Browsing by Subject "Stem cell"
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Item Open Access Angiogenic peptide nanofibers repair cardiac tissue defect after myocardial infarction(Acta Materialia Inc, 2017) Rufaihah, A. J.; Yasa, I. C.; Ramanujam, V. S.; Arularasu, S. C.; Kofidis, T.; Güler, Mustafa O.; Tekinay, A. B.Myocardial infarction remains one of the top leading causes of death in the world and the damage sustained in the heart eventually develops into heart failure. Limited conventional treatment options due to the inability of the myocardium to regenerate after injury and shortage of organ donors require the development of alternative therapies to repair the damaged myocardium. Current efforts in repairing damage after myocardial infarction concentrates on using biologically derived molecules such as growth factors or stem cells, which carry risks of serious side effects including the formation of teratomas. Here, we demonstrate that synthetic glycosaminoglycan (GAG) mimetic peptide nanofiber scaffolds induce neovascularization in cardiovascular tissue after myocardial infarction, without the addition of any biologically derived factors or stem cells. When the GAG mimetic nanofiber gels were injected in the infarct site of rodent myocardial infarct model, increased VEGF-A expression and recruitment of vascular cells was observed. This was accompanied with significant degree of neovascularization and better cardiac performance when compared to the control saline group. The results demonstrate the potential of future clinical applications of these bioactive peptide nanofibers as a promising strategy for cardiovascular repair. Statement of Significance We present a synthetic bioactive peptide nanofiber system can enhance cardiac function and enhance cardiovascular regeneration after myocardial infarction (MI) without the addition of growth factors, stem cells or other biologically derived molecules. Current state of the art in cardiac repair after MI utilize at least one of the above mentioned biologically derived molecules, thus our approach is ground-breaking for cardiovascular therapy after MI. In this work, we showed that synthetic glycosaminoglycan (GAG) mimetic peptide nanofiber scaffolds induce neovascularization and cardiomyocyte differentiation for the regeneration of cardiovascular tissue after myocardial infarction in a rat infarct model. When the peptide nanofiber gels were injected in infarct site at rodent myocardial infarct model, recruitment of vascular cells was observed, neovascularization was significantly induced and cardiac performance was improved. These results demonstrate the potential of future clinical applications of these bioactive peptide nanofibers as a promising strategy for cardiovascular repair.Item Open Access Characterization of enteric nervous system response to disease conditions in intestine(Bilkent University, 2022-01) Gönüllü, Nagihan GizaySmall intestine is one of the vital organs in gastrointestinal tract that is responsible for absorption of food, amino acids and create barrier against microbial invasion. Whereas large bowel is involved in the reabsorption of water and minerals. Intestinal epithelium is a highly regenerative tissue that it can renew its cells in a span of 4-5 days. In homeostatic state, the turnover rate of the epithelial cells is stable however, in case of inflammation and disease, the rate of proliferation and differentiation increase to regenerate the damaged tissue. Primary cilia (PC) are non-motile, microtubule-based organelles that extrude from plasma membrane. It functions as a sensory element to detect environmental cues. One of the highly studied disease models is ulcerative colitis is mainly characterized by the inflammation of the intestinal mucosal layer and generated by DSS administration. Additionally, high fat diet induced obesity, as a metabolic disease model, was shown to affect intestinal stem cell activity such that higher fat composition of diet causes shortening of small intestine and decrease in weight of tissue. Enteric nervous system is the endogenous nervous network surrounding the gastrointestinal tract and it controls many vital functions including digestion, blood flow, intestinal motility. The initial aim of this study was to reveal the response of intestinal stem cell niche in those stated disease conditions. After detecting ACOT7 protein as a global marker for enteric nervous system of myenteric and submucosal plexus layers, we hypothesized that subpopulations of ENS cells have a connection with intestinal niche