Browsing by Author "Danyeli, Ayca Ersen"

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Evaluation of the Efficacy of SiIdenafil Citrate Following Severe Head Trauma in an Experimental Rat Model
(TURKISH NEUROSURGICAL SOC, 2020-01-01) Kilicarslan, Bilal; Kilicarslan, Emel; Kizmazoglu, Ceren; Aydin, Hasan Emre; Kaya, Ismail; Danyeli, Ayca Ersen; Karabekir, Hamit Selim
AIM: To investigate the acute effects of sildenafil citrate in an experimental model of severe head trauma, and to compare it with the efficacy of mannitol, which is an osmotically active agent frequently used in clinical treatment of traumatic brain injury (TBI). MATERIAL and METHODS: Twenty-eight Wistar-derived albino strain female rats were randomized into four groups comprising seven rats each. These groups were designated as follows: Group I: sham
Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology
(WILEY, 2022-01-01) Cevik, Lokman; Landrove, Marilyn Vazquez; Aslan, Mehmet Tahir; Khammad, Vasilii; Garagorry Guerra, Francisco Jose; Cabello-Izquierdo, Yolanda; Wang, Wesley; Zhao, Jing; Becker, Aline Paixao; Czeisler, Catherine; Rendeiro, Anne Costa; Sousa Veras, Lucas Luis; Zanon, Maicon Fernando; Reis, Rui Manuel; Matsushita, Marcus de Medeiros; Ozduman, Koray; Pamir, M. Necmettin; Danyeli, Ayca Ersen; Pearce, Thomas; Felicella, Michelle; Eschbacher, Jennifer; Arakaki, Naomi; Martinetto, Horacio; Parwani, Anil; Thomas, Diana L.; Otero, Jose Javier
Aims Resource-strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. Methods We used simple information theory calculations on a brain cancer simulation model and real-world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H\&E and Olig2 stained images obtained from digital slides. An auto-adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH-mutant tumors. Results Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH-mutant tumors. The predictive models may facilitate the reduction of false-positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. Conclusions We posit that this approach provides an improvement on the cIMPACT-NOW workflow recommendations for IDH-mutant tumors and a framework for future resource and testing allocation.
Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma
(BMC, 2021-01-01) Ulgen, Ege; Can, Ozge; Bilguvar, Kaya; Boylu, Cemaliye Akyerli; Yuksel, Sirin Kilicturgay; Danyeli, Ayca Ersen; Sezerman, O. Ugur; Yakicier, M. Cengiz; Pamir, M. Necmettin; Ozduman, Koray
Background In the clinical setting, workflows for analyzing individual genomics data should be both comprehensive and convenient for clinical interpretation. In an effort for comprehensiveness and practicality, we attempted to create a clinical individual whole exome sequencing (WES) analysis workflow, allowing identification of genomic alterations and presentation of neurooncologically-relevant findings. Methods The analysis workflow detects germline and somatic variants and presents: (1) germline variants, (2) somatic short variants, (3) tumor mutational burden (TMB), (4) microsatellite instability (MSI), (5) somatic copy number alterations (SCNA), (6) SCNA burden, (7) loss of heterozygosity, (8) genes with double-hit, (9) mutational signatures, and (10) pathway enrichment analyses. Using the workflow, 58 WES analyses from matched blood and tumor samples of 52 patients were analyzed: 47 primary and 11 recurrent diffuse gliomas. Results The median mean read depths were 199.88 for tumor and 110.955 for normal samples. For germline variants, a median of 22 (14-33) variants per patient was reported. There was a median of 6 (0-590) reported somatic short variants per tumor. A median of 19 (0-94) broad SCNAs and a median of 6 (0-12) gene-level SCNAs were reported per tumor. The gene with the most frequent somatic short variants was TP53 (41.38\%). The most frequent chromosome-/arm-level SCNA events were chr7 amplification, chr22q loss, and chr10 loss. TMB in primary gliomas were significantly lower than in recurrent tumors (p = 0.002). MSI incidence was low (6.9\%). Conclusions We demonstrate that WES can be practically and efficiently utilized for clinical analysis of individual brain tumors. The results display that NOTATES produces clinically relevant results in a concise but exhaustive manner.
Towards Development of a Standard Terminology of the World Health Organization Classification of Tumors of the Central Nervous System in the Turkish Language, and a Perspective on the Practical Implications of the WHO Classification for Low and Middle Income Countries
(FEDERATION TURKISH PATHOLOGY SOC, 2022-01-01) Soylemezoglu, Figen; Oz, Buge; Egilmez, Reyhan; Pekmezci, Melike; Bozkurt, Suheyla; Danyeli, Ayca Ersen; Onguru, Onder; Kulac, Ibrahim; Tihan, Tarik
In our manuscript, we propose a common terminology in the Turkish language for the newly adopted WHO classification of the CNS tumors, also known as the WHO CNS 5th edition. We also comment on the applicability of this new scheme in low and middle income countries, and warn about further deepening disparities between the global north and the global south. This division, augmented by the recent COVID-19 pandemic, threatens our ability to coordinate efforts worldwide and may create significant disparities in the diagnosis and treatment of cancers between the ``haves{''} and the ``have nots{''}.
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, Ilhan
Despite 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.