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Öğe Cancer Treatment: An Epigenetic View(Thieme Medical Publ Inc, 2020) Aydin, Cansu; Kalkan, RasimeCancer can be identified as an uncontrolled growth and reproduction of cell. Accumulation of genetic aberrations (mutations of oncogenes and tumor-suppressor genes and epigenetic modifications) is one of the characteristics of cancer cell. Increasing number of studies highlighted importance of the epigenetic alterations in cancer treatment and prognosis. Now, cancer epigenetics have a huge importance for developing novel biomarkers and therapeutic target for cancer. In this review, we will provide a summary of the major epigenetic changes involved in cancer and preclinical results of epigenetic therapeutics.Öğe Customised targeted massively parallel sequencing enables more precisely diagnosis of patients with epilepsy(Wiley, 2022) Atli, Emine Ikbal; Atli, Engin; Yalcintepe, Sinem; Demir, Selma; Kalkan, Rasime; Eker, Damla; Gurkan, HakanBackground Advancement in genetic technology has led to the identification of an increasing number of genes in epilepsy. This will provide a lot of information in clinical practice and improve the diagnosis and treatment of epilepsy. Aim To show the importance of genes in the next-generation sequencing (NGS) panel during the evaluation of epilepsy and to emphasise the importance of genetic studies in different populations for the evaluation of genes that cause disease. Methods This was a single-centre retrospective cohort study of 80 patients who underwent NGS testing with a customised epilepsy panel. Results In a total of 54 (67.5%) out of 80 patients, pathogenic or likely pathogenic variants and variants of uncertain significance (VOUS) were identified according to the American College of Medical Genetics and Genomics criteria. Pathogenic or likely pathogenic variants (n = 35) were identified in 29 (36.25%) out of 80 individuals. VOUS (n = 34) were identified in 28 (35%) out of 80 patients. Pathogenic, likely pathogenic and VOUS were most frequently identified in TSC2 (n = 11), SCN1A (n = 6) and TSC1 (n = 5) genes. Other common genes were KCNQ2 (n = 3), AMT (n = 3), CACNA1H (n = 3), CLCN2 (n = 3), MECP2 (n = 2), ASAH1 (n = 2) and SLC2A1 (n = 2). Conclusions NGS-based testing panels contribute to the diagnosis of epilepsy and might change the clinical management by preventing unnecessary and potentially harmful diagnostic procedures and management in patients. Thus, our results highlight the benefit of genetic testing in children suffering with epilepsy.Öğe The Impacts of miRNAs in Glioblastoma Progression(Begell House Inc, 2016) Kalkan, Rasime; Atli, Emine IkbalmiRNAs are short noncoding RNA sequences that cause translational repression or mRNA degradation. A growing number of studies have sought new biomarkers in GBM that will be important in disease progression and prognosis and as potential therapeutic targets. miRNA-profiling studies in glioblastoma patients have found that aberrant miRNA expression can be used as a target to develop new biomarkers for disease detection and for determining prognosis or therapeutic response. In evaluating the tumor or its therapeutic response, genetic abnormalities such as mutations, epigenetic abnormalities, and aberrant miRNA expressions can be useful markers. This review summarizes the known miRNAs according their therapeutic importance and their use as disease progression biomarkers.Öğe Investigation of Genetic Alterations in Congenital Heart Diseases in Prenatal Period(Thieme Medical Publ Inc, 2022) Atli, Emine Ikbal; Atli, Engin; Yalcintepe, Sinem; Demir, Selma; Kalkan, Rasime; Akurut, Cisem; Ozen, YaseminThe prenatal diagnosis of congenital heart disease (CHD) is important because of mortality risk. The onset of CHD varies, and depending on the malformation type, the risk of aneuploidy is changed. To identify possible genetic alterations in CHD, G-banding, chromosomal microarray or if needed DNA mutation analysis and direct sequence analysis should be planned. In present study, to identify genetic alterations, cell culture, karyotype analysis, and single nucleotide polymorphism, array analyses were conducted on a total 950 samples. Interventional prenatal genetic examination was performed on 23 (2, 4%, 23/950) fetal CHD cases. Chromosomal abnormalities were detected in 5 out of 23 cases (21, 7%). Detected chromosomal abnormalities were 10q23.2 deletion, trisomy 18, 8p22.3-p23.2 deletion, 8q21.3-q24.3 duplication, 11q24.2q24.5 (9Mb) deletion, and 8p22p12 (16.8Mb) deletion. Our study highlights the importance of genetic testing in CHD.