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Shokoohi F, Stephens DA, Greenwood CMT. Identifying Differential Methylation in Cancer Epigenetics via a Bayesian Functional Regression Model. Biomolecules 2024; 14:639. [PMID: 38927043 PMCID: PMC11201607 DOI: 10.3390/biom14060639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
DNA methylation plays an essential role in regulating gene activity, modulating disease risk, and determining treatment response. We can obtain insight into methylation patterns at a single-nucleotide level via next-generation sequencing technologies. However, complex features inherent in the data obtained via these technologies pose challenges beyond the typical big data problems. Identifying differentially methylated cytosines (dmc) or regions is one such challenge. We have developed DMCFB, an efficient dmc identification method based on Bayesian functional regression, to tackle these challenges. Using simulations, we establish that DMCFB outperforms current methods and results in better smoothing and efficient imputation. We analyzed a dataset of patients with acute promyelocytic leukemia and control samples. With DMCFB, we discovered many new dmcs and, more importantly, exhibited enhanced consistency of differential methylation within islands and their adjacent shores. Additionally, we detected differential methylation at more of the binding sites of the fused gene involved in this cancer.
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Affiliation(s)
- Farhad Shokoohi
- Department of Mathematical Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - David A. Stephens
- Department of Mathematics and Statistics, McGill University, Montreal, QC H3A 0B9, Canada;
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada;
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC H3A 1G1, Canada
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2
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The Expanding Role of Cancer Stem Cell Marker ALDH1A3 in Cancer and Beyond. Cancers (Basel) 2023; 15:cancers15020492. [PMID: 36672441 PMCID: PMC9857290 DOI: 10.3390/cancers15020492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Aldehyde dehydrogenase 1A3 (ALDH1A3) is one of 19 ALDH enzymes expressed in humans, and it is critical in the production of hormone receptor ligand retinoic acid (RA). We review the role of ALDH1A3 in normal physiology, its identification as a cancer stem cell marker, and its modes of action in cancer and other diseases. ALDH1A3 is often over-expressed in cancer and promotes tumor growth, metastasis, and chemoresistance by altering gene expression, cell signaling pathways, and glycometabolism. The increased levels of ALDH1A3 in cancer occur due to genetic amplification, epigenetic modifications, post-transcriptional regulation, and post-translational modification. Finally, we review the potential of targeting ALDH1A3, with both general ALDH inhibitors and small molecules specifically designed to inhibit ALDH1A3 activity.
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3
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Zhang J, Gao X, Yu L. Roles of Histone Deacetylases in Acute Myeloid Leukemia With Fusion Proteins. Front Oncol 2021; 11:741746. [PMID: 34540702 PMCID: PMC8440836 DOI: 10.3389/fonc.2021.741746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Accurate orchestration of gene expression is critical for the process of normal hematopoiesis, and dysregulation is closely associated with leukemogenesis. Epigenetic aberration is one of the major causes contributing to acute myeloid leukemia (AML), where chromosomal rearrangements are frequently found. Increasing evidences have shown the pivotal roles of histone deacetylases (HDACs) in chromatin remodeling, which are involved in stemness maintenance, cell fate determination, proliferation and differentiation, via mastering the transcriptional switch of key genes. In abnormal, these functions can be bloomed to elicit carcinogenesis. Presently, HDAC family members are appealing targets for drug exploration, many of which have been deployed to the AML treatment. As the majority of AML events are associated with chromosomal translocation resulting in oncogenic fusion proteins, it is valuable to comprehensively understand the mutual interactions between HDACs and oncogenic proteins. Therefore, we reviewed the process of leukemogenesis and roles of HDAC members acting in this progress, providing an insight for the target anchoring, investigation of hyperacetylated-agents, and how the current knowledge could be applied in AML treatment.
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Affiliation(s)
- Juan Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Xuefeng Gao
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
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4
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Alzahrani AM, Shait Mohammed MR, Alghamdi RA, Ahmad A, Zamzami MA, Choudhry H, Khan MI. Urolithin A and B Alter Cellular Metabolism and Induce Metabolites Associated with Apoptosis in Leukemic Cells. Int J Mol Sci 2021; 22:ijms22115465. [PMID: 34067305 PMCID: PMC8196872 DOI: 10.3390/ijms22115465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/22/2021] [Accepted: 05/13/2021] [Indexed: 12/19/2022] Open
Abstract
Leukemia is persistently a significant cause of illness and mortality worldwide. Urolithins, metabolites of ellagic acid and ellagitannins produced by gut microbiota, showed better bioactive compounds liable for the health benefits exerted by ellagic acid and ellagitannins containing pomegranate and walnuts. Here, we assessed the potential antileukemic activities of both urolithin A and urolithin B. Results showed that both urolithin A and B significantly inhibited the proliferation of leukemic cell lines Jurkat and K562, among which urolithin A showed the more prominent antiproliferative capability. Further, urolithin treatment alters leukemic cell metabolism, as evidenced by increased metabolic rate and notable changes in glutamine metabolism, one-carbon metabolism, and lipid metabolism. Next, we evidenced that both urolithins equally promoted apoptosis in leukemic cell lines. Based on these observations, we concluded that both urolithin A and B alter leukemic cell metabolome, resulting in a halt of proliferation, followed by apoptosis. The data can be used for designing new combinational therapies to eradicate leukemic cells.
