TR-Dizin İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/396
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Article Glucosylceramide Synthase Is a Novel Biomarker of Midostaurin-Induced Cytotoxicity in Non-Mutant FLT3 Positive Acute Myeloid Leukemia Cells(2021) Şahin, Hande Nur; Adan, AysunAmaç: Glukozilseramid sentaz (GSS) tarafından sentezlenen gluko- zilseramid (GS) birçok kanser türünde hücre yaşamını ve proliferas- yonunu sağlamaktadır. Ancak, mutant olmayan Fms-benzeri tirozinkinase 3 (FLT3) pozitif akut miyeloid lösemi (AML) patogenezindekirolü açıklanmamıştır. Çoklu kinaz inhibitörü olan midostaurin mu- tant FLT3 AML tedavisinde etkili olmasına rağmen mutant olmayanFLT3 pozitif AML’deki klinik etkisi gözden kaçırılmıştır. Bu çalışmada,midostaurinin GSS inhibitörü ile kombinasyonunun yabanıl tip FLT3ifadesine sahip AML hücrelerindeki etkisinin belirlenmesi ve mole- küler mekanizmalarının açıklanması amaçlanmıştır. Gereç ve Yöntem: Midostaurin, PDMP (GSS inhibitörü) ve kombi- nasyonların THP1 hücreleri üzerindeki sitotoksik ve sitostatik etki- leri sırasıyla MTT testi ve PI boyaması ile akım sitometri kullanılarakbelirlenmiştir. Kombinasyon indeksleri (CI) Calcusyn programı ilehesaplanmıştır. GSS ifadesi western blot ile belirlenmiştir.Bulgular: Midostaurin GSS ifadesini baskılamıştır. FLT3 ve GSS’ınbirlikte inhibe edilmesi kontrolle karşılaştırıldığında hücre çoğal- masını baskılamıştır. Kombinasyonlar sinerjistik sitotoksik etki gös- termiştir (CI<1). Kombinasyon hücre döngüsünün G2/M fazındakihücre populasyonunu arttırmıştır. Sonuç: Mutant olmayan FLT3 AML’de GSS inhibisyonunun midosta- urin’in etkisini arttırdığı saptanmıştır. Detaylı mekanizma çalışmalarıyapıldıktan sonra kombinasyon tedavisinin midostaurin’in sınırlıklinik kullanımını arttırması açısından yeni bir yaklaşım olabileceğidüşünülmektedir.Article Design, Molecular Docking and Molecular Dynamics Simulation Studies of Novel Pyridinecarboxamide Derivatives as Potent HDAC6 Inhibitors(2025) Akçok, İsmailHiston deasetilazlar (HDACs), gen ifadesinin ve hücresel süreçlerin düzenlenmesinde önemli rol oynayan bir enzim ailesidir. HDAC enzimleri homolojilerine, hücresel lokalizasyonlarına ve yapısal özelliklerine göre dört ana sınıfa ayrılır. Sınıf IIb enzimlerinden biri olan HDAC6 enzimi, hücre göçü, bağışıklık tepkileri ve nöronal işlev gibi çeşitli fizyolojik süreçlerde önemli işlevlere sahiptir. HDAC6 aktivitesinin düzensizliği, nörodejeneratif hastalıklarda toksik protein agregatlarının birikimiyle ilişkilendirilmiştir; kanser hücrelerinde aşırı ifadesi veya değişen aktivitesi ise metastaz ve tümör oluşumuna sebep olabilmektedir. Bu çalışmada, potansiyel HDAC6 inhibitörleri tasarlanmış ve bu moleküllerin inhibisyon potansiyelleri, moleküler kenetlenme, moleküler dinamik simülasyonları ve MM-PBSA hesaplamalarını içeren in silico protokolleri kullanılarak araştırılmıştır. Tasarlanan moleküller arasında IA64, HDAC6 enzimine karşı en iyi bağlanma profilini göstermiştir ve ileri çalışmalar için öncü bir molekül olarak görülebilir.Article Dalak Tirozin Kinaz ve Histon Deasetilaz Enzim İnhibisyonunun FLT3-ITD(+) Akut Miyeloid Lösemi Hücreleri Üzerindeki Anti-Lösemik Etkisi(2025) Akcok, E. Basak Gencer; Şansaçar, MerveSpleen Tyrosine Kinase (Syk) crosstalk with paramount signaling pathways which has a major contribution in the progress of acute myeloid leukemia (AML) such as PI3K, NFκB and JAK/STAT signaling pathways. Several studies recorded that deregulated Histone Deacetylase (HDAC) enzymes are involved in the pathogenesis of AML. The study aims to reveal the effect of Syk and HDAC co-inhibition on MOLM-13 and MV4-11 AML cells which are harboring the receptor of FMS-like Tyrosine Kinase's (FLT3) Internal Tandem Duplication (ITD). AML cells were incubated using both R406 and HDAC inhibitors alone and in combination, and increasing concentrations of R406 and HDAC inhibitors revealed a significant reduction of MOLM-13 and MV4-11 cells’ viability using MTT cell viability test. Furthermore, the combination of R406 and VPA resulted in a reduction in the proliferation of both cells correlated with the synergistic effect of the two drugs revealed by the combination index (CI). Moreover, investigating apoptosis for the combined administration of drugs resulted in induced apoptosis in AML cells using Annexin-V/PI double staining. We observed also changes in the mRNA expression level of MYC after combination treatment via Real-time PCR analysis. Even though further studies are needed, targeting Syk and HDAC enzymes in AML cells may be a good strategy in the treatment of patients suffering from AML with FLT3 ITD (+) mutation.Article Developing a Label Propagation Approach for Cancer Subtype Classification Problem(TUBITAK, 2021) Güner, P.; Bakir-Güngör, B.; Coşkun, M.; Şahan, Pınar GünerCancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. © 2022 