Person: KASAVİ, CEYDA
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KASAVİ
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CEYDA
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Publication Open Access Gene co-expression network analysis revealed novel biomarkers for ovarian cancer(2022-10-01) KASAVİ, CEYDA; KASAVİ C.Ovarian cancer is the second most common gynecologic cancer and remains the leading cause of death of all gynecologic oncologic disease. Therefore, understanding the molecular mechanisms underlying the disease, and the identification of effective and predictive biomarkers are invaluable for the development of diagnostic and treatment strategies. In the present study, a differential co-expression network analysis was performed via meta-analysis of three transcriptome datasets of serous ovarian adenocarcinoma to identify novel candidate biomarker signatures, i.e. genes and miRNAs. We identified 439 common differentially expressed genes (DEGs), and reconstructed differential co-expression networks using common DEGs and considering two conditions, i.e. healthy ovarian surface epithelia samples and serous ovarian adenocarcinoma epithelia samples. The modular analyses of the constructed networks indicated a co-expressed gene module consisting of 17 genes. A total of 11 biomarker candidates were determined through receiver operating characteristic (ROC) curves of gene expression of module genes, and miRNAs targeting these genes were identified. As a result, six genes (CDT1, CNIH4, CRLS1, LIMCH1, POC1A, and SNX13), and two miRNAs (mir-147a, and mir-103a-3p) were suggested as novel candidate prognostic biomarkers for ovarian cancer. Further experimental and clinical validation of the proposed biomarkers could help future development of potential diagnostic and therapeutic innovations in ovarian cancer.Publication Open Access Idiopathic pulmonary arterial hypertension: network-based integration of multi-omics data reveals new molecular signatures and candidate drugs(2023-01-01) KASAVİ, CEYDA; KASAVİ C.Idiopathic pulmonary arterial hypertension (IPAH) is a progressive disease that affects the pulmonary arteries, resulting in increased pulmonary vascular resistance and right ventricular dysfunction, which can ultimately lead to heart failure and death. The molecular substrates of IPAH are poorly understood while diagnostics and therapeutics innovation remain as unmet needs for this debilitating disease. In this study, a network-based methodology was used to uncover the salient molecular mechanisms of IPAH to inform drug and diagnostic discovery, and personalized medicine. Expression profiling datasets associated with IPAH were obtained from the Gene Expression Omnibus database: GSE15197, GSE113439, GSE53408, and GSE67597. The comparative analysis of mRNA and miRNA expression data and the modular analysis of a transcriptome-based weighted gene coexpression network unraveled disease-specific gene and miRNA signatures. DEAD-box helicase 52 (DDx52), ESF1 nucleolar pre-RNA processing protein (ESF1), heterogeneous nuclear ribonuclearprotein A3 (MNRNPA3), Myosin VA (MYO5A), replication factor C subunit 1 (RFC1), and arginine and serine rich coiled coil 1 (RSRC1) were detected as the salient genes for IPAH. In addition, the salient gene-based drug repositioning analysis identified alvespimycin, tanespimycin, geldanamycin, LY294002, cephaeline, digoxigenin, lanatoside C, helveticoside, trichostatin A, phenoxybenzamine, genistein, pioglitazone, and rosiglitazone as potential drug candidates for IPAH. In conclusion, this study provides new molecular signatures in relation to IPAH and attendant potential drug candidates for further experimental and translational clinical research for patients with IPAH.Publication Open Access Genomic analysis provides new Insights into biotechnological and industrial potential of parageobacillus thermantarcticus M1(2022-06-01) KASAVİ, CEYDA; TOKSOY ÖNER, EBRU; YILDIZ S. Y., Finore I., Leone L., Romano I., Lama L., KASAVİ C., Nicolaus B., TOKSOY ÖNER E., Poli A.Parageobacillus thermantarcticus strain M1 is a Gram-positive, motile, facultative anaerobic, spore forming, and thermophilic bacterium, isolated from geothermal soil of the crater of Mount Melbourne (74 degrees 22 \" S, 164 degrees 40 \" E) during the Italian Antarctic Expedition occurred in Austral summer 1986-1987. Strain M1 demonstrated great biotechnological and industrial potential owing to its ability to produce exopolysaccharides (EPSs), ethanol and thermostable extracellular enzymes, such as an xylanase and a beta-xylosidase, and intracellular ones, such as xylose/glucose isomerase and protease. Furthermore, recent studies revealed its high potential in green chemistry due to its use in residual biomass transformation/valorization and as an appropriate model for microbial astrobiology studies. In the present study, using a systems-based approach, genomic analysis of P. thermantarcticus M1 was carried out to enlighten its functional characteristics. The elucidation of whole-genome organization of this thermophilic cell factory increased our understanding of biological mechanisms and pathways, by providing valuable information on the essential genes related to the biosynthesis of nucleotide sugar precursors, monosaccharide unit assembly, as well as the production of EPSs and ethanol. In addition, gene prediction and genome annotation studies identified genes encoding xylanolytic enzymes that are required for the conversion of lignocellulosic materials to high-value added molecules. Our findings pointed out the significant potential of strain M1 in various biotechnological and industrial applications considering its capacity to produce EPSs, ethanol and thermostable enzymes via the utilization of lignocellulosic waste materials.Publication Metadata only Multiomics data integration identifies new molecular signatures for abdominal aortic aneurysm and aortic occlusive disease: implications for early diagnosis, prognosis, and therapeutic targets(2022-05-01) KASAVİ, CEYDA; ARĞA, KAZIM YALÇIN; Kori M., Cig D., Arga K. Y., Kasavi C.Cardiovascular disease (CVD) is the leading cause of death among adults in developed countries. Among CVDs, abdominal aortic aneurysm (AAA) and aortic occlusive disease (AOD) are of great public health importance because of the high mortality rate in the elderly population. Despite significant molecular insights into AAA and AOD, the molecular mechanisms of these diseases remain unclear, and the current lack of robust diagnostic and prognostic biomarkers requires novel approaches to biomarker discovery and molecular targeting. In this study, we performed a comparative analysis of genome-wide expression data from patients with large AAA (n = 29), small AAA (n = 20), AOD (n = 9), and controls (n = 10). Specifically, we identified the differentially expressed genes and associated molecular pathways and biological processes (BPs) in each disease. Using a systems science approach, these data were linked to comprehensive human biological networks (i.e., protein-protein interaction, transcriptional regulatory, and metabolic networks) to identify molecular signatures of the salient mechanisms of AAA and AOD. Significant alterations in lipid metabolism and valine, leucine, and isoleucine metabolism, as well as neurodegenerative diseases and sex differences in the pathogenesis of AAA and AOD were identified. In the presence of aneurysm, size-dependent changes in lipid metabolism were observed. In addition, molecules and signaling pathways related to immunity, inflammation, infectious disease, and oxidative phosphorylation were identified in common. The results of the comparative and integrative analyzes revealed important clues to disease mechanisms and reporter molecules at various levels that warrant future development as potential prognostic biomarkers and putative therapeutic targets.