upon disease states. Our following goal was to identify subpopulations of ENS and ciliated cells. In order to assess our hypotheses, we conducted series of IHC experiments and confocal microscopy analyses. We found that ACOT7+ cells in ENS contain mainly distinct types of neuronal cell populations such as PHOX2B+ and HuCD+ cells. Further, we identified that glial cells are the main subpopulation of ENS changing their expression pattern in both colitis and obesity models. Also, we classified ciliated cells as a heterogenous population to be colocalized with several ENS and mesenchymal markers. Lastly, we analyzed the gut-brain axis response to DSS induced colitis in the brain of model animals with a focus on thalamus and insular cortex. We identified several thalamic regions showed similar expression pattern alterations which were observed in colon. Overall, the novelty of this thesis arises from the identification of ACOT7 as an ENS marker along with the detection of glial cell interaction with mesenchymal sub-populations. This interplay demonstrates a response upon disease states of both small intestine and colon.Item Open Access Endothelial progenitor cells display clonal restriction in multiple myeloma(BioMed Central Ltd., 2006) Braunstein, M.; Özçelik, T.; Baǧişlar, S.; Vakil, V.; Smith, E. L. P.; Dai, K.; Akyerli, C. B.; Batuman O. A.Background: In multiple myeloma (MM), increased neoangiogenesis contributes to tumor growth and disease progression. Increased levels of endothelial progenitor cells (EPCs) contribute to neoangiogenesis in MM, and, importantly, covary with disease activity and response to treatment. In order to understand the mechanisms responsible for increased EPC levels and neoangiogenic function in MM, we investigated whether these cells were clonal by determining X-chromosome inactivation (XCI) patterns in female patients by a human androgen receptor assay (HUMARA). In addition, EPCs and bone marrow cells were studied for the presence of clonotypic immunoglobulin heavy-chain (IGH) gene rearrangement, which indicates clonality in B cells; thus, its presence in EPCs would indicate a close genetic link between tumor cells in MM and endothelial cells that provide tumor neovascularization. Methods: A total of twenty-three consecutive patients who had not received chemotherapy were studied. Screening in 18 patients found that 11 displayed allelic AR in peripheral blood mononuclear cells, and these patients were further studied for XCI patterns in EPCs and hair root cells by HUMARA. In 2 patients whose EPCs were clonal by HUMARA, and in an additional 5 new patients, EPCs were studied for IGH gene rearrangement using PCR with family-specific primers for IGH variable genes (VH). Results: In 11 patients, analysis of EPCs by HUMARA revealed significant skewing (≥ 77% expression of a single allele) in 64% (n = 7). In 4 of these patients, XCI skewing was extreme (≥ 90% expression of a single allele). In contrast, XCI in hair root cells was random. Furthermore, PCR amplification with VH primers resulted in amplification of the same product in EPCs and bone marrow cells in 71 % (n = 5) of 7 patients, while no IGH rearrangement was found in EPCs from healthy controls. In addition, in patients with XCI skewing in EPCs, advanced age was associated with poorer clinical status, unlike patients whose EPCs had random XCI. Conclusion: Our results suggest that EPCs in at least a substantial subpopulation of MM patients are related to the neoplastic clone and that this is an important mechanism for upregulation of tumor neovascularization in MM. © 2006 Braunstein et al; licensee BioMed Central Ltd.Item Open Access In vivo magnetic resonance imaging of mesenchymal stem cells in myocardial infarction(Lippincott Williams & Wilkins, 2003) Kraitchman, D. L.; Heldman, A. W.; Atalar, Ergin; Amado, L. C.; Martin, B. J.; Pittenger, M. F.; Hare, J. M.; Bulte, J. W. M.Background - We investigated the potential of magnetic resonance imaging (MRI) to track magnetically labeled mesenchymal stem cells (MR-MSCs) in a swine myocardial infarction (MI) model. Methods and Results - Adult farm pigs (n=5) were subjected to closed-chest experimental MI. MR-MSCs (2.8 to 16×107 cells) were injected intramyocardially under x-ray fluoroscopy. MRIs were obtained on a 1.5T MR scanner to demonstrate the location of the MR-MSCs and were correlated with histology. Contrast-enhanced MRI demonstrated successful injection in the infarct and serial MSC tracking was demonstrated in two animals. Conclusion - MRI tracking of MSCs is feasible and represents