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Publication Metadata only Activation of toll-like receptor signaling in endothelial progenitor cells dictates angiogenic potential: from hypothesis to actual state(Springer, 2021) Avci, Cigir Biray; Saberianpour, Shirin; Ahmadi, Mahdi; Hassanpour, Mehdi; Bagheri, Hesam Saghaei; Rezaie, Jafar; Talebi, Mehdi; Roodbari, Fatemeh; Darabi, Masoud; Rahbarghazi, Reza; N/A; Heidarzadeh, Morteza; Sokullu, Emel; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; N/A; 163024Human endothelial progenitor cells (EPCs) were isolated from cord blood samples and enriched by magnetic activated cell sorting method based on the CD133 marker. Cells were incubated with different doses of bacterial lipopolysaccharide, ranging from 2, 5, 10, 50, 100, 200, 250, 500, to 1000 mu g/ml, for 48 h. The cell survival rate was determined by using MTT assay. To confirm activation of the toll-like receptor signaling pathway, PCR array analysis was performed. Protein levels of ERK1/2, p-ERK1/2, NF-kappa B and TRIF proteins were measured using western blotting. The content of TNF-alpha and lipoprotein lipase activity were analyzed by immunofluorescence imaging. Flow cytometric analysis of CD31 was performed to assess the maturation rate. Cell migration was studied by the Transwell migration assay. The expression of genes related to exosome biogenesis was measured using real-time PCR analysis. In vivo gel plug angiogenesis assay was done in nude mice. Lipopolysaccharide changed endothelial progenitor cells' survival in a dose-dependent manner with maximum viable cells in groups treated with 2 mu g/ml. PCR array analysis showed the activation of toll-like signaling pathways after exposure to LPS (p<0.05). Western blotting analysis indicated an induction of p-ERK1/2 and Erk1/2, NF-kappa B and TRIF in LPS-treated EPCs compared with the control (p<0.05). Immunofluorescence staining showed an elevation of TNF-alpha and lipoprotein lipase activity after lipopolysaccharide treatment (p<0.05). Lipopolysaccharide increased EPC migration and expression of exosome biogenesis-related genes (p<0.05). In vivo gel plug analysis revealed enhanced angiogenesis in cells exposed to bacterial lipopolysaccharide. Data highlighted the close relationship between the toll-like receptor signaling pathway and functional activity in EPCs.Publication Metadata only Antioxidant activity of CAPE (caffeic acid phenethyl ester) in vitro can protect human sperm deoxyribonucleic acid from oxidative damage(Elsevier, 2018) Ayla, Sule; Tunali, Gulden; Bilgic, Bulent E.; Sofuoglu, Kenan; Ozdemir, A. Arman; Tanriverdi, Gamze; Ozdemir, Semra; Soner, B. Cem; Ozturk, Bahar; Aslan, Esra Guler; Seckin, Ismail; N/A; Karahüseyinoğlu, Serçin; Faculty Member; School of Medicine; 110772Purpose: Sperm processing (e.g., centrifugation) used in preparation for assisted reproduction can result in excessive generation of reactive oxygen species (ROS) and potential sperm damage. The use of antioxidants during sperm processing has been shown to prevent iatrogenic sperm damage, including DNA damage. In this study, we evaluated the effect of caffeic acid phenethyl ester (CAPE) on oxidative stress mediated sperm dysfunction and DNA damage. Methods: Semen samples were obtained to liquefy at room temperature. After centrifugation and washing protocols, spermatozoa were incubated in a single step supplemented medium with either of 10, 50 or 100 mu mol/L CAPE for 2 hours at 36 degrees C. After incubation period, MDA levels of seminal plasma were measured. The fragmentation in sperm DNA was detected by light microscopy via use of an aniline blue assay, while ultrastructural morphology was analyzed by transmission electron microscopy. Results: Significant increase has been observed in percent chromatin condensation (assessed by aniline blue staining) and Malondialdehyde (Mmol/L) in oligoasthenoteratozoospermia group before the centrifugation (0.57 +/- 0.15). Incubation of samples with 100 mu mol/L CAPE after centrifugation resulted in a significantly lower percent chromatin condensation compared to samples incubated without CAPE (0.42 +/- 0.12) (P < 0.0033). Incubation of all samples with CAPE (10 mu mol/L, 50 mu mol/L, 100 mu mol/L.) after centrifugation resulted in a significantly lower percentage of Malondialdehyde levels. Conclusions: The data suggests that preincubation of spermatozoa with the antioxidant CAPE offers protection against oxidative DNA damage in vitro.Publication Open Access Antiviral activity of an N-allyl acridone against dengue virus(BioMed Central, 2015) Mazzucco, Maria B.; Talarico, Laura B.; Carro, Ana C.; Fascio, Mirta L.; D'Accorso, Norma B.; Garcia, Cybele C.; Damonte, Elsa B.; N/A; Vatansever, Sezen; PhD Student; Graduate School of Sciences and EngineeringBackground: Dengue virus (DENV), a member of the family Flaviviridae, is at present the most widespread causative agent of a human viral disease transmitted by mosquitoes. Despite the increasing incidence of this