Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - Scopus: 11Μdacs Platform: a Hybrid Microfluidic Platform Using Magnetic Levitation Technique and Integrating Magnetic, Gravitational, and Drag Forces for Density-Based Rare Cancer Cell Sorting(Elsevier, 2023) Keçili, Seren; Yılmaz, Esra; Özçelik, Özge Solmaz; Anıl İnevi, Müge; Günyüz, Zehra Elif; Yalçın Özuysal, Özden; Özçivici, Engin; Tekin, Hüseyin CumhurCirculating tumor cells (CTCs) are crucial indicators of cancer metastasis. However, their rarity in the bloodstream and the heterogeneity of their surface biomarkers present challenges for their isolation. Here, we developed a hybrid microfluidic platform (microfluidic-based density-associated cell sorting (µDACS) platform) that utilizes density as a biophysical marker to sort cancer cells from the population of white blood cells (WBCs). The platform utilizes the magnetic levitation technique on a microfluidic chip to sort cells based on their specific density ranges, operating under a continuous flow condition. By harnessing magnetic, gravitational, and drag forces, the platform efficiently separates cells. This approach involves a microfluidic chip equipped with a microseparator, which directs cells into top and bottom outlets depending on their levitation heights, which are inversely proportional to their densities. Hence, low-density cancer cells are collected from the top outlet, while high-density WBCs are collected from the bottom outlet. We optimized the sorting efficiency by varying the flow rates, and concentrations of the sorting medium's paramagnetic properties using standard densities of polymeric microspheres. To demonstrate the platform's applicability, we performed hybrid microfluidic sorting on MDA-MB-231 human breast cancer cells and U-937 human monocytes. The results showed efficient sorting of rare cancer cells (≥100 cells/mL) from serum samples, achieving a sorting efficiency of ∼70% at a fast-processing speed of 1 mL h−1. This label-free approach holds promise for rapid and cost-effective CTC sorting, facilitating in-vitro diagnosis and prognosis of cancer. © 2023 The Author(s)Research Project Erişkin kök hücrelerinde doku yönelimi ve dış mekanik etkilere bağlı gelişen altyapısal değişikliklerin karakterizasyonu(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2015) Özçivici, Engin; Yalçın Özuysal, Özden; Meşe Özçivici, GülistanMekanik titreşim uygulanması hem kemik hücrelerinde mineralizasyonu arttırdığı hem de kemik iliğindeki kök hücrelerini kemik yönelimine soktuğu için kemik kütlesini arttırıcı bir etkiye sahiptir. Mekanik sinyaller ayrıca yağ dokusu oluşumunu kemik iliği ve diğer yağ depolarında engeller özelliklere sahiptir. Kemik ve yağ hücrelerinin ortak bir hücre tipinden geldikleri düşünülürse, mekanik titreşim sinyalleri kullanılarak kemik oluşumu arttırılırken eşzamanlı olarak yağ oluşumu azaltılabilir. Halihazırda kemik iliği kök hücrelerinin bu tip mekanik titreşim sinyallerine duyarlı olup olmadığı ve eğer duyarlıysa bu sinyallere nasıl adapte olduğu henüz net olarak bilinmemektedir. Burada fare kemik iliğinden alınan mezenkimal D1-ORL-UVA kök hücreleri atıl durumda, kemik yöneliminde ya da yağ yönelimindeyken günlük mekanik titreşimlere (0.15g, 90 Hz, 15dk/gün) 7 gün boyunca maruz bırakıldı ve bu titreşimlerin hücrelerde yarattığı hücresel, morfolojik ve moleküler değişimler araştırıldı. Atıl durumdaki kök hücrelerde mekanik sinyaller hücre üremesini, hücrelerin toplam aktin miktarını ve kalınlığını arttırdığı gözlendi. Kemik yönelimi sırasında da mekanik sinyaller toplam aktin miktarı, aktin kalınlığı ve hücrelerin membran pürüzlülüklerini arttırdılar. Yağ yönelimi sırasında ise uygulanan mekanik kuvvetlerin hücrelerin yağ biriktirmesinden kaynaklanan morfolojik ve altyapısal etkileri geri çevirdiği gözlendi. Mekanik titreşimlerin ayrıca tüm yönelimler için hücrelerarası iletişimi arttırdıkları gözlendi. Sonuçlar