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Yayın Agmatine reverses Sub-chronic stress induced Nod-like receptor Protein 3 (NLRP3) activation and cytokine response in rats(John Wiley & Sons, Ltd, 2016) Sahin, Ceren; Albayrak, Ozgur; Akdeniz, Tuğba F.; Akbulut, Zeynep; Yanıkkaya Demirel, Gülderen; Arıcıoğlu, FeyzeThe activation of Nod-like receptor protein 3 (NLRP3) has lately been implicated in stress and depression as an initiatormechanism required for the production of interleukin (IL)-1band IL-18. Agmatine, an endogenous polyamine widely distributedin mammalian brain, is a novel neurotransmitter/neuromodulator, with antistress, anxiolytic and antidepressant-like effects. In thisstudy, we examined the effect of exogenously administered agmatine on NLRP3 inflammasome pathway/cytokine responses inrats exposed to restraint stress for 7 days. The rats were divided into three groups: stress, stress+agmatine (40 mg/kg; i.p.) andcontrol groups. Agmatine significantly down-regulated the gene expressions of all stress-induced NLRP3 inflammasomecomponents (NLRP3, NF-jB, PYCARD, caspase-1, IL-1band IL-18) in the hippocampus and prefrontal cortex (PFC) andreduced pro-inflammatory cytokine levels not only in both brain regions, but also in serum. Stress-reduced levels of IL-4 andIL-10, two major anti-inflammatory cytokines, were restored back to normal by agmatine treatment in the PFC. The findings ofthe present study suggest that stress-activated NLRP3 inflammasome and cytokine responses are reversed by an acute administra-tion of agmatine. Whether antidepressant-like effect of agmatine can somehow, at least partially, be mediated by the inhibition ofNLRP3 inflammasome cascade and relevant inflammatory responses requires further studies in animal models of depression.Yayın Capsaicin Alters the Expression of Genetic and Epigenetic Molecules In Hepatocellular Carcinoma Cell(Cellular & Molecular Biology Research Center, 2023) Ates, Beren; Oner, Cagri; Akbulut, Zeynep; Colak, ErtugrulCapsaicin is a natural product which is extracted from pepper and has the potential to be used in cancer treatment because of its anti- proliferative effects. The aim of the study was to determine the effect of capsaicin on the hepatocellular carcinoma cell proliferation and the expressions of related genetic markers as Ki-67, PI3K/AKT/mTOR and epigenetic markers as miR-126 and piR-Hep-1. The inhibitory concentration of capsaicin in HepG2 cells was determined. piR-Hep-1 and miR-126 expressions and Ki-67, PI3K, AKT and mTOR gene expressions were examined by RT-PCR. The inhibitory concentration of capsaicin for HepG2 cells was 200 nM and the decreased proliferation was observed at 24th hour. As epigenetic markers, an up regulation of miR-126 and down regulation of piR-Hep-1 expression were determined after treatment. Moreover, Ki-67, PI3K and mTOR gene expressions decreased while AKT gene expression increased after the treatment (p<0.001). According to the obtained data, capsaicin has an impact on proliferation both genetically and epigenetically. Furthermore, treatment of capsaicin effects miR-126 and piR-Hep-1 expressions which effect carcinogenesis in different way. Moreover, there are some clues which indicate that these two small non-coding RNA might affect each other and share the same target molecules post-transcriptionally.Yayın Çoğalma ve farklılaşma aşamasındaki karaciğer karsinoma hücrelerinde oksidatif stres (ros) üzerine tip 1 kollajenin etkileri1(İKSAD, 2021) Akbulut, Zeynep; Atay, Mertcan; Aktaş, Ranan Gülhan; Harem, İsmail Şah; Toptan, Müslüm; Bucak, FerayGiriş:Hepatosellüler Karsinoma (HCC), erken prognozu zor ve tedavi seçenekleri cok sınırlı olan bir kanser türüdür. Dünyada kansere bağlı mortalitenin önde gelen ikinci nedenidir. Hücrelerde reaktif oksijen türlerinin (ROS) aşırı üretilmesi, antioksidanların yeterli gelmemesine ve oksidatif stres denilen durumun ortaya çıkmasına neden olur. Amaç: Çalışma, hücre dışı matriksin en yaygın bileşenlerinden biri olan tip I kollajen varlığına bağlı olarak, HCC hücre hattı olan HepG2 hücrelerinde oksidatif stres üzerine etkilerini incelemeyi amaçlamaktadır. Yöntem: Klasik kültür