Araştırma Çıktıları
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Item DNA Fragmentation Simulation Method (FSM) and Fragment Size Matching Improve aCGH Performance of FFPE Tissues(PUBLIC LIBRARY SCIENCE, 2012-01-01) Craig, Justin M.; Vena, Natalie; Ramkissoon, Shakti; Idbaih, Ahmed; Fouse, Shaun D.; Ozek, Memet; Sav, Aydin; Hill, D. Ashley; Margraf, Linda R.; Eberhart, Charles G.; Kieran, Mark W.; Norden, Andrew D.; Wen, Patrick Y.; Loda, Massimo; Santagata, Sandro; Ligon, Keith L.; Ligon, Azra H.Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.Item Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype(OXFORD UNIV PRESS INC, 2015-01-01) Bergthold, Guillaume; Bandopadhayay, Pratiti; Hoshida, Yujin; Ramkissoon, Shakti; Ramkissoon, Lori; Rich, Benjamin; Maire, Cecile L.; Paolella, Brenton R.; Schumacher, Steven E.; Tabak, Barbara; Ferrer-Luna, Ruben; Ozek, Memet; Sav, Aydin; Santagata, Sandro; Wen, Patrick Yung; Goumnerova, Liliana C.; Ligon, Azra H.; Stiles, Charles; Segal, Rosalind; Golub, Todd; Grill, Jacques; Ligon, Keith L.; Chan, Jennifer A.; Kieran, Mark W.; Beroukhim, RameenPediatric low-grade gliomas (PLGGs), the most frequent pediatric brain tumor, comprise a heterogeneous group of diseases. Recent genomic analyses suggest that these tumors are mostly driven by mitogene-activated protein kinase (MAPK) pathway alterations. However, little is known about the molecular characteristics inherent to their clinical and histological heterogeneity. We performed gene expression profiling on 151 paraffin-embedded PLGGs from different locations, ages, and histologies. Using unsupervised and supervised analyses, we compared molecular features with age, location, histology, and BRAF genomic status. We compared molecular differences with normal pediatric brain expression profiles to observe whether those patterns were mirrored in normal brain. Unsupervised clustering distinguished 3 molecular groups that correlated with location in the brain and histological subtype. ``Not otherwise specified{''} (NOS) tumors did not constitute a unified class. Supratentorial pilocytic astrocytomas (PAs) were significantly enriched with genes involved in pathways related to inflammatory activity compared with infratentorial tumors. Differences based on tumor location were not mirrored in location-dependent differences in expression within normal brain tissue. We identified significant differences between supratentorial PAs and diffuse astrocytomas as well as between supratentorial PAs and dysembryoplastic neuroepithelial tumors but not between supratentorial PAs and gangliogliomas. Similar expression patterns were observed between childhood and adolescent PAs. We identified differences between BRAF-duplicated and V600E-mutated tumors but not between primary and recurrent PLGGs. Expression profiling of PLGGs reveals significant differences associated with tumor location, histology, and BRAF genomic status. Supratentorial PAs, in particular, are enriched in inflammatory pathways that appear to be tumor-related.Item Treatment Strategies for Dopamine Agonist-Resistant and Aggressive Prolactinomas: A Comprehensive Analysis of the Literature(GEORG THIEME VERLAG KG, 2021-01-01) Sari, Ramazan; Altinoz, Meric A.; Ozlu, Eylem Burcu Kahraman; Sav, Aydin; Danyeli, Ayca Ersen; Baskan, Ozdil; Er, Ozlem; Elmaci, IlhanDespite most of the prolactinomas can be treated with endocrine therapy and/or surgery, a significant percentage of these tumors can be resistant to endocrine treatments and/or recur with prominent invasion into the surrounding anatomical structures. Hence, clinical, pathological, and molecular definitions of aggressive prolactinomas are important to guide for classical and novel treatment modalities. In this review, we aimed to define molecular endocrinological features of dopamine agonist-resistant and aggressive prolactinomas for designing future multimodality treatments. Besides surgery, temozolomide chemotherapy and radiotherapy, peptide receptor radionuclide therapy, estrogen pathway modulators, progesterone antagonists or agonists, mTOR/akt inhibitors, pasireotide, gefitinib/lapatinib, everolimus, and metformin are tested in preclinical models, anecdotal cases, and in small case series. Moreover, chorionic gonadotropin, gonadotropin releasing hormone, TGF beta and PRDM2 may seem like possible future targets for managing aggressive prolactinomas. Lastly, we discussed our management of a unique prolactinoma case by asking which tumors' proliferative index (Ki67) increased from 5-6\% to 26\% in two subsequent surgeries performed in a 2-year period, exerted massive invasive growth, and secreted huge levels of prolactin leading up to levels of 