yüksek frekanslı ve düşük genlikli mekanik titreşimlerin mezenkimal kök hücrelerin yönelimlerini belirleyen faktörlere önemli etkilerde bulunduklarını düşündürmektedir. Klinik aşamaya ulaşabilirse bu sonuçlar ilaçtan bağımsız bir etkinin kemik erimesi ve obezite için kullanılabileceğini düşündürmektedir.Research Project Mekanik titreşimlerin meme kanseri hücrelerinin davranışlarına etkisi(2015) Özçivici, Engin; Yalçın Özuysal, ÖzdenHer geçen gün artan epidemiyolojik bulgular fiziksel egzersizin kanser üzerinde, özellikle meme, prostat ve kolon kanserlerinde önleyici bir etkisi olduğunu ortaya koymaktadır. Varolan bulgulara rağmen kanser ve fiziksel egzersiz arasındaki etkileşimin biyolojik mekanizması hücre kültürü ve hayvan deneyleriyle ortaya çıkarılamamıştır. Tıbbi literatür egzersizin kanser üzerindeki önleyici etkisini sistemler bazında oluşan bağışıklık, metabolik aktivite, dolaşımdaki hormonlar ve vücuttaki yağ oranları ile açıklamaya çalışmaktadır. Buna rağmen, mekanik kuvvetlerin sağlıklı hücreler üzerindeki düzenleyici etkisi düşünüldüğünde bu etkilerin kanserli hücreler üzerinde de etkin olabileceğinden şüphelenilmektedir. Mekanik kuvvetleri kanser hücrelerinin üreme ve organizasyon özelliklerini kontrol etmek için kullanma düşüncesi alternatifleri göz önüne alındığında (örneğin kemoterapi, ışın tedavisi) yan etkilerinin yokluğu ve sinyallerin doğallığı sebebiyle oldukça avantajlıdır. Bu konuda yeterli bilimsel çalışma olmamakla beraber aynı zamanda kanser dokusu (tümör) mikroçevresi düşünüldüğünde bazı engeller ortaya çıkmaktadır. Tümörde hücre dışı matrisi sağlıklı dokulara göre daha sertken, kanser hücreleri bozulan altyapısal özellikleri sebebiyle sağlıklı hücrelere göre çok daha yumuşaktır. Bu yüzden tümör dokularında oluşan kuvvetler “stress shielding” adı verilen prensip sebebiyle hücreleri değil daha sert olan hücre dışı matrisin yüklenmesini sağlarlar. Önerilen projede bu durumun önüne geçilmek için kanser hücreleri matriste oluşan kuvvetlerden bağımsız ve Newton prensipleriyle, yani ivmelenen kütlede oluşan kuvvetler sayesinde yüklenmeye maruz bırakılacaktır.Article Citation - WoS: 12Citation - Scopus: 12Sema6d Differentially Regulates Proliferation, Migration, and Invasion of Breast Cell Lines(American Chemical Society, 2022) Günyüz, Zehra Elif; Sahi İlhan, Ece; Küçükköse, Cansu; İpekgil, Doğaç; Tok, Güneş; Meşe, Gülistan; Özçivici, Engin; Yalçın Özuysal, ÖzdenSemaphorin 6D (SEMA6D), a member of the class 6 semaphorin family, is a membrane-associated protein that plays a key role in the development of cardiac and neural tissues. A growing body of evidence suggests that SEMA6D is also involved in tumorigenesis. In breast cancer, high SEMA6D levels are correlated with better survival rates. However, very little is known about the functional significance of SEMA6D in breast tumorigenesis. In the present study, we aimed to investigate the effects of SEMA6D expression on the normal breast cell line MCF10A and the breast cancer cell lines MCF7 and MDA MB 231. We demonstrated that SEMA6D expression increases the proliferation of MCF10A cells, whereas the opposite effect was observed in MCF7 cells. SEMA6D expression induced anchorage-independent growth in both cancer cell lines. Furthermore, migration of MCF10A and MCF7 cells and invasion of MDA MB 231 cells were elevated in response to SEMA6D overexpression. Accordingly, the genes related to epithelial-mesenchymal transition (EMT) were altered by SEMA6D expression in MCF10A and MCF7 cell lines. Finally, we provided evidence that SEMA6D levels were associated with the expression of the cell cycle, EMT, and Notch signaling pathway-related genes in breast cancer patients' data. We showed for the first time that SEMA6D overexpression has cell-specific effects on the proliferation, migration, and invasion of normal and cancer breast cell lines, which agrees with the gene expression data