Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Investigation of the Interactions Between Cancer Cells and the Microenvironment at the Cellular Level(Izmir Institute of Technology, 2022) Yöndem, Eyüp; Pesen Okvur, Devrim; Pesen Okvur, DevrimBreast cancer is the most frequently diagnosed cancer type and the first leading cause of cancer-related deaths in women. Breast tumor mass is not only harboring cancer cells but also several types of stromal cells, including fibroblasts. While all of these stromal cells may have a calamitous effect on cancer progression, fibroblasts which make up nearly 80% of tumor mass present unique characteristics such as extensive extracellular matrix (ECM) production. In the context of tumors, the activated cells are referred to as cancer-associated fibroblasts (CAF), expressing several markers such as αSMA, FSP1, FAP, vimentin, and PDGFRβ. However, an in-depth understanding of the transdifferentiation of fibroblasts to CAFs is lacking. ECM components may change when cells become cancerous, which can alter cell behavior, facilitating proliferation, differentiation, and migration. Decellularized ECM(dECM) has recently been considered one of the tools to study in-vitro cell-ECM interaction. In this work, we utilized cancer cell-derived ECM(ccECM) to investigate its effect on the differentiation of the fibroblast to CAFs by compering decellularization methods called the extraction buffer and the freeze-thaw cycle. Our study suggested that ccECM from MDA-MB-231 impacted the fibroblasts' behavior from proliferation to differentiation via its ECM components, including fibronectin and laminin. The fibroblasts cultured on ccECM showed increased CAFs markers indicated above. Overall, ccECM could be one of the intermediate steps in fibroblast differentiation, but in the future, the factors present in ccECM should be scrutinized to understand the mechanisms behind this effect.Master Thesis Plant-On Devices for Sed Screening(Izmir Institute of Technology, 2019) Yetgin, Ali; Pesen Okvur, Devrim; Canlı, KeremThanks to their roots, plants take the required molecules from the soil, therefore their research is important. The fact that absorption takes place from the root hair makes the observations necessary. The inadequacy of traditional methods requires the development of new methods to ensure their observations, especially during root studies. The fact that chip systems have the features that can overcome the problems has caused plant researches by using this method. The fact that environmental factors can be imitated in chip systems paves the way for abiotic stresses to work. Although abiotic stresses have been studied extensively on plants, seed germination and subsequent root extension and root hair formation have not been studied in detail except for the model organism (Arabidopsis thaliana). The use of chip system for plant studies of scientists have begun the 21st century is also reveals the need to do more work in this area. Researchers show that they are excited about the advantages they bring to the system and that necessary studies will be carried out in other side branches. It is thought that more research will be done by using chip systems after a short time. By using chip systems, a suitable environment for seed growth can be provided and environmental conditions can be simulated. By creating the desired controlled environment, it is possible to create a system which results in less time and less cost in order to replace the inconvenient and expensive method.Master Thesis Cellular Mechanosensing at a Distance(Izmir Institute of Technology, 2019) Can, Ali; Pesen Okvur, Devrim; Özçivici, EnginThe goal of the project is to determine differences in mechanical sensing at a distance between breast cancer cells and normal mammary epithelial cells. To achieve this goal, we aim to: 1. Optimize the device for mechanical sensing at a distance 2. Determine the effect of mechanical sensing at a distance on cell proliferation 3. Determine the effect of mechanical sensing at a distance on cell migration Breast cancer is one of the cancers with the highest incidence and mortality rates in women in Turkey as well as in the world. Tumor microenvironment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Biochemical aspects of the interactions of cancer cells with the constituents of the microenvironment are widely studied whereas biophysical studies are at limited numbers. There is increasing evidence that extracellular matrix can change the mechanics and function of cancer and stroma cells. It has been observed that cancer cells show different responses to soft and stiff tissues they are in direct contact with than normal cells. However, it is not known whether the distance at which cancer cells can feel the stiffness of a distant tissue is longer, the same or shorter than that of normal cells. The hypothesis we will test in this project is as follows: The distance at which cancer cells can feel the stiffness of a distant tissue is shorter than that of normal cells.Master Thesis Evaluation of Biophysical Aspedts of Cancer Using Lab-On Chip Devices(Izmir Institute of Technology, 2019) Tahmaz, İsmail; Pesen Okvur, Devrim; Sürmeli, Nur BaşakBreast cancer metastasis is really crucial point from cancer related deaths. As cancer cells from primary tumor are travelling through blood, they hang on to blood vessel and finally they exit from blood vessel into secondary site where is extracellular matrix and/or tissue/organ. This process commonly known as extravasation. Cancer cells sometimes can be highly aggressive when it exposed to hypoxia referred low oxygen amount by activating HIF1α. This transcription factor is activated in malignant cells, normal cells and endothelial cells