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    cfDNA in exhaled breath condensate (EBC) and contamination by ambient air: toward volatile biopsies
    (Iop Publishing Ltd, 2019) Koc, Altug; Goksel, Tuncay; Pelit, Levent; Korba, Korcan; Dizdas, Tugberk N.; Baysal, Ertan; Uzun, Umut C.; Kaya, Ozge Ozer; Ozyilmaz, Berk; Kutbay, Yasar B.; Ozdemir, Taha Resid; Kirbiyik, Ozgur; Erdogan, Kadri M.; Guvenc, Merve Saka; Kocal, Gizem Calibasi; Basbinar, Yasemin
    Exhaled breath is a source of volatile and nonvolatile biomarkers in the body that can be accessed non-invasively and used for monitoring. The collection of lung secretions by conventional methods such as bronchoalveolar lavage, induced sputum collection, and core biopsies is limited by the invasive nature of these methods. Non-invasive collection of exhaled breath condensate (EBC) provides fluid samples that are representative of airway lining fluids. Various volatile and nonvolatile biomarkers can be detected in volatile condensates, such as H2O2, nitric oxide, lipid mediators, cytokines, chemokines, DNA, and microRNAs. Studies have examined cell-freeDNA(cfDNA) in plasma samples from non-small-cell lung cancer patients, offering to new insights and fostering development of the liquid biopsy. However, few studies have examined cfDNA in EBC samples. This study examined whether EBC is an appropriate source of cfDNA using housekeeping-gene-specific primer probes and quantitative real-time polymerase chain reaction in healthy subjects. Ambient (room) air is contaminated with DNA, so caution is needed. Preliminary studies indicated that volatile biopsies are becoming an important diagnostic tool in lung cancer.
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    In Silico Approach to Molecular Profiling of the Transition from Ovarian Epithelial Cells to Low-Grade Serous Ovarian Tumors for Targeted Therapeutic Insights
    (Mdpi, 2024) Leblebici, Asim; Sancar, Ceren; Tercan, Bahar; Isik, Zerrin; Arayici, Mehmet Emin; Ellidokuz, Ender Berat; Basbinar, Yasemin
    This paper aims to elucidate the differentially coexpressed genes, their potential mechanisms, and possible drug targets in low-grade invasive serous ovarian carcinoma (LGSC) in terms of the biologic continuity of normal, borderline, and malignant LGSC. We performed a bioinformatics analysis, integrating datasets generated using the GPL570 platform from different studies from the GEO database to identify changes in this transition, gene expression, drug targets, and their relationships with tumor microenvironmental characteristics. In the transition from ovarian epithelial cells to the serous borderline, the FGFR3 gene in the Estrogen Response Late pathway, the ITGB2 gene in the Cell Adhesion Molecule, the CD74 gene in the Regulation of Cell Migration, and the IGF1 gene in the Xenobiotic Metabolism pathway were upregulated in the transition from borderline to LGSC. The ERBB4 gene in Proteoglycan in Cancer, the AR gene in Pathways in Cancer and Estrogen Response Early pathways, were upregulated in the transition from ovarian epithelial cells to LGSC. In addition, SPP1 and ITGB2 genes were correlated with macrophage infiltration in the LGSC group. This research provides a valuable framework for the development of personalized therapeutic approaches in the context of LGSC, with the aim of improving patient outcomes and quality of life. Furthermore, the main goal of the current study is a preliminary study designed to generate in silico inferences, and it is also important to note that subsequent in vitro and in vivo studies will be necessary to confirm the results before considering these results as fully reliable.
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    SALIVARY PRO-INFLAMMATORY CYTOKINES AND SALIVARY BACTERIAL CHALLENGE EFFECT ON DENTAL CARIES: A CLINICO-MOLECULAR CROSS-SECTIONAL STUDY (vol 1, pg 77, 2020)
    (Dokuz Eylul Univ Inst Health Sciences, 2022) Pakdemirli, Ahu; Kocal, Gizem Calibasi; Kilinc, Gulser; Daskin, Ezgi; Kemaloglu, Hande; Basbinar, Yasemin; Ellidokuz, Hulya
    [No Abstract Available]
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    Ubiquitin-Proteasome Axis, Especially Ubiquitin-Specific Protease-17 (USP17) Gene Family, is a Potential Target for Epithelial-Mesenchymal Transition in High-Grade Serous Ovarian Cancer
    (Sage Publications Inc, 2019) Yildirim, Nuri; Kocal, Gizem Calibasi; Isik, Zerrin; Saatli, Bahadir; Saygili, Ugur; Uysal, Tugba; Ulukus, Cagnur; Koyuncuoglu, Meral; Ellidokuz, Hulya; Basbinar, Yasemin
    Objectives: To investigate gene expression differences and related functions between primary tumor, malignant cells in ascites, and metastatic peritoneal implant in high-grade serous ovarian cancer. Methods: Biopsies from primary tumor, peritoneal implant, and ascites were collected from 10 patients operated primarily for high-grade, advanced-staged serous ovarian cancer. Total RNA isolation was performed from collected tissue biopsy and fluid samples, and RNA expression profile was measured. Messenger RNA expression profiles of 3 different groups were compared. Functional analyses of candidate genes were carried out by gene ontology and pathway analysis. Results: There were significant differences in the expression of 5 genes between primary tumor and peritoneal implant, 979 genes between primary tumor and malignant cells in ascites, and 649 genes between peritoneal implant and malignant cells in ascites. Three commonly enriched gene ontology functions between "primary tumor and malignant cells in the ascites" and "peritoneal implant and malignant cells in the ascites" were protein deubiquitination, ubiquitin-dependent protein catabolism, and apoptotic processes. All genes related to these functions belonged to USP17 gene family. Conclusion: Gene expression difference between primary tumor and the peritoneal implant is not as much as the difference between primary tumor and free cells in the ascites. These results show that malignant cells in the ascites return into its genetic origin after they invade on the peritoneum. Significantly increased expression of DUB-enzyme genes, SNAR gene family, and ribosomal pathway genes in epithelial-mesenchymal transition suggests that this regulation is ubiquitin-proteasome dependent. Especially, this is the first study that offers USP17 as a potential target for epithelial-mesenchymal transition.