Genetics and Biotechnology Research Center (BİLGEN)

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Open Access
Congenital pineoblastoma and parameningeal rhabdomyosarcoma: concurrent two embryonal tumors in a young infant
(Springer, 2006) Çorapçıoğlu, F.; Özek, M. M.; Sav, A.; Üren, Deniz
Background: Pineoblastomas are very rare brain tumors in fetus and neonates, comprising only 0.9% of congenital brain tumors. The occurrence of multiple tumors of different histopathologic types in the same individual is a rare event, most often encountered in hereditary cancer syndromes. Case Report: We report a female fetus presented with a congenital pineoblastoma at the 32nd week of gestation, with hydrocephalus and concurrent parameningeal embryonal rhabdomyosarcoma in early infancy. Results: Cytogenetic analysis showed normal karyotype in the peripheral blood of the patient, and p53 mutational analysis revealed no germ line mutations. Discussion: This is the first case with concurrent congenital pineoblastoma and parameningeal embryonal rhabdomyosarcoma in early infancy. We suggest that concurrence of these tumors could be due to mutations in other tumor suppressor genes or secondary to exposure to unknown in utero factors.
Open Access
Transforming growth factor-beta induces senescence in hepatocellular carcinoma cells and inhibits tumor growth
(American Association for the Study of Liver Disease, 2010) Şentürk, Şerif; Mumcuoğlu, Mine; Gürsoy-Yüzügüllü, Özge; Cingöz, Burcu; Akçalı, Kamil Can; Öztürk, Mehmet
Senescence induction could be used as an effective treatment for hepatocellular carcinoma (HCC). However, major senescence inducers (p53 and p16Ink4a) are frequently inactivated in these cancers.We tested whether transforming growth factor-β (TGF-β) could serve as a potential senescence inducer in HCC. First, we screened for HCC cell lines with intact TGF-β signaling that leads to small mothers against decapentaplegic (Smad)-targeted gene activation. Five cell lines met this condition, and all of them displayed a strong senescence response to TGF-β1 (1-5 ng/mL) treatment. Upon treatment, c-myc was down-regulated, p21Cip1 and p15Ink4b were up-regulated, and cells were arrested at G1. The expression of p16Ink4a was not induced, and the senescence response was independent of p53 status. A short exposure of less than 1 minute was sufficient for a robust senescence response. Forced expression of p21 Cip1 and p15Ink4b recapitulated TGF-β1 effects. Senescence response was associated with reduced nicotinamide adenine dinucleotide phosphate oxidase 4 (Nox4) induction and intracellular reactive oxygen species (ROS) accumulation. The treatment of cells with the ROS scavenger N-acetyl-L-cysteine, or silencing of the NOX4 gene, rescued p21Cip1 and p15Ink4b accumulation as well as the growth arrest in response to TGF-β. Human HCC tumors raised in immunodeficient mice also displayed TGF-β1-induced senescence. More importantly, peritumoral injection of TGF-β1 (2 ng) at 4-day intervals reduced tumor growth by more than 75%. In contrast, the deletion of TGF-β receptor 2 abolished in vitro senescence response and greatly accelerated in vivo tumor growth. Conclusion: TGF-β induces p53-independent and p16Ink4a-independent, but Nox4-dependent, p21Cip1-dependent, p15Ink4b-dependent, and ROS-dependent senescence arrest in well-differentiated HCC cells. Moreover, TGF-β-induced senescence in vivo is associated with a strong antitumor response against HCC.