Elsevier B.V., All rights reserved.Article Thermosensitive Pluronic® F127-Based in Situ Gel Formulation Containing Nanoparticles for the Sustained Delivery of Paclitaxel(2023) Unal, Sedat; Aktas, Yesim; Doğan, Osman; Tekeli, Merve CelikBone metastasis is one of the most encountered complications among cancer patients and majority of cancer types has led to bone metastasis. Paclitaxel (PCX) is an anticancer agent commonly used in cancer treatment. However, its clinical use is restricted owing to poor water solubility. PCL NPs were investigated to cope with solubility problem of PCX. The size, polydispersity index and zeta potential of PCL were 383.8±2.4 nm, 0.253±0.122 and +51.3±6.1 mV, respectively. The PCX encapsulation efficiency was 77.2±2.1%. Subsequently, in situ gellling system was prepared by using different Pluronic F-127 concentration in order to determine the optimum ratio. İn situ gel formulation containing 20% Pluronic F-127 was selected as the optimum formulation and subjected to characterization tests. The viscosity of in situ gelling system with CS/PCX-PCL NPs at room temperature (25 °C±0.1) and at body temperature (37 °C±0.1) were found 137.00 ±3.05 cP and 890.30 ±89.61 cP at 100 rpm, respectively. According to the release results, in situ gel provided prolonged release profile compared to PCL NPs alone. Consequently, in situ gel containing CS/PCX-PCL NP elucidated in detail is a promising approach for locally applicable injectable systems.Article Citation - WoS: 8Citation - Scopus: 10Lung Cancer Subtype Differentiation From Positron Emission Tomography Images(Tubitak Scientific & Technological Research Council Turkey, 2020-01-27) Ayyildiz, Oguzhan; Aydin, Zafer; Yilmaz, Bulent; Karacavus, Seyhan; Senkaya, Kubra; Icer, Semra; Kaya, Eser; Taşdemir, ArzuLung cancer is one of the deadly cancer types, and almost 85% of lung cancers are nonsmall cell lung cancer (NSCLC). In the present study we investigated classification and feature selection methods for the differentiation of two subtypes of NSCLC, namely adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). The major advances in understanding the effects of therapy agents suggest that future targeted therapies will be increasingly subtype specific. We obtained positron emission tomography (PET) images of 93 patients with NSCLC, 39 of which had ADC while the rest had SqCC. Random walk segmentation was applied to delineate three-dimensional tumor volume, and 39 texture features were extracted to grade the tumor subtypes. We examined 11 classifiers with two different feature selection methods and the effect of normalization on accuracy. The classifiers we used were the k-nearest-neighbor, logistic regression, support vector machine, Bayesian network, decision tree, radial basis function network, random forest, AdaBoostM1, and three stacking methods. To evaluate the prediction accuracy we performed a leave-one-out cross-validation experiment on the dataset. We also considered optimizing certain hyperparameters of these models by performing 10-fold cross-validation separately on each training set. We found that the stacking ensemble classifier, which combines a decision tree, AdaBoostM1, and logistic regression methods by a metalearner, was the most accurate method for detecting subtypes of NSCLC, and normalization of feature sets improved the accuracy of the classification method.Article Enlightening the Molecular Mechanisms of Type 2 Diabetes With a Novel Pathway Clustering and Pathway Subnetwork Approach(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Bakir-Gungor, Burcu; Yazici, Miray Unlu; Goy, Gokhan; Temiz, Mustafa; Ünlü Yazici, MirayType 2 diabetes mellitus (T2D) constitutes 90% of the diabetes cases, and it is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for T2D successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multigenic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three metaanalysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in silico approaches that proceed in top-down manner and bottom-up manner, and presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, PPI networks into GWAS can dissect leading molecular pathways, and it could offer improvement over traditional enrichment strategies.Article Cytotoxic and Cytostatic Effects of Targeting mTOR and Hedgehog Pathways in Acute Myeloid Leukemia(Istanbul Univ, 2022-12-29) Cicek, Enes; Kucuktas, Fulya Mina; Yenigul, Munevver; Akcok, Emel Basak GencerObjectives: Acute myeloid leukemia (AML) is a highly aggressive heterogeneous hematopoietic malignancy characterized by a rapid and abnormal proliferation of immature myeloid leukemia cells in the bone marrow and peripheral blood. Aberrant alterations in signal transduction pathways are strongly associated with the progression of AML. This study aimed to investigate cell viability and the cell cycle in AML cells