Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Epithelial-Mesenchymal Transition as a Potential Route for Dapt Resistance in Breast Cancer Cells(Walter de Gruyter GmbH, 2023) Tellı, Kubra; Ozuysal, Ozden Yalcın; Telli, Kübra; Yalçın Özuysal, ÖzdenObjectives: Notch is a conserved pathway involved in cell- fate determination and homeostasis. Its dysregulation plays a role in poor prognosis and drug resistance in breast cancer. Targeting Notch signaling via inhibition of the gamma- secretase complex is in the spotlight of modern cancer treat- ments. Gamma-secretase inhibitors (GSI) have shown suc- cessful clinical activity in treating cancers, yet the possible resistance mechanism remains unstudied. Modeling the resistance and understanding culprit molecular mechanisms can improve GSI therapies. Accordingly, the aim of this study is to generate and analyze GSI-resistant breast cancer cells. Methods: Gradually increasing doses of DAPT, a well-known GSI, were applied to MCF-7 breast cancer cell lines to generate resistance. Cell viability, migration and gene expressions were assessed by MTT, wound healing and qRT-PCR analyses. Results: DAPT-resistant MCF-7 cells exhibited abnormal expression of Notch receptors, Notch targets (HES1, HES5, HEY1), and epithelial-mesenchymal transition (EMT) markers (E-cadherin, ZO-1, SNAIL2, N-cadherin) to overcome the continuous increase in DAPT toxicity by increased migration through mesenchymal transition. Conclusions: This study prospects into the role of EMT in the potential resistance mechanism against DAPT treatment for breast cancer cells. Complementary targeting of EMT should be investigated further for a possible effect to potentiate DAPT’s anti-cancer effects.Article Citation - WoS: 4Citation - Scopus: 4Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells(Elsevier, 2022) Ayaz Güner, Şerife; Acar, Mustafa Burak; Boyvat, Dudu; Güner, Hüseyin; Bozalan, Habibe; Güzel, Melis; Yıldır, Selin Kübra; Altınsoy, Nilay; Fındık, Fatma; Karakükçü, Musa; Özcan, ServetAnalysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnetically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, followed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.Article Comparative Proteome Profiles of Methicillin-Resistant Staphylococcus Aureus in Response To Vanillic Acid and 2-Hydroxycinnamic Acid(Bentham Science Publishers, 2021) Keman, Deniz; Soyer, FerdaBackground: The ability of Staphylococcus aureus to cause severe infections and the difficulty of the treatments due to the multiple antibiotic resistance make this bacterium a lifethreatening human pathogen. This situation necessitates the exploration of novel antimicrobial compounds with known targets on bacteria. Phenolic acids naturally produced in plants as secondary metabolites are good candidates for being alternative antimicrobials for antibiotic-resistant bacteria. Objective: Investigation of protein profile of Methicillin-Resistant S. Aureus (MRSA) in the presence of subinhibitory concentrations of phenolic acids. Methods: MRSA was subjected to subinhibitory concentrations of Vanillic Acid (VA) and 2-Hydroxycinnamic Acid (2-HCA), separately, and the proteomic analyses were carried out by using liquid chromatography coupled to mass spectrometry. Results: Both phenolic acids elicited identification of differently expressed proteins that have roles in DNA replication, repair, RNA processing and transcription, protein synthesis, maintenance of cell homeostasis, several metabolic reactions in energy, carbohydrate and lipid metabolisms and also proteins related with the virulence and the pathogenicity of MRSA when compared with the control group. The numbers of the proteins identified were 444, 375, and 426 for control, VA-treated MRSA, and 2-HCA-treated MRSA, respectively, from which 256 were shared. While VA treatment resulted in 149 unidentified MRSA proteins produced in control, 2-HCA treatment resulted in 126 unidentified proteins. Data are available via ProteomeXchange with identifier PXD016922. Conclusion: The results obtained from this study might indicate the potential targets on bacteria and the effective use of phenolic acids in the battle with antibiotic-resistant pathogens.Article Citation - WoS: 2Citation - Scopus: 2Antiviral Microrna Expression Signatures Are Altered in Subacute Sclerosing Panencephalitis(Wolters Kluwer Medknow Publications, 2021) Tüfekçi, Kemal Uğur; Allmer, Jens; Çarman, Kürşat Bora; Bayram, Erhan; Topçu, Yasemin; Hız, Semra; Genç, Şermin; Yiş, UluçBackground: Subacute sclerosing panencephalitis (SSPE) is a chronic, progressive disease caused by a persistent infection of the