Cakan Lab. on Zebrafish Models


Zebrafish is a widely used, robust vertebrate model that is accessible for genetic modification, well suited for imaging, easy to manipulate, has a short generation time and low cost. Zebrafish has been increasingly used for disease modeling and cancer studies, and it has come forward as an attractive model for drug discovery and personalized medicine studies in recent years. 

Zebrafish larval xenografts are widely used to create cancer models and assess metastatic and/or angiogenic capacity of cancer cells. More recently, patient derived xenografts (PDX) of zebrafish have been demonstrated useful for testing treatment options as a tool for personalized medicine. Cancer cells are introduced to 2dpf(2 days post fetilization) zebrafish hosts by microinjection. Cells injected to yolk sac to form a tumor and dissemination of the metastatic cells into circulation is observed within few days of injection a powerful in vivo metastasis model. 

We generate zebrafish cancer models also by creating “humanized tumors” by overexpression of human oncogenes in selected tissues, creating tumors that are genetically and pathologically similar to human tumors. Availibility of various genetic tools allows  us to create time and space controlled expression of such oncogenes, in significantly shorter time and reduces cost than rodent models. Large amount of expression and mutation data available in the literature that postulate genes of prognostic value, metastatic signature and driver mutations in cancer. In vivo validation of these genes is often much slower than the sequence data generation. We are utilizing the unique advantages zebrafish offers to test the in vivo effects of such genes to speed up the validation process and contribute to identification of potential targets for therapy.

We collaborate with scientists in various research fields at iBG, offering expertise on state-of-the art zebrafish technology and facilitating wider use of this model organism. Highly collaborative research efforts supported by iBG ecosystem will undoubtedly yield to valuable findings and applications.


The zebrafish aquarium is operated by highly trained personnel, with high standards in compliance with EU-regulations, monitored with local ethics committee and  the Ministry of Food, Agriculture and Livestock.  iBG zebrafish facility houses an aquarium equipped with Techniplast Zebtec Multilinking system with 360 tanks capacity, and a Zebtec Standalone system with 60 tanks capacity used in the main room and the quarantine room respectively. In addition, the unit has embryo manipulation room that is equipped with stereomicroscopes  and microinjection equipment , two imaging rooms equipped with a fluorescent stereomicroscope and a brigthfield stereomicroscope with cameras. We maintain the facility equipment, give high standard zebraifsh care, train researchers for micromanipulation, genotyping, mutagenesis, transgenesis .. techniques.  As a group we aim to facilitate transfer of know-how, support efficient use of zebrafish model in the region by  creating a collaborative environment, and always offering expertise on state-of-the art zebrafish technology. 

Selected Publications

Aysim Gunes, Ezgi Bagirsakci, Evin Iscan, Gulcin Cakan-Akdogan, Umut Aykutlu, Serif Senturk, Gunes Ozhan, Esra Erdal, Deniz Nart, Funda Yilmaz Barbet, Nese Atabey. Thioredoxin interacting protein promotes invasion in hepatocellular carcinoma. Oncotarget. 2018 ; 9 (96): 36849-36866. doi:

Akdogan Y, Emrullahoglu M, Tatlidil D, Ucuncu M, Cakan-Akdogan G. EPR studies of intermolecular interactions and competitive binding of drugs in a drug-BSA binding model.. Physical chemistry chemical physics : PCCP. 2016 Aug ; 18 (32): 22531-9. doi:10.1039/c6cp04137j.


Cakan Lab. on Zebrafish Models

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