of clinical samples. This study lays the groundwork for future research into understanding the functional importance of SEMA6D in breast cancerArticle Citation - WoS: 5Citation - Scopus: 5Low Magnitude High Frequency Vibrations Expedite the Osteogenesis of Bone Marrow Stem Cells on Paper Based 3d Scaffolds(Springer, 2020) Karadaş, Özge; Meşe, Gülistan; Özçivici, EnginAnabolic effects of low magnitude high frequency (LMHF) vibrations on bone tissue were consistently shown in the literature in vivo, however in vitro efforts to elucidate underlying mechanisms are generally limited to 2D cell culture studies. Three dimensional cell culture platforms better mimic the natural microenvironment and biological processes usually differ in 3D compared to 2D culture. In this study, we used laboratory grade filter paper as a scaffold material for studying the effects of LHMF vibrations on osteogenesis of bone marrow mesenchymal stem cells in a 3D system. LMHF vibrations were applied 15 min/day at 0.1 g acceleration and 90 Hz frequency for 21 days to residing cells under quiescent and osteogenic conditions. mRNA expression analysis was performed for alkaline phosphatase (ALP) and osteocalcin (OCN) genes, Alizarin red S staining was performed for mineral nodule formation and infrared spectroscopy was performed for determination of extracellular matrix composition. The highest osteocalcin expression, mineral nodule formation and the phosphate bands arising from the inorganic phase was observed for the cells incubated in osteogenic induction medium with vibration. Our results showed that filter paper can be used as a model scaffold system for studying the effects of mechanical loads on cells, and LMHF vibrations induced the osteogenic differentiation of stem cells.Book Part Citation - Scopus: 15Stem Cell Culture Under Simulated Microgravity(Springer, 2020) Anıl İnevi, Müge; Sarıgil, Öykü; Kızılkaya, Melike; Meşe, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, EnginChallenging environment of space causes several pivotal alterations in living systems, especially due to microgravity. The possibility of simulating microgravity by ground-based systems provides research opportunities that may lead to the understanding of in vitro biological effects of microgravity by eliminating the challenges inherent to spaceflight experiments. Stem cells are one of the most prominent cell types, due to their self-renewal and differentiation capabilities. Research on stem cells under simulated microgravity has generated many important findings, enlightening the impact of microgravity on molecular and cellular processes of stem cells with varying potencies. Simulation techniques including clinostat, random positioning machine, rotating wall vessel and magnetic levitation-based systems have improved our knowledge on the effects of microgravity on morphology, migration, proliferation and differentiation of stem cells. Clarification of the mechanisms underlying such changes offers exciting potential for various applications such as identification of putative therapeutic targets to modulate stem cell function and stem cell based regenerative medicine. © Springer Nature Switzerland AG 2020.Article Citation - WoS: 18Citation - Scopus: 17Cnt Incorporated Polyacrilonitrile/Polypyrrole Nanofibers as Keratinocytes Scaffold(Trans Tech Publications, 2019) İnce Yardımcı, Atike; Aypek, Hande; Öztürk, Özgür; Yılmaz, Selahattin; Özçivici, Engin; Meşe, Gülistan; Selamet, YusufPolypyrrole (PPy) is an attractive scaffold material for tissue engineering with its non-toxic and electrically conductive properties. There has not been enough information about PPy usage in skin tissue engineering. The aim of this study is to investigate biocompatibility of polyacrilonitrile (PAN)/PPy nanofibrous scaffold for human keratinocytes. PAN/PPy bicomponent nanofibers were prepared by electrospinning, in various PPy