Open Access
The ability to generate senescent progeny as a mechanism underlying breast cancer cell heterogeneity
(Public Library of Science, 2010) Mumcuoğlu, Mine; Bağışlar, Sevgi; Yüzügüllü, Haluk; Alotaibi, Hani; Şentürk, Şerif; Telkoparan, Pelin; Gür-Dedeoğlu, Bala; Cingöz, Burcu; Bozkurt, B.; Tazebay, Uygar H.; Yuluğ, Işık G.; Akçalı, Kamil Can; Öztürk, Mehmet
Background Breast cancer is a remarkably heterogeneous disease. Luminal, basal-like, "normal-like", and ERBB2+ subgroups were identified and were shown to have different prognoses. The mechanisms underlying this heterogeneity are poorly understood. In our study, we explored the role of cellular differentiation and senescence as a potential cause of heterogeneity. Methodology/Principal Findings A panel of breast cancer cell lines, isogenic clones, and breast tumors were used. Based on their ability to generate senescent progeny under low-density clonogenic conditions, we classified breast cancer cell lines as senescent cell progenitor (SCP) and immortal cell progenitor (ICP) subtypes. All SCP cell lines expressed estrogen receptor (ER). Loss of ER expression combined with the accumulation of p21Cip1 correlated with senescence in these cell lines. p21Cip1 knockdown, estrogen-mediated ER activation or ectopic ER overexpression protected cells against senescence. In contrast, tamoxifen triggered a robust senescence response. As ER expression has been linked to luminal differentiation, we compared the differentiation status of SCP and ICP cell lines using stem/progenitor, luminal, and myoepithelial markers. The SCP cells produced CD24+ or ER+ luminal-like and ASMA+ myoepithelial-like progeny, in addition to CD44+ stem/progenitor-like cells. In contrast, ICP cell lines acted as differentiation-defective stem/progenitor cells. Some ICP cell lines generated only CD44+/CD24-/ER-/ASMA- progenitor/stem-like cells, and others also produced CD24+/ER- luminal-like, but not ASMA+ myoepithelial-like cells. Furthermore, gene expression profiles clustered SCP cell lines with luminal A and "normal-like" tumors, and ICP cell lines with luminal B and basal-like tumors. The ICP cells displayed higher tumorigenicity in immunodeficient mice. Conclusions/Significance Luminal A and "normal-like" breast cancer cell lines were able to generate luminal-like and myoepithelial-like progeny undergoing senescence arrest. In contrast, luminal B/basal-like cell lines acted as stem/progenitor cells with defective differentiation capacities. Our findings suggest that the malignancy of breast tumors is directly correlated with stem/progenitor phenotypes and poor differentiation potential.
Open Access
Aflatoxin genotoxicity is associated with a defective DNA damage response bypassing p53 activation
(John Wiley & Sons, 2011) Gürsoy-Yüzügüllü, Özge; Yüzügüllü, Haluk; Yılmaz, Mustafa; Öztürk, Mehmet
Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer deaths. Aflatoxins, which may play a causative role in 5-28% of HCCs worldwide, are activated in liver cells and induce principally G→T mutations, including the TP53 codon 249(G→T) hotspot mutation. The DNA damage checkpoint response acts as an antitumour mechanism against genotoxic agents, but its role in aflatoxin-induced DNA damage is unknown. Aim: We studied the DNA damage checkpoint response of human cells to aflatoxin B1 (AFB1). Methods and results: The treatment of HepG2 hepatoma cells with mutation-inducing doses (3-5μmol/l) of AFB1 induced DNA adducts, 8-hydroxyguanine lesions and DNA strand breaks that lasted several days. Persistent phospho-H2AX and 53BP1 foci were also detected, but cell growth was not affected. AFB1-exposed HepG2 cells formed phospho-H2AX and 53BP1 foci, but failed to phosphorylate both Chk1 and Chk2. Huh7 hepatoma and HCT116 colorectal cancer cell lines also exhibited a similarly incomplete checkpoint response. p53 phosphorylation also failed, and AFB1-exposed cells did not show p53-dependent G1 arrest or a sustained G2/M arrest. These observations contrasted sharply with the fully functional DNA damage response of cells to Adriamycin. Cotreatment of cells with AFB1 did not inhibit p53 and p21Cip1 accumulation induced by Adriamycin. Thus, the deficient checkpoint response to AFB1 was not due to an inhibitory effect, but could be explained by an inefficient activation. Conclusion: Genotoxic doses of AFB1 induce an incomplete and inefficient checkpoint response in human cells. This defective response may contribute to the mutagenic and carcinogenic potencies of aflatoxins.