1 605 671ng/dl in blood.Item Detection of KIAA1549-BRAF Fusion Transcripts in Formalin-Fixed Paraffin-Embedded Pediatric Low-Grade Gliomas(ELSEVIER SCIENCE INC, 2011-01-01) Tian, Yongji; Rich, Benjamin E.; Vena, Natalie; Craig, Justin M.; MacConaill, Laura E.; Rajaram, Veena; Goldman, Stewart; Taha, Hala; Mahmoud, Madeha; Ozek, Memet; Sav, Aydin; Longtine, Janina A.; Lindeman, Neal I.; Garraway, Levi A.; Ligon, Azra H.; Stiles, Charles D.; Santagata, Sandra; Chan, Jennifer A.; Kieran, Mark W.; Ligon, Keith L.Alterations of BRAF are the most common known genetic aberrations in pediatric gliomas. They frequently are found in pilocytic astrocytomas, where genomic duplications involving BRAF and the poorly characterized gene KIAA1549 create fusion proteins with constitutive B-Raf kinase activity. BRAF V600E point mutations are less common and generally occur in nonpilocytic tumors. The development of BRAF inhibitors as drugs has created an urgent need for robust clinical assays to identify activating lesions in BRAF. KIAA1549-BRAF fusion transcripts have been detected in frozen tissue, however, methods for FFPE tissue have not been reported. We developed a panel of FFPE-compatible quantitative RT-PCR assays for the most common KIAA1549-BRAF fusion transcripts. Application of these assays to a collection of 51 low-grade pediatric gliomas showed 97\% sensitivity and 91\% specificity compared with fluorescence in situ hybridization or array comparative genomic hybridization. In parallel, we assayed samples for the presence of the BRAF V600E mutation by PCR pyrosequencing. The data further support previous observations that these two alterations of the BRAF, KIAA1549 fusions and V600E point mutations, are associated primarily with pilocytic astrocytomas and nonpilocytic gliomas, respectively. These results show that fusion transcripts and mutations can be detected reliably in standard FFPE specimens and may be useful for incorporation into future studies of pediatric gliomas in basic science or clinical trials. (J Mal Diagn 2011, 13:669-677Item Desmoplastic infantile ganglioglioma: Report of an unusual case with a cranial defect(MEDKNOW PUBLICATIONS \& MEDIA PVT LTD, 2014-01-01) Basaran, Recep; Cakir, Fatma Betul; Isik, Nejat; Sav, Aydin; Elmaci, IlhanDesmoplastic infantile ganglioglioma (DIG) is a rare tumor that typically occurs in infants under the age of 24 months. These tumors commonly have a good prognosis after surgical resection despite their aggressive radiological appearances. Clinical signs are due to the large size of the tumor and include increased head circumference, bulging fontanel, sunset sign and seizures. We report an unusual DIG case who presented with parietal bulging associated with a bony defect. The patient was thought to have a leptomeningeal cystic formation, but on his cranial magnetic resonance imaging (MRI), we observed a centrally and homogeneously gadolinium-enhanced lesion fixed to the dura by its solid component. A surgical gross total resection was performed, and no residual tumor was observed on follow-up.Item Purely extradural spinal nerve root hemangioblastomas(MEDKNOW PUBLICATIONS \& MEDIA PVT LTD, 2016-01-01) Aytar, Murat Hamit; Yener, Ulas; Eksi, Murat Sakir; Kaya, Behram; Ozgen, Serdar; Sav, Aydin; Alanay, AhmetSpinal nerve root hemangioblastomas present mostly as intradural-extradurally. Purely extradural spinal nerve root hemangioblastoma is a very rare entity. In this study, we aimed to analyze epidemiological perspectives of purely extradural spinal nerve root hemangioblastomas presented in English medical literature in addition to our own exemplary case. PubMed/MEDLINE was searched using the terms ``hemangioblastoma,{''} ``extradural,{''} ``spinal,{''} and ``nerve root.{''} Demographical variables of age, gender, concomitant presence of von Hippel-Lindau (VHL) diseaseItem Monostotic fibrous dysplasia involving occipital bone: a case report and review of literature(AFRICAN FIELD EPIDEMIOLOGY NETWORK-AFENET, 2014-01-01) Basaran, Recep; Kaksi, Mustafa; Gur, Erdal; Efendioglu, Mustafa; Balkuv, Ece; Sav, AydinFibrous dysplasia (FD) is a progressive systemic bone tumour of young and it can be seen on cranial bones. FD is divided into three types according to radiological features. The second most common subtype is polyostotic subtype. With this article, we aimed to review and present clinical features, radiological examination, differential diagnosis and treatment management of a case of solitary monostotic fibrous dysplasia of occipital bone. 15 years old female patient admitted to our hospital for a bump and in the back of his head that she noticed 1 month ago. Her physical and neurological examination