WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Review Citation - WoS: 8Citation - Scopus: 8Long Noncoding Rnas in Human Cancer and Apoptosis(Bentham Science Publishers, 2023) Erdoğan, İpek; Sweef, Osama; Akgül, BünyaminGenome annotations have uncovered the production of at least one transcript from nearly all loci in the genome at some given time throughout the development. Surprisingly, many of these transcripts do not code for proteins and are relatively long in size, thus called long noncoding RNAs (lncRNAs). Next- and third-generation sequencing technologies have amassed numerous lncRNAs expressed under different phenotypic conditions, yet many remain to be functionally characterized. LncRNAs regulate gene expression by functioning as scaffold, decoy, signaling, and guide molecules both at the transcriptional and post-transcriptional levels, interacting with different types of macromolecules, such as proteins, DNA, and RNA. Here, we review the potential regulatory role of lncRNAs in apoptosis and cancer as some of these lncRNAs may have the diagnostic and therapeutic potential in cancer.Article Citation - WoS: 4Citation - Scopus: 5Development of Ab3-Type Novel Phthalocyanine and Porphyrin Photosensitizers Conjugated With Triphenylphosphonium for Higher Photodynamic Efficacy(American Chemical Society, 2022) Albakour, Mohamad; Önal, Emel; Tüncel, Özge; Erdoğan, İpek; Gümüşgöz Çelik, Gizem; Küçük, Tuǧba; Akgül, Bünyamin; Gürek, Ayşe Gül; Özçelik, SerdarThere are a number of lipophilic cations that can be chosen; the triphenylphosphonium (TPP) ion is particularly unique for mitochondrion targeting, mainly due to its simplicity in structure and ease to be linked to the target molecules. In this work, mitochondrion-targeted AB3-type novel phthalocyanine and porphyrin photosensitizers (PSs) were synthesized and their photophysical photochemical properties were defined. Fluorescence quantum yields (φF) are 0.009, 0.14, 0.13, and 0.13, and the singlet-oxygen quantum yields (φΔ) are 0.27, 0.75, 0.57, and 0.58 for LuPcPox(OAc), AB3TPP-Pc, AB3TPP-Por-C4, and AB3TPP-Por-C6, respectively. To evaluate the photodynamic efficacy of the TPP-conjugated PS cell viabilities of A549 and BEAS-2B lung cells were comparatively measured and IC-50 values were determined. AB3TPP-Por-C4, AB3TPP-Por-C6, and AB3TPP-Pc compounds compared to the reference molecules ZnPc and H2TPP were found to be highly cytotoxic (sub-micromolar concentration) under the light. LuPcPox(OAc) is the most effective molecule regarding cell killing (the activity). The cell killing of the TPP-conjugated porphyrin derivatives exhibits a similar response compared to LuPcPox(OAc) when the light absorbing factor of the PS is normalized at 660 nm: TPP-conjugated porphyrins absorb less light (lower extinction coefficient) but produce more radical species (higher singlet-oxygen quantum yield) and therefore effectively kill the cells. The singlet oxygen-producing capacity of AB3TPP-Pc is almost 3 times higher compared to LuPcPox(OAc) and 50% more efficient with respect to ZnPc, suggesting that TPP-conjugated phthalocyanine may serve as a good photosensitizer for photodynamic therapy (PDT). The high singlet oxygen generation capacity of these novel TPP-conjugated porphyrin and phthalocyanine PS suggests that they might be useful for PDT requiring lower photosensitizer concentration and reduced energy deposited through less light exposure.Article Citation - WoS: 14Citation - Scopus: 15Noncoding Rnas in Apoptosis: Identification and Function(TÜBİTAK, 2022) Tüncel, Özge; Kara, Merve; Yaylak, Bilge; Erdoğan, İpek; Akgül, BünyaminApoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.Article Citation - WoS: 7Citation - Scopus: 8Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-Coding Rna as a Modulator of Proliferation and Metastasis in Hela Cells(Frontiers Media S.A., 2021) Gürer, Dilek Cansu; Erdoğan, İpek; Ahmadov, Ulvi; Başol, Merve; Sweef, Osama; Çakan Akdoğan, Gülçin; Akgül, BünyaminCisplatin is a well-known cancer chemotherapeutic agent but how extensively long non-coding RNA (lncRNA) expression is modulated by cisplatin is unknown. It is imperative to employ a comprehensive approach to obtain a better account of cisplatin-mediated changes in the expression of lncRNAs. In this study, we used a transcriptomics approach to profile lncRNAs in cisplatin-treated HeLa cells, which resulted in identification of 10,214 differentially expressed lncRNAs, of which 2,500 were antisense lncRNAs. For functional analyses, we knocked down one of the cisplatin inducible lncRNAs, death receptor 5 antisense (DR5-AS) lncRNA, which resulted in a morphological change in HeLa cell shape without inducing any cell death. A second round of transcriptomics-based profiling revealed differential expression of genes associated with immune system, motility and cell cycle in DR5-AS knockdown HeLa cells. Cellular analyses showed that DR5-AS reduced cell proliferation and caused a cell cycle arrest at S and G2/M phases. Moreover, DR5-AS knockdown reduced the invasive