a preferred method for studying the engraftment of MSCs in MI.Item Open Access Patterned carbon nanotubes as a new three-dimensional scaffold for mesenchymal stem cells(Elsevier, 2013) Bitirim, Verda Ceylan; Küçükayan-Doğu, Gökçe; Bengü, Erman; Akçalı, Kamil CanWe investigated the cellular adhesive features of mesenchymal stem cells (MSC) on non-coated and collagen coated patterned and vertically aligned carbon nanotube (CNT) structures mimicking the natural extra cellular matrix (ECM). Patterning was achieved using the elasto-capillary induced by water treatment on the CNT arrays. After confirmation with specific markers both at transcript and protein levels, MSCs from different passages were seeded on either collagen coated or non-coated patterned CNTs. Adhesion and growth of MSCs on the patterned CNT arrays were examined using scanning electron microscopy image analysis and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-tetrazolium bromide (MTT) assays. The highest MSC count was observed on the non-coated patterned CNTs at passage zero, while decreasing numbers of MSCs were found at the later passages. Similarly, MTT assay results also revealed a decrease in the viability of the MSCs for the later passages. Overall, the cell count and viability experiments indicated that MSCs were able to better attach to non-coated patterned CNTs compared to those coated with collagen. Therefore, the patterned CNT surfaces can be potentially used as a scaffold mimicking the ECM environment for MSC growth which presents an alternative approach to MSC-based transplantation therapy applications.Item Open Access Prediction of prognosis and chemosensitivity in breast cancer(Bilkent University, 2020-09) Akbar, Muhammad WaqasBreast cancer (BC) is responsible for the highest mortality and morbidity out of all the cancers in women which is primarily due to both inter and intra-tumoral molecular heterogeneity. This heterogeneity arises from stemness, epithelial to mesenchymal transition and the type of treatment given to patients. These three biological processes are highly related with each other. Traditional therapy when given to breast cancer patients generally results in the transition of epithelial cells to mesenchymal phenotype. Because treatment targets primarily non-stem cells, it can leave stem cells alive which can later result in a relapse of cancer. In this study we aimed to identify such markers that could classify breast cancer patients into stem/mesenchymal or non-stem/epithelial like phenotypes, to determine how generalized the above stated hypotheses are. We developed a gene list of 15 genes we term as CSC/non-CSC gene list (CNCL) which classifies tumors into stemness and/or EMT based phenotypes and can also classify tumor cells based on their relative sensitivity to treatment with traditional therapeutics such as paclitaxel and doxorubicin. When classified into stem/mesenchymal (CS/M) and non-stem/epithelial (NS/E) phenotypes, we showed that Lapatinib and Midostaurin have a specific growth inhibitory effects on NS/E cells, and CS/M cells, respectively. Surprisingly the CNCL showed prognostic significance only for patients who were treated with paclitaxel in neoadjuvant setting, while it could not prognosticate most other BC cohorts. We argue that this is due to the dynamic plasticity of these tumors, as studied within the third aim of this thesis. Secondly, we aimed to identify chemotherapy biomarkers for paclitaxel, cisplatin and doxorubicin to stratify patients in groups that will or will not benefit from these drugs. Using biomarkers, we selected for this purpose, we performed linear regression analysis using breast cancer cell lines to generate cytotoxicity prediction models which can predict IC50 values for these drugs, based on the expression of two genes in each model. Two models were selected for doxorubicin and cisplatin, and three models were selected for paclitaxel. All models were validated both in silico and in vitro. Thirdly, we aimed to evaluate breast cancer plasticity that occurs upon treatment or when a tumor metastasizes. We noted that some breast tumors not only switch their clinical subtype but also change their molecular subtype upon treatment or metastasis. As breast cancer patient treatment in the routine practice is routed based on breast cancer subtype, it is very important to identify the subtype switches which can be critical for changes in treatment decisions. Additionally, we also identified metastatic biomarkers using large number of cohorts. Lastly, as CNCL genes did not show any