Researcher: Özkan, Sena Nur
Name Variants
Özkan, Sena Nur
Email Address
Birth Date
4 results
Search Results
Now showing 1 - 4 of 4
Publication Metadata only Stencil-based selective surface functionalization of silicon nanowires in 3D device architectures for next-generation biochemical sensors(American Chemical Society, 2024) Esfahani, Mohammad Nasr; Leblebici, Yusuf; Department of Mechanical Engineering; Department of Mechanical Engineering; Ali, Basit; Özkan, Sena Nur; Akıncı, Seçkin; Öztürk, Ece; Alaca, Burhanettin Erdem; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Health Sciences; College of Engineering; School of MedicineSurface functionalization of 1D materials such as silicon nanowires is a critical preparation technology for biochemical sensing. However, existing nonselective functionalization techniques result in nonlocal binding and contamination, with potential device damage risks. Associated risks are further exacerbated for next-generation devices of a 3D nature with challenging topographies. Such 3D devices draw inspiration from the out-of-plane evolution of planar transistors to FinFETs and to today's gate-all-around transistors. This study is the first reported technological work addressing stencil-based surface decoration and selective functionalization of a suspended silicon nanowire building block embedded within such a device that involves two-order-of-magnitude thicker features compared to the nanowire critical dimensions. A gold pattern resolution of 3.0 mu m atop the silicon nanowires is achieved with a stencil aperture critical dimension of 2.2 mu m, accompanied by a die-level registration accuracy of 1.2 +/- 0.3 mu m. Plasma-enhanced chemical vapor deposition-based silicon nitride stencil membranes as large as 300 x 300 mu m2 are used to define the apertures without any membrane fracture during fabrication and membrane cleaning. The pattern-blurring aspect as a resolution-limiting factor is assessed by using 24 individual nanowire devices. Finally, gold-patterned silicon nanowires are functionalized using thiolated heparin and employed for selective attachment and detection of the human recombinant basic fibroblast growth factor (FGF-2). With the potential involvement in angiogenesis, the process of new blood vessel formation crucial for tumor growth, FGF-2 can serve as a potential prognostic biomarker in oncology. Demonstrated selectively on nanowires with high pattern resolution, the proposed functionalization approach offers possibilities for parallel sensing using vast nanowire arrays embedded in 3D device architectures developed for next-generation biochemical sensors in addition to serving various encapsulation and packaging needs.Publication Metadata only Growth and organotypic branching of lung-specific microvascular cells on 2D and in 3D lung-derived matrices(N/A, 2024) Özkan, Sena Nur; Öztürk, Ece; Graduate School of Health Sciences; School of MedicineTissue-specific endothelial cells have vital roles in maintenance and functioning of native tissues with constant reciprocal crosstalk with resident cells. Three-dimensional (3D) physio-mimetic in vitro models which incorporate lung-specific microvasculature are needed to model lung-related diseases which involve modulation of endothelial cell behavior like cancer. In this study, we investigated the growth kinetics, morphological changes and responses to biological cues of lung microvasculature on two-dimensional (2D) and in lung matrix-derived 3D hydrogels. HUVEC and HULEC-5a cells were cultured on 2D and compared for their growth, morphologies, and responses to varying growth medium formulations. Brightfield and immunofluorescence imaging was performed to assess differences in morphology. For 3D cultures, native bovine lungs were decellularized, lyophilized, solubilized, and reconstituted into hydrogel form in which endothelial cells were embedded. Cell growth and organotypic branching was monitored in 3D hydrogels in the presence of varying biological cues including lung cancer cell secretome. HUVEC and HULEC-5a cells demonstrated comparable growth and morphology on 2D. However, in 3D lung-derived ECM hydrogels, tissue-specific HULEC-5a cells exhibited much better adaptation to their microenvironment, characterized by enhanced organotypic branching and longer branches. HULEC-5a growth was responsive to lung cancer cell-conditioned medium in both 2D and 3D conditions. In 3D, the concentration of ECM ligand significantly affected cell growth in long-term culture where molecular crowding had an inhibitory role. Our data reveals that HULEC-5a cells offer a reliable alternative to frequently pursued HUVECs with comparable growth and morphology. Due to their intrinsic program for cellular crosstalk with resident cells, the use of tissue-specific endothelium constitutes