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Kaehler M, Cascorbi I. Molecular Mechanisms of Tyrosine Kinase Inhibitor Resistance in Chronic Myeloid Leukemia. Handb Exp Pharmacol 2023; 280:65-83. [PMID: 36882601 DOI: 10.1007/164_2023_639] [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] [Indexed: 03/09/2023]
Abstract
The hematopoietic neoplasm chronic myeloid leukemia (CML) is a rare disease caused by chromosomal reciprocal translocation t(9;22)(q34:q11) with subsequent formation of the BCR-ABL1 fusion gene. This fusion gene encodes a constitutively active tyrosine kinase, which results in malignant transformation of the cells. Since 2001, CML can be effectively treated using tyrosine kinase inhibitors (TKIs) such as imatinib, which prevent phosphorylation of downstream targets by blockade of the BCR-ABL kinase. Due to its tremendous success, this treatment became the role model of targeted therapy in precision oncology. Here, we review the mechanisms of TKI resistance focusing on BCR-ABL1-dependent and -independent mechanisms. These include the genomics of the BCR-ABL1, TKI metabolism and transport and alternative signaling pathways.
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Affiliation(s)
- Meike Kaehler
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany.
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2
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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3
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Wu DL, Wang Y, Zhang TJ, Chu MQ, Xu ZJ, Yuan Q, Ma JC, Lin J, Qian J, Zhou JD. SLIT2 promoter hypermethylation predicts disease progression in chronic myeloid leukemia. Eur J Med Res 2022; 27:259. [PMID: 36411451 PMCID: PMC9677675 DOI: 10.1186/s40001-022-00899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation plays a crucial role in the progression of myeloid neoplasms. Previously, our literature reported that slit guidance ligand 2 (SLIT2) promoter methylation was associated with disease progression and indicated a poor prognosis in patients with myelodysplastic syndrome. Herein, we further investigated the clinical implications and role of SLIT2 promoter methylation in patients with chronic myeloid leukemia (CML). METHODS The level of SLIT2 promoter methylation was determined in 104 CML patients, and its clinical significance was analyzed. Moreover, demethylation studies were performed in K562 cells to determine the epigenetic mechanism by which SLIT2 promoter methylation is regulated in CML. RESULTS The level of SLIT2 promoter methylation was similar between CML patients and controls. However, deeper analysis revealed that the SLIT2 promoter methylation level in the accelerated phase (AP) and blast crisis (BC) was markedly higher than that in the chronic phase (CP) and controls. Additionally, a marked difference was identified between the SLIT2 promoter hypermethylated and non-hypermethylated groups among CML patients grouped by clinical stage. The frequency of SLIT2 hypermethylation was markedly increased with the progression of clinical stage, that is, it was the lowest in CP samples (12/80, 15%), higher in AP samples (4/8, 50%) and the highest in BC samples (11/16, 69%). Importantly, the level/density of SLIT2 promoter methylation was significantly higher in the advanced stage than in the early stage among the 6 tested paired CML patients. Epigenetically, the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 expression was decreased in patients with CML. SLIT2 promoter hypermethylated cases had a markedly lower SLIT2-IT1 expression level than SLIT2 promoter non-hypermethylated cases. Moreover, SLIT2-IT1 and miR-218 expression was remarkably upregulated in a dose-dependent manner after demethylation treatment of K562 cells. CONCLUSIONS Hypermethylation of the SLIT2 promoter is correlated with disease progression in CML. Furthermore, SLIT2 promoter methylation may function by regulating the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 during CML progression.
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Affiliation(s)
- De-long Wu
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,Department of Oncology, Dongtai People’s Hospital, Dongtai, Jiangsu People’s Republic of China
| | - Yun Wang
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Ting-juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Department of Oncology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Ming-qiang Chu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Ji-chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jun Qian
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jing-dong Zhou
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
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4
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Properties of Leukemic Stem Cells in Regulating Drug Resistance in Acute and Chronic Myeloid Leukemias. Biomedicines 2022; 10:biomedicines10081841. [PMID: 36009388 PMCID: PMC9405586 DOI: 10.3390/biomedicines10081841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Notoriously known for their capacity to reconstitute hematological malignancies in vivo, leukemic stem cells (LSCs) represent key drivers of therapeutic resistance and disease relapse, posing as a major medical dilemma. Despite having low abundance in the bulk leukemic population, LSCs have developed unique molecular dependencies and intricate signaling networks to enable self-renewal, quiescence, and drug resistance. To illustrate the multi-dimensional landscape of LSC-mediated leukemogenesis, in this review, we present phenotypical characteristics of LSCs, address the LSC-associated leukemic stromal microenvironment, highlight molecular aberrations that occur in the transcriptome, epigenome, proteome, and metabolome of LSCs, and showcase promising novel therapeutic strategies that potentially target the molecular vulnerabilities of LSCs.
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5
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Chromosomal Instability in Chronic Myeloid Leukemia: Mechanistic Insights and Effects. Cancers (Basel) 2022; 14:cancers14102533. [PMID: 35626137 PMCID: PMC9140097 DOI: 10.3390/cancers14102533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/15/2022] Open
Abstract
The most recent two decades have seen tremendous progress in the understanding and treatment of chronic myeloid leukemia, a disease defined by the characteristic Philadelphia chromosome and the ensuing BCR::ABL fusion protein. However, the biology of the disease extends beyond the Philadelphia chromosome into a nebulous arena of chromosomal and genetic instability, which makes it a genetically heterogeneous disease. The BCR::ABL oncoprotein creates a fertile backdrop for oxidative damage to the DNA, along with impairment of genetic surveillance and the favoring of imprecise error-prone DNA repair pathways. These factors lead to growing chromosomal instability, manifested as additional chromosomal abnormalities along with other genetic aberrations. This worsens with disease progression to accelerated and blast phase, and modulates responses to tyrosine kinase inhibitors. Treatment options that target the genetic aberrations that mitigate chromosome instability might be a potential area for research in patients with advanced phase CML.
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6
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Kamachi K, Ureshino H, Watanabe T, Yoshida N, Yamamoto Y, Kurahashi Y, Fukuda-Kurahashi Y, Hayashi Y, Hirai H, Yamashita S, Ushijima T, Okada S, Kimura S. Targeting DNMT1 by demethylating agent OR-2100 increases tyrosine kinase inhibitors-sensitivity and depletes leukemic stem cells in chronic myeloid leukemia. Cancer Lett 2022; 526:273-283. [PMID: 34875342 DOI: 10.1016/j.canlet.2021.11.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
ABL1 tyrosine kinase inhibitors (TKIs) dramatically improve the prognosis of chronic myeloid leukemia (CML), but 10-20% of patients achieve suboptimal responses with low TKIs sensitivity. Furthermore, residual leukemic stem cells (LSCs) are involved in the molecular relapse after TKIs discontinuation. Aberrant DNA hypermethylation contributes to low TKIs sensitivity and the persistence of LSCs in CML. DNMT1 is a key regulator of hematopoietic stem cells, suggesting that aberrant DNA hypermethylation targeting DNMT1 represents a potential therapeutic target for CML. We investigated the efficacy of OR-2100 (OR21), the first orally available single-compound prodrug of decitabine. OR21 exhibited anti-tumor effects as a monotherapy, and in combination therapy it increased TKI-induced apoptosis and induction of tumor suppressor genes including PTPN6 encoding SHP-1 in CML cells. OR21 in combination with imatinib significantly suppressed tumor growth in a xenotransplant model. OR21 and combination therapy decreased the abundance of LSCs and inhibited engraftment in a BCR-ABL1-transduced mouse model. These results demonstrate that targeting DNMT1 using OR21 exerts anti-tumor effects and impairs LSCs in CML. Therefore, combination treatment of TKIs and OR21 represents a promising treatment strategy in CML.
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Affiliation(s)
- Kazuharu Kamachi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan; Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Ureshino
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan; Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.
| | - Tatsuro Watanabe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Nao Yoshida
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuta Yamamoto
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan; OHARA Pharmaceutical Co., Ltd, Japan
| | - Yuki Fukuda-Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan; OHARA Pharmaceutical Co., Ltd, Japan
| | - Yoshihiro Hayashi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Hideyo Hirai
- Laboratory of Stem Cell Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Shinya Kimura
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan; Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
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7
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Chattopadhyaya S, Ghosal S. DNA methylation: a saga of genome maintenance in hematological perspective. Hum Cell 2022; 35:448-461. [DOI: 10.1007/s13577-022-00674-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/13/2022] [Indexed: 12/21/2022]
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8
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Krishnan V, Kim DDH, Hughes TP, Branford S, Ong ST. Integrating genetic and epigenetic factors in chronic myeloid leukemia risk assessment: toward gene expression-based biomarkers. Haematologica 2021; 107:358-370. [PMID: 34615339 PMCID: PMC8804571 DOI: 10.3324/haematol.2021.279317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Cancer treatment is constantly evolving from a one-size-fits-all towards bespoke approaches for each patient. In certain solid cancers, including breast and lung, tumor genome profiling has been incorporated into therapeutic decision-making. For chronic phase chronic myeloid leukemia (CML), while tyrosine kinase inhibitor therapy is the standard treatment, current clinical scoring systems cannot accurately predict the heterogeneous treatment outcomes observed in patients. Biomarkers capable of segregating patients according to outcome at diagnosis are needed to improve management, and facilitate enrollment in clinical trials seeking to prevent blast crisis transformation and improve the depth of molecular responses. To this end, gene expression (GE) profiling studies have evaluated whether GE signatures at diagnosis are clinically informative. Patient material from a variety of sources has been profiled using microarrays, RNA sequencing and, more recently, single-cell RNA sequencing. However, differences in the cell types profiled, the technologies used, and the inherent complexities associated with the interpretation of genomic data pose challenges in distilling GE datasets into biomarkers with clinical utility. The goal of this paper is to review previous studies evaluating GE profiling in CML, and explore their potential as risk assessment tools for individualized CML treatment. We also review the contribution that acquired mutations, including those seen in clonal hematopoiesis, make to GE profiles, and how a model integrating contributions of genetic and epigenetic factors in resistance to tyrosine kinase inhibitors and blast crisis transformation can define a route to GE-based biomarkers. Finally, we outline a four-stage approach for the development of GE-based biomarkers in CML.