Open Access
mESAdb: microRNA expression and sequence analysis database
(Oxford University Press, 2011) Kaya, Koray D.; Karakülah, G.; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen
MicroRNA expression and sequence analysis database (http://konulab.fen. bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.
Open Access
Synthesis of novel 6-(4-substituted piperazine-1-yl)-9-(β-dribofuranosyl)purine derivatives, which lead to senescence-induced cell death in liver cancer cells
(ACS, 2012) Tunçbilek, M.; Güven, Ebru Bilget; Önder, T.; Çetin-Atalay, Rengül
Novel purine ribonucleoside analogues (9-13) containing a 4-substituted piperazine in the substituent at N-6 were synthesized and evaluated for their cytotoxicity on Huh7, HepG2, FOCUS, Mahlavu liver, MCF7 breast, and HCT116 colon carcinoma cell lines. The purine nucleoside analogues were analyzed initially by an anticancer drug-screening method based on a sulforhodamine B assay. Two nucleoside derivatives with promising cytotoxic activities (11 and 12) were further analyzed on the hepatoma cells. The N-6-(4-Trifluoromethylphenyl)piperazine analogue 11 displayed the best antitumor activity, with IC50 values between 5.2 and 9.2 mu M. Similar to previously described nucleoside analogues, compound 11 also interferes with cellular ATP reserves, possibly through influencing cellular kinase activities. Furthermore, the novel nucleoside analogue 11 was shown to induce senescence-associated cell death, as demonstrated by the SA beta-gal assay. The senescence-dependent cytotoxic effect of 11 was also confirmed through phosphorylation of the Rb protein by p15(INK4b) overexpression in the presence of this compound.
Open Access
Novel anti-HER2 monoclonal antibodies: synergy and antagonism with tumor necrosis factor-α
(BioMed Central, 2012) Ceran, Ceyhan; Çokol, M.; Cingöz, S.; Taşan, İpek; Öztürk, Mehmet; Yağcı, Tamer
Background: One-third of breast cancers display amplifications of the ERBB2 gene encoding the HER2 kinase receptor. Trastuzumab, a humanized antibody directed against an epitope on subdomain IV of the extracellular domain of HER2 is used for therapy of HER2-overexpressing mammary tumors. However, many tumors are either natively resistant or acquire resistance against Trastuzumab. Antibodies directed to different epitopes on the extracellular domain of HER2 are promising candidates for replacement or combinatorial therapy. For example, Pertuzumab that binds to subdomain II of HER2 extracellular domain and inhibits receptor dimerization is under clinical trial. Alternative antibodies directed to novel HER2 epitopes may serve as additional tools for breast cancer therapy. Our aim was to generate novel anti-HER2 monoclonal antibodies inhibiting the growth of breast cancer cells, either alone or in combination with tumor necrosis factor-α (TNF-α). Methods: Mice were immunized against SK-BR-3 cells and recombinant HER2 extracellular domain protein to produce monoclonal antibodies. Anti-HER2 antibodies were characterized with breast cancer cell lines using immunofluorescence, flow cytometry, immunoprecipitation, western blot techniques. Antibody epitopes were localized using plasmids encoding recombinant HER2 protein variants. Antibodies, either alone or in combination with TNF-α, were tested for their effects on breast cancer cell proliferation. Results: We produced five new anti-HER2 monoclonal antibodies, all directed against conformational epitope or epitopes restricted to the native form of the extracellular domain. When tested alone, some antibodies inhibited modestly but significantly the growth of SK-BR-3, BT-474 and MDA-MB-361 cells displaying ERBB2 amplification. They had no detectable effect on MCF-7 and T47D cells lacking ERBB2 amplification. When tested in combination with TNF-α, antibodies acted synergistically on SK-BR-3 cells, but antagonistically on BT-474 cells. A representative anti-HER2 antibody inhibited Akt and ERK1/2 phosphorylation leading to cyclin D1 accumulation and growth arrest in SK-BR-3 cells, independently from TNF-α. Conclusions: Novel antibodies against extracellular domain of HER2 may serve as potent anti-cancer bioactive molecules. Cell-dependent synergy and antagonism between anti-HER2 antibodies and TNF-α provide evidence for a complex interplay between HER2 and TNF-α signaling pathways. Such complexity may drastically affect the outcome of HER2-directed therapeutic interventions.