in blood vessel when oxygen amount decreased to certain levels and it induce several genes expression such as VEGF, LOX, Angiopoietin-like-4 etc. In this study we investigated effect of HIF1α which is hypoxia indicator on breast cancer extravasation by comparing to normal oxygen level. This study represents both anemic hypoxia physiologically and lead to understand underlying mechanism of extravasation into extracellular matrix related to low oxygen circulating through blood. In addition to HIF1α effects, dynamic perfusion mimicking blood flow was applied to determine effects on extravasation. For this purpose, lab-on-a chip device was utilized for real time visualization. In conclusion, although hypoxia is giving permission MDAMB231 to extravasate because of reshaping of vascular geometry, less extravasated cancer cells observed in matrix during hypoxia under both static and flow condition when compared to normoxic and static conditions. Moreover, it was shown that flow triggers extravasation distance in normoxia against static condition and normal breast epithelial cells extravasated away in hypoxia comparing breast cancer cells by means of flow.Master Thesis Mimicking the Tumor Microenvironment in Lab-On Devices(Izmir Institute of Technology, 2019) Bilgen, Müge; Pesen Okvur, Devrim; Sürmeli, Nur BaşakBreast cancer is one of the cancers with the highest incidence and mortality rates in women in the world. The leading cause of death for cancer patients is tumor metastasis. Cancer cells can extravasate the blood vessel, go through the distant organs and form the metastasis. Tumor microenvironment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Biochemical aspects of the interactions of cancer cells with the constituents of the microenvironment are widely studied whereas biophysical studies are at limited numbers. There is increasing evidence that extracellular matrix can change the mechanics and function of cancer and stroma cells. It has been observed that cancer cells show different responses to soft and stiff tissues they are in direct contact with than normal cells. New cell culture setups should be developed to better understand the interactions of cancer cells with their microenvironment. To develop a three dimensional (3D) in vitro model will allow the study of stiffness which is one of the mechanical features of extracellular matrix features first, 3D (dimensional) Controlled in vitro Microenvironments (CivMs) that mimic a blood vessel and its neighboring tissue in vivo will be fabricated using UV lithography. Monolayer which was formed by endothelial cells play a role in pathophysiological processes, so it shows a barrier role between both blood and tissues. To form a blood vessel bEnd.3 cell line was used. Collagen which is the most abundant protein in connective tissues were used to mimic extracellular matrix. pH value of collagen was changed and represented two different stiffness value. Here, the in vitro model we define as controlled in vitro microenvironments (CivM) is a lab-on-a-chip (LOC) application. In this microenvironment; MDA-MB-231 cells which are known to be invasive and MCF10A which is normal mammary epithelial cells were used as control. LOC devices were used to investigate cancer cell extravasation which is the prominent step of metastasis and extracellular matrix relation.Master Thesis Lab-on-a-chip devices for drug screening(Izmir Institute of Technology, 2019) Gökçe, Begüm; Pesen Okvur, Devrim; Çağır, AliBreast cancer is one of the cancers with the highest incidence and mortality rates in women in Turkey as well as in the world. Tumor micro environment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Research has shown that cell shape, adhesion, migration, response to growth factors and drugs are different in 2D and 3D culture. Today, only 8 out of 100 anti-cancer clinical trial gives effective results. 3D cell culture systems have shown to be a necessary step between in vitro, in vivo and clinical studies. Therefore, it is necessary to better understand the interactions of cancer cells with their micro environment, for which new cell culture setups are required. The most apparent disadvantage of widely used 3D cell culture setups is the lack of stromal cells. The systems to be developed should both provide a 3D environment and comprise multiple cell types. The drug screen in 3D tri-culture method with a lab-on-a-chip device, that will be developed in this study will be able to answer these needs. Cell lines that represent different breast cancer types alone or together with stromal cells were cultured in 3D in the to be developed lab-on-a-chip; by determining the effects of drugs with different targets on the viability and distribution of cells, a drug screening method is developed.Master Thesis Interactions of Cancer Cells and Macrophages on the Egf-Egfr Axis: Chemotaxis, Haptotaxis or Direct Contact?