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Affiliation(s)
- Vaidehi Krishnan
- Cancer and Stem Cell Biology Signature Research Program, Duke-NUS Medical School, Singapore, Singapore; International Chronic Myeloid Leukemia Foundation
| | - Dennis Dong Hwan Kim
- International Chronic Myeloid Leukemia Foundation; Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto
| | - Timothy P Hughes
- International Chronic Myeloid Leukemia Foundation; School of Medicine, University of Adelaide, Adelaide, Australia; South Australian Health and Medical Research Institute, Adelaide, Australia; Department of Haematology, Royal Adelaide Hospital, Adelaide
| | - Susan Branford
- International Chronic Myeloid Leukemia Foundation; School of Medicine, University of Adelaide, Adelaide, Australia; Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, Australia; School of Pharmacy and Medical Science, University of South Australia, Adelaide
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Program, Duke-NUS Medical School, Singapore, Singapore; International Chronic Myeloid Leukemia Foundation; Department of Haematology, Singapore General Hospital, Singapore, Singapore; Department of Medical Oncology, National Cancer Centre Singapore; Department of Medicine, Duke University Medical Center, Durham, NC.
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9
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DNA Methylation and Intra-Clonal Heterogeneity: The Chronic Myeloid Leukemia Model. Cancers (Basel) 2021; 13:cancers13143587. [PMID: 34298798 PMCID: PMC8307727 DOI: 10.3390/cancers13143587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/24/2023] Open
Abstract
Chronic Myeloid Leukemia (CML) is a model to investigate the impact of tumor intra-clonal heterogeneity in personalized medicine. Indeed, tyrosine kinase inhibitors (TKIs) target the BCR-ABL fusion protein, which is considered the major CML driver. TKI use has highlighted the existence of intra-clonal heterogeneity, as indicated by the persistence of a minority subclone for several years despite the presence of the target fusion protein in all cells. Epigenetic modifications could partly explain this heterogeneity. This review summarizes the results of DNA methylation studies in CML. Next-generation sequencing technologies allowed for moving from single-gene to genome-wide analyses showing that methylation abnormalities are much more widespread in CML cells. These data showed that global hypomethylation is associated with hypermethylation of specific sites already at diagnosis in the early phase of CML. The BCR-ABL-independence of some methylation profile alterations and the recent demonstration of the initial intra-clonal DNA methylation heterogeneity suggests that some DNA methylation alterations may be biomarkers of TKI sensitivity/resistance and of disease progression risk. These results also open perspectives for understanding the epigenetic/genetic background of CML predisposition and for developing new therapeutic strategies.
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10
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Kaehler M, Cascorbi I. Pharmacogenomics of Impaired Tyrosine Kinase Inhibitor Response: Lessons Learned From Chronic Myelogenous Leukemia. Front Pharmacol 2021; 12:696960. [PMID: 34262462 PMCID: PMC8273252 DOI: 10.3389/fphar.2021.696960] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/17/2021] [Indexed: 12/25/2022] Open
Abstract
The use of small molecules became one key cornerstone of targeted anti-cancer therapy. Among them, tyrosine kinase inhibitors (TKIs) are especially important, as they were the first molecules to proof the concept of targeted anti-cancer treatment. Since 2001, TKIs can be successfully used to treat chronic myelogenous leukemia (CML). CML is a hematologic neoplasm, predominantly caused by reciprocal translocation t(9;22)(q34;q11) leading to formation of the so-called BCR-ABL1 fusion gene. By binding to the BCR-ABL1 kinase and inhibition of downstream target phosphorylation, TKIs, such as imatinib or nilotinib, can be used as single agents to treat CML patients resulting in 80 % 10-year survival rates. However, treatment failure can be observed in 20-25 % of CML patients occurring either dependent or independent from the BCR-ABL1 kinase. Here, we review approved TKIs that are indicated for the treatment of CML, their side effects and limitations. We point out mechanisms of TKI resistance focusing either on BCR-ABL1-dependent mechanisms by summarizing the clinically observed BCR-ABL1-mutations and their implications on TKI binding, as well as on BCR-ABL1-independent mechanisms of resistances. For the latter, we discuss potential mechanisms, among them cytochrome P450 implications, drug efflux transporter variants and expression, microRNA deregulation, as well as the role of alternative signaling pathways. Further, we give insights on how TKI resistance could be analyzed and what could be learned from studying TKI resistance in CML in vitro.
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Affiliation(s)
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
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11
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Wang L, Li L, Chen R, Huang X, Ye X. Understanding and Monitoring Chronic Myeloid Leukemia Blast Crisis: How to Better Manage Patients. Cancer Manag Res 2021; 13:4987-5000. [PMID: 34188552 PMCID: PMC8236273 DOI: 10.2147/cmar.s314343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/13/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic myeloid leukemia (CML) is triggered primarily by the t(9;22) (q34.13; q11.23) translocation. This reciprocal chromosomal translocation leads to the formation of the BCR-ABL fusion gene. Patients in the chronic phase (CP) experience a good curative effect with tyrosine kinase inhibitors. However, cases are treatment refractory, with a dismal prognosis, when the disease has progressed to the accelerated phase (AP) or blast phase (BP). Until now, few reports have provided a comprehensive description of the mechanisms involved at different molecular levels. Indeed, the underlying pathogenesis of CML evolution comprises genetic aberrations, chromosomal translocations (except for the Philadelphia chromosome), telomere biology, and epigenetic anomalies. Herein, we provide knowledge of the biology responsible for blast transformation of CML at several levels, such as genetics, telomere biology, and epigenetic anomalies. Because of the limited treatment options available and poor outcomes, only the therapeutic response is monitored regularly, which involves BCR-ABL transcript level assessment and immunologic surveillance, with the optimal treatment strategy for patients in CP adapted to evaluate disease recurrence or progression. Overall, selecting optimal treatment endpoints to predict survival and successful TFR improves the quality of life of patients. Thus, identifying risk factors and developing risk-adapted therapeutic options may contribute to a better outcome for advanced-phase patients.
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Affiliation(s)
- Lulu Wang
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,Program in Clinical Medicine, School of Medicine of Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Li Li
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Rongrong Chen
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,Program in Clinical Medicine, School of Medicine of Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xianbo Huang
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiujin Ye
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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12
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Jones R, Wijesinghe S, Wilson C, Halsall J, Liloglou T, Kanhere A. A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1. iScience 2021; 24:102273. [PMID: 33851096 PMCID: PMC8022221 DOI: 10.1016/j.isci.2021.102273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 01/10/2023] Open
Abstract
DNA methyl transferase-1 or DNMT1 maintains DNA methylation in the genome and is important for regulating gene expression in cells. Aberrant changes in DNMT1 activity and DNA methylation are commonly observed in cancers and many other diseases. Recently, a number of long intergenic non-protein-coding RNAs or lincRNAs have been shown to play a role in regulating DNMT1 activity. CCDC26 is a nuclear lincRNA that is frequently mutated in cancers and is a hotbed for disease-associated single nucleotide changes. However, the functional mechanism of CCDC26 is not understood. Here, we show that this lincRNA is concentrated on the nuclear periphery. Strikingly, in the absence of CCDC26 lincRNA, DNMT1 is mis-located in the cytoplasm, and the genomic DNA is significantly hypomethylated. This is accompanied by double-stranded DNA breaks and increased cell death. These results point to a previously unrecognized mechanism of lincRNA-mediated subcellular localization of DNMT1 and regulation of DNA methylation.