Open Access
Patterned carbon nanotubes as a new three-dimensional scaffold for mesenchymal stem cells
(Elsevier, 2013) Bitirim, Verda Ceylan; Küçükayan-Doğu, Gökçe; Bengü, Erman; Akçalı, Kamil Can
We investigated the cellular adhesive features of mesenchymal stem cells (MSC) on non-coated and collagen coated patterned and vertically aligned carbon nanotube (CNT) structures mimicking the natural extra cellular matrix (ECM). Patterning was achieved using the elasto-capillary induced by water treatment on the CNT arrays. After confirmation with specific markers both at transcript and protein levels, MSCs from different passages were seeded on either collagen coated or non-coated patterned CNTs. Adhesion and growth of MSCs on the patterned CNT arrays were examined using scanning electron microscopy image analysis and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-tetrazolium bromide (MTT) assays. The highest MSC count was observed on the non-coated patterned CNTs at passage zero, while decreasing numbers of MSCs were found at the later passages. Similarly, MTT assay results also revealed a decrease in the viability of the MSCs for the later passages. Overall, the cell count and viability experiments indicated that MSCs were able to better attach to non-coated patterned CNTs compared to those coated with collagen. Therefore, the patterned CNT surfaces can be potentially used as a scaffold mimicking the ECM environment for MSC growth which presents an alternative approach to MSC-based transplantation therapy applications.
Open Access
Genetics and epigenetics of liver cancer
(Elsevier, 2013) Özen, Çiğdem; Yıldız, Gökhan; Dağcan, Alper Tunga; Çevik, Dilek; Örs, Ayşegül; Keleş, Umut; Topel, Hande; Öztürk, Mehmet
Hepatocellular carcinoma (HCC) represents a major form of primary liver cancer in adults. Chronic infections with hepatitis B (HBV) and C (HCV) viruses and alcohol abuse are the major factors leading to HCC. This deadly cancer affects more than 500,000 people worldwide and it is quite resistant to conventional chemo- and radiotherapy. Genetic and epigenetic studies on HCC may help to understand better its mechanisms and provide new tools for early diagnosis and therapy. Recent literature on whole genome analysis of HCC indicated a high number of mutated genes in addition to well-known genes such as TP53, CTNNB1, AXIN1 and CDKN2A, but their frequencies are much lower. Apart from CTNNB1 mutations, most of the other mutations appear to result in loss-of-function. Thus, HCC-associated mutations cannot be easily targeted for therapy. Epigenetic aberrations that appear to occur quite frequently may serve as new targets. Global DNA hypomethylation, promoter methylation, aberrant expression of non-coding RNAs and dysregulated expression of other epigenetic regulatory genes such as EZH2 are the best-known epigenetic abnormalities. Future research in this direction may help to identify novel biomarkers and therapeutic targets for HCC.
Open Access
Novel object recognition is not affected by age despite age-related brain changes
(Scientific Research Publishing, 2013) Aktoprak, İlay; Dinç, Pelin; Günay, Gizem; Adams, Michelle M.
