Browsing by Subject "Cancer stem cells"

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Open Access
Alterations in the molecular properties of neural stem cells from aged brains and brain tumors
(2017-06) Burhan, Özge Pelin
It is known that new neuron formation in the brain continues throughout the life of an organism. In the adult human brain, it was proven that neurogenesis in the hippocampus is higher than expected, almost 700 new neurons are formed in a day. The formation of new neurons is supported by the stem cell subpopulation in the brain. With learning and the formation of new memories, the neuron production increases. However, changes in the cognitive abilities with advancing age are thought to be caused by the functional and molecular alterations in the stem cell populations. Molecular changes in neural stem cells throughout aging were found to be deterrents of the increased risk of cancer with age, such as tumor suppressor mechanisms. However, the activation and overlap of tumor suppressing mechanisms result in senescence in stem cells that have accumulated oncogenic mutations, which causes the stem cell pool exhaustion. It is thought that cancer cells acquire stem cell-like properties in order to have the unlimited proliferation and self-renewal properties, which are characteristics of both healthy and cancer stem cells. Neural cancer stem cells have the ability to produce glial and neural cells, like normal stem cells. The cancer stem cell subpopulations are implicated in the growth of tumor tissues. Hence, it is important to identify and characterize cancer stem cells and make a distinction between cancer and non-cancer stem cells. In this project, this issue was addressed by studying the marker expressions of brain tumor tissues obtained from humans, which confirmed that the cancer cells do express stem cell and progenitor cell markers, such as Sox2 and Vimentin. The presence of mature neurons was also established by the mature neuronal marker NeuN. In order to determine whether these stem cells may be different in young and old subjects, a study was also carried out in young and old zebrafish neural stem cells in order to identify the expression differences between the groups. The presence of proliferating stem cells and differentiated cells were identified in cell culture. This analysis of neural stem cells in old and young zebrafish revealed 18 differentially-expressed genes. The results indicated a higher differentiation rate in old zebrafish stem cells, which may be due to the increased loss of neural cells in the old zebrafish brain. The development of markers that could be widely used for the diagnosis of cancer and the identification of cell types is important. For reliable diagnosis and identification of cancer cells, multiple cellular markers are used. Hence the distinction of cell types based on light scattering differences would speed up the process of diagnosis, and the elimination of marker used for the distinction of cell types would be beneficial. The final project mentioned in this thesis involves the analysis of C6 (rat glioma) cell line for scattering properties and cell cycle arrest. A general method for definition of a scatter data interval for C6 cells in different stages was developed and can be applied to other cell types and diseases. These studies show that the proliferation and stem cell markers’ expressions differ between cancer and healthy stem cells, and the expression of neuroprotective genes is differentially upregulated in old zebrafish neural stem cells compared to the young. This data could contribute to the knowledge on normal and cancer stem cell expression differences, as well as how age affects the expression, and supply information required for the development of a cancer stem cell identification and targeting methods.
Open Access
Autologous anti-SOX2 antibody responses reflect intensity but not frequency of antigen expression in small cell lung cancer
(BioMed Central Ltd., 2014) Atakan, S.; Bayiz, H.; Sak, S.; Poyraz, A.; Vural, B.; Yildirim, A. S.; Demirag, F.; Gure, A. O.
Background: Anti-SOX2 antibody responses are observed in about 10 to 20% of small cell lung cancer (SCLC) patients. The aim of this study was to determine whether such responses reflect a particular pattern of SOX2 protein expression in the tumor and whether this pattern associates with clinical outcome. Methods. Paraffin embedded tumor tissues, obtained from SCLC patients who had no evidence of paraneoplastic autoimmune degeneration, were evaluated for SOX2 expression by immunohistochemistry for both intensity and extent of staining. Sera from the same patients were tested for autologous antibodies against recombinant SOX2 by enzyme-linked immunosorbent assay (ELISA). Correlates between overall survival and various clinical parameters including SOX2 staining and serology were determined. Results: SOX2 protein expression was observed in tumor tissue in 89% of patients. Seventeen patients (29%) were seropositive for SOX2 antibodies and, in contrast to SOX2 staining, the presence of antibody correlated with limited disease stage (p = 0.05). SOX2 seropositivity showed a significant association with the intensity of SOX2 staining in the tumor (p = 0.02) but not with the frequency of SOX2 expressing cells. Conclusion: Anti-SOX2 antibodies associate with better prognosis (limited stage disease) while SOX2 protein expression does not; similar to reports from some earlier studies. Our data provides an explanation for this seemingly contrasting data for the first time as SOX2 antibodies can be observed in patients whose tumors contain relatively few but strongly staining cells, thus supporting the possible presence of active immune-surveillance and immune-editing targeting SOX2 protein in this tumor type. © 2014 Atakan et al.; licensee BioMed Central Ltd.
Open Access
Cancer stem cell biology
(Trakya Üniversitesi, 2019) Chau, Tieu Lan; Xhafa, Erta; Göktuna, Serkan İsmail
Cancer is becoming the leading cause of death all around the world. To develop better therapeutic options against cancer, we need a thorough understanding of tumor development and dissemination. As our knowledge increases, it becomes apparent that cancer is a very complex disease and this complexity is partially due to the great level of heterogeneity even within the same tumor mass. Therefore, there is a pressing need to decipher complex regulations and interactions of the tumor cells that lead to different hierarchies. Concepts of tumor-initiating and self-renewing stem cells have long been proposed to explain the emergence of a vast number of progenies within monoclonal neoplastic growth. It is now known that cancer stem cells which are found in many cancers have many roles in tumor development and dissemination. Many fascinating properties of cancer stem cells draw further attention to clarify their involvement in tumor cell plasticity, epithelial to mesenchymal transition, chemotherapy resistance and to develop therapeutic strategies for their targeting. Here we summarized recent efforts to illustrate the progress in our understanding of the biology of cancer stem cells.
Open Access
Characterization of chemosensitivity profiles of breast cancer cell lınes, with and without stem cell like features = Kök-hücre özelliği olan ve olmayan meme kanseri hücre hatlarının ilaç hassasiyet profillerinin tanımlanması
(2014) Akbar, Muhammad Waqas
Breast cancer is the second most common cause of death worldwide from cancer due to complications with its diagnosis and resistance to therapy. Recent studies have shown that breast tumors when compared with other solid tumors also contain a subpopulation termed as cancer stem cells (CSCs). CSCs are hard to kill due to their therapy resistant capacities. These unharmed cells then result into relapse of tumor after treatment. Some established breast cancer cell lines also behave in similar fashion to CSCs in overall manner thus termed as CSC like cell lines. This study primarily focuses on characterizing CSC like cell lines from non CSC like cell lines based upon their gene expression and prediction of drugs which can target these groups separately. In this study two databases, Cancer Cell Line Encyclopedia (CCLE) and Cancer Genome Project (CGP), were used which contain gene expression data and drugs cytotoxicity data for most of the established cancer cell lines. Breast cancer cell lines gene expression data was used to predict two gene lists which can separate breast cancer cell lines into CSC like and non CSC like cell lines by in silico analysis. These gene lists were named as Patentable and Non Patentable. Additionally four drugs were predicted which can target CSC like group (Midostaurin and Elesclomol) and non CSC like group (Panobinostat and Lapatinib) separately. Later these findings were validated in vitro. Non Patentable gene list could not be validated due to low concordance with microarray data. On the other hand, Patentable gene list was validated and was found concordant with microarray data. Out of four selected drugs, Panobinostat and Lapatinib showed increased toxicity to non CSC like cell lines while only Midostaurin showed toxicity to CSC like cell lines. To investigate further that cell lines were grown in 3D cell culture conditions, to increase their stem cell like properties (stemness). But only one cell line MDA-MB-157 which was found as CSC like, showed expected behavior. Additionally this cell line increased resistance to Lapatinib and Panobinostat and became more sensitive to Midostaurin. Correlation analysis showed some genes as potential biomarkers for selected drugs. In conclusion, in this study various genes are proposed to differentiate CSC like cell lines from non CSC like cell lines. And Midostaurin can be potential drug to treat CSC like cells while Lapatinib and Panobinostat showed increased activity against non CSC like cell lines.
Open Access
Contribution of notch signaling on HCC stem cell status and utilizing TLR agonists and notch inhibition to improve HCC theraphy
(2014) Ertuna, Yusuf İsmail
Hepatocellular carcinoma (HCC) is the seventh most common cancer type worldwide, and ranked third place among cancer-related deaths within both sexes. As in many solid tumors, HCC shelters a cancer stem cell subpopulation, and is held responsible for the resistance developed during chemo-and-radio-therapy of HCC. The only option to cure HCC is liver transplantation, which is the bottleneck to provide a remedy to patients due to limited availability. Understanding the stem cell behavior of HCC would critically contribute to develop effective eradication strategies. In this study, a panel of 17 HCC cell lines was evaluated for their CSC status. Of these cell lines, six of them were determined to be positive for CD133 expression, a cardinal CSC marker. Next, HepG2, Huh7 and Hep3B-TR, (a desensitized TGF-beta-1 receptor clone) were selected and Notch activity vs. CSC fraction was investigated by analyzing CD133+/EpCAM+ levels. Our results revealed that DAPT (a notch inhibitor) led to a drop in CD133+/EpCAM+ levels in HepG2 and Huh7 by half, but not in Hep3B-TR cells, implicating a possible TGFβ1R involvement on CSC generation/maintenance. Treatment of cells with a notch ligand, Jagged-1, however, had little or no positive effect on CD133+/EpCAM+ expressions in all tested cells. Additionally, HCC cells' response to different TLR ligands and the resulting transcript expressions of TLRs were investigated by PCR. Of note, TLRs are widely used in immunotherapy of cancers. Here we aimed to combine Notch inhibitor along with selected TLR ligand, thereby improving tumor clearance in athymic mice xenografted with HCC. We found that in three selected cell lines upon TLR2 ligand stimulation, TLR5 and TLR7 were highly upregulated. Afterwards, treating these HCC cell lines with these ligands we observed that TLR3, TLR7/8 and TLR9 levels were activated. In the final part of this study, tumor-bearing mice with Huh7, were subjected to a combination therapy with TLR ligands +/- DAPT. We demonstrated that combination therapy comprising TLR3, 7/8 and 9 ligands and DAPT (only two injections, a week apart) induced significant tumor regression.
Open Access
Image processing algorithms for histopathological images
(2016-03) Oğuz, Oğuzhan
Conventionally, a pathologist examines cancer cell morphologies under microscope. This process takes a lot of time and is subject to human mistakes. Computer aided diagnosis (CAD) systems and modules aim to help pathologists in their work to decrease the time consumption and the human mistakes. This thesis proposes a CAD module and algorithms which assist the pathologist in segmentation, detection and the classi cation problems in histopatholgic images. A multi-resolution super-pixel based segmentation algorithm is developed to measure the cell size, count the number of cells and track the motion of cells in Mesenchymal Stem Cell (MSC) images. The proposed algorithm is compared with Simple Linear Iterative Clustering (SLIC) algorithm. It is experimentally observed that in the segmentation stage, the cell detection rate is increased by 7% and the false alarm is decreased by 5%. In addition to this, two novel decision rules for merging similar neighboring super-pixels are proposed. One dimensional version of the Scale Invariant Feature Transform (SIFT) based merging algorithm is developed and applied to the histograms of the neighboring super-pixels to determine the similar regions. It is also shown that the merging process can be made with the use of wavelets. Moreover, it is shown that region covariance and codi erence matrices can be used in detection of cancer stem cells (CSC) and a CAD module for the CSC detection in liver cancer tissue images are developed. The system locates CSCs in CD13 stained liver tissue images. The method has an online learning approach which improves the accuracy of detection. It is experimentally shown that, applying the proposed approach with the user guidance, increases the overall detection quality and accuracy up to 25% compared to using region descriptors alone. Also, the proposed module is compared with the similar plug-ins of ImageJ and Fiji. It is shown that, when the similar features are used, the implemented module achieves approximately 20% better classi cation results compared to the plug-ins of Imagej and Fiji. Furthermore, the proposed 1-D SIFT algorithm is expanded and used in classi cation of the cancer tissues images stained with Hematoxylin and Eosin (H&E) stain, which is a cost e ective routine compared to the immunohistochemistry (IHC) procedure. The 1-D SIFT algorithm is able to classify healthy and cancerous tissue images with up to 91% accuracy in H&E stained images in our data set.
