Research

Our research interests are in the direction of developing tools and methods for quantitative biology. We aim to modify traditional batch culture methods and develop novel microfabricated tools, mostly compatible with microscopy, to precisely measure and quantitatively characterize cellular behavior for various cell types ranging from bacteria to mammalian cells. Production of diagnostic and monitoring devices for point-of-care testing using obtained quantitative data and developed technologies for fundamental biological concepts are among our primary research goals.

One of our current projects integrates our biology and engineering knowledge and skills is in the concept of hepatocellular carcinoma (HCC). HCC is the most common type of liver cancer. It causes 626,000 deaths worldwide per year. Although early-stage liver cancer can sometimes be treated with partial hepatectomy, liver transplantation, ablation, and embolization, the sorafenib treatment (Nexavar, Bayer HealthCare Pharmaceuticals–Onyx Pharmaceuticals), is the only approved systemic therapy for advanced HCC. Sorafenib is a multikinase inhibitor that inhibits tumor-cell proliferation and tumor angiogenesis and increases the rate of apoptosis. However, the molecular mechanisms by which sorafenib exerts its antitumor activity has not been fully elucidated. We aim to develop microfluidic tools to investigate the cellular signaling network underlying HCC, sorafenib effect, and HCC progression on sorafenib. Therefore, it will be a tool for personalized medicine. Although the device is purposed to develop for HCC, it has a great potential to be used for other cancer types especially for the ones which metastases more than HCC.

Thanks to Supports by TUBITAK 2232, TOGD, and Sabanci University.

Dielectrophoresis (DEP) is an active area of research for detection, concentration, separation, and manipulation of cells and molecules. DEP does not involve cell-labeling or cell-modification steps compared to other detection and separation techniques, it is based on the polarizability of living cells, which depends strongly on cellular composition, morphology, phenotype, and on the frequency of the applied electrical field, without causing significant cellular damage or death. We adapt and develop dielectrophoretic devices to make them major cell-characterization tools thereby DEP can rapidly and precisely aid therapy decisions and contribute understanding the mechanism of diseases. DEP-based characterization methods can become a part of routine screening methods and may lead to develop novel disease detection markers and methods.

Large-scale phenotyping of crop plants under stress conditions has been limited due to inadequateness of available tools and its cost. Recently, high-throughput phenotyping has been possible using microfluidic and microelectromechanical systems (MEMS) in plant biology. In previous studies characterizations of seeds under abiotic stress conditions were not being able to accurately examined at the phenotypic level and most of the studies were mainly focusing only on their genotype, without analyzing their phenotypes in detail. To enable efficient and high-throughput phenotypic assays and link them to genetics, we develop microfluidic platforms and generate quantitative data for Arabidopsis thaliana seeds and drought conditions.

Thanks to Supports by Sabanci University.

It is increasingly recognized that infiltrating immune cells contribute to the pathogenesis of a wide range of solid tumors. The paracrine signaling between the tumor and the immune cells alters the functional state of individual tumor cells and, correspondingly, the anticipated response to radiation or chemotherapies, which is of great importance to clinical oncology. In this work, we measure proteins secretions both single-cell and population levels using microfluidic devices and correlate the results with macrophage phenotype, tumor invasiveness and epithelial-mesenchymal transitions.

Coming Soon!