capacity of HeLa cells in zebrafish xenograft model. These results suggest that cisplatin-mediated pleiotropic effects, such as reduction in cell proliferation, metastasis and cell cycle arrest, may be mediated by lncRNAs. © Copyright © 2021 Gurer, Erdogan, Ahmadov, Basol, Sweef, Cakan-Akdogan and Akgül.Conference Object Citation - WoS: 2Incorporation of Equisetum Arvense Extract Into Silk Fibroin-Hyaluronic Acid Sponge Matrices for Wound Dressing Applications(Elsevier, 2012) Uslu, Mehmet Emin; Erdoğan, İpek; Bayraktar, OğuzEquisetum arvense extract has frequently been investigated for its antioxidant capacity, antimicrobial and antitumor properties. However, one of the challenges in natural compound investi-gations is to maintain the stability of polyphenolic compounds during their storage and applications. For this purpose extracts can be incorporated into different forms of biomaterial. In this research silk fibroin (SF) and hyaluronic acid (HA) was used as sponge matri-ces for wound dressing application.Conference Object In Vitro Antitumor Activity of Sarcopoterium Spinosum Leaf Extract With Bioactive Natural Compounds(Elsevier, 2013) Süngüç, Ceren; Erdoğan, İpek; Uslu, Mehmet Emin; Bayraktar, OğuzCancer cell lines cause generation of reactive oxygen species and free radicals at high levels (Wang and Yi, 2008). Then generated free radicals lead to breakdown of the structure of DNA, lipid or protein (Gul et al., 2011). When plant extracts including antioxidant phytochemicals are exposed to the redox reactions, the harmful effects of free radicals are effectively prevented. The aim of present research was to evaluate the antitumor potential of the extract derived from Sarcopoterium spinosum leaves. The leaves of S. spinosum were collected in Izmir, Turkey. Total phenol content of ethanolic.Conference Object Investigation of Anti-Tumoral Activity of Cistus Creticus Extract Against Pc-3 Cell Line(Elsevier, 2013) Erdoğan, İpek; Süngüç, Ceren; Uslu, Mehmet Emin; Bayraktar, OğuzRecent studies have revealed that plant extracts show cytotoxic activities against cancer cell lines by ceasing cell division in particular phases (Xu et al., 2012, Yıldırım et al., 2013). Expression of specific genes was found to be activated according to pathway in which cell death occurs. Objective of this study was to identify antitumoural effect of Cistus creticus, which is a perennial shrub, found in Mediterranean region, against prostate cancer cell line by measuring the cytotoxic activities and apoptotic gene expression levels.Article Citation - WoS: 19Citation - Scopus: 24Intracytoplasmic Re-Localization of Mirisc Complexes(Frontiers Media S.A., 2018) Akgül, Bünyamin; Erdoğan, İpekMicroRNAs (miRNAs) are a conserved class of non-coding RNAs of 22 nucleotides that post-transcriptionally regulate gene expression through translational repression and/or mRNA degradation. A great progress has been made regarding miRNA biogenesis and miRNA-mediated gene regulation. Additionally, an ample amount of information exists with respect to the regulation of miRNAs. However, the cytoplasmic localization of miRNAs and its effect on gene regulatory output is still in progress. We provide a current review of the cytoplasmic miRNA localization in metazoans. We then discuss the dynamic changes in the intracytoplasmic localization of miRNAs as a means to regulate their silencing activity. We then conclude our discussion with the potential molecules that could modulate miRNA localization.Article Citation - WoS: 8Wound Healing Effects of Various Fractions of Olive Leaf Extract (ole) on Mouse Fibroblasts(Ars Docendi, 2018) Erdoğan, İpek; Bayraktar, Oğuz; Uslu, Mehmet Emin; Tüncel, ÖzgeOlive (Olea europaea) leaf has been introduced as a potential therapeutic in wound healing owing to combined antioxidant and antimicrobial activity. Comparison of crude extract and its fractions in terms of antioxidant capacity, antimicrobial and cytotoxic activity to gain insight about cell migration rate under exogenous stress of H2O2, as a hallmark of wound healing constituted the objective of this study. Oleuropein-containing fraction exerted the highest cell migration rate among other fractions that contains hydroxytyrosol, verbascoside and luteolin, whilst treatment with high concentrations (50 mu g/ml) of this fraction simultaneously with H2O2 caused a dramatic decline in cell migration, resulting in the loss of cell adherence. Results overall indicated that active compounds caused an imbalance in redox signaling beyond a critical concentration. Comparison of fractions and crude extract also revealed that crude extract promoted cell migration by 20%, which may be attributed to synergistic effect of undefined phenolics.Article Citation - WoS: 11Citation - Scopus: 13Transcriptomics Analysis of Circular Rnas Differentially Expressed in Apoptotic Hela Cells(Frontiers Media S.A., 2019) Yaylak, Bilge; Erdoğan, İpek; Akgül, BünyaminApoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-alpha and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis.