Browsing by Author "Akyerli, Cemaliye B."

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Analysis of Mitochondrial DNA Control Region D-Loop in Gliomas: Result of 52 Patients
(TURKISH NEUROSURGICAL SOC, 2021-01-01) Yuksel, Sirin Kilicturgay; Ozduman, Koray; Yilmaz, Engin; Pamir, M. Necmettin; Akyerli, Cemaliye B.
AIM: To investigate the effect of mitochondrial DNA (mtDNA) variants mainly in D-loop on glioma biology. MATERIAL and METHODS: Sanger sequencing of D-loop (15971-16451 bp) for 52 glioma patients was performed and the variations were statistically analyzed for gender, WHO classification, morphological grade, IDH/TERT status. RESULTS: Total of 122 variations (51 unique) were identified in 52 patients. C16223T, T16189C, T16311C and T16126C variants were frequently detected. The total variation number was statistically non-significant among the analyzed categories. When individual variants were considered, T16311C and T16224C were statistically significant for WHO classification (p=0.033), morphological grade (p=0.036) and gender (p=0.039), respectively. CONCLUSION: Total variation number in D-loop was not found to be related with clinical variables. Our data suggests that individual variants may play a critical role in glioma biology.
IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation
(NATURE PUBLISHING GROUP, 2016-01-01) Oktay, Yavuz; Ulgen, Ege; Can, Ozge; Akyerli, Cemaliye B.; Yuksel, Sirin; Erdemgil, Yigit; Durasi, I. Melis; Henegariu, Octavian Ioan; Nanni, E. Paolo; Selevsek, Nathalie; Grossmann, Jonas; Erson-Omay, E. Zeynep; Bai, Hanwen; Gupta, Manu; Lee, William; Turcan, Sevin; Ozpinar, Aysel; Huse, Jason T.; Sav, M. Aydin; Flanagan, Adrienne; Gunel, Murat; Sezerman, O. Ugur; Yakicier, M. Cengiz; Pamir, M. Necmettin; Ozduman, Koray
The single nucleotide polymorphism rs55705857, located in a non-coding but evolutionarily conserved region at 8q24.21, is strongly associated with IDH-mutant glioma development and was suggested to be a causal variant. However, the molecular mechanism underlying this association has remained unknown. With a case control study in 285 gliomas, 316 healthy controls, 380 systemic cancers, 31 other CNS-tumors, and 120 IDH-mutant cartilaginous tumors, we identified that the association was specific to IDH-mutant gliomas. Odds-ratios were 9.25 (5.17-16.52
Lack of hotspot mutations other than TP53 R249S in aflatoxin B1 associated hepatocellular carcinoma
(WALTER DE GRUYTER GMBH, 2020-01-01) Akyerli, Cemaliye B.; Yuksel, Sirin K.; Yakicier, M. Cengiz
Objective: Despite the recent advances in diagnosis and treatment of hepatocellular carcinoma (HCC), it is still a major health problem. Therefore, understanding the molecular mechanism is very important. Our aim is to investigate the molecular basis of aflatoxin B1 (AFB1) induced HCC other than the hotspot TP53 p.Arg249Ser (c.747G>T) (R249S) mutation. Methods: 525 genes previously reported to be involved in carcinogenesis with mutations in different cancer types were analyzed by next generation sequencing for 525 cancer-gene panel (Roche/NimbleGen) in one tumor sample (T29) and one cell line (MAHLAVU) carrying TP53 R249S mutation. Additionally, ARID2 and BCORL1 genes were analyzed by Sanger sequencing for MAHLAVU and Primary Liver Carcinoma/Poliomyelitis Research Foundation/5 (PLC/PRF/5) cell lines. Results: No other common gene mutations were found in the analyzed T29 and MAHLAVU samples and also no genetic variation possibly associated with AFB1 was detected in PLC/PRF/5 cell line and 68 COSMIC HCC samples. Likewise, no pathogenic mutation was detected in ARID2 and BCORL1 genes of MAHLAVU and PLC/PRF/5 cell lines. Conclusion: No fingerprint mutations were detected in the analyzed genes. To the best of our knowledge, other hotspot mutations appear to be absent if not at a very low frequency in HCC carrying TP53 R249S mutation.
Sensitive Detection of Molecular Targets in Cancer by Minisequencing
(Acıbadem Mehmet Ali Aydınlar Üniversitesi, 2021-12-01) Yüksel, Şirin K.; Akyerli, Cemaliye B.
ABSTRACT Purpose: Molecular alterations leading to specific mutations are essential for tumor development and survival. Accurate analysis of these molecular targets is important for diagnosis, early detection, forecasting of prognosis and aiding in the treatment of different cancer types. Therefore, for sensitive analysis of molecular markers, we aimed to optimize and use minisequencing protocols besides Sanger sequencing. Methods and Materials: Sanger sequencing and minisequencing were performed for IDH1 R132, IDH2 R140/R172 and TERT promoter C228/C250 mutations using genomic DNA isolated from glioma samples. Minisequencing reactions were performed with detection primers using SnaPshot Multiplex Ready Reaction Mix and run on an automated capillary electrophoresis. Multiplex peaks were analyzed with GeneMapper Software. Results: In the multiplex minisequencing analyses, peaks corresponding to wild type alleles and different mutations were detected. The presence of the peaks next to the wild type peaks points to the presence of variations in that location and the nature of the mutation can be identified according to the color. Conclusions: Identification of molecular markers in cancer is very important. Minisequencing is a reliable method for the detection of molecular targets.