2016 – 2021 Gebze Technical University, Institute of Natural and Applied Sciences, Molecular Biology and Genetics Doctorate Program
Thesis Advisor: Prof. Dr. Ayşe Gül Gürek
Thesis co-advisor: Prof. Dr. Gülderen Yanıkkaya Demirel
Thesis Title: Evaluation of Novel Zinc, Indium and Silicon Phthalocyanines' Anti-Cancer Properties
2013 – 2016 Yeditepe University, Institute of Health Sciences, Molecular Medicine Master Program
Thesis Advisor: Prof. Dr. Gülderen Yanıkkaya Demirel
Thesis Title: Effect of Testosterone Propionate on Bone Marrow Derived Mesenchymal Stem Cells’ Proliferation and Viability
2009 – 2013 İstanbul University, Faculty of Science, Biology Department
Division of Molecular and Cellular Biology
RESEARCH, TEACHING, or OTHER INTERESTS
Multidisciplinary, Immunology, Cancer Research, General Biochemistry, Genetics and Molecular Biology
Immunological Biomarkers in Oral Leukoplakia According to Oral Intraepithelial Neoplasia (OIN) Classification: A Comparative Analysis of Salivary and Plasma Cytokines Hakan Yülek, Gaye Keser, Başak Aru, Filiz Namdar Pekiner, Gülderen Yanıkkaya Demirel Journal of Oral Pathology and Medicine, 2026 Background Oral leukoplakia (OL) is the most common oral potentially malignant disorder, defined as a white patch or plaque not attributable to other causes. While OL carries an inherent risk of malignant transformation, the underlying immunological changes remain poorly characterized. This study aimed to profile a broad panel of cytokines in saliva and plasma of OL patients in comparison to healthy controls, in order to elucidate local and systemic immunoinflammatory alterations associated with OL. Methods Thirty patients with clinically and histopathologically confirmed OL and 30 age‐ and gender‐matched healthy controls were enrolled. Detailed clinical examinations were performed, including lesion characterization and psychosocial assessments. Unstimulated whole saliva and peripheral blood samples were collected, and concentrations of 13 cytokines/chemokines (IL‐1β, IL‐6, IL‐8/CXCL8, IL‐10, IL‐12p70, IL‐17A, IL‐18, IL‐23, IL‐33, TNF‐α, IFN‐γ, IFN‐α2, and MCP‐1/CCL2) were measured using a multiplex bead‐based immunoassay. Group comparisons were performed using appropriate statistical tests ( χ 2 /Fisher's exact test for categorical variables and t ‐test or Mann–Whitney U test for continuous variables), with statistical significance set at p < 0.05. Results OL patients (mean age 52.4 ± 10.7 years) and controls (59.9 ± 12.8 years) showed no significant differences in gender, socioeconomic status, or psychological scores. Salivary levels of IL‐1β, TNF‐α, MCP‐1, IL‐8, and IL‐18 were significantly lower in OL patients compared to controls ( p < 0.01 for all), whereas other salivary cytokines (IFN‐α2, IFN‐γ, IL‐6, IL‐10, IL‐12p70, IL‐17A, IL‐23, IL‐33) showed no significant differences. In contrast, plasma levels of IFN‐α2, IL‐6, IL‐12p70, IL‐17A, IL‐18, and IL‐33 were significantly higher in OL patients than in controls ( p < 0.05), indicating systemic inflammation, while plasma IL‐1β, IFN‐γ, TNF‐α, MCP‐1, IL‐8, IL‐10, and IL‐23 did not differ. No significant differences in salivary cortisol, liver enzymes, or hepatitis viral markers were observed between groups. Across histopathological subgroups, cytokine concentrations did not significantly differ between lesions graded as hyperkeratosis, OIN1, OIN2, or OIN3, although a trend toward higher plasma IL‐6, IL‐17A, and IL‐18 levels was observed in cases with higher OIN grades. Conclusion These findings shed light on the inflammatory profile of OL. The decrease in salivary IL‐1β, IL‐8, TNF‐α, and MCP‐1 may indicate a more suppressed local immune response, whereas the higher plasma levels of IL‐6, IL‐17A, IL‐18, and IL‐33 tend to be seen in lesions showing greater degrees of dysplasia. In particular, patients with higher OIN grades often display this systemic inflammatory shift, which may signal an increased risk of progression.