(Izmir Institute of Technology, 2017) Önal, Sevgi; Pesen Okvur, Devrim; Bulmuş Zareie, Esma VolgaBreast cancer cells (BCC) and macrophages are known to interact via epidermal growth factor (EGF) produced by macrophages and colony stimulating factor-1 (CSF-1) produced by BCC. Despite contradictory findings, this interaction is perceived as a paracrine loop. Yet, the underlying mechanism of interaction remains unclear. Here, we investigated interactions of BCC with macrophages in 2D and 3D. BCC did not show chemotaxis to macrophages in custom designed 3D cell-on-a-chip devices, which was in agreement with ELISA results showing that macrophage-derived-EGF was not secreted into macrophage-conditioned-medium. Live cell imaging of BCC in the presence and absence of iressa showed that macrophages but not macrophage-derivedmatrix modulated adhesion and motility of BCC in 2D. 3D co-culture experiments in matrigel and collagen showed that BCC changed their multicellular organization in the presence of macrophages. In custom designed 3D co-culture cell-on-a-chip devices, macrophages reduced and promoted migration of BCC in matrigel and collagen, respectively. Furthermore, adherent but not suspended BCC endocytosed EGFR when in contact with macrophages. Collectively, our data revealed that macrophages showed chemotaxis towards BCC-derived-CSF-1 whereas BCC required direct contact to interact with macrophage-derived-EGF. We propose that the interaction between cancer cells and macrophages is a paracrine-juxtacrine loop of CSF-1 and EGF, respectively.Master Thesis Antiproliferative Properties of 2'-alkoxymethyl Substituted Klavuzon Derivatives(Izmir Institute of Technology, 2017) Yıldız, Mehmet Salih; Pesen Okvur, Devrim; Çağır, Ali; Çağır, Ali; Pesen Okvur, DevrimOne of the main objectives of studies on anticancer agents is that the agent is expected to show a high cytotoxic activity on cancer cells and show a less cytotoxic effect on the contrary in healthy cells or never show cytotoxic activity. (R)- goniothalamin, isolated from the Goniothalamus plant, is a styryl lactone and has been found to have a selective antiproliferative property on cancer cells in studies conducted. The Michael acceptor feature in the structure of goniothalamin is thought to be covalently bonded to the nucleophilic side chains of the enzymes and show activity in this way. In previous studies, it has been shown that 1-naphthyl substituted 5,6-dihydro- 2H-pyran-2-one derivatives and 4'-methyl klavuzon derivatives exhibit higher cytotoxic activity on cancer cells than goniothalamin. In this study, antiproliferative properties of newly synthesized 2'-alkoxymethyl substituted klavuzon derivatives have been examined and MIA PaCa-2 pancreatic cancer cell lines and HPDEC pancreatic healthy cell lines were used. MTT cell viability tests were performed at the first step of this study. As a result of this study, it has been observed that the 2'-isobutoxymethylklavuzon derivative has selective cytotoxic activity on the MIA PaCa-2 cell line. It showed activity at lower concentrations than goniothalamin. Cytotoxic activities of the compounds are associated with the size of the R group at position 2’-. Methoxymethyl substituted the worst selective activity among these compounds whereas isobutoxy derivative the best selective one. In the second stage of the study, the inhibition on topoisomerase I enzyme was studied. The 2'-alkoxymethyl klavuzon derivatives were found to have Topo I enzyme inhibition properties depending on concentration and time manner. The study continued with choices methoxy and isobutoxy derivatives and these two compounds caused an arrest at G1 phase and DNA damage. Also, isobutoxy derivative induced apoptosis in the MIA PaCa-2 pancreatic cancer cell lines.Master Thesis Comparison Od Side Effects of Anti-Cancer Drugs in 2d and 3d And, Classical and Cell-On Cultures(Izmir Institute of Technology, 2016) Kankale, Deniz; Pesen Okvur, Devrim; Çağır, AliThe studies that aim to assess the effects of drugs developed against cancer at the cellular level use multiwell plates. However, these classical systems fail to reproduce the in-vivo like microenvironment necessary for realistic assessment. In addition, classical cell culture systems use high amount of materials increasing cost. On the other hand, lab-on-a-chip systems use minimal volumes of reagents and more importantly can mimic the in-vivo microenvironment via spatial and temporal control. Furthermore, it is known that cell response to drugs can be very different in 2D and 3D cell culture setups. Doxorubicin is a widely used anticancer drug. Here, doxorubicin uptake by highly metastatic human breast cancer cell line MDA-MB-231 and normal mammary epithelial cell line MCF10A were investigated using 2D and 3D, classical and cell-on-a-chip cultures. Drug uptake at 24, 48 and 72 hours various concentrations of the drug determined by measuring signal intensities from fluorescence microscopy images of cells. For cell viability assay, cells were stained with dapi and two cell lines were compared in systems. According to results, it was observed that 3D cell culture environment in chip provides more in-vivo like environment with less reagent consumption and cell viability is not correlated only with drug uptake.Master Thesis Invadopodia Formation on Nanometer Scale Protein Patterns(Izmir Institute of Technology, 2014) Batı, Gizem; Pesen Okvur, Devrim; Özyüzer, LütfiHow the positions of invadopodium in the cell are determined and if they have an adhesivefunction are not known. Using fluorescence microscopy and antibodies that recognize actin, cortactin and MT1-MMP proteins, invadopodia formed by breast cancer cells plated on protein nanopatterns of different geometeries and components after stimulation with epidermal growth factor which is known to induce invadopodia formation, were examined. Invadopodia formation was studied for the first time on nanometer scale, single and double active component, protein patterns with equal distance and gradient spacings. The results show that: • On K-casein-fibronectin nanopatterns, invadopodia prefer to form on K-casein which blocks cell adhesion rather than on fibronectin nanodots which promote cell adhesion. • On Laminin-fibronectin nanopatterns, invadopodia prefer to form on laminin rather than on fibronectin nanodots. • On gradient patterns, invadopodia prefer areas with wide spacings. These results support the hypotheses that the positions where invadopodia form can be determined by surface protein nanopatterns and that cell adhesion is not required at points where invadopodia will form.