Oktay Lab. on Neuro-Genomics

Overview

Next generation sequencing (NGS) technologies have revolutionized our approach to studying the genetic basis of diseases and caused a paradigm shift in biological sciences. With the cost of whole genome sequencing (WGS) well-below the much-anticipated $1000 level, it is now affordable to sequence the whole genome of hundreds to thousands of patients or healthy people. As a result, our knowledge of genome and its regulation in health and disease has increased tremendously: Since the completion of the Human Genome Project (HGP), millions of variants and mutations have been identified and thousands of them have been associated with both inherited and sporadic diseases. So far, an overwhelming majority of clinical genomics studies have focused on the “exome” – protein-coding parts of the genome, mainly due to its much lower cost compared to WGS. ENCODE (Encyclopedia of DNA Elements) Project and similar efforts have provided peek into the functional organization of the genome, however, our knowledge of how genomic information is utilized is far from complete and limited. A better understanding of such fundamental principles of genome regulation will undoubtedly help us explain the molecular basis of pathologic disease states. The overarching goal of our research efforts is to unravel these principles within the context of nervous system disorders.

Research Interests

The overarching goal of the Neuro-genomics Lab at IBG is the elucidation of mechanisms leading from genomic variation to diseases of the human nervous system. Our efforts can be grouped into two stages: Identification of such variants (i.e. in neurodevelopmental disorders) and their modeling in cellular and animal models with the help of genome editing tools.

Elucidation of the cellular mechanisms underlying the genetic predisposition to complex diseases and phenotypes of the nervous system is a major focus of our lab. In this respect, we utilize tools of the functional genomics to understand the molecular basis of genetic susceptibility to lethal brain tumors, namely gliomas. A multidisciplinary approach using genomic, epigenomic, transcriptomic, bioinformatic and cell biology methods is employed to achieve an integrative understanding of the early stages of gliomagenesis, as well as to identify prognostic biomarkers and therapeutic targets. We have recently identified the molecular basis of genetic predisposition to IDH-mutant gliomas and established the proto-oncogene MYC as the culprit of 8q24-associated glioma risk.

Another major focus of our research is to develop models and methods that will facilitate identification of DNA variants that cause or contribute to the etiopathogenesis of neurodevelopmental diseases. To this end, we perform whole-exome sequencing of trios and multiplex families to identify candidate variants, and test them with functional studies in cell and animal models, frequently employing CRISPR/Cas9 genome-editing tools. We have recently identified several new disease genes and variants in a large consanguineous cohort of neurodevelopmental disorders. Our current efforts are aimed towards finding therapeutic targets by utilizing a multi-omic analyses of this cohort.

A better grasp of the genotype-phenotype relationships in neurodevelopmental, as well as neurooncological, diseases is a must to translate the power of genomics into clinical benefit. Our multi-disciplinary approach will be expected to provide valuable guidance to development of therapeutic, prognostic and diagnostic tools.

Methodological Approach

  • Determination of variants and mutations that cause diseases: targeted sequence analysis of genes that encode proteins and functional genome elements, RNA-sequencing, analysis of patient samples with whole exome and whole genome sequencing.
  • Functional studies of identified variants and mutations in cell culture and animal models: The development of cell and animal models by CRISPR-Cas9 genome-forming technology is applied in our laboratory.

Research Highlights

Our recent work on low-grade gliomas (LGGs) has focused on understanding the genetic basis of genetic predisposition to IDH-mutated gliomas, which comprise 70-80 % of LGGs. These studies were conducted by a multi-disciplinary approach that employed transcriptomic, proteomic, immunohistochemical, clinical and epidemiologic analyses of tumor and blood samples from LGG patients. A manuscript based on these studies is under review. Also, a TUBITAK 1001 grant has recently (2015) been awarded for 3 years to study the mechanistic basis of 8q24.21-associated genetic predisposition to glioma. Within this project, neural stem cell (NSC) lines are being edited by using the CRISPR-Cas9 system to obtain isogenic cell lines that differ at only the disease-associated variants/loci, in the absence and presence of IDH1-R132H mutation due to the strict association of these variants with IDH1/2 mutations. An integrated analysis of these cells will be carried out by 4C-seq, RNA-seq, enhancer assays, etc.