Open Access
Intracellular functions of RNA-binding protein, Musashi1, in stem and cancer cells
(BioMed Central, 2020) Forouzanfar, M.; Lachinani, L.; Dormiani, K.; Nasr-Esfahani, M. H.; Güre, Ali Osmay; Ghaedi, K.
RNA-binding protein, musashi1 (MSI1), is a main protein in asymmetric cell division of the sensory organ precursor cells, whereas its expression is reported to be upregulated in cancers. This protein is a critical element in proliferation of stem and cancer stem cells, which acts through Wnt and Notch signaling pathways. Moreover, MSI1 modulates malignancy and chemoresistance of lung cancer cells via activating the Akt signaling. Due to the main role of MSI1 in metastasis and cancer development, MSI1 would be an appropriate candidate for cancer therapy. Downregulation of MSI1 inhibits proliferation of cancer stem cells and reduces the growth of solid tumors in several cancers. On the other hand, MSI1 expression is regulated by microRNAs in such a way that several different tumor suppressor miRNAs negatively regulate oncogenic MSI1 and inhibit migration and tumor metastasis. The aim of this review is summarizing the role of MSI1 in stem cell proliferation and cancer promotion.
Open Access
Predicting chemotherapy sensitivity profiles for breast cancer cell lines with and without stem cell-like features
(Bentham Science Publishers B.V., 2013) Isbilen, M.; Senses, K. M.; Gure, A. O.
Our current understanding of cancer-stem cells (CSCs) is that they are slow growing, generally mesenchymallike cells capable of generating tumors. Convincing evidence for the existence of such cells comes from recent lineage tracing experiments. CSCs have been reported as being resistant to conventional drug treatment and have been considered as being responsible for failure of chemotherapy. Recently, several databases aiming the genetic characterization of a large number of cancer cell lines have been made publicly available. In addition to gene expression data, these databases contain cytotoxicity information for all cell lines for a number of drugs as well. It is possible to classify known cell lines derived from a given tumor, based on how similar they are to CSCs, or in other words, to define their stem-ness, using gene-lists that define such cells. Using two such, independently generated, gene lists we found that breast cancer cell lines could be categorized into two distinct groups which we designate CSC-like and non-CSC-like. We then identified drugs to which the two groups were most sensitive to. We also generated sensitivity profiles for all drugs, within one such database, to identify chemotherapeutics with preferential action on breast cancer. We believe this is a straight-forward approach for swiftly identifying drugs that would selectively target a subpopulation of cells for any given tumor type. © 2013 Bentham Science Publishers.
Open Access
Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers
(Nature Publishing Group, 2019-02) Siddiqui, A.; Gollavilli, P. N.; Schwab, A.; Vazakidou, M. E.; Ersan, Pelin G.; Ramakrishnan, M.; Pluim, D.; Coggins, Si’A.; Saatçi, Ö.; Annaratone, L.; Schellens, J. HM; Kim, B.; Asangani, İ. A.; Rasheed, S. A. K.; Marchiò, C.; Şahin, Özgür; Ceppi, P.
Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC). In vitro, TS knockdown increased the population of CD24+ differentiated cells, and attenuated migration and sphere-formation. RNA-seq profiling indicated repression of epithelial-to-mesenchymal transition (EMT) signature genes upon TS knockdown, and TS-deficient cells showed an increased ability to invade and metastasize in vivo, consistent with the occurrence of a partial EMT phenotype. Mechanistically, TS enzymatic activity was found essential for maintenance of the EMT/stem-like state by fueling a dihydropyrimidine dehydrogenase—dependent pyrimidine catabolism. In patient tissues, TS levels were found significantly higher in poorly differentiated and in triple negative BC, and strongly correlated with worse prognosis. The present study provides the rationale to study in-depth the role of NM at the crossroads of proliferation and differentiation, and depicts new avenues for the design of novel drug combinations for the treatment of BC.