pathogen, there are no antiviral drugs or vaccines currently available for treatment or prevention. In a previous screening assay, we identified a group of N-allyl acridones as effective virus inhibitors. Here, the antiviral activity and mode of action targeted to viral RNA replication of one of the most active DENV-2 inhibitors was further characterized. Results: The compound 10-allyl-7-chloro-9(10H)-acridone, designated 3b, was active to inhibit the in vitro infection of Vero cells with the four DENV serotypes, with effective concentration 50% (EC50) values in the range 12.5-27.1 mu M, as determined by virus yield inhibition assays. The compound was also effective in human HeLa cells. No cytotoxicity was detected at 3b concentrations up to 1000 mu M. Mechanistic studies demonstrated that virus entry into the host cell was not affected, whereas viral RNA synthesis was strongly inhibited, as quantified by real time RT-PCR. The addition of exogenous guanosine together with 3b rescued only partially the infectivity of DENV-2. Conclusions: The acridone derivative 3b selectively inhibits the infection of Vero cells with the four DENV serotypes without a direct interaction with the host cell or the virion but interfering specifically with the intracellular virus multiplication. The mode of antiviral action for this acridone apparently involves the cellular enzyme inosine-monophospahe dehydrogenase together with another still unidentified target related to DENV RNA synthesis.Publication Metadata only Artificial intelligence based methods for hot spot prediction(Current Biology Ltd, 2022) N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Övek, Damla; Abalı, Zeynep; Zeylan, Melisa Ece; Keskin, Özlem; Gürsoy, Attila; Tunçbağ, Nurcan; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 26605; 8745; 245513Proteins interact through their interfaces to fulfill essential functions in the cell. They bind to their partners in a highly specific manner and form complexes that have a profound effect on understanding the biological pathways they are involved in. Any abnormal interactions may cause diseases. Therefore, the identification of small molecules which modulate protein interactions through their interfaces has high thera-peutic potential. However, discovering such molecules is challenging. Most protein-protein binding affinity is attributed to a small set of amino acids found in protein interfaces known as hot spots. Recent studies demonstrate that drug-like small molecules specifically may bind to hot spots. Therefore, hot spot prediction is crucial. As experimental data accumulates, artificial intelligence begins to be used for computational hot spot prediction. First, we review machine learning and deep learning for computational hot spot prediction and then explain the significance of hot spots toward drug design.Publication Open Access beta III-Tubulin: a novel mediator of chemoresistance and metastases in pancreatic cancer(Impact Journals, 2015) McCarroll, Joshua A.; Sharbeen, George; Liu, Jie; Youkhana, Janet; Goldstein, David; McCarthy, Nigel; Limbri, Lydia F.; Dischl, Dominic; Ceyhan, Gueralp O.; Johns, Amber L.; Biankin, Andrew V.; Kavallaris, Maria; Phillips, Phoebe A.; N/A; Erkan, Murat Mert; Faculty Member; School of Medicine; 214689Pancreatic cancer is a leading cause of cancer-related deaths in Western societies. This poor prognosis is due to chemotherapeutic drug resistance and metastatic spread. Evidence suggests that microtubule proteins namely, beta-tubulins are dysregulated in tumor cells and are involved in regulating chemosensitivity. However, the role of beta-tubulins in pancreatic cancer are unknown. We measured the expression of different beta-tubulin isotypes in pancreatic adenocarcinoma tissue and pancreatic cancer cells. Next, we used RNAi to silence beta III-tubulin expression in pancreatic cancer cells, and measured cell growth in the absence and presence of chemotherapeutic drugs. Finally, we assessed the role of beta III-tubulin in regulating tumor growth and metastases using an orthotopic pancreatic cancer mouse model. We found that beta III-tubulin is highly expressed in pancreatic adenocarcinoma tissue and pancreatic cancer cells. Further, we demonstrated that silencing beta III-tubulin expression reduced pancreatic cancer cell growth and tumorigenic potential in the absence and presence of chemotherapeutic drugs. Finally, we demonstrated that suppression of beta III-tubulin reduced tumor growth and metastases in vivo. Our novel data demonstrate that beta III-tubulin is a key player in promoting pancreatic cancer growth and survival, and silencing its expression may be a potential therapeutic strategy to increase the long-term survival of pancreatic cancer patients.Publication Open Access BRD9-containing non-canonical BAF complex maintains somatic cell transcriptome and acts as a barrier to human reprogramming(Elsevier, 2022) Philpott, M.; Cribbs, A.P.; Dunford, J.E.; Sigua, L.H.; Qi, J.; Oppermann, U.; Department of Molecular Biology