Group Members

Oktay Lab. on Neuro-Genomics

Group Leader

Yavuz OKTAY
yavuz.oktay@ibg.edu.tr
+90 232 299 41 00 (5141)
+9 02322994164

Semra HIZ Senior Researcher semra.hiz@ibg.edu.tr

Burcu Ekinci PhD Student burcu.ekinci@msfr.ibg.edu.tr

Aykut Kuruoğlu PhD Student aykut.kuruoglu@msfr.ibg.edu.tr

Fadime Öztoprak PhD Student fadime.oztoprak@msfr.ibg.edu.tr

Ece Sönmezler MSc Student ece.sonmezler@msfr.ibg.edu.tr

Kaan Okay MSc Student kaan.okay@msfr.ibg.edu.tr

Ebru Diler MSc Student ebru.diler@msfr.ibg.edu.tr

Tutku Yaraş MSc Student tutku.yaras@msfr.ibg.edu.tr

News

Our lab has become part of newly established MRC-ICGNMD center on neuromuscular diseases

International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD) has just been established and awarded 5-year funding by the Medical Research Council (MRC)-UK. The centre brings together clinicians and researchers from UK, Turkey, India, South Africa, Brazil and Zambia to advance genomic medicine in neuromuscular diseases. The inauguration ceremony of the centre took place on April 3, 2019 at House of Lords in London, with attendance by Turkish counsellor and Prof. Lord Kakkar among the audience.


Selected Publications

Ege Ulgen, Ozge Can, Kaya Bilguvar, Yavuz Oktay, Cemaliye Akyerli, Ayça Danyeli, Cengiz Yakicier, Ugur Sezerman, Necmettin Pamir Koray Özduman. Whole Exome Sequencing-Based Analysis Identifies DNA Damage Repair Deficiency as a Major Contributor to Gliomagenesis in Adult Diffuse Gliomas. J Neurosurg. 2019 Apr doi:10.3171/2019.1.JNS182938.

Canem Kavurma, Erhan Bayram, Aylin Özbek, Semra Ayşe Hız. ‘My Child Doesn’t Eat!’; Parental Feeding Strategies, Parental Attitudes and Family Functioning of Children with Poor Appetite. J Basic Clin Health Sci. 2018 Feb ; 2 20-24. doi:10.30621/jbachs.2018.275.

Erhan Bayram, Meral Torun Bayram, Uluç Yiş. Evaluation of the body composition with bioelectrical impedence analysia in epileptic patients treated with valproic acid. Neurology Asia. 2018 ; 23 (2): 131-136.

İpek Polat, Semra Hız. Hipoksik İskemik Beyin Hasarı. Turkiye Klinikleri J Pediatr Sci . 2018 ; 14 (1): 30-36.

Semra Gürsoy, Esra Ataman, Özlem Giray Bozkaya, Engin Köse, Müge Ayanoğlu, Ayşe İpek Polat, Nur Arslan, Semra Hız Kurul, Derya Erçal. Identification of the largest homozygous glycine decarboxylase gene deletion in a Turkish infant. Pediatrics and Neonatology. 2018 Dec ; 59 (6): 632-633. doi:10.1016/j.pedneo.2018.01.011.

Akyerli CB, Yüksel Ş, Can Ö, Erson-Omay EZ, Oktay Y, Coşgun E, Ülgen E, Erdemgil Y, Sav A, von Deimling A, Günel M, Yakıcıer MC, Pamir MN, Özduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. J Neurosurg. 2018 Apr ; 128 (4): 1102-1114. doi:10.3171/2016.11.JNS16973.

