Characterization of sorting nexin 3 (SNX3) function

Öyken, Merve
Sorting nexin 3 (SNX3) belongs to the sorting nexins family involved in endocytic trafficking network. SNX3 only has a PX domain, which facilitates binding to the phosphatidyl inositol-3-phosphate on endosomes and has a role in formation of the retromer complex on early endosomes. Endocytosed receptors go through internalization and recycle back to plasma membrane, Trans-Golgi Network or alternatively are degraded in the lysosomes. Earlier, we found that SNX3 messenger RNA (mRNA) is upregulated via alternative polyadenylation in breast cancers. Therefore, we hypothesized that deregulated expression of SNX3 may change the dynamics of endocytic trafficking of membrane receptors in cancer cells. In order to test our hypothesis, we developed different RNA interference (RNAi) models of SNX3 in cancer cell lines and observed that WLS (Wntless, one of the known cargos of SNX3) and EGFR (Epidermal Growth Factor Receptor, possible cargo of SNX3) levels were altered in SNX3 silenced cells compared with the controls. We used proximity-based ligation approach to demonstrate possible interaction between SNX3 and EGFR, used immunostaining to determine subcellular localization of SNX3 and several mutants we generated that showed deregulated ubiquitylation and abnormal subcellular localization. Overall, we showed that SNX3 modulates EGFR protein levels and that ubiquitylation may be important for SNX3 function. Understanding the role of SNX3 and the endocytic trafficking may have future implications for targeted therapies against EGFR.


Sorting nexin 3 (SNX3) is an immediate and sustained target of EGF stimulation in EGFR positive breast cells
Çiçek, Esra; Erson Bensan, Ayşe Elif; Department of Biology (2021-9-10)
Sorting nexin 3 (SNX3) is a member of the sorting nexins family, which is involved in the endocytic trafficking network. SNX3 only has a PX domain, which helps endosomes bind to phosphatidyl inositol-3-phosphate and plays a role in the constitution of the retromer complex on early endosomes. Endocytosed receptors are internalized and recycled back to the plasma membrane, the Trans-Golgi Network, or are degraded in the lysosomes. The current understanding of SNX3 function in recycling Epidermal Growth Factor...
Evaluation of crossover techniques in genetic algorithm based optimum structural design
Hasançebi, Oğuzhan (1998-08-21)
Crossover is one of the three basic operators in ally genetic algorithm (GA). Several crossover techniques have been proposed and their relative merits are currently under investigation. This paper starts with a brief discussion of the working scheme of genetic algorithms (GAs) and crossover techniques commonly used in previous GA applications. Next, these techniques are tested on two truss size optimization problems, and are evaluated with respect to exploration and exploitation aspects of the search proce...
Improving the scalability of ILP-based multi-relational concept discovery system through parallelization
Mutlu, Ayşe Ceyda; Karagöz, Pınar; Kavurucu, Yusuf (2012-03-01)
Due to the increase in the amount of relational data that is being collected and the limitations of propositional problem definition in relational domains, multi-relational data mining has arisen to be able to extract patterns from relational data. In order to cope with intractably large search space and still to be able to generate high-quality patterns. ILP-based multi-relational data mining and concept discovery systems employ several search strategies and pattern limitations. Another direction to cope w...
Investigation of Stationarity for Graph Time Series Data Sets
Güneyi, Eylem Tuğçe; Vural, Elif (2021-01-07)
Graphs permit the analysis of the relationships in complex data sets effectively. Stationarity is a feature that facilitates the analysis and processing of random time signals. Since graphs have an irregular structure, the definition of classical stationarity does not apply to graphs. In this study, we study how stationarity is defined for graph random processes and examine the validity of the stationarity assumption with experiments on synthetic and real data sets.
A minimum distance bound for quasi-nD-cyclic codes
Özbudak, Ferruh (Elsevier BV, 2016-09-01)
We provide a new concatenated structure for multidimensional quasi-cyclic (QnDC) codes over F-q and we give a trace representation for their codewords, which extends the known representations of QC and nD cyclic codes. Based on these results, we obtain a minimum distance bound for QnDC dyclic codes. Since QnDC codes are naturally related to nD convolutional codes, this bound also applies to a special class of 1-generator 2D convolutional codes.
Citation Formats
M. Öyken, “Characterization of sorting nexin 3 (SNX3) function,” Thesis (Ph.D.) -- Graduate School of Natural and Applied Sciences. Biology., Middle East Technical University, 2020.