Unveiling the Anticancer Potential of Verbascum aydogdui: Isolation, Characterization, and In Vitro Studies Şerife Sena Günaydın, Anita Barta, Ayşe Nur Çaldıran, Başak Aru, Mehtap Tekşen, Judit Hohmann, Hasan Kırmızıbekmez Chemistry and Biodiversity, 2026 Cytotoxic activity‐guided fractionation of the ethanolic extract of Verbascum aydogdui , an endemic halophyte plant to Türkiye, resulted in the isolation of 16 secondary metabolites, including eight triterpene saponins, mulleinsaponins III ( 1 ), ilwensisaponin A ( 2 ), buddlejasaponin I ( 3 ), mulleinsaponin IV ( 4 ), ilwensisaponins D ( 5 ), ilwensisaponin C ( 6 ), craniosaponin A ( 7 ) and buddlejasaponin Ia ( 8 ), six iridoid glycosides, aucubine ( 9 ), eurostoside ( 10 ), geniposidic acid ( 11 ), nigroside III ( 13 ), 6‐ O ‐β‐D‐glucopyranosylaucubine ( 12 ), 6‐ O ‐[3‐ O ‐( E ‐feruloyl)‐α‐L‐rhamnopyranosyl]‐aucubine ( 14 ), and two phenylethanoid glycosides, verbascoside ( 15 ) and alyssonoside ( 16 ). Compounds 1 – 5 displayed significant cytotoxicity against PC3, HEPG2, HGC27, A375, MCF7, and SW480 cancer cell lines with half‐maximal inhibitory concentration values of 17.6–85.1 µM, being 2 and 3 the most cytotoxic ones. Thus, 2 and 3 were further assayed for their cell death mechanisms, including apoptosis and necrosis. Compound 2 exerted anti‐cancer effects in all cancer cell lines tested, except for MCF7, especially via inducing apoptosis. Its apoptotic activity was predominantly mediated by a significant increase in p53 and p21 expressions in all cancer lines tested, but for SW480. This is the first bioactivity and phytochemical study on V. aydogdui . Our results indicated that 2 could be a potential anticancer natural product that merits further in vitro and in vivo studies.
Indole ring linked thiazolidone hybrid molecules as potent tubulin inhibitors Abdulrahman Abba, Naz Unal, Zulal Sevgi Dede, Ipek Bedir, Dilek Telci, Başak Aru, Gülderen Yanıkkaya Demirel, Güneş Yıldırım Akdeniz, Ahmet Can Timuçin, Burcin Gungor, Hülya Akgün Letters in Drug Design and Discovery, 2025 Tubulin inhibitors are a prominent class of antineoplastic agents for cancer therapy, with many established drugs originating from plant-derived compounds such as vinca alkaloids and taxanes. A new series of twenty-four 5-(substituted) benzylidene-2-{[2-(3H-indol-3-yl)ethyl]imino}-3-phenyl-1,3-thiazolidin-4-one derivatives (1−24) was synthesized based on assuming that it would inhibit tubulin polymerization, successfully. To assess their biological potential these derivatives were subjected to a comprehensive screening including cytotoxic activity using various cancer cell lines, cell death studies, cell motility and migration analysis, assessment of the compounds' ability to inhibit tubulin polymerization, and computational analysis. Out of the twenty-four synthesized compounds, specifically compounds 8, 10, 15, 21, and 23 demonstrated a desirable selective cytotoxic effect against the MCF7 cancer cell line compared to the healthy epithelial counterparts. Mechanistic studies confirmed that these five active compounds functioned as tubulin polymerization inhibitors, exhibiting an inhibitory mechanism similar to that of vinblastine. Computational analyses strongly supported these findings, demonstrating that the five active compounds possessed a high affinity binding to the tubulin structure. Compound 15 was identified as the most potent derivative, causing significant cell cycle arrest and inducing a distinct apoptotic effect in MCF7 cells. 2-{[2-(3H-indol-3-yl)ethyl]imino}-3-phenyl-5-[(3-hydroxy-4-methoxy phenyl)methylidene]-1,3-thiazolidin-4-one (15) represents a novel chemical series targeting microtubules. This compound emerged as a promising potential hit molecule due to its selective cytotoxicity against MCF7 cells, potent vinblastine-like tubulin polymerization inhibition. • Novel indole-thiazolidine hybrid molecules synthesized as anticancer agents. • The five compounds exerted antiproliferative action on MCF7 cells, selectively. • Compounds inhibitory actions on tubulin polymerization supported by computational analysis. • Tubulin polymerization was defected upon compound 15 treatment which caused apoptosis. • Compound 15 possessing 3-hydroxy-5-methoxy emerged as a potential hit molecule.
Citrate-Enhanced PCL Scaffolds for Bone Tissue Engineering Muge Musmula, Oguz Sogut, Basak Aru, Gizem Gurel, Serdar Sezer, Gulderen Yanıkkaya Demirel, Umran Aydemir Sezer Advanced Materials Interfaces, 2025 Filling key bone deficiencies with functional grafts and providing structural support is essential for 3D scaffold creation in bone tissue engineering. This study develop a new composite ink based on polycaprolactone (PCL) combined with FDA‐approved citrate‐based plasticizers to improve PCL for bone regeneration. This method increase PCL's mechanical strength, flexibility, and bioactivity. Four scaffold models, triple hexagon, grid, gyroid, and zigzag, are created utilizing composite ink filaments and precision extrusion‐based additive manufacturing. Chemical characterisation, mechanical compression, cellular proliferation, osteocyte differentiation, and gene expression assessments of scaffold models assess scaffold suitability for bone tissue engineering. Compared to pure PCL scaffolds, PCL/TBC and PCL/ATBC composite scaffolds increase cell growth by up to 35%. In the PCL/TBC group, gene expression analysis show considerable upregulation of osteogenic markers as ALP and BMP. The receptor activator of nuclear factor‐kappa B ligand (RANKL), which inhibits apoptosis and forms osteoclasts, is not expressed in any group. The created groups have increased osteoinductive capacity, according to these data. These findings demonstrate the PCL/TBC composite ink and tri‐hexagon scaffold model's ability to aid bone repair through 3D printing.