by targeting the Hedgehog and mTOR signaling pathways with rapamycin and GANT61. Materials and Method: The antiproliferative effect of rapamycin and GANT61 was assessed by the MTT cell viability assay in two AML cell lines: CMK and MOLM-13. The effect of the inhibitors on cell-cycle distribution was determined using propidium iodide staining and measured with flow cytometry. Results: Rapamycin, an mTOR inhibitor, and GANT61, a Gli-1 inhibitor, decreased the cell proliferation of CMK and MOLM-13 cells. The IC20 values, which is the drug concentration that inhibits cell growth by 20%, were combined and administered to the cells. The results show the drugs to have a combinatorial inhibitory effect on CMK cells but not on MOLM-13 cells. In addition, the combination of drugs arrested the cells during the G0/G1 phase. Conclusion: This study suggests a novel combination therapy approach for AML via mTOR and Hedgehog signaling pathway inhibition using rapamycin and GANT61, respectively. It also suggest further studies be performed to reveal the mechanism of action.Article Citation - WoS: 3Combined Effect of Midostaurin and Sphingosine Kinase-1 Inhibitor on FMS-Like Tyrosine Kinase 3 (FLT3) Wild Type Acute Myeloid Leukemia Cells(Walter de Gruyter Gmbh, 2022-02-01) Sahin, Hande Nur; Adan, AysunObjectives Therapeutic potential of clinically approved FLT3 inhibitor midostaurin has been neglected in wild-type FLT3 positive acute myeloid leukemia (AML). Sphingosine kinase-1 (SK-1) having anti-proliferative functions is studied in various cancers, but not in FLT3 wild-type AML. We aimed to develop new therapeutic strategies to combat FLT3 wild-type AML by combining midostaurin with SK-1 inhibitor (SKI II) in THP1 cells. Methods The anti-proliferative effects of midostaurin, SKI II and in combination on THP1 cells were determined by MTT assay. The combination indexes were calculated using calcusyn software. SK-1 expression and PARP cleavage were checked by western blot. Cell cycle distributions (PI staining) and apoptosis (annexin-V/PI dual staining) were assessed by flow cytometry for each agent alone and in combinations. Results Midostaurin decreased SK-1 protein level. Midostaurin, SKI II and certain combinations decreased cell viability in a dose dependent manner. The combined anti-leukemic effects of the aforementioned drug combination afforded additive effect. Co-administration induced both necrosis and apoptosis via phosphatidylserine externalization, PARP cleavage and cell cycle arrest at G0/G1 and S phases. Conclusions Targeting sphingosine kinase-1 together with FLT3 inhibition could be a novel mechanism to increase limited clinic response to midostaurin in wild-type FLT3 overexpressing AML after further pre-clinical studies.Article Apatinib Sensitizes Human Breast Cancer Cells Against Navitoclax and Venetoclax Despite Up-Regulated Bcl-2 and Mcl-1 Gene Expressions(Kare Publ, 2021) Kavakcioglu Yardimci, Berna; Ozgun Acar, Ozden; Semiz, Asli; Sen, Alaattin; Acar, Ozden Ozgun; Yardımcı, Berna KavakcıoğluOBJECTIVE Defects in apoptotic cell death which restrict the success of conventional cytotoxic therapies have pivotal roles in a number of pathological conditions including cancer. However, a novel drug class targeting pro-survival Bcl-2 protein family members has been developed with the understanding of the structures and interactions of Bcl-2 proteins. Within this new class, Bcl-2/Bcl-xL inhibitor Navitoclax and Bcl-2 specific inhibitor Venetoclax have been shown to demonstrate strong anticancer activities on several types of cancers. But their low affinity to other anti-apoptotic proteins limits their clinical usage. Here, we investigated the cytotoxic and apoptotic effects of Navitoclax/Venetoclax and their combinations with specific tyrosine kinase inhibitor Apatinib on estrogen receptor (ER)-positive MCF-7 and ER-negative MDA-MB-231 breast cancer cell lines. METHODS MTT assay was used for the evaluation of the inhibition of cancer cell proliferation. ELISA test and Quantitative real-time PCR assay was performed to determine the role of caspase-3, Bak, Bax, Bcl-2, Bcl-xL and Mcl-1 proteins in the inhibition of cell proliferation triggered by the tested agents. RESULTS We found that aggressive MDA-MB-231 cell line was more sensitive to all tested agents. Apatinib significantly enhanced Navitoclax/Venetoclax mediated inhibition of cell viability in both cancer cell lines despite up-regulation in the expression levels of Bcl-2 and Mcl-1 genes. We further demonstrated significant Bak/Bax and caspase-3 expression in less aggressive MCF-7 cells. CONCLUSION Our findings have impacts on Navitoclax/Venetoclax plus Apatinib based therapy for breast adenocarcinoma. On the other hand, further studies should be conducted to elucidate the mechanisms underlying synergistic effects of Navitoclax/Venetoclax plus Apatinib combinations.