Oktay Y., Boylu C.A., Özduman K.. Gliom gelişiminde genetik yatkınlığın rolü. Türk Nöroşir Derg. 2017 Mar ; 27 (2): 122-130.

Engin Köse, Uluc Yis, Semra Hiz, Nur Arslan. A novel mutation in the glycine decarboxylase gene in patient with non-ketotic hyperglycinemia. Neurosciences. 2017 Apr ; 22 (2): 131-133. doi:10.17712/nsj.2017.2.20160468.

Semra Hız-Kurul, Semra Gürsoy, Müge Ayanoğlu, Uluç Yiş, Derya Erçal. Expanding spectrum of SCN1A-related phenotype with novel mutations. Turk J Pediatr. 2017 ; 59 (5): 570-575. doi:10.24953/turkjped.2017.05.010.

Oktay Y., Boylu C.A., Özduman K. Gliom gelişiminde genetik yatkınlığın rolü. Türk Nöroşir Derg. 2017 Mar ; 27 (2): 122-130. doi: .

Projects

Tubitak - RD : GLİOM OLUŞUMUNDA ROL OYNAYAN KALICI EPİGENOMİK DEĞİŞİMLERİN IDH1-TERT-MYC EKSENİNDE KARAKTERİZASYONU , 2018-06-15/2021-02-15

UİDB-COST - RD : GLİOMLARA YATKINLIK SAĞLAYAN 8Q24.21 BÖLGESİNDEKİ SNP RS55705857'NİN MOLEKÜLER ETKİ MEKANİZMALARININ ORTAYA ÇIKARILMASI , 2015-06-01/2018-12-15

UİDB-COST - RD : PAKİGRİLİ HASTALARDA GÖRÜLEN DNA DİZİ VARİANTLARININ IPSC'LERDE VE ZEBRABALIĞINDA GENOM DÜZENLEME ARAÇLARI ILE MODELLENEREK KİŞİYE YÖNELİK TIP UYGULAMALARINA OLANAK TANIYACAK YÖNTEM VE PLATFORMLARIN GELİŞTİRİLMESİ , 2018-06-01/2021-06-01

Tubitak - RD : PEDİATRİK NÖROGENETİK HASTALIKLARDA YENİ NESİL DİZİLEME UYGULAMALARININ TANISAL ETKİNLİĞİNİ ARTTIRMAYA YÖNELİK BÜTÜNCÜL BİR YAKLAŞIM , 2019-02-15/2021-02-15

Tubitak - RD : Obsesif-kompulsif Bozukluk ile NLRP3 İnflamazom Aktivitesi İlişkisinin Araştırılması , 2018-04-01/2019-04-01

DEU BAP - RD : Sendromik Olmayan‚ Otizm Spektrum Bozukluğu Tanılı İkisi de Etkilenmiş İkiz Çocuk ve Ergenlerin ve Anne Babalarının Genomlarının Tüm Genom Dizileme Yöntemi ile Analizi , 2017-01-01/2018-01-31

BRITISH COUNCIL / TÜBİTAK ORTAK - RD : Türkiye'de Akraba Evliliklerine Bağlı Nörogenetik Hastalık Yükünün Araştırılmasında Yeni Genomik Yaklaşımlar , 2016-12-01/2019-08-01

UİDB-COST - RD : Tekrar Artışı ile Giden Nörogelişimsel Hastalıkların Tanı ve DNA Analizine Yönelik CRISPR/Cas Aracılı Üçüncü Nesil DNA Dizileme Yöntemleri Geliştirilmesi ,

Open Positions

Looking for motivated MSc candidates!    

Awards

  • Yavuz OKTAY - Young Investigator (GEBİP) Awards by Turkish Academy of Sciences (TÜBA), 2017

Contact

Oktay Lab. on Neuro-Genomics

Group Leader

Yavuz OKTAY
yavuz.oktay@ibg.edu.tr
+90 232 299 41 00 (5141)
+9 02322994164