT, which could provide helpful insight into the pathogenesis of DVT.
Citation Count: 0
Screening of EPCR gene mutations in children with acute lymphoblastic leukemia
(Wolters Kluwer Medknow Publications, 2018) Bali, Dilara F. A.; Ozkan, Didem T.; Kurekci, Emin; Akar, Nejat; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
[No Abstract Available]
Citation Count: 0
Screening of single nucleotide polymorphism in CD95 (APO-1/FAS) promoter region (G-1377A) in children with acute leukemia
(Wolters Kluwer Medknow Publications, 2018) Akin, Dilara F.; Ozkan, Didem T.; Kurekci, Emin; Akar, Nejat; Tıbbi Laboratuvar Teknikleri / Medical Laboratory Techniques
Background CD95 is a cell surface receptor involved in apoptotic signal transmission. Deregulation of this pathway results in downregulation of apoptosis and subsequent persistence of a malignant clone. A single nucleotide polymorphism resulting in guanine-to-adenine (G>A) transition in the CD95 promoter region (position - 1377) is thought to reduce stimulatory protein 1 transcription factor binding and decrease CD95 expression. The purpose of this study is to examine a genetic polymorphism in the core promoter region of CD95 and to evaluate association between its frequency and clinical findings. Patients and methods G-1377A in the CD95 promoter region was genotyped by polymerase chain reaction and restriction endonuclease analysis finally were sequenced by Sanger Sequecing. Results Among 146 patients, CD95 G-1377A (rs2234767) single nucleotide polymorphism carriers frequencies have been identified as 25% (n=37) GA and AA 4% (n=6). This polymorphism of the distribution of the CD95 gene in children with acute leukemia will be a guide for future studies. Conclusion This polymorphism of the distribution of the CD95 gene in children with acute leukemia will be a guide for future studies. (c) 2018 The Egyptian Journal of Haematology