was normal. On cranial CT examination we detected a bony defect. Her gadolinium enhanced cranial MRI revealed bony defect along with massive gadolinium enhancement in adjacent tissue. On histopathologic examinationItem Intradural Solitary Fibrous Tumor of the Lumbar Spine: A Distinctive Case Report(HINDAWI LTD, 2015-01-01) Basaran, Recep; Kaksi, Mustafa; Onoz, Mustafa; Balkuv, Ece; Sav, AydinBackground. Solitary fibrous tumors are ubiquitous mesenchymal neoplasms of putative fibroblastic origin. They were originally described in the pleura but subsequently have been reported in many extraserosal sites. Solitary fibrous tumors may also occur in the meninges, central nervous system parenchyma, and spinal cord. Case. A 67-year-old male patient with progressive lower extremity weakness, urinary urgency, and sexual dysfunction has been admitted to our hospital. On his lumbar MRI, we detected an intradural lesion posterior to the L3 vertebral corpus. We resected the lesion by L3 total laminectomy. Immunohistological findings revealed strong and diffuse immunopositivity with vimentin, CD34, and bcl-2. Ki-67 proliferation index was 5-8\%. We did not detect any recurrence 12 months after his operation. Conclusion. SFT is mostly seen in young and middle-aged patients and should be considered among differential diagnosis in cases suffering from pain, hypoesthesia, and urinary dysfunction. Gross total resection should be primary treatment. Tumors that have high Ki-67 labeling should be followed up for potential recurrences.Item Neuroprotective Effect of Memantine on Hippocampal Neurons in Infantile Rat Hydrocephalus(TURKISH NEUROSURGICAL SOC, 2011-01-01) Cabuk, Burak; Etus, Volkan; Bozkurt, Suheyla Uyar; Sav, Aydin; Ceylan, SavasAIM:The effect of memantine administration on hippocampal neurons of the infantile rats with kaolin induced hydrocephalus was investigated. MATERIAL and METHODS: Hydrocephalus was induced by injecting kaolin into the cisterna magna of 3-weeks old Sprague-Dawley rat pups. One group received a single daily dose of 20mg/kg memantine i.p. following hydrocephalus induction for a period of two weeks. By the end of the two-week period, animals were radiologically evaluated by magnetic resonance imaging and then sacrificed to get their cerebrums removed. Both immunohistochemical analysis of nitric oxide synthase activity and quantification of spared neurons in CA1, CA2 and CA3 regions of hippocampus were performed. RESULTS: In hydrocephalus-induced rats considerable neuronal loss associated with significantly increased nitric oxide synthase immunoreactivity were determined in all hippocampal regions. However, memantine treated rats showed significantly higher number of spared neuron counts and reduced nitric oxide synthase immunoreactivity in CA1 and CA2 regions compared with the non-treated rats. CONCLUSION:The findings of the study show that hippocampal neurons may constitute important targets for injury secondary to hydrocephalic process in experimental infantile hydrocephalus. Early anti-excitotoxic treatment with memantine seems to have a neuroprotective effect especially in the CA1 and CA2 subunits of the hippocampus.Item Spinal Intramedullary Metastasis of Breast Cancer(HINDAWI LTD, 2014-01-01) Basaran, Recep; Tiryaki, Mehmet; Yavuzer, Dilek; Efendioglu, Mustafa; Balkuv, Ece; Sav, AydinObjective. Breast cancer accounts for approximately one-third of all cancers in females. Approximately 8.5 \% of all central nervous system metastases are located in the spinal cord. These patients have rapidly progressing neurological deficits and require immediate examination. The aim of surgery is decompression of neural tissue and histological evaluation of the tumor. In this paper, we present a case of breast cancer metastasis in thoracic spinal intramedullary area which had been partially excised and then given adjuvant radiotherapy. Case. A 43-year-old female patient with breast cancer for 8 years was admitted to our hospital with complaints of weakness in both legs. Eight years ago, she received chemotherapy and radiotherapy. On her neurological examination, she had paraparesis (left lower extremity: 2/5, right lower extremity: 3/5) and urinary incontinence. Spinal MRI revealed a gadolinium enhancing intramedullary lesion. Pathologic examination of the lesion was consistent with breast carcinoma metastasis. The patient has been taken into radiotherapy. Conclusion. Spinal intramedullary metastasis of breast cancer is an extremely rare situation, but it has a high morbidity and mortality rate. Microsurgical resection is necessary for preservation or amelioration of neurological state and also for increased life expectancy and quality.