prognostic importance in terms of both overall survival and metastasis free survival, we checked if the same is true for melanoma. We used Melanin A (MLANA) and Inhibin (INHBA) genes as the markers for invasive/proliferative, stem/non-stem and mesenchymal/epithelial phenotypes. High INHBA expression, which is epithelial, proliferative and non-stem phenotype biomarker, was associated with poor survival and high MLANA expression, which is mesenchymal, invasive and stem phenotype marker, was associated with good prognosis in melanoma patients. Therefore, these findings in melanoma supported our results in breast cancer.Item Open Access Targeting PI3K/AKT/mTOR pathway identifies differential expression and functional role of IL8 in liver cancer stem cell enrichment(American Association for Cancer Research, 2019) Kahraman, D. C.; Kahraman, Tamer; Çetin-Atalay, R.Activation of the PI3K/Akt/mTOR pathway is an important signaling mechanism involved in the development and the progression of liver cancer stem cell (LCSC) population during acquired Sorafenib resistance in advanced hepatocellular carcinoma (HCC). Therefore, identification of novel therapeutic targets involving this pathway and acting on LCSCs is highly essential. Here, we analyzed the bioactivities and the molecular pathways involved in the action of small-molecule PI3K/Akt/mTOR pathway inhibitors in comparison with Sorafenib, DNA intercalators, and DAPT (CSC inhibitor) on CD133/EpCAM-positive LCSCs. Sorafenib and DNA intercalators lead to the enrichment of LCSCs, whereas Rapamycin and DAPT significantly reduced CD133/EpCAM positivity. Sequential treatment with Rapamycin followed by Sorafenib decreased the ratio of LCSCs as well as their sphere formation capacity, as opposed to Sorafenib alone. Under the stress of the inhibitors, differential expression analysis of 770 cancer pathway genes using network-based systems biology approach singled out IL8 expression association with LCSCs. Furthermore, IL8 secretion and LCSC enrichment ratio was also positively correlated. Following IL8 inhibition with its receptor inhibitor Reparixin or siRNA knockdown, LCSC features of HCC cells were repressed, and sensitivity of cells to Sorafenib increased significantly. Furthermore, inflammatory cytokines (IL8, IL1β, and IL11) were also upregulated upon treatment with HCC-approved kinase inhibitors Sorafenib and Regorafenib. Hence, chemotherapeutic stress alters inflammatory cytokine gene expression in favor of hepatic CSC population survival. Autocrine IL8 signaling is identified as a critical event, and its inhibition provides a promising complimentary therapeutic approach for the prevention of LCSC population enrichment.Item Restricted Türkiye’deki kemik iliği nakli uygulamalarının tarihçesi(Bilkent University, 2021) Aksu, Ahmet Burak; Geçit, Zeynep Begüm; Aygar, Emre; Ecerkale, Begüm; Turan, ZeynepKemik iliği nakli lösemi, lenf bezi kanseri ve kemik iliği yetmezliği gibi hastalıkların tedavisinde kullanılan ve sağlıklı bir vericiden toplanmış olan kemik iliğinin veya kemik iliği kök hücrelerinin hastaya nakledilmesi ile gerçekleştirilen bir tedavi yöntemidir. Kemik iliği nakli yöntemi dünyada 1960’lı yıllar itibariyle kullanılmaya başlanmış ve 1970’li yıllar itibariyle kullanımı yaygınlaşmıştır. Türkiye’de yöntemin ilk uygulanışı resmi verilere göre 1978 yılına dayansa da kemik iliği naklinin yaygın bir tedavi yöntemi haline gelmesi uzun sürmemiştir. Türk hekimlerinin başarılı uygulamaları sayesinde Türkiye’deki nakil uygulamaları dünyadaki gelişmeleri kısa sürede yakalamış ve Türkiye dünyanın önemli nakil merkezlerinden biri haline gelmiştir. 1978 yılında Hacettepe Üniversitesi bünyesinde Prof. Dr. Korkut Özerkan ile başlayan kemik iliği nakli uygulamalarını 1984 yılında GATA’da ilk otolog kemik iliği naklini gerçekleştiren Prof. Dr. Önder Berk ve ekibi ve daha sonra 1992 yılında gerçekleştirilen ilk periferik kök hücre nakli uygulaması ile Ankara Üniversitesi takip etmiştir. Dünyada olduğu gibi Türkiye’de de çocuk hastaların kemik iliği nakli yöntemiyle tedavisi erişkin hastalara göre daha geç başlamış ve 1990’lı yılların başında ilk uygulama İstanbul Üniversitesi Tıp Fakültesi’nde gerçekleştirilmiştir. Bu araştırmada Türkiye’deki kemik iliği naklinin tarihi, bu tarihi yaşayanların gözünden sosyal ve kısmen bilimsel yönden incelenmiştir. Aynı zamanda süreç içerisinde yaşanan zorluklar, yüksek teknoloji ve üst düzey uzman insan kaynağı gerektiren bu işlemin Türkiye’de yaygınlaşması, gelişmesi ve hekimlerin yetişmesinde hangi yöntemlerin kullanıldığı gibi bilgiler de anlatılmıştır.