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Affiliation(s)
- Rhian Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susanne Wijesinghe
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, UK
| | - Claire Wilson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John Halsall
- Institute of Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Triantafillos Liloglou
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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13
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Valent P, Orfao A, Kubicek S, Staber P, Haferlach T, Deininger M, Kollmann K, Lion T, Virgolini I, Winter G, Hantschel O, Kenner L, Zuber J, Grebien F, Moriggl R, Hoermann G, Hermine O, Andreeff M, Bock C, Mughal T, Constantinescu SN, Kralovics R, Sexl V, Skoda R, Superti-Furga G, Jäger U. Precision Medicine in Hematology 2021: Definitions, Tools, Perspectives, and Open Questions. Hemasphere 2021; 5:e536. [PMID: 33623882 PMCID: PMC7892291 DOI: 10.1097/hs9.0000000000000536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
During the past few years, our understanding of molecular mechanisms and cellular interactions relevant to malignant blood cell disorders has improved substantially. New insights include a detailed knowledge about disease-initiating exogenous factors, endogenous (genetic, somatic, epigenetic) elicitors or facilitators of disease evolution, and drug actions and interactions that underlie efficacy and adverse event profiles in defined cohorts of patients. As a result, precision medicine and personalized medicine are rapidly growing new disciplines that support the clinician in making the correct diagnosis, in predicting outcomes, and in optimally selecting patients for interventional therapies. In addition, precision medicine tools are greatly facilitating the development of new drugs, therapeutic approaches, and new multiparametric prognostic scoring models. However, although the emerging roles of precision medicine and personalized medicine in hematology and oncology are clearly visible, several questions remain. For example, it remains unknown how precision medicine tools can be implemented in healthcare systems and whether all possible approaches are also affordable. In addition, there is a need to define terminologies and to relate these to specific and context-related tools and strategies in basic and applied science. To discuss these issues, a working conference was organized in September 2019. The outcomes of this conference are summarized herein and include a proposal for definitions, terminologies, and applications of precision and personalized medicine concepts and tools in hematologic neoplasms. We also provide proposals aimed at reducing costs, thereby making these applications affordable in daily practice.
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Affiliation(s)
- Peter Valent
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | - Alberto Orfao
- Servicio Central de Citometria, Centro de Investigacion del Cancer (IBMCC; CSIC/USAL), IBSAL, CIBERONC and Department of Medicine, University of Salamanca, Spain
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Staber
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | | | - Michael Deininger
- Division of Hematology and Hematologic Malignancies, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Thomas Lion
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
- Children’s Cancer Research Institute, Vienna, Austria
| | - Irene Virgolini
- Department of Nuclear Medicine, Medical University of Innsbruck, Austria
| | - Georg Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Oliver Hantschel
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps-University of Marburg, Germany
| | - Lukas Kenner
- Pathology of Laboratory Animals, University of Veterinary Medicine, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, Unit for Functional Cancer Genomics, University of Veterinary Medicine Vienna, Austria
| | - Gregor Hoermann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - Olivier Hermine
- Imagine Institute Université Paris Descartes, Sorbonne, Paris Cité, Paris, France
- Department of Hematology, Necker Hospital, Paris, France
| | - Michael Andreeff
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tariq Mughal
- Division of Hematology & Oncology, Tufts University Medical Center, Boston, Massachusetts, USA
| | - Stefan N. Constantinescu
- de Duve Institute and Ludwig Cancer Research Brussels, Université catholique de Louvain, Brussels, Belgium
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Radek Skoda
- Departement of Biomedicine, University of Basel, Switzerland
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrich Jäger
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
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14
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An integrative model of pathway convergence in genetically heterogeneous blast crisis chronic myeloid leukemia. Blood 2021; 135:2337-2353. [PMID: 32157296 DOI: 10.1182/blood.2020004834] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
Targeted therapies against the BCR-ABL1 kinase have revolutionized treatment of chronic phase (CP) chronic myeloid leukemia (CML). In contrast, management of blast crisis (BC) CML remains challenging because BC cells acquire complex molecular alterations that confer stemness features to progenitor populations and resistance to BCR-ABL1 tyrosine kinase inhibitors. Comprehensive models of BC transformation have proved elusive because of the rarity and genetic heterogeneity of BC, but are important for developing biomarkers predicting BC progression and effective therapies. To better understand BC, we performed an integrated multiomics analysis of 74 CP and BC samples using whole-genome and exome sequencing, transcriptome and methylome profiling, and chromatin immunoprecipitation followed by high-throughput sequencing. Employing pathway-based analysis, we found the BC genome was significantly enriched for mutations affecting components of the polycomb repressive complex (PRC) pathway. While transcriptomically, BC progenitors were enriched and depleted for PRC1- and PRC2-related gene sets respectively. By integrating our data sets, we determined that BC progenitors undergo PRC-driven epigenetic reprogramming toward a convergent transcriptomic state. Specifically, PRC2 directs BC DNA hypermethylation, which in turn silences key genes involved in myeloid differentiation and tumor suppressor function via so-called epigenetic switching, whereas PRC1 represses an overlapping and distinct set of genes, including novel BC tumor suppressors. On the basis of these observations, we developed an integrated model of BC that facilitated the identification of combinatorial therapies capable of reversing BC reprogramming (decitabine+PRC1 inhibitors), novel PRC-silenced tumor suppressor genes (NR4A2), and gene expression signatures predictive of disease progression and drug resistance in CP.
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15
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Schmitz U, Shah JS, Dhungel BP, Monteuuis G, Luu PL, Petrova V, Metierre C, Nair SS, Bailey CG, Saunders VA, Turhan AG, White DL, Branford S, Clark SJ, Hughes TP, Wong JJL, Rasko JE. Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients. Cancers (Basel) 2020; 12:cancers12123738. [PMID: 33322625 PMCID: PMC7764299 DOI: 10.3390/cancers12123738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary This study provides new insights into the changing transcriptomic and epigenomic landscapes in chronic myeloid leukaemia (CML) patients who are receiving tyrosine kinase inhibitor (TKI) therapy (often life-long). Alternative splicing, vital for cellular homeostasis, is dysregulated in human cancers. Remarkably, we found abnormal splicing patterns despite molecular remission in peripheral blood cells of chronic-phase CML patients. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Abstract Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
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Affiliation(s)
- Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Jaynish S. Shah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Geoffray Monteuuis
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
| | - Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
| | - Cynthia Metierre
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Shalima S. Nair
- Kinghorn Centre for Clinical Genomics Core Facility, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Verity A. Saunders
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
| | - Ali G. Turhan
- APHP, Division of Hematology, Paris Sud University Hospitals and Inserm U935 INGESTEM Pluripotent Stem Cell Infrastructure 78 Rue du Général Leclerc, 94275 Le Kremlin Bicetre, France;
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Susan Branford
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Susan J. Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Timothy P. Hughes
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Department of Haematology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5001, Australia
| | - Justin J.-L. Wong
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Correspondence: ; Tel.: +61-2-9565-6160
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16
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Elsayed FM, Nafea DA, El-Attar LM, Saied MH. Epigenetic silencing of the DAPK1 gene in Egyptian patients with chronic myeloid Leukemia. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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17
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Heller G, Nebenfuehr S, Bellutti F, Ünal H, Zojer M, Scheiblecker L, Sexl V, Kollmann K. The Effect of CDK6 Expression on DNA Methylation and DNMT3B Regulation. iScience 2020; 23:101602. [PMID: 33205015 PMCID: PMC7648139 DOI: 10.1016/j.isci.2020.101602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/31/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
CDK6 is frequently overexpressed in various cancer types and functions as a positive regulator of the cell cycle and as a coregulator of gene transcription. We provide evidence that CDK6 is involved in the process of DNA methylation, at least in ALL. We observe a positive correlation of CDK6 and DNMT expression in a large number of ALL samples. ChIP-seq analysis reveals CDK6 binding to genomic regions associated with DNA methyltransferases (DNMTs). ATAC-seq shows a strong reduction in chromatin accessibility for DNMT3B in CDK6-deficient BCR-ABL + Cdk6-/- cells, accompanied by lower levels of DNMT3B mRNA and less chromatin-bound DNMT3B, as shown by RNA-seq and chromatome analysis. Motif analysis suggests that ETS family members interact with CDK6 to regulate DNMT3B. Reduced representation bisulfite sequencing analysis uncovers reversible and cell line-specific changes in DNA methylation patterns upon CDK6 loss. The results reveal a function of CDK6 as a regulator of DNA methylation in transformed cells.
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Affiliation(s)
- Gerwin Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, 1090 Vienna, Austria.,Comprehensive Cancer Center, Vienna, Austria.,Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Sofie Nebenfuehr
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Florian Bellutti
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Huriye Ünal
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Markus Zojer
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Lisa Scheiblecker
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Veronika Sexl
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Karoline Kollmann
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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18
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Komorowski L, Fidyt K, Patkowska E, Firczuk M. Philadelphia Chromosome-Positive Leukemia in the Lymphoid Lineage-Similarities and Differences with the Myeloid Lineage and Specific Vulnerabilities. Int J Mol Sci 2020; 21:E5776. [PMID: 32806528 PMCID: PMC7460962 DOI: 10.3390/ijms21165776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Philadelphia chromosome (Ph) results from a translocation between the breakpoint cluster region (BCR) gene on chromosome 9 and ABL proto-oncogene 1 (ABL1) gene on chromosome 22. The fusion gene, BCR-ABL1, is a constitutively active tyrosine kinase which promotes development of leukemia. Depending on the breakpoint site within the BCR gene, different isoforms of BCR-ABL1 exist, with p210 and p190 being the most prevalent. P210 isoform is the hallmark of chronic myeloid leukemia (CML), while p190 isoform is expressed in majority of Ph-positive B cell acute lymphoblastic leukemia (Ph+ B-ALL) cases. The crucial component of treatment protocols of CML and Ph+ B-ALL patients are tyrosine kinase inhibitors (TKIs), drugs which target both BCR-ABL1 isoforms. While TKIs therapy is successful in great majority of CML patients, Ph+ B-ALL often relapses as a drug-resistant disease. Recently, the high-throughput genomic and proteomic analyses revealed significant differences between CML and Ph+ B-ALL. In this review we summarize recent discoveries related to differential signaling pathways mediated by different BCR-ABL1 isoforms, lineage-specific genetic lesions, and metabolic reprogramming. In particular, we emphasize the features distinguishing Ph+ B-ALL from CML and focus on potential therapeutic approaches exploiting those characteristics, which could improve the treatment of Ph+ B-ALL.
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Affiliation(s)
- Lukasz Komorowski
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Elżbieta Patkowska
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiry Gandhi 14, 02-776 Warsaw, Poland;
| | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
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19
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Ismail MA, Samara M, Al Sayab A, Alsharshani M, Yassin MA, Varadharaj G, Vezzalini M, Tomasello L, Monne M, Morsi H, Qoronfleh MW, Zayed H, Cook R, Sorio C, Modjtahedi H, Al-Dewik NI. Aberrant DNA methylation of PTPRG as one possible mechanism of its under-expression in CML patients in the State of Qatar. Mol Genet Genomic Med 2020; 8:e1319. [PMID: 32700424 PMCID: PMC7549574 DOI: 10.1002/mgg3.1319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Background Several studies showed that aberrant DNA methylation is involved in leukemia and cancer pathogenesis. Protein tyrosine phosphatase receptor gamma (PTPRG) expression is a natural inhibitory mechanism that is downregulated in chronic myeloid leukemia (CML) disease. The mechanism behind its downregulation has not been fully elucidated yet. Aim This study aimed to investigate the CpG methylation status at the PTPRG locus in CML patients. Methods Peripheral blood samples from CML patients at time of diagnosis [no tyrosine kinase inhibitors (TKIs)] (n = 13), failure to (TKIs) treatment (n = 13) and healthy controls (n = 6) were collected. DNA was extracted and treated with bisulfite treatment, followed by PCR, sequencing of 25 CpG sites in the promoter region and 26 CpG sites in intron‐1 region of PTPRG. The bisulfite sequencing technique was employed as a high‐resolution method. Results CML groups (new diagnosed and failed treatment) showed significantly higher methylation levels in the promoter and intron‐1 regions of PTPRG compared to the healthy group. There were also significant differences in methylation levels of CpG sites in the promoter and intron‐1 regions amongst the groups. Conclusion Aberrant methylation of PTPRG is potentially one of the possible mechanisms of PTPRG downregulation detected in CML.
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Affiliation(s)
- Mohamed A Ismail
- School of Life Science, Pharmacy and Chemistry, Faculty of Science, Engineering & ComputingFaculty of Science, Engineering & Computing, Kingston University London, Kingston-Upon-Thames, UK.,Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Muthanna Samara
- Department of Psychology, Kingston University London, Kingston upon Thames, London, UK
| | - Ali Al Sayab
- Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Mohamed Alsharshani
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine and Pathology (DLMP), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Mohamed A Yassin
- Department of Medical Oncology, National Centre for Cancer Care and Research, Hamad Medical Corporation (HMC), Doha, Qatar
| | | | - Marzia Vezzalini
- General Pathology Division, Department of Medicine, University of Verona, Verona, Italy
| | - Luisa Tomasello
- Wexner Medical Center, Biomedical Research Tower, The Ohio State University, Columbus, OH, USA
| | - Maria Monne
- Centro di Diagnostica Biomolecolare e Citogenetica Emato-Oncologica, San Francesco" Hospital, Nuoro, Italy
| | - Hisham Morsi
- Quality of Life unit, National Center for Cancer Care and Research, (NCCCR), Hamad Medical Corporation (HMC), Doha, Qatar
| | - M Walid Qoronfleh
- World Innovation Summit for Healthcare (WISH), Qatar Foundation, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, Biomedical Research Center, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Richard Cook
- School of Life Science, Pharmacy and Chemistry, Faculty of Science, Engineering & ComputingFaculty of Science, Engineering & Computing, Kingston University London, Kingston-Upon-Thames, UK
| | - Claudio Sorio
- General Pathology Division, Department of Medicine, University of Verona, Verona, Italy
| | - Helmout Modjtahedi
- School of Life Science, Pharmacy and Chemistry, Faculty of Science, Engineering & ComputingFaculty of Science, Engineering & Computing, Kingston University London, Kingston-Upon-Thames, UK
| | - Nader I Al-Dewik
- School of Life Science, Pharmacy and Chemistry, Faculty of Science, Engineering & ComputingFaculty of Science, Engineering & Computing, Kingston University London, Kingston-Upon-Thames, UK.,Qatar Medical Genetic Center (QMGC), Hamad General Hospital (HGH), and Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar.,College of Health and Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar.,Department of Pediatrics, Women's Wellness and Research Center (WWRC), HMC, Doha, Qatar
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20
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Lee D, Lee S, Kim S. PRISM: methylation pattern-based, reference-free inference of subclonal makeup. Bioinformatics 2020; 35:i520-i529. [PMID: 31510697 PMCID: PMC6612819 DOI: 10.1093/bioinformatics/btz327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation Characterizing cancer subclones is crucial for the ultimate conquest of cancer. Thus, a number of bioinformatic tools have been developed to infer heterogeneous tumor populations based on genomic signatures such as mutations and copy number variations. Despite accumulating evidence for the significance of global DNA methylation reprogramming in certain cancer types including myeloid malignancies, none of the bioinformatic tools are designed to exploit subclonally reprogrammed methylation patterns to reveal constituent populations of a tumor. In accordance with the notion of global methylation reprogramming, our preliminary observations on acute myeloid leukemia (AML) samples implied the existence of subclonally occurring focal methylation aberrance throughout the genome. Results We present PRISM, a tool for inferring the composition of epigenetically distinct subclones of a tumor solely from methylation patterns obtained by reduced representation bisulfite sequencing. PRISM adopts DNA methyltransferase 1-like hidden Markov model-based in silico proofreading for the correction of erroneous methylation patterns. With error-corrected methylation patterns, PRISM focuses on a short individual genomic region harboring dichotomous patterns that can be split into fully methylated and unmethylated patterns. Frequencies of such two patterns form a sufficient statistic for subclonal abundance. A set of statistics collected from each genomic region is modeled with a beta-binomial mixture. Fitting the mixture with expectation-maximization algorithm finally provides inferred composition of subclones. Applying PRISM for two AML samples, we demonstrate that PRISM could infer the evolutionary history of malignant samples from an epigenetic point of view. Availability and implementation PRISM is freely available on GitHub (https://github.com/dohlee/prism). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dohoon Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Sangseon Lee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Department of Computer Science and Engineering, Seoul National University, Seoul, Korea.,Bioinformatics Institute, Seoul National University, Seoul, Korea
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21
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Mechanisms of Disease Progression and Resistance to Tyrosine Kinase Inhibitor Therapy in Chronic Myeloid Leukemia: An Update. Int J Mol Sci 2019; 20:ijms20246141. [PMID: 31817512 PMCID: PMC6940932 DOI: 10.3390/ijms20246141] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by the presence of the BCR-ABL1 fusion gene, which encodes a constitutive active tyrosine kinase considered to be the pathogenic driver capable of initiating and maintaining the disease. Despite the remarkable efficacy of tyrosine kinase inhibitors (TKIs) targeting BCR-ABL1, some patients may not respond (primary resistance) or may relapse after an initial response (secondary resistance). In a small proportion of cases, development of resistance is accompanied or shortly followed by progression from chronic to blastic phase (BP), characterized by a dismal prognosis. Evolution from CP into BP is a multifactorial and probably multistep phenomenon. Increase in BCR-ABL1 transcript levels is thought to promote the onset of secondary chromosomal or genetic defects, induce differentiation arrest, perturb RNA transcription, editing and translation that together with epigenetic and metabolic changes may ultimately lead to the expansion of highly proliferating, differentiation-arrested malignant cells. A multitude of studies over the past two decades have investigated the mechanisms underlying the closely intertwined phenomena of drug resistance and disease progression. Here, we provide an update on what is currently known on the mechanisms underlying progression and present the latest acquisitions on BCR-ABL1-independent resistance and leukemia stem cell persistence.
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22
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Bugler J, Kinstrie R, Scott MT, Vetrie D. Epigenetic Reprogramming and Emerging Epigenetic Therapies in CML. Front Cell Dev Biol 2019; 7:136. [PMID: 31380371 PMCID: PMC6652210 DOI: 10.3389/fcell.2019.00136] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disorder characterized by BCR-ABL1, an oncogenic fusion gene arising from the Philadelphia chromosome. The development of tyrosine kinase inhibitors (TKIs) to overcome the constitutive tyrosine kinase activity of the BCR-ABL protein has dramatically improved disease management and patient outcomes over the past 20 years. However, the majority of patients are not cured and developing novel therapeutic strategies that target epigenetic processes are a promising avenue to improve cure rates. A number of epigenetic mechanisms are altered or reprogrammed during the development and progression of CML, resulting in alterations in histone modifications, DNA methylation and dysregulation of the transcriptional machinery. In this review these epigenetic alterations are examined and the potential of epigenetic therapies are discussed as a means of eradicating residual disease and offering a potential cure for CML in combination with current therapies.