measles virus. Despite extensive efforts, the exact neurodegeneration mechanism in SSPE remains unknown. MicroRNAs (miRNAs) have emerged as an essential part of cellular antiviral defense mechanisms and can be modulated by antiviral cytokines Such as interferon-beta (IFN-beta). Aims and Objectives: In this study, we aimed to elucidate the role of antiviral miRNAs in the pathogenesis of SSPE and analyze the interaction between host antiviral miRNAs and virus genes. Materials and Methods: Thirty-seven patients who were followed with SSPE and age-matched healthy children were included in the study. Peripheral blood mononuclear cell levels of miR-196b, miR-296, miR-431, and miR-448 were analyzed using quantitative polymerase chain reaction. Target predictions and pathway constructions of deregulated miRNAs were assessed. Results: Here, we showed that IFN-beta-modulated miR-196b, miR-296, and miR-431 were significantly upregulated in patients with SSPE compared with healthy controls. Besides, sequence complementarity analysis showed that miR-296 and miR-196b predicted binding regions in measles virus genomic RNA. Conclusion: Our findings suggest that antiviral miRNAs are upregulated in patients with SSPE, which could be a part of the host antiviral defense mechanism. </p>Article Citation - WoS: 8Citation - Scopus: 8Simple High-Performance Liquid Chromatographic Method for Determination of Donepezil Hcl in Pharmaceutical Formulations(ACG Publications, 2020) Bulduk, İbrahim; Aydın, Beyza SultanDonepezil HCl is a hydrochloride salt of a piperidine derivative acetylcholinesterase inhibitor and, it uses in treatment demantia of Alzheimer’s disease. In this study, a sensitive and rapid HPLC-UV method was developed and validated for determination of Donepezil HCl in API and tablet dosage forms. Chromatographic separation was performed using a Ace 5 C18 (5 ?m, 250 x 4.6 mm) by using isocratic phosphate buffer at pH:2.0 and acetonitrile (55:45, v/v) mobile phase was used at the rate of 1.2 mL/min. The column temperature was set at 30 ?C and the UV detection was recorded at 268 nm. The method was validated with respect to specificity, precision, accuracy, linearity, repeatability and reproducibility parameters in a concentration range of 25-125 µg/mL. The limit of detection (LOD) and limit of quantification (LOQ) were determined as 1.40 and4.20 µg/mL, respectively. The uncertainty budget of the measurement for Donepezil HCl was estiamted as 5.80 % at 95% confidence level (k = 2).Article Citation - WoS: 2Citation - Scopus: 2Identification of Cytoplasmic Sialidase Neu2-Associated Proteins by Lc-ms/Ms(Türk Biyokimya Derneği, 2019) Akyıldız Demir, Seçil; Seyrantepe, VolkanBackground: Cytoplasmic sialidase (NEU2) plays an active role in removing sialic acids from oligosaccharides, gly-copeptides, and gangliosides in mammalian cells. NEU2 is involved in various cellular events, including cancer metabolism, neuronal and myoblast differentiation, proliferation, and hypertrophy. However, NEU2-interacting protein(s) within the cell have not been identified yet. Objective: The aim of this study is to investigate NEU2 interacting proteins using two-step affinity purification (TAP) strategy combined with mass spectrometry analysis. Methods: In this study, NEU2 gene was cloned into the pCTAP expression vector and transiently transfected to COS-7 cells by using PEI. The most efficient expression time of NEU2- tag protein was determined by real-time PCR and Western blot analysis. NEU2-interacting protein(s) were investigated by using TAP strategy combined with two different mass spectrometry experiment; LC-MS/MS and MALDI TOF/TOF. Results: Here, mass spectrometry analysis showed four proteins; a-actin, beta-actin, calmodulin and histone H1.2 proteins are associated with NEU2. The interactions between NEU2 and actin filaments were verified by Western blot analysis and immunofluorescence analysis. Conclusions: Our study suggests that association of NEU2 with actin filaments and other protein(s) could be important for understanding the biological role of NEU2 in mammalian cells.Editorial Citation - WoS: 3Citation - Scopus: 4La médecine de précision en oncologie: challenges, enjeux et nouveaux paradigmes(John Libbey Eurotext Ltd, 2019) Cox, Stephanie; Rousseau-Tsangaris, Marina; Abou-Zeid, Nancy; Dalle, Stephane; Leurent, Pierre; Cutivet, Arnaud; Baran, YusufL'oncologie médicale a pris, depuis quelques années, un tournant substantiel en intégrant la dimension génomique dans la prise de décision thérapeutique. En raison de l'accès aux technologies de séquençage (exome complet, séquençage ciblé du génome, séquençage de l'ARN, ADN