ve iki boyutlu tip I kollajen kaplı kültür kaplarında HepG2 hücreler 37C° ve %5CO2 içeren kültür ortamında kültüre edildi. Hücreler kültür yüzeyini %60-70 oranında kapladıkları çoğalma aşamasında, tüm yüzeyi kaplayarak farklılaşmaya başladıkları dönemde ve 1 hafta sonra olmak üzere üç periyotta inverted mikroskop altında incelendi ve ROS seviyeleri analiz edildi. Tüm gruplarda ROS analizi yapılan hücre sayısı 200.000 olarak sabitlendi. Bulgular: Tip I kollajen varlığında kültüre edilen hücrelerde ROS seviyesi çoğalma aşaması ve tam konfluent olmaya başladığı farklılaşma aşamasında, kontrol grubu hücrelere göre daha yüksek bulurken, 1 hafta sonraki farklılaşmaya devam ettiği dönemde anlamlı olarak düşüş göstermiştir. Ayrıca hücrelerin tip I kollajen varlığında morfolojik olarak değişikler gösterdiği gözlenmiştir. Sonuç:Elde edilen sonuçlar, tip I kollajenin HepG2 hücrelerin, farklılaşma dönemde ROS seviyesi üzerinde etki gösterdiği görülmüştür. Kanser hücrelerinde ROS seviyesinin azalmasına neden olan mekanizmaların araştırılması, oksidatif stres ve yeni kematerapotiklerin geliştirilmesi ilgili çalışmalara katkı sağlayabilir.Yayın Culturing, Freezing, Processing, and Imaging of Entire Organoids and Spheroids While Still in a Hydrogel(Journal of Visualized Experiments, 2022) Tok, Olgu Enis; Demirel, Gamze; Saatci, Yusuf; Akbulut, Zeynep; Kayalar, Özgecan; Aktas, Ranan GülhanOrganoids and spheroids, three-dimensional growing structures in cell culture labs, are becoming increasingly recognized as superior models compared to two-dimensional culture models, since they mimic the human body better and have advantages over animal studies. However, these studies commonly face problems with reproducibility and consistency. During the long experimental processes -with transfers of organoids and spheroids between different cell culture vessels, pipetting, and centrifuging -these susceptible and fragile 3D growing structures are often damaged or lost. Ultimately, the results are significantly affected, since the 3D structures cannot maintain the same characteristics and quality. The methods described here minimize these stressful steps and ensure a safe and consistent environment for organoids and spheroids throughout the processing sequence while they are still in a hydrogel in a multipurpose device. The researchers can grow, freeze, thaw, process, stain, label, and then examine the structure of organoids or spheroids under various high-tech instruments, from confocal to electron microscopes, using a single multipurpose device. This technology improves the studies' reproducibility, reliability, and validity, while maintaining a stable and protective environment for the 3D growing structures during processing. In addition, eliminating stressful steps minimizes handling errors, reduces time taken, and decreases the risk of contamination.Yayın The effects of low-dose sorafenib on epithelial-mesenchymal transition and multidrug resistance markers in HepG2 cell line(Prusa Medical Publishing, 2023) Dönmez Çakıl, Yaprak; Akbulut, Zeynep; Demirel, Gamze; Güneş Özünal, Zeynep; Aktaş, Gülhan RananObjectives: Sorafenib is an orally administered tyrosine kinase inhibitor in hepatocellular cancer. Low sorafenib concentrations are attained during pharmacotherapy due to pharmacokinetic profile and patient inadherence. Resistance to treatment is a limitation to improving survival. Underlying mechanisms include epithelial-mesenchymal transition. The aim of the study was to evaluate epithelial-mesenchymal transition and multidrug resistance-related parameters in HepG2 cells following low-dose and short-term sorafenib treatment. Methods: Epithelial-mesenchymal transition and multidrug resistance-related markers were examined by quantitative PCR, flow cytometry, and confocal laser scanning microscopy. Results: An increase in epithelial marker E-cadherin and downregulation of mesenchymal markers Vimentin and Snail1 were detected by gene expression analysis. While P-glycoprotein expression increased, multidrug resistance protein 1, and breast cancer resistance protein mRNA levels did not alter after sorafenib treatment. The accumulation of