Browsing by Author "Oztop, Sidika"

Now showing 1 - 4 of 4

Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice
(2020) Hanifehnezhad, Alireza; Kehribar, Ebru Sahin; Oztop, Sidika; Sheraz, Ali; Kasirga, Serkan; Ergunay, Koray; Onder, Sevgen; Yilmaz, Erkan; Engin, Doruk; Oguzoglu, T. Cigdem; Seker, Urartu Ozgur Safak; Yilmaz, Engin; Ozkul, Aykut; 0000-0001-5653-6080; 33015402; AAJ-7911-2020
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently a global pandemic with unprecedented public health, economic and social impact. The development of effective mitigation strategies, therapeutics and vaccines relies on detailed genomic and biological characterization of the regional viruses. This study was carried out to isolate SARS-CoV-2 viruses circulating in Anatolia, and to investigate virus propagation in frequently-used cells and experimental animals. We obtained two SARS-CoV-2 viruses from nasopharngeal swabs of confirmed cases in Vero E6 cells, visualized the virions using atomic force and scanning electron microscopy and determined size distribution of the particles. Viral cytopathic effects on Vero E6 cells were initially observed at 72 h post-inoculation and reached 90% of the cells on the 5th day. The isolates displayed with similar infectivity titers, time course and infectious progeny yields. Genome sequencing revealed the viruses to be well-conserved, with less than 1% diversity compared to the prototype virus. The analysis of the viral genomes, along with the available 62 complete genomes from Anatolia, showed limited diversity (up to 0.2% on deduced amino acids) and no evidence of recombination. The most prominent sequence variation was observed on the spike protein, resulting in the substitution D614G, with a prevalence of 56.2%. The isolates produced non-fatal infection in the transgenic type I interferon knockout (IFNAR(-/-)) mice, with varying neutralizing antibody titers. Hyperemia, regional consolidation and subpleural air accumulation was observed on necropsy, with similar histopathological and immunohistochemistry findings in the lungs, heart, stomach, intestines, liver, spleen and kidneys. Peak viral loads were detected in the lungs, with virus RNA present in the kidneys, jejunum, liver, spleen and heart. In conclusion, we characterized two local isolates, investigated in vitro growth dynamics in Vero E6 cells and identified IFNAR-/- mice as a potential animal model for SARS-CoV-2 experiments.
Gastric Carcinoma with Lymphoid Stroma: A Combination of Mismatch Repair Deficient Medullary Type and Epstein-Barr Virus-associated Gastric Carcinomas
(2022) Uner, Meral; Isik, Aynur; Oztop, Sidika; Karabulut, Erdem; Demirkol-Canli, Secil; Akyol, Aytekin; https://orcid.org/0000-0001-5653-6080; 35188817; AAJ-7911-2020
Gastric carcinomas consist of a heterogeneous group of neoplasms with broad cytological and architectural variations. Gastric carcinomas with lymphoid stroma show poor correlation between their histomorphology and biological behavior. This contrast causes a need for more detailed analysis and molecular exploration of lymphoid stroma-rich gastric carcinomas with medullary like features and lack of glandular differentiation. In this study, we performed a detailed retrospective analysis of 53 gastric carcinomas among 654 gastric tumors from surgical resection specimens, all of which had no prominent glandular differentiation. Morphological and clinical data were compared with immunohistochemistry (MLH1, PMS2, MSH2 and MSH6 for mismatch repair mechanism deficiency; CD2, CD8 and CD163 for immune infiltration; and PD-1, PD-L1, LMP-1, ERBB2 and ki-67) besides EBER in situ hybridization and molecular studies (PCR based microsatellite instability and BRAF V600E mutation analysis). Morphological, immunohistochemical and molecular findings lead us to classify lymphoid stroma-rich advanced gastric carcinomas (n = 40/53) into two distinct entities originating from two different pathogenetic pathway: one is gastric carcinomas revealing predominantly medullary type morphology with defective DNA mismatch repair mechanism (n = 30/53) and the other is EBV associated carcinomas (n = 10/53). In addition, we suggest that biomarker based classification algorithms besides morphological evaluation are necessary to identify these two entities. Distinguishing these entities is crucial to apply different treatment strategies, including alternative treatments such as immunotherapy.
A Highly Potent SARS-CoV-2 Blocking Lectin Protein
(2022) Ahan, Recep E.; Hanifehnezhad, Alireza; Kehribar, Ebru S.; Oguzoglu, Tuba C.; Foldes, Katalin; Ozcelik, Cemile E.; Filazi, Nazlican; Oztop, Sidika; Palaz, Fahreddin; Onder, Sevgen; Bozkurt, Eray U.; Ergunay, Koray; Ozkul, Aykut; Seker, Urartu Ozgur Safak; https://orcid.org/0000-0001-5653-6080; 35426678; AAJ-7911-2020
The COVID-19 (coronavirus disease-19) pandemic affected more than 180 million people around the globe, causing more than five million deaths as of January 2022. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the new coronavirus, has been identified as the primary cause of the infection. The number of vaccinated people is increasing; however, prophylactic drugs are highly demanded to ensure secure social contact. A number of drug molecules have been repurposed to fight against SARS-CoV-2, and some of them have been proven to be effective in preventing hospitalization or ICU admissions. Here, we demonstrated griffithsin (GRFT), a lectin protein, to block the entry of SARS-CoV-2 and its variants, Delta and Omicron, into the Vero E6 cell lines and IFNAR(-/-) mouse models by attaching to the spike protein of SARS-CoV-2. Given the current mutation frequency of SARS-CoV-2, we believe that GRFT protein-based drugs will have a high impact in preventing the transmission of both the Wuhan strain as well as any other emerging variants, including Delta and Omicron variants, causing the high-speed spread of COVID-19.
RAB25 confers resistance to chemotherapy by altering mitochondrial apoptosis signaling in ovarian cancer cells
(2020) Temel, Sehime Gulsun; Giray, Asli; Karaka, Bahriye; Gul, Ozgur; Kozanoglu, Ilknur; Celik, Husnu; Basaga, Huveyda; Acikbas, Ufuk; Sucularli, Ceren; Oztop, Sidika; Aka, Yeliz; Kutuk, Ozgur; 0000-0001-5653-6080; 0000-0001-9854-7220; 0000-0002-5268-1210; 32901335; AAJ-7911-2020; AAH-1671-2019; AAE-1241-2021
Ovarian cancer remains one of the most frequent causes of cancer-related death in women. Many patients with ovarian cancer suffer from de novo or acquired resistance to chemotherapy. Here, we report that RAB25 suppresses chemotherapy-induced mitochondrial apoptosis signaling in ovarian cancer cell lines and primary ovarian cancer cells. RAB25 blocks chemotherapy-induced apoptosis upstream of mitochondrial outer membrane permeabilization by either increasing antiapoptotic BCL-2 proteins or decreasing proapoptotic BCL-2 proteins. In particular, BAX expression negatively correlates with RAB25 expression in ovarian cancer cells. BH3 profiling assays corroborated that RAB25 decreases mitochondrial cell death priming. Suppressing RAB25 by means of RNAi or RFP14 inhibitory hydrocarbon-stapled peptide sensitizes ovarian cancer cells to chemotherapy as well as RAB25-mediated proliferation, invasion and migration. Our data suggest that RAB25 is a potential therapeutic target for ovarian cancer.