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Affiliation(s)
| | | | | | - David Vetrie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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Zhang TJ, Wen XM, Zhou JD, Gu Y, Xu ZJ, Guo H, Ma JC, Yuan Q, Chen Q, Lin J, Qian J. SOX30 methylation correlates with disease progression in patients with chronic myeloid leukemia. Onco Targets Ther 2019; 12:4789-4794. [PMID: 31417278 PMCID: PMC6592060 DOI: 10.2147/ott.s210168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/28/2019] [Indexed: 11/23/2022] Open
Abstract
Background Our previous study has reported that aberrant SOX30 methylation was associated with poor prognosis in AML, and it correlated with disease progression in MDS. Herein, we further determined SOX30 methylation and its clinical significance in the other myeloid malignance - chronic myeloid leukemia (CML). Methods SOX30 methylation was examined by real-time quantitative methylation-specific PCR and bisulfite sequencing PCR, whereas SOX30 expression was detected by real-time quantitative PCR. Results SOX30 methylation was identified in 11% (10/95) CML patients. SOX30 methylation was associated with lower hemoglobin and platelets (P=0.006 and 0.032, respectively). Importantly, significant differences were observed in the distributions of clinical stages and cytogenetics (P=0.006 and 0.002, respectively). The frequency of SOX30 methylation in chronic phase (CP) stage occurred with lowest frequency (4/74, 5%), higher in accelerated phase (AP) stage (1/7, 14%), and the highest in blast crisis (BC) stage (12/31, 39%). In addition, SOX30 methylated patients tended to have a higher level of BCR-ABL transcript than SOX30 non-methylated patients (P=0.063). In two paired CML patients, SOX30 methylation showed lower density in CP stage (19% and 17%, respectively), and was significantly increased in BC stage (89% and 69%, respectively) during disease progression. Additionally, SOX30 methylated CML patients presented a lower SOX30 transcript level than SOX30 non-methylated CML patients (P=0.046). Conclusion Our study revealed that SOX30 methylation correlated with disease progression in chronic myeloid leukemia.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Hong Guo
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Qian Yuan
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China
| | - Qin Chen
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology , Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City , Zhenjiang, Jiangsu, People's Republic of China
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Abstract
PURPOSE OF REVIEW In this review, we emphasize up-to-date practical cytogenetic and molecular aspects of chronic myeloid leukemia (CML) and summarize current knowledge on tyrosine kinase inhibitor (TKI) resistance and treatment response monitoring of CML. RECENT FINDINGS The introduction of TKIs has changed the natural course of CML and markedly improved patient survival. Over the past decades, many research efforts were devoted to elucidating the leukemogenic mechanisms of BCR-ABL1 and developing novel TKIs. More recent studies have attempted to answer new questions that have emerged in the TKI era, such as the cytogenetic and molecular bases of treatment failure and disease progression, the clinical impact of genetic aberrations in Philadelphia chromosome (Ph)-positive and Ph-negative cells, and the biological significance of Ph secondarily acquired during therapy of other hematological neoplasms. Recent progresses in the understanding of the cytogenetic and molecular mechanisms underlying therapeutic failure and disease progression have improved the risk stratification of CML and will be helpful in the design of novel therapeutic strategies.
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Affiliation(s)
- Ting Zhou
- Department of Pathology & Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0072, Houston, TX, 77030, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0072, Houston, TX, 77030, USA.
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25
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Nteliopoulos G, Bazeos A, Claudiani S, Gerrard G, Curry E, Szydlo R, Alikian M, Foong HE, Nikolakopoulou Z, Loaiza S, Khorashad JS, Milojkovic D, Perrotti D, Gale RP, Foroni L, Apperley JF. Somatic variants in epigenetic modifiers can predict failure of response to imatinib but not to second-generation tyrosine kinase inhibitors. Haematologica 2019; 104:2400-2409. [PMID: 31073075 PMCID: PMC6959189 DOI: 10.3324/haematol.2018.200220] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 05/06/2019] [Indexed: 11/09/2022] Open
Abstract
There are no validated molecular biomarkers to identify newly-diagnosed individuals with chronic-phase chronic myeloid leukemia likely to respond poorly to imatinib and who might benefit from first-line treatment with a more potent second-generation tyrosine kinase inhibitor. Our inability to predict these ‘high-risk’ individuals reflects the poorly understood heterogeneity of the disease. To investigate the potential of genetic variants in epigenetic modifiers as biomarkers at diagnosis, we used Ion Torrent next-generation sequencing of 71 candidate genes for predicting response to tyrosine kinase inhibitors and probability of disease progression. A total of 124 subjects with newly-diagnosed chronic-phase chronic myeloid leukemia began with imatinib (n=62) or second-generation tyrosine kinase inhibitors (n=62) and were classified as responders or non-responders based on the BCRABL1 transcript levels within the first year and the European LeukemiaNet criteria for failure. Somatic variants affecting 21 genes (e.g. ASXL1, IKZF1, DNMT3A, CREBBP) were detected in 30% of subjects, most of whom were non-responders (41% non-responders, 18% responders to imatinib, 38% non-responders, 25% responders to second-generation tyrosine kinase inhibitors). The presence of variants predicted the rate of achieving a major molecular response, event-free survival, progression-free survival and chronic myeloid leukemia-related survival in the imatinib but not the second-generation tyrosine kinase inhibitors cohort. Rare germline variants had no prognostic significance irrespective of treatment while some pre-leukemia variants suggest a multi-step development of chronic myeloid leukemia. Our data suggest that identification of somatic variants at diagnosis facilitates stratification into imatinib responders/non-responders, thereby allowing earlier use of second-generation tyrosine kinase inhibitors, which, in turn, may overcome the negative impact of such variants on disease progression.
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Affiliation(s)
| | - Alexandra Bazeos
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Simone Claudiani
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Gareth Gerrard
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
| | - Edward Curry
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College, London, UK
| | - Richard Szydlo
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Mary Alikian
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Hui En Foong
- Imperial College Healthcare NHS Trust, London, UK
| | - Zacharoula Nikolakopoulou
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Sandra Loaiza
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Jamshid S Khorashad
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Dragana Milojkovic
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Danilo Perrotti
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore MD, USA
| | - Robert Peter Gale
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
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26
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Vatanmakanian M, Tavallaie M, Ghadami S. Imatinib independent aberrant methylation of NOV/CCN3 in chronic myelogenous leukemia patients: a mechanism upstream of BCR-ABL1 function? Cell Commun Signal 2019; 17:38. [PMID: 31014357 PMCID: PMC6480731 DOI: 10.1186/s12964-019-0350-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Background The NOV gene product, CCN3, has been reported in a diverse range of tumors to serve as a negative growth regulator, while acting as a tumor suppressor in Chronic Myelogenous Leukemia (CML). However, the precise mechanism of its silencing in CML is poorly understood. In the current study, we aimed to query if the gene regulation of CCN3 is mediated by the promoter methylation in the patients with CML. In addition, to clarify whether the epigenetic silencing is affected by BCR-ABL1 inhibition, we assessed the methylation status in the patients at different time intervals following the tyrosine kinase inhibition using imatinib therapy, as the first-line treatment for this type of leukemia. Methods To address this issue, we applied bisulfite-sequencing technique as a high-resolution method to study the regulatory segment of the CCN3 gene. The results were analyzed in newly diagnosed CML patients as well as following imatinib therapy. We also evaluated the correlation of CCN3 promoter methylation with BCR-ABL1 levels. Results Our findings revealed that the methylation occurs frequently in the promoter region of CML patients showing a significant increase of the methylated percentage at the CpG sites compared to normal individuals. Interestingly, this hypermethylation was indicated to be independent of BCR-ABL1 titers in both groups, which might suggest a mechanism beyond the BCR-ABL1 function. Conclusion Despite suggesting that the CCN3 hypermethylation acts as a molecular mechanism independent of BCR-ABL1 function in CML patients, this scenario requires further validation by complementary experiments. In the case of acting upstream of BCR-ABL1 signaling, the methylation marker can provide early detection and a novel platform for targeted epigenetic modifiers for efficient treatment in imatinib resistant patients.
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Affiliation(s)
- Mousa Vatanmakanian
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Mahmood Tavallaie
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Shirin Ghadami
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran.
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27
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Chen X, Huang J, Zhang S, Mo F, Su S, Li Y, Fang L, Deng J, Huang H, Luo Z, Zheng J. Electrochemical Biosensor for DNA Methylation Detection through Hybridization Chain-Amplified Reaction Coupled with a Tetrahedral DNA Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2019; 11:3745-3752. [PMID: 30624036 DOI: 10.1021/acsami.8b20144] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is a key factor in the pathogenesis of gene expression diseases or malignancies. Thus, it has become a significant biomarker for the diagnosis and prognosis of these diseases. In this paper, we designed an ultrasensitive and specific electrochemical biosensor for DNA methylation detection. The platform consisted of stem-loop-tetrahedron composite DNA probes anchoring at a Au nanoparticle-coated gold electrode, a restriction enzyme digestion of HpaII, and signal amplification procedures including electrodeposition of Au nanoparticles, hybridization chain reaction, and horseradish peroxidase enzymatic catalysis. Under optimal conditions, the design showed a broad dynamic range from 1 aM to 1 pM and a detection limit of about 0.93 aM. The approach also showed ideal specificity, repeatability, and stability. The recovery test demonstrated that the design is a promising platform for DNA methylation detection under clinical circumstances and could meet the need for cancer diagnosis.
