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    Identification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a Bioinformatics Study
    (Taylor & Francis Inc, 2023) Hekmatshoar, Yalda; Rahbar Saadat, Yalda; Ozkan, Tulin; Bozkurt, Sureyya; Karadag Gurel, Aynur
    Imatinib (IMA) and nilotinib are the first and second generations of BCR-ABL tyrosine kinase inhibitors, which widely applied in chronic myeloid leukemia (CML) treatment. Here we aimed to provide new targets for CML treatment by transcriptome analysis. Microarray data GSE19567 was downloaded and analyzed from Gene Expression Omnibus (GEO) to identify common genes, which are downregulated or upregulated in K562-imatinib and K562-nilotinib treated cells. The differentially expressed genes (DEGs) were assessed, and STRING and Cytoscape were used to create the protein-protein interaction (PPI) network. In imatinib and nilotinib treated groups' comparison, there were common 626 upregulated and 268 downregulated genes, which were differentially expressed. The GO analysis represented the enrichment of DEGs in iron ion binding, protein tyrosine kinase activity, transcription factor activity, ATP binding, sequence-specific DNA binding, cytokine activity, the mitochondrion, sequence-specific DNA binding, plasma membrane and cell-cell adherens junction. KEGG pathway analysis revealed that downregulated DEGs were associated with pathways including microRNAs in cancer and PI3K-Akt signaling pathway. Furthermore, upregulated DEGs were involved in hematopoietic cell lineage, lysosome and chemical carcinogenesis. Among the upregulated genes, MYH9, MYH14, MYL10, MYL7, MYL5, RXRA, CYP1A1, FECH, AKR1C3, ALAD, CAT, CITED2, CPT1A, CYP3A5, CYP3A7, FABP1, HBD, HMBS and PPOX genes were found as hub genes. Moreover, 20 downregulated genes, YARS, AARS, SARS, GARS, CARS, IARS, RRP79, CEBPB, RRP12, UTP14A, PNO1, CCND1, DDX10, MYC, WDR43, CEBPG, DDIT3, VEGFA, PIM1 and TRIB3 were identified as hub genes. These genes have the potential to become target genes for diagnosis and therapy of CML patients.
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    Inhibition of O6-methylguanine-DNA-methyltransferase (MGMT) by lomeguatrib reduces multiple myeloma cell viability and impairs DNA repair in MGMT-proficient cells
    (Wiley, 2024) Akcora-Yildiz, Dilara; Ozkan, Tulin; Cetintav, Bekir; Yukselten, Yunus; Calis, Seyma; Sevim-Nalkiran, Hatice; Turkel, Nezaket
    The function of direct DNA damage repair protein, namely MGMT in MM, and the impact of MGMT on melphalan treatment remains unclear. We showed a significantly higher MGMT mRNA expression in CD138+ myeloma cells than in matched CD138-nontumorigenic cells derived from newly diagnosed and relapsed/refractory MM patients using qPCR. However, using gene expression databases, a similar expression of MGMT was observed during disease progression. MGMT depletion by its specific inhibitor lomeguatrib reduced myeloma cell viability, impaired S phase entry and DNA repair, and increased DNA damage and apoptosis. Apoptosis and DNA damage were further elevated by combined treatment with lomeguatrib and melphalan in RPMI 8226 cells. This is the first study demonstrating MGMT inhibition enhances DNA damage-induced apoptosis and melphalan cytotoxicity in MGMT-proficient MM cells and suggesting using lomeguatrib might have clinical importance in treating MM and overcoming melphalan resistance in MGMT-proficient patients.
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    Phenotypic and functional characterization of subpopulation of Imatinib resistant chronic myeloid leukemia cell line
    (Elsevier Urban & Partner Sp Z O O, 2023) Hekmatshoar, Yalda; Gurel, Aynur Karadag; Ozkan, Tulin; Saadat, Yalda Rahbar; Koc, Asli; Karabay, Arzu Zeynep; Bozkurt, Sureyya
    Purpose: Chronic myeloid leukemia (CML) is a hematological malignancy characterized by the presence of BCR-ABL protein. Imatinib (IMA) is considered as the first line therapy in management of CML which particularly targets the BCR-ABL tyrosine kinase protein. However, emergence of resistance to IMA hinders its clinical efficiency. Hence, identifying novel targets for therapeutic approaches in CML treatment is of great importance. Here, we characterize a new subpopulation of highly adherent IMA-resistant CML cells that express stemness and adhesion markers compared to naive counterparts.Materials and methods: We performed several experimental assays including FISH, flow cytometry, and gene expression assays. Additionally, bioinformatics analysis was performed by normalized web-available microarray data (GSE120932) to revalidate and introduce probable biomarkers. Protein-protein interactions (PPI) network was analyzed by the STRING database employing Cytoscape v3.8.2.Results: Our findings demonstrated that constant exposure to 5 & mu;M IMA led to development of the adherent phenotype (K562R-adh). FISH and BCR-ABL expression analysis indicated that K562R-adh cells were derived from the original cells (K562R). In order to determine the role of various genes involved in epi-thelial-mesenchymal transition (EMT) and stem cell characterization, up/down-regulation of various genes including cancer stem cell (CSC), adhesion and cell surface markers and integrins were observed which was similar to the findings of the GSE120932 dataset.Conclusion: Treating CML patients with tyrosine kinase inhibitors (TKIs) as well as targeting adhesion molecules deemed to be effective approaches in prevention of IMA resistance emergence which in turn may provide promising effects in the clinical management of CML patients.