Age-related memory impairments show a progressive decline across lifespan. Studies have demonstrated equivocal results in biological and behavioral outcomes of aging. Thus, in the present study we examined the novel object recognition task at a delay period that has been shown to be impaired in aged rats of two different strains. Moreover, we used a strain of rats, Fisher 344XBrown Norway, which have published age-related biological changes in the brain. Young (10 month old) and aged (28 month old) rats were tested on a standard novel object recognition task with a 50-minute delay period. The data showed that young and aged rats in the strain we used performed equally well on the novel object recognition task and that both young and old rats demonstrated a righthanded side preference for the novel object. Our data suggested that novel object recognition is not impaired in aged rats although both young and old rats have a demonstrated side preference. Thus, it may be that genetic differences across strains contribute to the equivocal results in behavior, and genetic variance likely influences the course of cognitive aging.
Open Access
Comparative evaluation of in vitro cytotoxic effects among parent abietyl alcohol and novel fatty acid ester derivatives against MCF7 and hepatocellular carcinoma cell lines
(Pakistan Journal of Pharmaceutical Sciences, 2014) Mustufa, Muhammad Ayaz; Aslam, A.; Özen, Çiğdem; Hashmi, I. A.; Naqvi, N.; Öztürk, Mehmet; Ali, F. I.
Synthesis of twelve hitherto unreported esters of abietyl alcohol and screening of these esters against four cancer cell lines including one breast cancer line MCF7 and four hepatocellular carcinoma cell lines (HCC) Huh7, Hep3B, Snu449 and Plc has been determined using SRB assay. The Cell cycle progression showed changes in cellular behaviour after 48 and 72 hours in MCF7 and Huh7 cell lines. Abietyl alcohol was obtained from the reduction of abietic acid, a tricyclic diterpene, isolated from oleoresin of Pinus longifolia Roxberghii.
Open Access
Gene expression changes in aging zebrafish (Danio rerio) brains are sexually dimorphic
(BioMed Central, 2014) Arslan-Ergül, Ayça; Adams, Michelle M.
Background: Brain aging is a multi-factorial process due to both genetic and environmental factors. The zebrafish has recently become a popular model organism for examining aging and age-related diseases because as in humans they age gradually and exhibit cognitive decline. Few studies have examined the biological changes in the aging brain that may contribute to these declines and none have examined them within individuals with respect to gender. Our aim was to identify the main genetic pathways associated with zebrafish brain aging across gender. We chose males and females from specific age groups (young, 7.5-8.5 months and old, 31-36 months) based on the progression of cognitive decline in zebrafish. RNA was isolated from individual brains and subjected to microarray and qPCR analysis. Statistical analyses were performed using a two-way ANOVA and the relevant post-hoc tests. Results: Our results demonstrated that in the brains of young and old male and female zebrafish there were over 500 differentially expressed genes associated with multiple pathways but most notably were those related to neurogenesis and cell differentiation, as well as brain and nervous system development. Conclusions: The gene expression of multiple pathways is altered with age and differentially expressed in males and females. Future studies will be aimed at determining the causal relationships of age-related changes in gene expression in individual male and female brains, as well as possible interventions that counteract these alterations.
Open Access
Evaluation of inhibitory effects of benzothiazole and 3-amino-benzothiazolium derivatives on DNA topoisomerase II by molecular modeling studies
(Taylor and Francis, 2014) Akı-Yalçın, E.; Ertan-Bolelli, T.; Taşkın-Tok, T.; Öztürk, Ö.; Ataei, S.; Özen, Çiğdem; Yıldız, I.; Yalçın, I.
There has been considerable interest in DNA topoisomerases over the last decade, as they have been shown to be one of the major cellular targets in anticancer drug development. Previously we synthesized some benzothiazole derivatives and corresponding benzothiazolium forms, and tested their DNA inhibitory activity to develop novel antitumor agents. Among the 12 prepared compounds, compound BM3 (3-aminobenzothiazole-3-ium 4-methylbenzene sulfonate) exhibited extreme topoisomerase II inhibitory activity compared with the reference drug etoposide. We also tried to determine the DNA and enzyme binding abilities of BM3 and found that BM3 acted on topoisomerase II first at low doses, while it had also showed DNA minor groove binding properties at higher doses. In this study the interactions between DNA topoisomerase II and the compounds were examined in detail by molecular modelling studies such as molecular docking and pharmacophore analysis performed using Discovery Studio 3.5. As a result, it was found that benzothiazolium compounds exhibited a totally different mechanism than benzothiazoles by binding to the different amino acids at the active site of the protein molecule. 3-Aminobenzothiazoliums are worthy of carrying onto anticancer studies; BM3 especially would be a good anticancer candidate for preclinical studies.