circulant. . .) facilité par la mise en place de plateformes de biologie moléculaire et la diminution des coûts par échantillon, la caractérisation moléculaire est devenue un outil supplémentaire à la disposition du clinicien, s'ajoutant au diagnostic histologique et immunohistochimique et aux données d'imagerie radiologique. Cette approche moléculaire a permis d'identifier de nouvelles formes nosologiques et permet, au-delà de l'aspect cognitif, de renseigner sur les altérations qui sont à prendre en compte dans les décisions thérapeutiques (biomarqueurs prédictifs, activation de voies spécifiques, mutations de résistance). C'est dans ce contexte de profond et rapide changement de pratique médicale et scientifique qu'il a été proposé de réfléchir collectivement aux nouveaux enjeux sous la forme d'un workshop à l'occasion de Biovision qui s'est tenu à Lyon, du 4 au 6 avril 2017.Article Citation - WoS: 3Citation - Scopus: 3Frequency and Levels of Potential Drug-Drug Interactions in Tuberculosis Patients of a Teaching Hospital in Pakistan(Colegio de Farmaceuticos de la Provincia de Buenos Aires, 2016) Uddin, Fayyaz; Khan, Nasar; Ghani, Shamsul; Khan, Saeed A.Polypharmacy in tuberculosis is used to prevent occurrence of resistance to mycobacteria. However, drug-drug interaction is one of the undesirable consequences of polypharmacy, that may lead to ineffective medication or change in therapeutic response. The objective of the study was to identify prevalence, types and nature of potential drug-drug interactions in tuberculosis patients at Khyber Teaching Hospital, Peshawar Pakistan. Medical records of 409 randomly-selected patients were reviewed for pDDIs using Micromedex Database. Results show that total 304 interacting-combinations lead to 1437 potential drug-drug interactions. 87.5% of the these potential drug-drug interactions were of moderate and major severity (i.e., 65.6% and 44.3% respectively). With regards to scientific-evidence, almost 50% of the potential drug-drug interactions were good documented while 34.7% had fair level of documentation. Furthermore, we have listed some of the interacting drug combinations, particularly most frequent major and moderate interactions, will help health care professionals to review their established therapeutic strategy for tuberculosis patients in their clinical settings.Article Citation - WoS: 24Citation - Scopus: 29Il-17, Il-21, and Il-22 Cytokines of T Helper 17 Cells in Cancer(Mary Ann Liebert, 2019) Nalbant, AytenCD4(+) T helper (Th) cells are important regulators of cellular immune response. Newly discovered interleukin (IL)-17-producing CD4(+) T cells are known as T helper 17 cells (Th17). They are distinct subset from the T helper type 1 (Th1) and 2 (Th2) lineages. The differentiation of Th17 cells has been intensively studied; however, the role of Th17 cells in different diseases including cancer is still under investigation. Besides IL-17 family cytokines, Th17 cells produce IL-22, IL-21, and IL-26. The dysregulated function of Th17 cells and their cytokines could contribute to pathology of diseases, including cancer. The role of cytokines of Th17 cells such as IL-17, IL-21, and IL-22 in cancer will be discussed in this review.Article Citation - WoS: 18Citation - Scopus: 17Cnt Incorporated Polyacrilonitrile/Polypyrrole Nanofibers as Keratinocytes Scaffold(Trans Tech Publications, 2019) İnce Yardımcı, Atike; Aypek, Hande; Öztürk, Özgür; Yılmaz, Selahattin; Özçivici, Engin; Meşe, Gülistan; Selamet, YusufPolypyrrole (PPy) is an attractive scaffold material for tissue engineering with its non-toxic and electrically conductive properties. There has not been enough information about PPy usage in skin tissue engineering. The aim of this study is to investigate biocompatibility of polyacrilonitrile (PAN)/PPy nanofibrous scaffold for human keratinocytes. PAN/PPy bicomponent nanofibers were prepared by electrospinning, in various PPy concentrations and with carbon nanotube (CNT) incorporation. The average diameter of electrospun nanofibers decreased with increasing PPy concentration. Further, agglomerated CNTs caused beads and disordered parts on the surface of nanofibers. Biocompatibility of these PAN/PPy and PAN/PPy/CNT scaffolds were analyzed in vitro. Both scaffolds provided adhesion and proliferation of keratinocytes. Nanofiber diameter did not significantly influence the morphology of cells. However, with increasing number of cells, cells stayed among nanofibers and this affected their shape and size. In this study, we demonstrated that PAN/PPy and PAN/PPy/CNT scaffolds enabled the growth of keratinocytes, showing their biocompatibility.