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Jiang L, Hong H, Xiang S, Li H, Ji J, Lan M, Luo B. Integrated gene co-expression network analysis and experimental validation revealed potential targets of human urine extract CDA-II in treating chronic myeloid leukemia. Genomics 2024; 116:110806. [PMID: 38325533 DOI: 10.1016/j.ygeno.2024.110806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/24/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Cell differentiation agent II (CDA-II) exhibits potent anti-proliferative and apoptosis-inducing properties against a variety of cancer cells. However, its mechanism of action in chronic myeloid leukemia (CML) remains unclear. METHODS Cell counting Kit 8 (CCK-8) and flow cytometry were used to investigate the effects of CDA-II on the biological characteristics of K562 cells. Gene (mRNA and lncRNA) expression profiles were analyzed by bioinformatics to screen differentially expressed genes and to perform enrichment analysis. The Pearson correlation coefficients of lncRNAs and mRNAs were calculated using gene expression values, and a lncRNA/mRNA co-expression network was constructed. The MCODE and cytoHubba plugins were used to analyze the co-expression network. RESULTS The Results, derived from CCK-8 and flow cytometry, indicated that CDA-II exerts dual effects on K562 cells: it inhibits their proliferation and induces apoptosis. From bioinformatics analysis, we identified 316 mRNAs and 32 lncRNAs. These mRNAs were predominantly related to the meiotic cell cycle, DNA methylation, transporter complex and peptidase regulator activity, complement and coagulation cascades, protein digestion and absorption, and cell adhesion molecule signaling pathways. The co-expression network comprised of 163 lncRNA/mRNA interaction pairs. Notably, our analysis results implicated clustered histone gene families and five lncRNAs in the biological effects of CDA-II on K562 cells. CONCLUSION This study highlights the hub gene and lncRNA/mRNA co-expression network as crucial elements in the context of CDA-II treatment of CML. This insight not only enriches our understanding of CDA-II's mechanism of action but also might provide valuable clues for subsequent experimental studies of CDA-II, and potentially contribute to the discovery of new therapeutic targets for CML.
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Affiliation(s)
- Lei Jiang
- Department of Critical Care Medicine, Intensive Care Unit, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China
| | - Haoyuan Hong
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Shulin Xiang
- Department of Critical Care Medicine, Intensive Care Unit, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China
| | - Han Li
- Department of Hematology, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China
| | - Jianyu Ji
- Department of Critical Care Medicine, Intensive Care Unit, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China
| | - Mei Lan
- Department of Hematology, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China
| | - Bin Luo
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China; Department of Hematology, The People's Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning 530021, China.
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Zenebe B, Nigussie H, Belay G, Seboka N. A review on characterization of BCR - ABL transcript variants for molecular monitoring of chronic myeloid leukemia phenotypes. Hematology 2023; 28:2284038. [PMID: 37982440 DOI: 10.1080/16078454.2023.2284038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal myeloproliferative growth of human pluripotent stem cells which is estimated to occur at a rate of 1/100000 populations every year worldwide. A characteristic feature of this disease is the presence of the Philadelphia chromosome genotype, which results from the reciprocal translocation between human chromosomes 9 and 22. Two types of major genotypes are involved, which consequently result in two major types of expressed fusion mRNA transcripts: b3a2 and b2a2, i.e. major breakpoint segments (happening after exon 13 & after exon 14) of the BCR gene on chromosome 22 fuze with the ABL1 gene breakpoint (happening after exon 2) on chromosome 9, forming two genotypes coding for two transcripts: b3a2 (e14a2) and b2a2 (e13a2). The protein 'p210 BCR-ABL1', a protein which characteristically exhibits a high tyrosine kinase activity which is followed by the activation of various cellular processes that lead to increased cellular proliferation and cancer, is coded by both major BCR - ABL1 mRNA transcripts. Recent developments in the treatment of CML through molecular monitoring of the disease have managed to reduce patient morbidity and mortality. Advanced molecular techniques are aimed at detecting BCR-ABL1 transcript levels to monitor treatment response. Transcript typing is necessary to detect minimal residual disease and to achieve molecular response by helping to provide selective therapy based on the type of transcript identified, as transcript type is correlated with the disease course.The purpose of this review is to discuss: the role of the BCR-ABL1 fusion gene in the pathogenesis of CML; the role of BCR-ABL1 transcript characterization in the molecular monitoring of CML therapy; the association of BCR - ABL1 transcript types with different CML phenotypes, molecular responses, and treatment responses; and the laboratory techniques employed to detect and characterize BCR - ABL1 transcripts.