Open Access
Synthesis and characterization of amino acid conjugates of oleanolic acid and their in vitro cytotoxic effect on HCC cell lines
(Pakistan Journal of Pharmaceutical Sciences, 2014) Mustufa, Muhammad Ayaz; Hashmi, I. A.; Manzoor, S.; Ahmed, A.; Ahmed, V.; Aslam, A.; Özen, Çiğdem; Naqvi, N.; Öztürk, Mehmet; Ali, F. I.
Oleanolic acid (3β-hydroxy-olean-12-en-28-oic acid; OA-01), a pentacyclic triterpene, exhibit a wide range of pharmacological and biological activities. We have isolated oleanolic acid from methanolic extract of Periploca aphylla, collected from surroundings of Karachi in the month of February. Furthermore, four known and two new C-28 amino acid conjugates of oleanolic acid were prepared to explore potential of these compounds on HCCs and one breast cancer cell line. Cytotoxic effects revealed that as compare to parent compound (OA-01), two derivatives OA-04 (p<0.0001) and OA-06 (p<0.01) showed significantly increased/higher inhibition rates.
Open Access
Synthesis and preliminary mechanistic evaluation of 5-(p-tolyl)-1-(quinolin-2-yl)pyrazole-3-carboxylic acid amides with potent antiproliferative activity on human cancer cell lines
(Elsevier, 2014) Cankara-Pirol, Ş.; Çalışkan, B.; Durmaz, İrem; Atalay, Rengül; Banoğlu, E.
We synthesized a series of novel amide derivatives of 5-(p-tolyl)-1-(quinolin-2-yl)pyrazole-3-carboxylic acid and assessed their antiproliferative activities against three human cancer cell lines (Huh7, human liver; MCF7, breast and HCT116, colon carcinoma cell lines) with the sulforhodamine B assay. Compound 4j with 2-chloro-4-pyridinyl group in the amide part exhibited promising cytotoxic activity against all cell lines with IC50values of 1.6 μM, 3.3 μM and 1.1 μM for Huh7, MCF7 and HCT116 cells, respectively, and produced dramatic cell cycle arrest at SubG1/G1 phase as an indicator of apoptotic cell death induction. On the basis of their high potency in cellular environment, these straightforward pyrazole-3-carboxamide derivatives may possess potential in the design of more potent compounds for intervention with cancer cell proliferation.
Open Access
A series of 2,4(1H,3H)-quinazolinedione derivatives: synthesis and biological evaluation as potential anticancer agents
(Bentham Science Publishers, 2016) Akgün, H.; Us-Yılmaz, D.; Çetin-Atalay, Rengül; Gözen, Damla
A series of 6,7-disubstituted-3-{2-[4-(substituted)piperazin-1-yl]-2-oxoethyl}quinazoline- 2,4(1H,3H)-dione derivatives (7-34) were synthesized and their structures were elucidated on the basis of analytical and spectral (UV, IR, 1H-NMR, 13C-NMR and MS) data. These synthesized compounds were evaluated for their in vitro cytotoxicities against a panel of three human cancer cell lines. According to the cytotoxicity screening results, 3-{2-[4-(4-chlorobenzyl)piperazin-1-yl]-2-oxoethyl} quinazoline-2,4(1H,3H)-dione (7) presented the highest activity against HUH-7, MCF-7 and HCT-116 cell line with the IC50 values of 2.5, 6.8 and 4.9 µM, respectively.

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