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Affiliation(s)
- Xi Chen
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | | | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
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28
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Karabulutoglu M, Finnon R, Imaoka T, Friedl AA, Badie C. Influence of diet and metabolism on hematopoietic stem cells and leukemia development following ionizing radiation exposure. Int J Radiat Biol 2018; 95:452-479. [PMID: 29932783 DOI: 10.1080/09553002.2018.1490042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE The review aims to discuss the prominence of dietary and metabolic regulators in maintaining hematopoietic stem cell (HSC) function, long-term self-renewal, and differentiation. RESULTS Most adult stem cells are preserved in a quiescent, nonmotile state in vivo which acts as a "protective state" for stem cells to reduce endogenous stress provoked by DNA replication and cellular respiration as well as exogenous environmental stress. The dynamic balance between quiescence, self-renewal and differentiation is critical for supporting a functional blood system throughout life of an organism. Stress-conditions, for example ionizing radiation exposure can trigger the blood forming HSCs to proliferate and migrate through extramedullary tissues to expand the number of HSCs and increase hematopoiesis. In addition, a wealth of investigation validated that deregulation of this balance plays a critical pathogenic role in various different hematopoietic diseases including the leukemia development. CONCLUSION The review summarizes the current knowledge on how alterations in dietary and metabolic factors could alter the risk of leukemia development following ionizing radiation exposure by inhibiting or even reversing the leukemic progression. Understanding the influence of diet, metabolism, and epigenetics on radiation-induced leukemogenesis may lead to the development of practical interventions to reduce the risk in exposed populations.
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Affiliation(s)
- Melis Karabulutoglu
- a Cancer Mechanisms and Biomarkers group, Biological Effects Department, Centre for Radiation, Chemical and Environmental Hazards , Public Health England , Didcot , UK.,b CRUK & MRC Oxford Institute for Radiation Oncology, Department of Oncology , University of Oxford , Oxford , UK
| | - Rosemary Finnon
- a Cancer Mechanisms and Biomarkers group, Biological Effects Department, Centre for Radiation, Chemical and Environmental Hazards , Public Health England , Didcot , UK
| | - Tatsuhiko Imaoka
- c Department of Radiation Effects Research, National Institute of Radiological Sciences , National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Anna A Friedl
- d Department of Radiation Oncology , University Hospital, LMU Munich , Munich , Germany
| | - Christophe Badie
- a Cancer Mechanisms and Biomarkers group, Biological Effects Department, Centre for Radiation, Chemical and Environmental Hazards , Public Health England , Didcot , UK
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29
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Elias MH, Azlan H, Sulong S, Baba AA, Ankathil R. Aberrant DNA methylation at HOXA4 and HOXA5 genes are associated with resistance to imatinib mesylate among chronic myeloid leukemia patients. Cancer Rep (Hoboken) 2018; 1:e1111. [PMID: 32721103 DOI: 10.1002/cnr2.1111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Imatinib mesylate is a molecularly targeted tyrosine kinase inhibitor drug. It is effectively used in the treatment of chronic myeloid leukemia (CML) patients. However, development of resistance to imatinib mesylate as a result of BCR-ABL dependent and BCR-ABL independent mechanisms has emerged as a daunting problem in the management of CML patients. Between these mechanisms, BCR-ABL independent mechanisms are still not robustly understood. AIM To investigate the correlation of HOXA4 and HOXA5 promoter DNA hypermethylation with imatinib resistance among CML patients. METHODS AND RESULTS Samples from 175 Philadelphia positive CML patients (83 good response and 92 BCR-ABL non-mutated imatinib resistant patients) were subjected to Methylation Specific High Resolution Melt Analysis for methylation levels quantification of the HOXA4 and HOXA5 promoter regions. Receiver operating characteristic curve analysis was done to elucidate the optimal methylation cut-off point followed by multiple logistic regression analysis. Log-Rank analysis was done to measure the overall survival difference between CML groups. The optimal methylation cut-off point was found to be at 62.5% for both HOXA4 and HOXA5. Chronic myeloid leukemia patients with ≥63% HOXA4 and HOXA5 methylation level were shown to have 3.78 and 3.95 times the odds, respectively, to acquire resistance to imatinib. However, overall survival of CML patients that have ≤62% and ≥ 63% methylation levels of HOXA4 and HOXA5 genes were found to be not significant (P-value = 0.126 for HOXA4; P-value = 0.217 for HOXA5). CONCLUSION Hypermethylation of the HOXA4 and HOXA5 promoter is correlated with imatinib resistance and with further investigation, it could be a potential epigenetic biomarker in supplement to the BCR-ABL gene mutation in predicting imatinib treatment response among CML patients but could not be considered as a prognostic marker.
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Affiliation(s)
- Marjanu Hikmah Elias
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Husin Azlan
- Haemato-Oncology Unit, Department of Internal Medicine, Universiti Sains Malaysia Hospital, Kota Bharu, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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30
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Singh N, Tripathi AK, Sahu DK, Mishra A, Linan M, Argente B, Varkey J, Parida N, Chowdhry R, Shyam H, Alam N, Dixit S, Shankar P, Mishra A, Agarwal A, Yoo C, Bhatt MLB, Kant R. Differential genomics and transcriptomics between tyrosine kinase inhibitor-sensitive and -resistant BCR-ABL-dependent chronic myeloid leukemia. Oncotarget 2018; 9:30385-30418. [PMID: 30100996 PMCID: PMC6084383 DOI: 10.18632/oncotarget.25752] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/28/2018] [Indexed: 01/11/2023] Open
Abstract
Previously, it has been stated that the BCR-ABL fusion-protein is sufficient to induce Chronic Myeloid Leukemia (CML), but additional genomic-changes are required for disease progression. Hence, we profiled control and tyrosine kinase inhibitors (TKI) alone or in combination with other drug-treated CML-samples in different phases, categorized as drug-sensitive and drug-resistant on the basis of BCR-ABL transcripts, the marker of major molecular-response. Molecular-profiling was done using the molecular-inversion probe-based-array, Human Transcriptomics-Array2.0, and Axiom-Biobank genotyping-arrays. At the transcript-level, clusters of control, TKI-resistant and TKI-sensitive cases were correlated with BCR-ABL transcript-levels. Both at the gene- and exon-levels, up-regulation of MPO, TPX2, and TYMS and down-regulation of STAT6, FOS, TGFBR2, and ITK lead up-regulation of the cell-cycle, DNA-replication, DNA-repair pathways and down-regulation of the immune-system, chemokine- and interleukin-signaling, TCR, TGF beta and MAPK signaling pathways. A comparison between TKI-sensitive and TKI-resistant cases revealed up-regulation of LAPTM4B, HLTF, PIEZO2, CFH, CD109, ANGPT1 in CML-resistant cases, leading to up-regulation of autophagy-, protein-ubiquitination-, stem-cell-, complement-, TGFβ- and homeostasis-pathways with specific involvement of the Tie2 and Basigin signaling-pathway. Dysregulated pathways were accompanied with low CNVs in CP-new and CP-UT-TKI-sensitive-cases with undetectable BCR-ABL-copies. High CNVs (previously reported gain of 9q34) were observed in BCR-ABL-independent and -dependent TKI, non-sensitive-CP-UT/AP-UT/B-UT and B-new samples. Further, genotyping CML-CP-UT cases with BCR-ABL 0-to-77.02%-copies, the identified, rsID239798 and rsID9475077, were associated with FAM83B, a candidate for therapeutic resistance. The presence of BCR-ABL, additional genetic-events, dysregulated-signaling-pathways and rsIDs associated with FAM83B in TKI-resistant-cases can be used to develop a signature-profile that may help in monitoring therapy.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar Tripathi
- Department of Clinical Hematology, King George's Medical University, Lucknow, India
| | - Dinesh Kumar Sahu
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Archana Mishra
- Department of Cardio Thoracic and Vascular Surgery, King George's Medical University, Lucknow, India
| | | | | | | | - Niranjan Parida
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontics, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Shivani Dixit
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Avinash Agarwal
- Department of Medicine, King George's Medical University, Lucknow, India
| | - Chris Yoo
- Systems Imagination, Scottsdale, Arizona, USA
| | | | - Ravi Kant
- All India Institute of Medical Sciences, Rishikesh, India
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31
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Vicente-Dueñas C, González-Herrero I, Sehgal L, García-Ramírez I, Rodríguez-Hernández G, Pintado B, Blanco O, Criado FJG, Cenador MBG, Green MR, Sánchez-García I. Dnmt1 links BCR-ABLp210 to epigenetic tumor stem cell priming in myeloid leukemia. Leukemia 2018; 33:249-278. [PMID: 29955131 PMCID: PMC6326950 DOI: 10.1038/s41375-018-0192-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/20/2018] [Accepted: 05/30/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Inés González-Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Lalit Sehgal
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Idoia García-Ramírez
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Guillermo Rodríguez-Hernández
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Belén Pintado
- Transgenesis Facility CNB-CBMSO, CSIC-UAM, Madrid, Spain
| | - Oscar Blanco
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Javier García Criado
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - María Begoña García Cenador
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - Michael R Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Isidro Sánchez-García
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. .,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain.