Öğe Methylation of RAR? is a New Clinical Biomarker for Treatment in Higher-grade Gliomas(Wolters Kluwer Medknow Publications, 2023) Toprak, Cigdem; Atli, Emine Ikbal; Kalkan, RasimeBackground: The dysregulation of various pathways and cellular processes contributes to the carcinogenic transition from low-grade gliomas to high-grade gliomas. The altered tumor microenvironment, altered epigenetic state, and high mutation heterogeneity are critical factors in glial tumors. The morphogen retinoic acid (RA) controls the homeostasis, regeneration, and development of the brain. RA receptor (RAR) gene methylation has been shown in different types of glial tumors. Aims and Objectives: This study assessed the RAR beta gene as a potential therapeutic target in gliomas. Materials and Methods: Using in silico methods, potential drugs targeting the RAR beta gene were compared based on temozolomide's effectiveness in treating gliomas. Results and Conclusion: Computational techniques can be used to identify drug-mediated pathways. This in silico study holds promise for RARB and RARB-targeted treatment strategies in gliomas.Öğe A Pilot Study of Identification Genetic Background of Craniosynostosis Cases(Lippincott Williams & Wilkins, 2021) Atli, Emine Ikbal; Yalcintepe, Sinem; Atli, Engin; Demir, Selma; Mail, Cisem; Eker, Damla; Kalkan, RasimeThe early fusion of the cranial sutures was described as a craniosynostosis. The early diagnosis and management of craniosynostosis is very important. Environmental factors and genetic abnormalities plays a key role during the development of craniosynostosis. Syndromic craniosynostosis cases are related with autosomal dominant disorders but nearly half of the affected cases carry a new mutation. In this study, in order to identify the genetic etiology of craniosynostosis the authors analyzed 20 craniosynostosis patients by using conventional karyotype, aCGH, sanger sequencing, next generation sequencing (NGS) and Multiplex ligation-dependent probe amplification (MLPA) techniques. The authors identified mutations on FGFR2 and FGFR3 genes which were associated with Muenke syndrome, Crouzon syndrome and skeletal dysplasia syndromes. NGS applied all of the cases and 7 clinical variations in 5 different gene were detected in %20 of cases. In addition to these abnormalities; del(11)(q14.1q22.2), del(17)(q21.31), dup(22)(q13.31) and t(2;16)(q37;p13) have been identified in our cohort which are not previously detected in craniosynostosis cases. Our study demonstrates the importance of detailed genetic analysis for the diagnosis, progression and management of the craniosynostosis.Öğe RAR? gene methylation is a candidate for primary glioblastoma treatment planning.(Makerere Univ, Fac Med, 2016) Atli, Emine Ikbal; Kalkan, Rasime; Ozdemir, Muhsin; Aydin, Hasan Emre; Arslantas, Ali; Artan, SevilhanBackground: We screened RAR beta methylation in primary glioblastoma multiforme (GBM) and the results were evaluated based on the clinical data and treatment type. Objective: The objective of this study was to find new areas for the usage of MS-HRM applications in the determination of methylation levels in primary GBM samples and it shows the association of RAR beta methylation with the clinical outcome. Methods: In our study, tumor samples were collected during surgical resection by the Department of Neurosurgery. The clinical and radiologic data was carefully reviewed, compared, and evaluated with the histological results. The methylation status of RAR beta was determined by using MS-HRM. Results: RAR beta gene methylation was detected in 24 out of 40 cases (60%), with different quantitative methylation levels. The mean survival time was 19 months form ethylated cases and 15 months for the non-methylated cases. The survival time of the patients who received treatment was 25 months and the survival time of the patients who received radiotherapy alone or where no treatment protocol applied was 15-20 months. Therefore, a significant difference in survival rates has been observed (P< 0.05). This study indicates a potential prognostic value for GBM treatment planning. Conclusion: Our study is the first study to investigate RAR beta methylation in primary GBMs. We conclude that the RAR beta gene could be a new prognostic and predictive candidate marker to designate the treatment protocol for primary GBMs.
