Cihangir Yandım

Cihangir Yandım
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Cihangir verified their affiliation via an institutional email.
Verified
Cihangir verified their affiliation via an institutional email.
İzmir University of Economics

Doctor of Philosophy

About

27
Publications
3,236
Reads
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373
Citations
Introduction
A broad-minded scientist with substantial experience in gene regulation, epigenetics, genomics, drug discovery and cancer research in laboratory and clinical trial settings.
Additional affiliations
February 2018 - present
İzmir University of Economics
Position
  • Professor (Assistant)
Education
September 2014 - September 2017
Institute of Cancer Research
Field of study
  • Cancer Therapeutics
October 2007 - May 2012
Independent Researcher
Independent Researcher
Field of study
  • Molecular Genetics and Epigenetics / Faculty of Medicine
September 2003 - June 2007
Bilkent University
Field of study
  • Molecular Biology and Genetics

Publications

Publications (27)
Article
Despite an overwhelming number of cancer literature reporting the links between patient survival and the expression levels of genes or mutations/single nucleotide variations (SNVs) on them, there is only limited information on repeat elements, which make at least half the human genome. Here, we analysed RNA-seq data obtained from primary pancreatic...
Article
PI3K pathway is heavily emphasized in cancer where PIK3CA, which encodes for the p110α subunit of PI3Kα, presents itself as the second most common mutated gene. A lot of effort has been put in developing PI3K inhibitors, opening promising avenues for the treatment of cancer. Among these, PI3Kα specific inhibitor alpelisib was approved by FDA for br...
Article
MTHFR (Methylenetetrahydrofolate reductase) is a pivotal enzyme involved in one-carbon metabolism, which is critical for the proliferation of cancer cells. In line with this, published literature showed that MTHFR knockdown caused impaired growth of multiple types of cancer cells. Moreover, higher MTHFR expression levels were linked to shorter over...
Article
Full-text available
The glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma’s molecular pathology and patient survival remains largely unexplored. In this stu...
Article
Full-text available
Background Although DNA repair mechanisms function to maintain genomic integrity, in cancer cells these mechanisms may negatively affect treatment efficiency. The strategy of targeting cancer cells via inhibiting DNA damage repair has been successfully used in breast and ovarian cancer using PARP inhibitors. Unfortunately, such strategies have not...
Article
Inorganic pyrophosphatase 1 (PPA1) is pivotal to cellular metabolism as it facilitates the hydrolysis of PPi—a by‐product of various metabolic processes that influence cell growth and differentiation. Overexpression of PPA1 enzyme has been linked to diminished patient survival and was shown to influence tumor cell dynamics, thereby positioning it a...
Article
Background and Objectives Hepatocellular carcinoma (HCC) is a primary cancer that poorly responds to treatment. Molecular cancer studies led to the development of kinase inhibitors, among which sorafenib stands out as a multi-kinase inhibitor approved by FDA for first line use in HCC patients. However, the efficiency of sorafenib was shown to be co...
Article
Full-text available
Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various...
Article
Full-text available
Replicative cellular senescence is the main cause of aging. It is important to note that early senescence is linked to tissue regeneration, whereas late senescence is known to trigger a chronically inflammatory phenotype. Despite the presence of various genome-wide studies, there is a lack of information on distinguishing early and late senescent p...
Article
Full-text available
AKT, a critical effector of the phosphoinositide 3-kinase (PI3K) signalling cascade, is an intensely pursued therapeutic target in oncology. Two distinct classes of AKT inhibitors have been in clinical development, ATP-competitive and allosteric. Class-specific differences in drug activity are likely the result of differential structural and confor...
Article
Full-text available
Introduction Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE –proximal gene expression associations from RNA-sequencing data are still missing. Implementation Herein,...
Conference Paper
Full-text available
Repetitive DNA elements, which constitute more than half of the human genome with more than a thousand types of distinct motifs 1,2 , are normally hardly expressed in healthy cells with a stable genome 3. Notably, a common feature of breast cancer is genomic instability, which is associated with heterogeneity and resistance to treatment 4. The cont...
Article
Limited studies on breast cancer indicated pathogenic changes in the expressions of some repeat elements. A global analysis was much needed within this context to distinguish the most significant repeats from more than a thousand repeat motifs. Utilising a previously presented RNA-seq dataset, we studied expression changes of all repeats in ER+/HER...
Article
Full-text available
Background: The last decade witnessed a number of genome-wide studies on human pre-implantation, which mostly focused on genes and provided only limited information on repeats, excluding the satellites. Considering the fact that repeats constitute a large portion of our genome with reported links to human physiology and disease, a thorough understa...
Conference Paper
Full-text available
More than half of the human genome comprises repetitive DNA sequences, which are referred as "junk" DNA and are often overlooked. Indeed, these sequences are usually not included in sequencing analyses due to problems arisen by their repetitive nature. Still, last decade witnessed an increase in the number of studies that linked repeatome with dise...
Article
Full-text available
Heterochromatinisation of pericentromeres, which in mice consist of arrays of major satellite repeats, are important for centromere formation and maintenance of genome stability. The dysregulation of this process has been linked to genomic stress and various cancers. Here we show in mice that the proteasome binds to major satellite repeats and prot...
Data
Transcription of major satellite peaks in G1 phase and minor satellite in G2/M phase of the cell cycle. (A) Cell fractions enriched at specific phases of the cell cycle, were obtained by centrifugal elutriation. Top panel: representative images of the FACS profiles after PI staining of non-elutriated cells and three different fractions of elutriate...
Data
The effect of the proteasome inhibition on the distribution and levels of HP1α. (A) Delocalisation of HP1α from chromocentres upon proteasome inhibition. NIH3T3 cells were treated with 20μM MG132 for 8h and immunolabeled with HP1α antibody (green) and co-stained with DAPI (blue). Scale bar 10μm. (B) Total HP1α protein levels remain similar upon pro...
Data
List of primers used throughout this study. (TIF)
Conference Paper
Full-text available
Objective : To assess the effect of twice daily dosing of nicotinamide on (1) maximum tolerated dose (MTD), (2) side effects and (3) frataxin expression in patients with Friedreich's ataxia. Background : Nicotinamide is a histone deacetylase (HDAC) inhibitor which we have recently shown to increase Frataxin (FXN) expression in patients with Friedre...
Article
Full-text available
Background: Friedreich's ataxia is a progressive degenerative disorder caused by deficiency of the frataxin protein. Expanded GAA repeats within intron 1 of the frataxin (FXN) gene lead to its heterochromatinisation and transcriptional silencing. Preclinical studies have shown that the histone deacetylase inhibitor nicotinamide (vitamin B3) can re...
Article
Full-text available
This is an exciting time in the study of Friedreich's ataxia. Over the last 10 years much progress has been made in uncovering the mechanisms, whereby the Frataxin gene is silenced by (GAA)n repeat expansions and several of the findings are now ripe for testing in the clinic. The discovery that the Frataxin gene is heterochromatinised and that this...
Thesis
Heterochromatin is implicated in the negative regulation of gene expression. To understand the effects of heterochromatin on RNA polymerase-II (RNAPII) mediated transcription, this study focused on the FXN gene where abnormal silencing induced by expanded (GAA)n repeats causes Friedreich's ataxia (FRDA), an incurable neurological disorder. Here, th...

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