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32
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Li Z, Luo J. Research on epigenetic mechanism of SFRP2 in advanced chronic myeloid leukemia. Biochem Biophys Res Commun 2018; 501:64-72. [DOI: 10.1016/j.bbrc.2018.04.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
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33
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Maupetit-Mehouas S, Court F, Bourgne C, Guerci-Bresler A, Cony-Makhoul P, Johnson H, Etienne G, Rousselot P, Guyotat D, Janel A, Hermet E, Saugues S, Berger J, Arnaud P, Berger MG. DNA methylation profiling reveals a pathological signature that contributes to transcriptional defects of CD34 + CD15 - cells in early chronic-phase chronic myeloid leukemia. Mol Oncol 2018; 12:814-829. [PMID: 29575763 PMCID: PMC5983208 DOI: 10.1002/1878-0261.12191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022] Open
Abstract
Despite the high efficiency of tyrosine kinase inhibitors (TKI), some patients with chronic myeloid leukemia (CML) will display residual disease that can become resistant to treatment, indicating intraclonal heterogeneity in chronic‐phase CML (CP‐CML). To determine the basis of this heterogeneity, we conducted the first exhaustive characterization of the DNA methylation pattern of sorted CP‐CML CD34+CD15− (immature) and CD34−CD15+ (mature) cells at diagnosis (prior to any treatment) and compared it to that of CD34+CD15− and CD34−CD15+ cells isolated from healthy donors (HD). In both cell types, we identified several hundreds of differentially methylated regions (DMRs) showing DNA methylation changes between CP‐CML and HD samples, with only a subset of them in common between CD34+CD15− and CD34−CD15+ cells. This suggested DNA methylation variability within the same CML clone. We also identified 70 genes that could be aberrantly repressed upon hypermethylation and 171 genes that could be aberrantly expressed upon hypomethylation of some of these DMRs in CP‐CML cells, among which 18 and 81, respectively, were in CP‐CML CD34+CD15− cells only. We then validated the DNA methylation and expression defects of selected candidate genes. Specifically, we identified GAS2, a candidate oncogene, as a new example of gene the hypomethylation of which is associated with robust overexpression in CP‐CML cells. Altogether, we demonstrated that DNA methylation abnormalities exist at early stages of CML and can affect the transcriptional landscape of malignant cells. These observations could lead to the development of combination treatments with epigenetic drugs and TKI for CP‐CML.
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Affiliation(s)
- Stéphanie Maupetit-Mehouas
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France.,Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Franck Court
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France
| | - Céline Bourgne
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Agnès Guerci-Bresler
- Hématologie Clinique, CHRU Nancy, Hôpitaux de Brabois, Vandoeuvre-lès-Nancy, France
| | | | - Hyacinthe Johnson
- Institut d'Hématologie de Basse Normandie, CHU de Caen, Caen Cedex 9, France
| | - Gabriel Etienne
- Hématologie Clinique, Institut Bergonié, Bordeaux Cedex, France
| | - Philippe Rousselot
- Centre Hospitalier de Versailles, service d'Hématologie et d'Oncologie, Le Chesney, France
| | - Denis Guyotat
- Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Alexandre Janel
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Eric Hermet
- Hématologie Clinique Adulte, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Sandrine Saugues
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Juliette Berger
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Philippe Arnaud
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France
| | - Marc G Berger
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
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34
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Cheng L, Tang Y, Chen X, Zhao L, Liu S, Ma Y, Wang N, Zhou K, Zhou J, Zhou M. Deletion of MBD2 inhibits proliferation of chronic myeloid leukaemia blast phase cells. Cancer Biol Ther 2018; 19:676-686. [PMID: 29565710 DOI: 10.1080/15384047.2018.1450113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aberrant methylation of tumour suppressor genes is associated with the progression to a blast crisis in chronic myeloid leukaemia (CML). Methyl-CpG-binding domain protein 2 (MBD2) has been studied as a "reader" of DNA methylation in many cancers, but its role in CML is unclear. We constructed cell models of a homozygous deletion mutation of MBD2 using gene-editing technology in K562 cells and BV173 cells. Here, we demonstrated that the deletion of MBD2 inhibited cell proliferation capacity in vitro. MBD2 deletion also significantly inhibited K562 cell proliferation in a xenograft tumour model in vivo. Additionally, the JAK2/STAT3 signalling pathway, which is abnormally active in CML, was inhibited by MBD2 deletion, and MBD2 deletion could up-regulate the expression of SHP1. In conclusion, our findings suggest that MBD2 is a candidate therapeutic strategy for the CML blast phase.
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Affiliation(s)
- Ling Cheng
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Ying Tang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Xing Chen
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Lei Zhao
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Songya Liu
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Yanna Ma
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Na Wang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Kuangguo Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Jianfeng Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Mi Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
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35
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Behzad MM, Shahrabi S, Jaseb K, Bertacchini J, Ketabchi N, Saki N. Aberrant DNA Methylation in Chronic Myeloid Leukemia: Cell Fate Control, Prognosis, and Therapeutic Response. Biochem Genet 2018; 56:149-175. [DOI: 10.1007/s10528-018-9841-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/18/2018] [Indexed: 01/24/2023]
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36
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Ruggiu M, Oberkampf F, Ghez D, Cony-Makhoul P, Beckeriche F, Cano I, Taksin AL, Benbrahim O, Ghez S, Farhat H, Rigaudeau S, de Gunzburg N, Lara D, Terre C, Raggueneau V, Garcia I, Spentchian M, De Botton S, Rousselot P. Azacytidine in combination with tyrosine kinase inhibitors induced durable responses in patients with advanced phase chronic myelogenous leukemia. Leuk Lymphoma 2017; 59:1659-1665. [PMID: 29179634 DOI: 10.1080/10428194.2017.1397666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Although the tyrosine kinase inhibitor (TKI) era has brought great improvement in outcome in chronic myelogenous leukemia (CML), prognosis of accelerated phase or myeloid blast crisis patients or of de novo Philadelphia chromosome-positive acute myeloid leukemia remains poor. We conducted a retrospective study on patients with advanced phase disease treated with a TKI and azacytidine. Sixteen patients were eligible. Median age was 64.9 years, the median number of previous therapies was 2.5 lines, and median follow-up was 23.1 months. Hematologic response (HR) rate was 81.3%. Median overall survival (OS), event free survival and relapse-free survival (RFS) were 31.5, 23.3, and 32.2 months, respectively. All except one patient were treated as out-patients after the first cycle. Five patients were bridged to allogenic hematopoietic stem cells transplant. The combination of a TKI and azacytidine is a safe and efficient regiment for patients with CML patients in advanced phases.
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Affiliation(s)
- Mathilde Ruggiu
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Florence Oberkampf
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - David Ghez
- b Hematology Department , Institut Gustave Roussy , Villejuif , France
| | | | | | - Isabelle Cano
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Anne L Taksin
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Omar Benbrahim
- e Hematology Department , Hôpital La Source , Orléans , France
| | - Stéphanie Ghez
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Hassan Farhat
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Sophie Rigaudeau
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Noémie de Gunzburg
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Diane Lara
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France
| | - Christine Terre
- f Hematology Laboratory , Centre Hospitalier de Versailles , Versailles , France
| | - Victoria Raggueneau
- f Hematology Laboratory , Centre Hospitalier de Versailles , Versailles , France
| | - Isabel Garcia
- f Hematology Laboratory , Centre Hospitalier de Versailles , Versailles , France
| | - Marc Spentchian
- f Hematology Laboratory , Centre Hospitalier de Versailles , Versailles , France
| | | | - Philippe Rousselot
- a Hematology Department , Centre Hospitalier de Versailles , Versailles , France.,g UMR1173, Université Versailles Saint-Quentin-en-Yvelines , Paris , France
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37
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Rahmani M, Talebi M, Hagh MF, Feizi AAH, Solali S. Aberrant DNA methylation of key genes and Acute Lymphoblastic Leukemia. Biomed Pharmacother 2017; 97:1493-1500. [PMID: 29793312 DOI: 10.1016/j.biopha.2017.11.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a dynamic process influencing gene expression by altering either coding or non-coding loci. Despite advances in treatment of Acute Lymphoblastic Leukemia (ALL); relapse occurs in approximately 20% of patients. Nowadays, epigenetic factors are considered as one of the most effective mechanisms in pathogenesis of malignancies. These factors are reversible elements which can be potentially regarded as therapy targets and disease prognosis. DNA methylation, which primarily serves as transcriptional suppressor, mostly occurs in CpG islands of the gene promoter regions. This was shown as a key epigenetic factor in inactivating various tumor suppressor genes during cancer initiation and progression. We aimed to review methylation status of key genes involved in hematopoietic malignancies such as IKZF1, CDKN2B, TET2, CYP1B1, SALL4, DLC1, DLX family, TP73, PTPN6, and CDKN1C; and their significance in pathogenesis of ALL. The DNA methylation alterations in promoter regions of the genes have been shown to play crucial roles in tumorigenesis. Methylation -based inactivation of these genes has also been reported as associated with prognosis in acute leukemia. In this review, we also addressed the association of gene expression and methylation pattern in ALL patients.
