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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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    Liquid biopsy for EGFR mutations in non-small cell lung cancer cases by RT-PCR
    (European Respiratory Soc Journals Ltd, 2018) Koc, Altug; Goksel, Tuncay; Komurcuoglu, Berna; Kaya, Ozge Ozer; Ozyilmaz, Berk; Gursoy, Pinar; Kutbay, Yasar B.; Kirbiyik, Ozgur; Ozdemir, Taha Resid; Erdogan, Kadri Murat; Guvenc, Merve Saka; Kocal, Gizem Calibasi; Baskin, Yasemin
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    Salivary Pro-Inflammatory Cytokines and Salivary Bacterial Challenge Effect on Dental Caries: A Clinico-Molecular Cross-Sectional Study
    (2020) Pakdemirli, Ahu; Kocal, Gizem Calibasi; Kılınç, Gülser; Daşkın, Ezgi; Başpınar, Yasemin; Kemaloğlu, Hande; Ellidokuz, Hülya
    Objectives: Objective of this study is to determine the correlation between salivary cytokine concentrations and cariogram value high (C1) and low (C2) experience in people. in this direction, saliva cytokines showed a significant correlation with the patient’s caries experience.Patients and Methods: Unstimulated whole saliva samples were collected from 38 appropriate populations of patients aged between 20 to 57 years old. All patients’ DMF (decay/missing/filled) values were higher than 0. Twenty-one caries activity groups (C1) and 17 caries non-activity groups (C2) patients were collected for this study. Procedures of the clinical evaluation were the collection of saliva samples and oral examination. the whole saliva from 38 patients with C1 and C2 was investigated for the existence of GM-CSF, TNF?, IFN-g, IL-2, IL-4, IL-6, IL-8, and IL-10.Results: the study population consisted of 38 subjects with a mean age of 34.76±14.43 years. Likewise, there was a significant interaction between salivary flow rate, S. Mutans number, number of Lactobacillus, number of meals and IL-6, a significant difference in caries activity groups.Conclusion: Salivary cytokines demonstrated significant interactions to caries experience of the patient.
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    Salivary Pro-Inflammatory Cytokines and Salivary Bacterial Challenge Effect on Dental Caries: A Clinico-Molecular Cross-Sectional Study
    (2020) Pakdemirli, Ahu; Kemaloğlu, Hande; Kılınç, Gülser; Ellidokuz, Hülya; Kocal, Gizem Calibasi; Daşkın, Ezgi; Başpınar, Yasemin
    Objectives: Objective of this study is to determine the correlation between salivary cytokine concentrations and cariogram value high (C1) and low (C2) experience in people. In this direction, saliva cytokines showed a significant correlation with the patient’s caries experience.Patients and Methods: Unstimulated whole saliva samples were collected from 38 appropriate populations of patients aged between 20 to 57 years old. All patients’ DMF (decay/missing/filled) values were higher than 0. Twenty-one caries activity groups (C1) and 17 caries non-activity groups (C2) patients were collected for this study. Procedures of the clinical evaluation were the collection of saliva samples and oral examination. The whole saliva from 38 patients with C1 and C2 was investigated for the existence of GM-CSF, TNF?, IFN-g, IL-2, IL-4, IL-6, IL-8, and IL-10.Results: The study population consisted of 38 subjects with a mean age of 34.76±14.43 years. Likewise, there was a significant interaction between salivary flow rate, S. Mutans number, number of Lactobacillus, number of meals and IL-6, a significant difference in caries activity groups.Conclusion: Salivary cytokines demonstrated significant interactions to caries experience of the patient.
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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.