and Genetics; N/A; Sevinç, Kenan; Cavga, Ayşe Derya; Kelekçi, Simge; Can, Hazal; Yıldız, Abdullah Burak; Yılmaz, Alperen; Ayar, Enes Sefa; Ata, Deniz; Önder, Tamer Tevfik; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Sciences and Engineering; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 42946Epigenetic reprogramming to pluripotency requires extensive remodeling of chromatin landscapes to silence existing cell-type-specific genes and activate pluripotency genes. ATP-dependent chromatin remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of recently identified Bromodomain-containing protein 9 (BRD9) and the associated non-canonical BRG1-associated factors (ncBAF) complex in reprogramming remains unknown. Here, we show that genetic or chemical inhibition of BRD9, as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, increase human somatic cell reprogramming efficiency and can replace KLF4 and c-MYC. We find that BRD9 is dispensable for human induced pluripotent stem cells under primed but not under naive conditions. Mechanistically, BRD9 inhibition downregulates fibroblast-related genes and decreases chromatin accessibility at somatic enhancers. BRD9 maintains the expression of transcriptional regulators MN1 and ZBTB38, both of which impede reprogramming. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers chromatin-based barriers to reprogramming.Publication Open Access C-Abl is not activated in DNA damage-induced and Tap63-mediated oocyte apoptosis in human ovary(Springer, 2018) Department of Molecular Biology and Genetics; N/A; N/A; Bildik, Gamze; Ayhan, Ceyda Açılan; Şahin, Gizem Nur; Karahüseyinoğlu, Serçin; Öktem, Özgür; Teaching Faculty; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; School of Medicine; Graduate School of Health Sciences; N/A; N/A; N/A; 110772; 102627There is a controversy in literature as to whether c-Abl is crucial for the induction of TAp63-mediated apoptosis and whether that inhibition of c-Abl with imatinib, which was designed to inhibit the oncogenic kinase BCR-ABL and c-kit, protects oocytes from chemotherapy-induced apoptosis in mice. No human data are available on this issue. We therefore aimed to explore whether genomic damage induced by chemotherapy drug cisplatin activates c-Abl along with TAp63 and the inhibition of c-Abl with imatinib prevents cisplatin-induced oocyte death and follicle loss in human ovary. Exposure to cisplatin induced DNA damage, activated TAp63 and SAPK/JNK pathway, and triggered apoptosis in the oocytes and granulosa cells. However, TAp63 activation after cisplatin was not associated with any increase in the expression of c-Abl. Imatinib did not prevent cisplatin-induced apoptosis of the granulosa cells or oocytes. Moreover, treatment with this drug resulted in the formation of bizarre shaped follicles lacking oocytes and increased follicular atresia by inducing apoptosis of granulosa cells and oocytes. Similar toxic effects were observed when ovarian tissue samples were incubated with a c-kit antagonist drug anti-CD117, but not with another c-Abl tyrosine kinase inhibitor GNF-2, which lacks an inhibitory action on c-kit. Intraperitoneal administration of imatinib to the xenografted animals produced similar histomorphological abnormalities in the follicles in human ovarian grafts and did not prevent cisplatin-induced follicle loss when co-administered with cisplatin. Our findings provide, for the first time, a molecular evidence for ovarian toxicity of this drug in human. Furthermore, this study together with two previous case reports of a severely compromised ovarian response to gonadotropin stimulation and premature ovarian failure in patients, while receiving imatinib, further heighten the concerns about its potential gonadotoxicity on human ovary and urge caution in its use in young female patients.Publication Metadata only Celcular and molecular dynamics of in-vitro 2D and 3D cultured blastocysts throughout the implantation process(Amer Soc Cell Biology, 2016) Yucel, D.; N/A; Karahüseyinoğlu, Serçin; Şahin, Gizem Nur; Kocabay, Ahmet; Taşkın, Ali Cihan; Faculty Member; PhD Student; Other; Other; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Health Sciences; N/A; N/A; N/A; N/A; N/A; Koç University Hospital; 110772; N/A; N/A; 291296N/APublication Metadata only Celcular and molecular dynamics of in-vitro 2D and 3D cultured blastocysts throughout the implantation process(Amer Soc Cell Biology, 2016) Yucel, D.; N/A; Karahüseyinoğlu, Serçin; Şahin, Gizem Nur; Kocabay, Ahmet; Taşkın, Ali Cihan; Faculty Member; PhD Student; Other; Other; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Health Sciences; N/A; N/A; N/A; N/A; N/A; Koç University Hospital; 110772; N/A; N/A; 291296N/APublication Metadata only Cell scientist to watch - Elif Nur Fırat-Karalar(Company Biologists Ltd, 2019) Breuer, Manuel; N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; N/A; Faculty Member; Department of Molecular Biology and Genetics; N/A; College of Sciences; N/A; 206349N/A