Identification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a Bioinformatics Study

• Published in: Nucleosides, nucleotides & nucleic acids Vol. 43; no. 7; pp. 664 - 684
• Main Authors: Hekmatshoar, Yalda, Rahbar Saadat, Yalda, Ozkan, Tulin, Bozkurt, Sureyya, Karadag Gurel, Aynur
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 02.07.2024; Taylor & Francis Ltd
• Subjects: 1-Phosphatidylinositol 3-kinase; Abl protein; AKT protein; BCR protein; Bioinformatics; Carcinogenesis; Cell lineage; Chronic myeloid leukemia; CYP3A7 protein; Cytochrome P450; DNA microarrays; Down-regulation; Fusion protein; Gene expression; gEO; Hematopoietic stem cells; Imatinib; Kinases; miRNA; Myc protein; Myeloid leukemia; nilotinib; Nucleotide sequence; Protein-tyrosine kinase; Proteins; Retinoid X receptor α; Signal transduction; Transcriptomes; gEO; imatinib; Chronic myeloid leukemia; nilotinib; gene expression; bioinformatics
• ISSN: 1525-7770; 1532-2335; 1532-2335
• DOI: 10.1080/15257770.2023.2296021

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.