concentrations and with carbon nanotube (CNT) incorporation. The average diameter of electrospun nanofibers decreased with increasing PPy concentration. Further, agglomerated CNTs caused beads and disordered parts on the surface of nanofibers. Biocompatibility of these PAN/PPy and PAN/PPy/CNT scaffolds were analyzed in vitro. Both scaffolds provided adhesion and proliferation of keratinocytes. Nanofiber diameter did not significantly influence the morphology of cells. However, with increasing number of cells, cells stayed among nanofibers and this affected their shape and size. In this study, we demonstrated that PAN/PPy and PAN/PPy/CNT scaffolds enabled the growth of keratinocytes, showing their biocompatibility.Conference Object Citation - WoS: 3Citation - Scopus: 4Biofabrication of Cellular Structures Using Weightlessness as a Biotechnological Tool(IEEE, 2019) Anıl İnevi, Müge; Sarıgil, Öykü; Yaman, Sena; Yalçın Özuysal, Özden; Meşe, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, EnginGravity is an important biomechanical signal effecting the morphology and function of organisms. Reduction of gravitational forces, as experienced during spaceflight, cause alterations in the biological systems. Magnetic levitation technique is one of the most recent ground-based technology to mimic weightlessness environment. In addition to providing a platform to investigate biological effects of the weightlessness, this platform presents a novel opportunity to biofabricate 3-dimensional (3D) structures in a scaffold-and nozzle-free fashion. In this study, various controllable self-assembled 3D living structures were fabricated via magnetic levitation technique. This strategy may offer an easy and cost-effective opportunity for a wide range of space biotechnology researches.Conference Object Citation - WoS: 4Citation - Scopus: 5Application of Magnetic Levitation Induced Weightlessness To Detect Cell Lineage(IEEE, 2019) Sarıgil, Öykü; Anıl İnevi, Müge; Yılmaz, Esra; Çağan, Melike; Meşe, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, EnginIdentification and classification of bone marrow cells is an important step for molecular biology and therapeutic studies related to bone marrow disorders such as osteoporosis or obesity. In this study, we applied magnetic levitation technology to induce a weightlessness environment to detect adipocytes and osteoblasts based on their single cell density. This biotechnological method can be used for separation of heterogeneous populations such as bone marrow once adapted to a continuous microfluidic platform.Article Citation - WoS: 79Citation - Scopus: 94Biofabrication of in Situ Self Assembled 3d Cell Cultures in a Weightlessness Environment Generated Using Magnetic Levitation(Nature Publishing Group, 2018) Anıl İnevi, Müge; Yaman, Sena; Arslan Yıldız, Ahu; Meşe, Gülistan; Yalçın Özuysal, Özden; Tekin, Hüseyin Cumhur; Özçivici, EnginMagnetic levitation though negative magnetophoresis is a novel technology to simulate weightlessness and has recently found applications in material and biological sciences. Yet little is known about the ability of the magnetic levitation system to facilitate biofabrication of in situ three dimensional (3D) cellular structures. Here, we optimized a magnetic levitation though negative magnetophoresis protocol appropriate for long term levitated cell culture and developed an in situ 3D cellular assembly model with controlled cluster size and cellular pattern under simulated weightlessness. The developed strategy outlines a potential basis for the study of weightlessness on 3D living structures and with the opportunity for real-time imaging that is not possible with current ground-based simulated weightlessness techniques. The low-cost technique presented here may offer a wide range of biomedical applications in several research fields, including mechanobiology, drug discovery and developmental biology.