the ABC transporter substrate rhodamine 123 in the cells increased following the treatment, corresponding to a less efficient efflux of rhodamine 123 and a possible effect on other transporters and mechanisms. Conclusions: The results indicate a protective effect of sorafenib against epithelial-mesenchymal transition and upregulation in P-glycoprotein expression, which is, however, not sufficient to cause less intracellular rhodamine 123 accumulation. The effects of low-dose and short-term sorafenib on epithelial-mesenchymal transition and multidrug resistance-related markers might contribute to enlightening new treatment strategies in hepatocellular cancer.Yayın MECHANICAL STIFFNESS OF PEGDA BASED HYDROGELS AFFECTS FORMATION OF HEPG2 SPHEROIDS IN 3D SCAFFOLDS(Wiley, 2021) Ulugöl, R. K.; Demirel, Gamze; Akbulut, Zeynep; Yener, Nese; Tok, Olgu Enis; Decker, Heather; Mellot, A. J.[Abstract Not Available]Yayın Modulation of YAP1 expression and other related signaling pathways in HepG2 cells by extracellular matrix, contact inhibition and cell density(American Association for the Study of Liver Diseases, 2022) Aktas, Ranan; Akbulut, Zeynep; Maraş, Hatice; Çakıl Dönmez, Yaprak; Kayalı, Damla; Karagoz Koroglu, Ayca; Sitar, Mustafa Erinc; Kısakol, Batuhan; Baysan, MehmetBackground: Hippo-YAP pathway is a key modulator in liver development, regeneration and the metabolism . Cell density, cell contact, the actin cytoskeleton, and extracellular matrix (ECM) composition have been shown to be involved in regulation of this pathway . The intervention of this pathway in hepatocellular carcinoma remains a central focus . The study aimed to examine how YAP1 integrate mechanical cues with the response to signal transduction pathways and to multiple aspects of cell behavior, proliferation, protein/lipid secretion, apoptosis/necrosis, adhesion, and stemness . Methods: HepG2 cells were cultured on uncoated (1), or Type I collagen (2), standard matrigel (3) or high concentration-matrigel coated surfaces (4) for 6 weeks . The cells were examined at 60% or 100%confluency, and at the end of each week by qRT-PCR, confocal microscopy, MTT, ELISA, and flow cytometry. Expression of 84 genes including YAP1, cell adhesion molecules (Inhibin, Cadherin, Na-K ATPase), apoptotic/necrotic changes, viability, protein/ lipid secretion, and existence of 7 different cancer stem cells were compared with Spearmen correlation test . Results: YAP1 gene expression changed significantly in Group1. Contact inhibition with 100% confluency caused deacrease at YAP1 in all groups . It was always low in group4 when compared with the others . Strong correlation between the YAP1, Actin-beta, and most of the genes in TGFB, AKT-P13 and RAS/RAF/MAPK pathways were clear (Graph I) . Positive correlation between cholesterol /LDL/HDL secretion; negative correlation between protein secretion, necrosis and CD133 (+) cells were notable . Conclusion: Herein, we described for the first time how liver cancer cells translate complex and dynamic changes at the external cues into signaling conduits that impact on YAP and other related gene expressions as well as on metabolic and morphological features of the cells . The study demonstrated the striking changes through the receptor of integrin alpha2beta1 that is stimulated by type I collagen . Changes in group 3 and 4 suggest that growth factors in stroma is another important factor at the response related to YAP1 expression. To our knowledge, this is the first study demonstrates Actin and YAP1 interaction at the gene expression level .Yayın Monitoring T-Cell kinetics in the early recovery period of lung transplantation cases by copy number levels of T-Cell receptor excision circle(International Institute of Anticancer Research., 2023) Akdeniz, F. Tuğba; Akbulut, Zeynep; Vayvada, Mustafa; Kalamanoğlu, Merih; Yeğinsu, Ali; Yanıkkaya Demirel, Gülderen; Asım Kutlu, CemalLung transplantation is a lifesaving procedure for patients with end-stage lung diseases. T-Cell receptor excision circle (TREC) is cireular DNA produced during T-Cell receptor gene rearrangement in the thymus and indicates naive T-cell migration from the thymus...