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Affiliation(s)
- Benyam Zenebe
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nigussie Seboka
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
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Fu J, Si L, Zhou Y, Li D, Wang R. Distinct N7-methylguanosine profiles of circular RNAs in drug-resistant acute myeloid leukemia. Sci Rep 2023; 13:14704. [PMID: 37679400 PMCID: PMC10485064 DOI: 10.1038/s41598-023-41974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Post-transcriptional methylation modifications, such as the N7-methylguanosine (m7G) modification, are increasingly acknowledged for their role in the development and resistance to chemotherapy in acute myeloid leukemia (AML). This study employed MeRIP-seq technology to investigate the m7G sites within circular RNAs (circRNAs) derived from human AML cells and drug-resistant AML cells, in order to identify these sites more comprehensively. In addition, a detailed analysis of the relationship between m7G and drug-resistant AML was conducted. The bioinformatics analysis was utilized to predict the functions of specific methylated transcripts. The findings revealed a significant difference in m7G level between AML cells and drug-resistant AML cells, suggesting a potentially critical role of m7G in circRNAs in drug-resistant AML development. The methylation of M7G could affect the circRNA-miRNA-mRNA co-expression during the development of AML resistance, which could further influence the regulation of resistance-associated target genes in AML. Furthermore, gene ontology analysis indicated that the distinct distribution pattern of circRNAs with m7G methylation in drug-resistant AML cells was correlated with metabolism-related pathways. These results suggested a potential association between drug-resistant AML and m7G methylation of circRNAs. Moreover, the results revealed a novel role of m7G RNA methylation in circRNAs in the progression of AML chemoresistance.
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Affiliation(s)
- Jinqiu Fu
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Libo Si
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yao Zhou
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Dong Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Ran Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China.
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Shanmuganathan N, Wadham C, Shahrin N, Feng J, Thomson D, Wang P, Saunders V, Kok CH, King RM, Kenyon RR, Lin M, Pagani IS, Ross DM, Yong ASM, Grigg AP, Mills AK, Schwarer AP, Braley J, Altamura H, Yeung DT, Scott HS, Schreiber AW, Hughes TP, Branford S. Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention. Haematologica 2023; 108:2380-2395. [PMID: 36951160 PMCID: PMC10483360 DOI: 10.3324/haematol.2022.282184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The BCR::ABL1 gene fusion initiates chronic myeloid leukemia (CML); however, evidence has accumulated from studies of highly selected cohorts that variants in other cancer-related genes are associated with treatment failure. Nevertheless, the true incidence and impact of additional genetic abnormalities (AGA) at diagnosis of chronic phase (CP)-CML is unknown. We sought to determine whether AGA at diagnosis in a consecutive imatinib-treated cohort of 210 patients enrolled in the TIDEL-II trial influenced outcome despite a highly proactive treatment intervention strategy. Survival outcomes including overall survival, progression-free survival, failure-free survival, and BCR::ABL1 kinase domain mutation acquisition were evaluated. Molecular outcomes were measured at a central laboratory and included major molecular response (MMR, BCR::ABL1 ≤0.1%IS), MR4 (BCR::ABL1 ≤0.01%IS), and MR4.5 (BCR::ABL1 ≤0.0032%IS). AGA included variants in known cancer genes and novel rearrangements involving the formation of the Philadelphia chromosome. Clinical outcomes and molecular response were assessed based on the patient's genetic profile and other baseline factors. AGA were identified in 31% of patients. Potentially pathogenic variants in cancer-related genes were detected in 16% of patients at diagnosis (including gene fusions and deletions) and structural rearrangements involving the Philadelphia chromosome (Ph-associated rearrangements) were detected in 18%. Multivariable analysis demonstrated that the combined genetic abnormalities plus the EUTOS long-term survival clinical risk score were independent predictors of lower molecular response rates and higher treatment failure. Despite a highly proactive treatment intervention strategy, first-line imatinib-treated patients with AGA had poorer response rates. These data provide evidence for the incorporation of genomically-based risk assessment for CML.
