Serap ERKEK ÖZHAN
In our lab, we aim to investigate the mechanisms that cause loss of function of chromatin modifiers, which are subunits of MLL complex, and frequently mutated both in cancer and in rare disease. We recently got a TUSEB project to study the function of KMT2D in one rare disease, Kabuki Syndrome. We would be interested to join to the future projects, characterizing the epigenetic mechanisms in rare diseases.
Lymphoid cancer biology, genomics, transcriptomics, epigenomics
I have several years of experience on NK/T cell lymphoma (NKTCL) pathogenesis. It is a rare and aggressive subtype of non-Hodgkin lymphoma. NKTCL is relatively more common in east Asian countries. Through my collaborations in China, I can obtain a good number of NKTCL samples for research projects. I may contribute to the development of a diagnostic kit based on the KIR expression profile, as an example.
Computational biophysics, in silico methods in life sciences
We use tools of high-performance computing, molecular modeling and statistical physics to understand how the local exposure or compaction of chromatin affects the progression of DNA-templated processes. In the context of rare diseases, we study the Rahman syndrome where we demonstrated that a mutated linker histone H1 impairs efficient chromatin condensation.
Developmental biology, neuroscience, Wnt signaling, tissue regeneration, zebrafish disease models
Danio rerio, commonly known as zebrafish, is a very convenient scientific model organism for studies including vertebrate developmental genetics, cell biology, toxicology, high-throughput screening of drug libraries and human diseases. Evolution of zebrafish to an attractive vertebrate model is due to a variety of essential scientific reasons such as having a high degree of sequence and functional homology with mammals, having a fully sequenced genome, easy maintenance, producing large number of offspring, and fast and transparent embryogenesis. Nevertheless, the organism takes its main power from the well-established transgenic tools, live-cell imaging and cell lineage tracing methodologies, forward and reverse genetic approaches and micromanipulation techniques. We have a zebrafish facility that harbors approximately 12.000 fish and is fully equipped with systems of micromanipulation, imaging and behavioral assay. Our group has successfully established various zebrafish techniques including embryo micromanipulation, generation of transgenic lines, CRISPR/Cas9-based genome editing and behavioral assays. We can generate zebrafish models to study the mechanisms of various rare diseases and test potential therapies.
Nur ARSLAN / Zeynep ÖZBEK
Inherited metabolic disorders/ Rare eye disorders
We are working on rare and undiagnosed patients with inherited metabolic origin or component. We have access to patient relatad clinical and biological data. Moreover, we can create organoid models for inherited metabolic disorders in Erdal Lab.
Biochemistry, Protein engineering, Antibody engineering
Our lab can contribute to protein design, expression, purification and characterization studies with the help of IBG-Pharma platform. We can produce recombinant proteins/enzymes in microbial systems. We can also produce recombinant antibodies in both microbial and mammalian sytems. After production, we can purify and characterize the generated protein. Characterization techniques include various biohemical and biophysical characterizations including binding kinetics analysis.
Work on rare immunological diseases. Support the deep phenotyping of patient material. Establishing mouse models for rare diseases and using those to investigate the underlying mechanisms of rare diseases of interest.
Cancer biology and Genetics
Atabey Lab has been working to define the mechanisms responsible for the aggressive phenotype in different cancers, especially liver and colorectal cancer. We perform genomics, transcriptomics, and proteomics analyses using cancer cell lines, 3D co-culture systems, genetically modified animal models, and patient materials. Our collaborations, which started within the scope of a COST project in recent years, resulted in an EU grant application to analyze RNA modifications during carcinogenesis in FAP patients with high-throughput methods. In this context, our studies and collaborations would contribute to the newly established rare and undiagnosed diseases platform, especially in rare cancers.
Yavuz OKTAY / Semra HIZ
Molecular Biology and Genetics
Our laboratory's main focus is developing disease models for a wide range of nervous system originating diseases, with an emphasis on Rare Diseases. We employ tools of genetics, cell biology, genomics, and bioinformatics. We hope to be able to contribute to the Platform by collaborations, joint project applications, etc.
Computational analyses and interpretation of NGS data sets
Gülçin ÇAKAN AKDOĞAN
Zebrafish models as a tool for disease modeling and drug testing for efficacy and toxicity. Development of drug screening platforms and targeted drug delivery methods
I would like to contribute to the platform by generation of mutant or transgenic zebrafish lines and investigating disease mechanisms in these models. Another important contribution will be to test potential drugs, to conduct drug repurposing or drug discovery studies. We have proven capacity to develop genetically modified disease models and study the mechanistic aspects of related pathologies. As part of one 1001 project we have generated the first in vivo model of macular cornea dystrophy.
Genetically modified mouse models, transgenic mice
Our contributions will be in two areas. First, as a service platform that develops genetically modified mouse models, we can collaborate with researchers and generate preclinical models for rare diseases. We have already generated numerous knockout and knockin mice utilizing the CRISPR technique. We can do this fast and efficiently. We have the tools to generate more sophisticated models (including conditional knockout, gene knockin, pronuclear injection for transgene integration, ESC microinjection etc.) and we will happily make more complex models if there is demand. Second, we have already established or in the process of establishing novel mouse models for a number of rare genetic disorders. We need partners for detailed characterization of the phenotypes in these mice. These models include mutations in the following genes: ATG9B, HIST1H1E, Tousled-like kinase 2, TRAPPC4.
Rare Disease Biobank
IBG-BIOBANK include work towards identifying new methods to preserve samples and related data in line with biobanking good laboratory practices and at the highest quality, as well as in a way that makes follow-up possible and that protects the safety of samples and data. These activities also include those aim at developing disease-relevant cell/tissue assay models.