Browsing by Subject "qPCR"

Now showing 1 - 2 of 2

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
Effects of aging on gene expression levels of inflammatory, cytoskeletal and microglial markers in the brain using the zebrafish (Danio Rerio) model organism
(2021-01) Aydoğan, Hande Özge
Age-related cognitive decline burdens the elderly population, limiting their abil-ity to socialize and be independent. To be able to develop proper treatments, healthy aging should be examined. Previous studies focusing on healthy brain aging revealed that abnormal microglial activation was observed. Aging microglia exhibits 0partial loss of motility due to cytoskeletal changes, leading to decreases in their ability to respond to environmental cues. Thus, a more inﬂammatory phe-notype was observed in microglia. These disruptions of the previously established homeostasis in the brain could be the underlying reason for cognitive decline ex-perienced during aging. To understand these changes during aging in the brain, cytoskeletal, microglial, and inﬂammation-related markers were investigated by using both in silico and in vivo approaches. In silico analyses were performed on mice hippocampus and the whole brain revealed that the genes involved in the actin cytoskeleton reorganization (Arpc1b), neurogenesis (Erbb4), and proinﬂam-matory related pathways (Il1b, P2x7r, Elf2b) showed diﬀerential gene expression levels among diﬀerent age groups, genders, and tissue of origin. On the other hand, no diﬀerential expression was observed in microglial (Coro1a and Aif1) and anti-inﬂammatory markers (Tgfb1 and Il10). To further validate these re-sults in vivo, quantitative polymerase chain reaction (qPCR) was performed on young and old zebraﬁsh brains. According to the results, only two genes showed marginally signiﬁcant diﬀerences among young and old brains: arpc1b and p2x7r. These results collectively could mean 1) the overall microglia population does not change during aging, 2) the brain does not exhibit imbalances in terms of pro-and anti-inﬂammatory cytokines, and 3) neurogenesis. Furthermore, the signiﬁ-cant changes observed in arpc1b and p2x7r indicated the iii iv importance of the cytoskeleton and inﬂammation-related pathways in the correct functioning of the cells. Therefore, this study showed that in silico analysis are the reliable indica-tors of in vivo experiments, zebraﬁsh can be used as a gerontological model, and the importance of cytoskeleton in motile cells. However, to understand these de-scribed relations, further investigation on the protein level of these genes should be done.