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MESH Headings
- Humans
- Imatinib Mesylate/therapeutic use
- Antineoplastic Agents/therapeutic use
- Philadelphia Chromosome
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myeloid, Chronic-Phase/drug therapy
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG).
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide
| | - NurHezrin Shahrin
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Jinghua Feng
- Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Daniel Thomson
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Paul Wang
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Verity Saunders
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide
| | - Chung Hoow Kok
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
| | - Rob M King
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Rosalie R Kenyon
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ming Lin
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ilaria S Pagani
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - David M Ross
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Flinders University and Medical Centre, Adelaide
| | - Agnes S M Yong
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); The University of Western Australia Medical School, Western Australia
| | - Andrew P Grigg
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Clinical Hematology, Austin Hospital and University of Melbourne, Melbourne
| | - Anthony K Mills
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Princess Alexandra Hospital, Brisbane
| | - Anthony P Schwarer
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Box Hill Hospital, Melbourne
| | - Jodi Braley
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - Haley Altamura
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - David T Yeung
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia; School of Biological Sciences, University of Adelaide, Adelaide
| | - Timothy P Hughes
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Susan Branford
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
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Kamyabi R, Jahandideh A, Panahi N, Muhammadnejad S. Synergistic cytotoxicity effect of the combination of chitosan nanoencapsulated imatinib mesylate and quercetin in BCR-ABL positive K562 cells. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2023; 26:359-366. [PMID: 36865043 PMCID: PMC9922367 DOI: 10.22038/ijbms.2023.68472.14934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/18/2022] [Indexed: 03/04/2023]
Abstract
Objectives Intolerable side effects and resistance to chemotherapeutic drugs have encouraged scientists to develop new methods of drug combinations with fewer complications. This study aimed to investigate the synergistic effects of quercetin and imatinib encapsulated in chitosan nanoparticles on cytotoxicity, apoptosis, and cell growth of the K562 cell line. Materials and Methods Imatinib and quercetin were encapsulated in chitosan nanoparticles and their physical properties were determined using standard methods and SEM microscope images. BCR-ABL positive K562 cells were cultured in a cell culture medium, cytotoxicity of drugs was determined by MTT assay and the effects of nano drugs on apoptosis in cells were investigated by Annexin V-FITC staining. The expression level of genes associated with apoptosis in cells was measured by real-time PCR. Results The IC50 for the combination of the nano drugs at 24 and 48 hr was 9.324 and 10.86 μg/ml, respectively. The data indicated that the encapsulated form of drugs induced apoptosis more effectively than the free form (P<0.05). Moreover, the synergistic effect of nano drugs in statistical analysis was proved (P=0.001). The combination of nano drugs resulted in the caspase 3, 8, and TP53 genes upregulation (P=0.001). Conclusion The results of the present study showed that the encapsulated form of imatinib and quercetin nano drugs with chitosan has more cytotoxicity than the free form of the drugs. In addition, the combination of imatinib and quercetin as a nano-drug complex has a synergistic effect on the induction of apoptosis in imatinib-resistant K562 cells.
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Affiliation(s)
- Rohollah Kamyabi
- Department of Veterinary Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Jahandideh
- Department of Veterinary Surgery, Science and Research Branch, Islamic Azad University, Tehran, Iran,Corresponding author: Alireza Jahandideh. Department of Veterinary Surgery, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Negar Panahi
- Department of Veterinary Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Samad Muhammadnejad
- Gene Therapy Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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