a vital aspect for modeling physiological and pathological processes. Furthermore, our study is the first demonstration of the synergy between lung-specific microvasculature with lung-specific ECM within a 3D in vitro model.Publication Metadata only Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness(Wiley, 2024) Arlov, Oystein; Cunningham, Katherine; Vunjak-Novakovic, Gordana; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kızılel, Seda; Kuşoğlu, Alican; Örnek, Deniz; Dansık, Aslı; Özkan, Sena Nur; Sarıca, Sevgi; Yangın, Kardelen; Özdinç, Şevval; Solcan, Nuriye; Doğanalp, Efe Can; Karaoğlu, İsmail Can; Solaroğlu, İhsan; Bulutay, Pınar; Fırat, Pınar Arıkan; Erus, Suat; Tanju, Serhan; Dilege, Şükrü; Tunçbağ, Nurcan; Öztürk, Ece; Uzun, Ceren; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Health Sciences; Graduate School of Sciences and Engineering; School of MedicineTumor extracellular matrices (ECM) exhibit aberrant changes in composition and mechanics compared to normal tissues. Proteoglycans (PG) are vital regulators of cellular signaling in the ECM with the ability to modulate receptor tyrosine kinase (RTK) activation via their sulfated glycosaminoglycan (sGAG) side chains. However, their role on tumor cell behavior is controversial. Here, it is demonstrated that PGs are heavily expressed in lung adenocarcinoma (LUAD) patients in correlation with invasive phenotype and poor prognosis. A bioengineered human lung tumor model that recapitulates the increase of sGAGs in tumors in an organotypic matrix with independent control of stiffness, viscoelasticity, ligand density, and porosity, is developed. This model reveals that increased sulfation stimulates extensive proliferation, epithelial-mesenchymal transition (EMT), and stemness in cancer cells. The focal adhesion kinase (FAK)-phosphatidylinositol 3-kinase (PI3K) signaling axis is identified as a mediator of sulfation-induced molecular changes in cells upon activation of a distinct set of RTKs within tumor-mimetic hydrogels. The study shows that the transcriptomic landscape of tumor cells in response to increased sulfation resembles native PG-rich patient tumors by employing integrative omics and network modeling approaches.Publication Open Access Different decellularization methods in bovine lung tissue reveals distinct biochemical composition, stiffness, and viscoelasticity in reconstituted hydrogels(American Chemical Society (ACS), 2023) N/A; N/A; N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Kuşoğlu, Alican; Yangın, Kardelen; Özkan, Sena Nur; Sarıca, Sevgi; Örnek, Deniz; Solcan, Nuriye; Karaoğlu, İsmail Can; Kızılel, Seda; Bulutay, Pınar; Fırat, Pınar Arıkan; PhD Student; PhD Student; PhD Student; PhD Student; Master Student; Master Student; PhD Student; Faculty Member; Teaching Faculty; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; Graduate School of Sciences and Engineering; Graduate School of Health Sciences; Graduate School of Health Sciences; Graduate School of Health Sciences; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; School of Medicine; School of Medicine; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 28376; 133565; 207545Extracellula r matri x (ECM)-derived hydrogels are in demand for use in lung tissue engineering to mimic the native microenvironment of cells in vitro. Decellularization of native tissues has been pursued for preser v i n g organotypic ECM while eliminating cellular content and reconstitution into scaffolds which allows re-cellularization for modeling homeostasis, regeneration, or diseases. Achieving mechanical stabi l i t y and understanding the effects of the decellularization process on mechanical parameters of the reconstituted ECM hydrogels present a challenge in the field. Stiffness and viscoelasticity are important characteristics of tissue mechanics that regulate crucial cellular processes and their in vitro representation in engineered models is a current aspiration. The effect of decellulariza-tion on viscoelastic properties of resulting ECM hydrogels has not yet been addressed. The aim of this study was to establish bovine lung tissue decellularization for the first time via pursuing four different protocols and characterization of reconstituted decellularized lung ECM hydrogels for biochemical and mechanical properties. Our data reveal that bovine lungs provide a reproducible alternative to human lungs for disease modeling with optimal retention of ECM components upon decellularization. We demonstrate that the decellularization method significa n t l y affects ECM content, stiffness, and viscoelastic properties of resulting hydrogels. Lastly, we examined the impact of these aspects on viabi l i t y , morphology, and growth of lung cancer cells, healthy bronchial epithelial cells, and patient-derived lung organoids.