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Affiliation(s)
- Mina Rahmani
- Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Stem cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Talebi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Farshdousti Hagh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saeed Solali
- Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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38
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Kaehler M, Ruemenapp J, Gonnermann D, Nagel I, Bruhn O, Haenisch S, Ammerpohl O, Wesch D, Cascorbi I, Bruckmueller H. MicroRNA-212/ABCG2-axis contributes to development of imatinib-resistance in leukemic cells. Oncotarget 2017; 8:92018-92031. [PMID: 29190894 PMCID: PMC5696160 DOI: 10.18632/oncotarget.21272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/08/2017] [Indexed: 12/27/2022] Open
Abstract
BCR-ABL-independent resistance against tyrosine kinase inhibitor is an emerging problem in therapy of chronic myeloid leukemia. Such drug resistance can be linked to dysregulation of ATP-binding cassette (ABC)-transporters leading to increased tyrosine kinase inhibitor efflux, potentially caused by changes in microRNA expression or DNA-methylation. In an in vitro-imatinib-resistance model using K-562 cells, microRNA-212 was found to be dysregulated and inversely correlated to ABC-transporter ABCG2 expression, targeting its 3'-UTR. However, the functional impact on drug sensitivity remained unknown. Therefore, we performed transfection experiments using microRNA-mimics and -inhibitors and investigated their effect on imatinib-susceptibility in sensitive and resistant leukemic cell lines. Under imatinib-treatment, miR-212 inhibition led to enhanced cell viability (p = 0.01), reduced apoptosis (p = 0.01) and cytotoxicity (p = 0.03). These effects were limited to treatment-naïve cells and were not observed in cells, which were resistant to various imatinib-concentrations (0.1 μM to 2 μM). Further analysis in treatment-naïve cells revealed that miR-212 inhibition resulted in ABCG2 upregulation and increased ABCG2-dependent efflux. Furthermore, we observed miR-212 promoter hypermethylation in 0.5 and 2 μM IM-resistant sublines, whereas ABCG2 methylation status was not altered. Taken together, the miR-212/ABCG2-axis influences imatinib-susceptibility contributing to development of imatinib-resistance. Our data reveal new insights into mechanisms initiating imatinib-resistance in leukemic cells.
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Affiliation(s)
- Meike Kaehler
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johanna Ruemenapp
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Daniel Gonnermann
- Institute of Immunology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inga Nagel
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Oliver Bruhn
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sierk Haenisch
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Henrike Bruckmueller
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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39
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Ferrando AA, López-Otín C. Clonal evolution in leukemia. Nat Med 2017; 23:1135-1145. [PMID: 28985206 DOI: 10.1038/nm.4410] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/26/2017] [Indexed: 02/06/2023]
Abstract
Human leukemias are liquid malignancies characterized by diffuse infiltration of the bone marrow by transformed hematopoietic progenitors. The accessibility of tumor cells obtained from peripheral blood or through bone marrow aspirates, together with recent advances in cancer genomics and single-cell molecular analysis, have facilitated the study of clonal populations and their genetic and epigenetic evolution over time with unprecedented detail. The results of these analyses challenge the classic view of leukemia as a clonal homogeneous diffuse tumor and introduce a more complex and dynamic scenario. In this review, we present current concepts on the role of clonal evolution in lymphoid and myeloid leukemia as a driver of tumor initiation, disease progression and relapse. We also discuss the implications of these concepts in our understanding of the evolutionary mechanisms involved in leukemia transformation and therapy resistance.
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Affiliation(s)
- Adolfo A Ferrando
- Department of Pediatrics, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Spain
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40
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Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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41
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Shen N, Jiang L, Li Q, Cui J, Zhou S, Cheng F, Zhong Z, Meng L, You Y, Zhu X, Zou P. The epigenetic effect of microRNA in BCR-ABL1-positive microvesicles during the transformation of normal hematopoietic transplants. Oncol Rep 2017; 38:3278-3284. [DOI: 10.3892/or.2017.5966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/16/2017] [Indexed: 11/06/2022] Open
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42
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Expression differences of genes in the PI3K/AKT, WNT/b-catenin, SHH, NOTCH and MAPK signaling pathways in CD34+ hematopoietic cells obtained from chronic phase patients with chronic myeloid leukemia and from healthy controls. Clin Transl Oncol 2017; 20:542-549. [DOI: 10.1007/s12094-017-1751-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
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43
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Koschmieder S, Vetrie D. Epigenetic dysregulation in chronic myeloid leukaemia: A myriad of mechanisms and therapeutic options. Semin Cancer Biol 2017; 51:180-197. [PMID: 28778403 DOI: 10.1016/j.semcancer.2017.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/13/2017] [Accepted: 07/28/2017] [Indexed: 01/08/2023]
Abstract
The onset of global epigenetic changes in chromatin that drive tumor proliferation and heterogeneity is a hallmark of many forms of cancer. Identifying the epigenetic mechanisms that govern these changes and developing therapeutic approaches to modulate them, is a well-established avenue pursued in translational cancer medicine. Chronic myeloid leukemia (CML) arises clonally when a hematopoietic stem cell (HSC) acquires the capacity to produce the constitutively active tyrosine kinase BCR-ABL1 fusion protein which drives tumor development. Treatment with tyrosine kinase inhibitors (TKI) that target BCR-ABL1 has been transformative in CML management but it does not lead to cure in the vast majority of patients. Thus novel therapeutic approaches are required and these must target changes to biological pathways that are aberrant in CML - including those that occur when epigenetic mechanisms are altered. These changes may be due to alterations in DNA or histones, their biochemical modifications and requisite 'writer' proteins, or to dysregulation of various types of non-coding RNAs that collectively function as modulators of transcriptional control and DNA integrity. Here, we review the evidence for subverted epigenetic mechanisms in CML and how these impact on a diverse set of biological pathways, on disease progression, prognosis and drug resistance. We will also discuss recent progress towards developing epigenetic therapies that show promise to improve CML patient care and may lead to improved cure rates.
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Affiliation(s)
- Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.
| | - David Vetrie
- Epigenetics Unit, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom.
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44
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Krejcova L, Richtera L, Hynek D, Labuda J, Adam V. Current trends in electrochemical sensing and biosensing of DNA methylation. Biosens Bioelectron 2017. [PMID: 28641203 DOI: 10.1016/j.bios.2017.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA methylation plays an important role in physiological and pathological processes. Several genetic diseases and most malignancies tend to be associated with aberrant DNA methylation. Among other analytical methods, electrochemical approaches have been successfully employed for characterisation of DNA methylation patterns that are essential for the diagnosis and treatment of particular diseases. This article discusses current trends in the electrochemical sensing and biosensing of DNA methylation. Particularly, it provides an overview of applied electrode materials, electrode modifications and biorecognition elements applications with an emphasis on strategies that form the core DNA methylation detection approaches. The three main strategies as (i) bisulfite treatment, (ii) cleavage by restriction endonucleases, and (iii) immuno/affinity reaction were described in greater detail. Additionally, the availability of the reviewed platforms for early cancer diagnosis and the approval of methylation inhibitors for anticancer therapy were discussed.
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Affiliation(s)
- Ludmila Krejcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, CZ-166 28 Prague, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - David Hynek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Jan Labuda
- Institute of Analytical Chemistry, Slovak University of Technology in Bratislava, Radlinskeho 9, SK-812 37 Bratislava, Slovakia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic.
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45
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Byun HM, Eshaghian S, Douer D, Trent J, Garcia-Manero G, Bhatia R, Siegmund K, Yang AS. Impact of Chromosomal Rearrangement upon DNA Methylation Patterns in Leukemia. Open Med (Wars) 2017; 12:76-85. [PMID: 28730166 PMCID: PMC5444343 DOI: 10.1515/med-2017-0014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/22/2017] [Indexed: 12/31/2022] Open
Abstract
Genomic instability, including genetic mutations and chromosomal rearrangements, can lead to cancer development. Aberrant DNA methylation occurs commonly in cancer cells. The aim of this study is to determine the effects of a specific chromosomal lesion the BCR-ABL translocation t(9:22), in establishing DNA methylation profiles in cancer. Materials and methods We compared DNA methylation of 1,505 selected promoter CpGs in chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL) with and without the Philadelphia chromosome t(9:22), CD34+ hematopoietic stem cells transfected with BCR-ABL, and other tumors without BCR-ABL (acute promyelocytic leukemia (APL) and gastrointestinal stromal tumors (GIST). In this study, the DNA methylation profile of CML was more closely related to APL, another myeloid leukemia, than Ph+ ALL. Although DNA methylation profiles were consistent within a specific tumor type, overall DNA methylation profiles were no influenced by BCR-ABL gene translocation in the cancers and tissues studied. We conclude that DNA methylation profiles may reflect the cell of origin in cancers rather than the chromosomal lesions involved in leukemogenesis.
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Affiliation(s)
- Hyang-Min Byun
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE4 5PLUnited Kingdom
| | - Shahrooz Eshaghian
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
| | - Dan Douer
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
| | - Jonathen Trent
- Department of Sarcoma, University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ravi Bhatia
- Department of Hematology, City of Hope Cancer Center, Duarte, CA, USA
| | - Kim Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Allen S Yang
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
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