Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Optimization of a Liver Organ on Chip System for the Investigation of Breast Cancer Cell Invasion(01. Izmir Institute of Technology, 2023) Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyThere are many challenges in creating an accurate and physiologically relevant three-dimensional (3D) model of the liver such as finding the suitable liver extracellular matrix (ECM) components and cell types for the development of cell-laden liver-on-a-chip systems. In recent years, precision tissue slice-based methods are used to reduce the problems caused by the cell-laden liver-on-a-chip system complexity. However, these methods require sophisticated tools which are not easily accessible. This study focuses on the development of a 3D liver model using simple and cost-effective methods. To achieve this, we aimed to optimize liver tissue size, maintenance and culture medium, scaffold gel, and viability assay. The needle method was found to be the easiest, most efficient, and cheap method for tissue processing as the equipment used was easily accessible and evaded enzymatic steps. Moreover, consistent samples that were all similar and in the desired size were easy to obtain. In addition to these, functionality and viability were analysed for 72 hours to assess the physiological state of the liver after tissue processing. Based on these findings a novel liver-on-a-chip system was successfully developed and as the next step, the invasion of the MDA-MB-231 breast cancer cell line towards the liver was investigated with and without the presence of C-X-C chemokine receptor type 4 (CXCR4) antagonists AMD3100 and AMD3465. In conclusion, this study demonstrated the development of a novel 3D model for the liver and provided a platform for studying breast cancer invasion with its potential implications for cancer therapy research.Master Thesis Role of Human Aprataxin Protein in P53-Related Cellular Processes in Breast Cells(01. Izmir Institute of Technology, 2021) Doğan, Hülya; Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; 01. Izmir Institute of Technology; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of ScienceAprataxin encoded by APTX, which is the human homolog of yeast HNT3, reverses adenylation damages emerged from abortive DNA ligation during ribonucleotide and base excision repair. Thus, it corrects AMP-modified nucleic acid termini and protects genome integrity as a DNA ligase "proofreader". Role of HNT3, which is a candidate p53-related gene, against DNA oxidative and alkylating damage indicates its antioxidant importance. Besides, previous studies demonstrated that absence of Aprataxin gives rise to ROS generation and oxidative stress in addition to mitochondrial dysfunction. Also, role of Aprataxin in drug and radiotherapy sensitivity was shown in many cancer. Since conformation of cysteine residues in p53 DNA-binding domain can be modified by oxidizing environment, functionality can be influenced by defective APTX. Although p53-Aprataxin interaction has been shown by co-immunoprecipitation, effects of APTX on p53 pathway were not studied. Aim of this study is to investigate Aprataxin-driven changes in p53-regulated processes in p53 wild-type cells through. According to results, Aprataxin overexpression leads to cell cycle arrest in low stress levels. However, it triggers cell death against induced stress in MCF10A cells. Moreover, apoptotic assay on MCF10A APTX Crispr cells indicated elevated level of basal cell death. Also, expression analysis of p53 targets in APTX knockdown MCF7 cells revealed that extrinsic apoptosis pathway might be induced. Consequently, these results help us to gain insight into how Aprataxin affects activity of p53 pathway. Further investigation providing stress accumulation based assays and protein level analysis is needed to figure out whether resulting changes are p53-dependent or not.Master Thesis Investigating the Effect of Human Sacm1l Gene in the P53 Wild Type Breast Epithelial Mcf10a and Breast Cancer Mcf7 Cells(01. Izmir Institute of Technology, 2021) Efe, Eda; Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; 01. Izmir Institute of Technology; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Sciencep53, tumor suppressor protein, plays role in the regulation of many cellular processes. Thus, p53 activity is controlled by a series of mechanisms, one of which is a redox reaction. However, redox regulation of p53 is not well defined in the literature. As a candidate of antioxidant, Sac1 gene mutation resulted in decreased levels of human p53 protein in transformed yeast, but the human homolog of Sac1 (SACM1L) has not been studied yet. SACM1L is known to function as a phosphoinositide phosphatase, hydrolyzes PI4P in the Golgi and ER. Previous studies demonstrated SACM1L depletion in HeLa cells led to decreased viability and arrest at the G2/M phase. However, no data were found on the association between the SACM1L and either directly p53 or p53 mediated cellular processes. We aimed to investigate the role of SACM1L in p53 controlled cellular processes like cell cycle and apoptosis in p53 wild type (wt) breast epithelial cells MCF10A and breast cancer cells MCF7 in the presence or absence of SACM1L gene. We demonstrated that SACM1L knockout MCF7 cells were arrested in the G1 phase, and number of proliferating cells was reduced, whereas overexpression of SACM1L did not change the proliferation, and cell cycle. Further, the rate of apoptosis was increased in SACM1L overexpressing and knockout MCF10A and MCF7 cells, supported by the findings of transcriptional analysis for p53 target genes. In conclusion, the greatest effect of SACM1L was observed in the apoptosis, but the underlying mechanisms are still unclear and must be further studied.