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Affiliation(s)
- Abdulaziz Musa Alzahrani
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
| | - Mohammed Razeeth Shait Mohammed
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raed Ahmed Alghamdi
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
| | - Abrar Ahmad
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
| | - Mazin A. Zamzami
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hani Choudhry
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.A.); (M.R.S.M.); (R.A.A.); (A.A.); (M.A.Z.); (H.C.)
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
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5
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MLL5 improves ATRA driven differentiation and promotes xenotransplant engraftment in acute promyelocytic leukemia model. Cell Death Dis 2021; 12:371. [PMID: 33824267 PMCID: PMC8024355 DOI: 10.1038/s41419-021-03604-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/15/2022]
Abstract
Although the mixed lineage leukemia 5 (MLL5) gene has prognostic implications in acute promyelocyte leukemia (APL), the underlying mechanism remains to be elucidated. Here, we demonstrate the critical role exerted by MLL5 in APL regarding cell proliferation and resistance to drug-induced apoptosis, through mtROS regulation. Additionally, MLL5 overexpression increased the responsiveness of APL leukemic cells to all-trans retinoic acid (ATRA)-induced differentiation, via regulation of the epigenetic modifiers SETD7 and LSD1. In silico analysis indicated that APL blasts with MLL5high transcript levels were associated with retinoic acid binding and downstream signaling, while MLL5low blasts displayed decreased expression of epigenetic modifiers (such as KMT2C, PHF8 and ARID4A). Finally, APL xenograft transplants demonstrated improved engraftment of MLL5-expressing cells and increased myeloid differentiation over time. Concordantly, evaluation of engrafted blasts revealed increased responsiveness of MLL5-expressing cells to ATRA-induced granulocytic differentiation. Together, we describe the epigenetic changes triggered by the interaction of MLL5 and ATRA resulting in enhanced granulocytic differentiation.
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Sharma M, Bhavani C, Suresh SB, Paul J, Yadav L, Ross C, Srivastava S. Gene expression profiling of CD34(+) cells from patients with myeloproliferative neoplasms. Oncol Lett 2021; 21:204. [PMID: 33574943 PMCID: PMC7816297 DOI: 10.3892/ol.2021.12465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/08/2020] [Indexed: 01/01/2023] Open
Abstract
Myeloproliferative neoplasms (MPN) are clonal disorders characterized by the increased proliferation of hematopoietic stem cell precursors and mature blood cells. Mutations of Janus kinase 2 (JAK2), Calreticulin (CALR) and MPL (myeloproliferative leukemia virus) are key driver mutations in MPN. However, the molecular profile of triple negative MPN has been a subject of ambiguity over the past few years. Mutations of, methylcytosine dioxygenase TET2, polycomb group protein ASXL1 and histone-lysine N-methyltransferase EZH2 genes have accounted for certain subsets of triple negative MPNs but the driving cause for majority of cases is still unexplored. The present study performed a microarray-based transcriptomic profile analysis of bone marrow-derived CD34(+) cells from seven MPN samples. A total of 21,448 gene signatures were obtained, which were further filtered into 472 upregulated and 202 downregulated genes. Gene ontology and protein-protein interaction (PPI) network analysis highlighted an upregulation of genes involved in cell cycle and chromatin modification in JAK2V617F negative vs. positive MPN samples. Out of the upregulated genes, seven were associated with the hematopoietic stem cell signature, while forty-seven were associated with the embryonic stem cell signature. The majority of the genes identified were under the control of NANOG and E2F4 transcription factors. The PPI network indicated a strong interaction between chromatin modifiers and cell cycle genes, such as histone-lysine N-methyltransferase SUV39H1, SWI/SNF complex subunit SMARCC2, SMARCE2, chromatin remodeling complex subunit SS18, tubulin β (TUBB) and cyclin dependent kinase CDK1. Among the upregulated epigenetic markers, there was a ~10-fold increase in MYB expression in JAK2V617F negative samples. A significant increase in total CD34 counts in JAK2V617F negative vs. positive samples (P<0.05) was also observed. Overall, the present data showed a distinct pattern of expression in JAK2V617F negative vs. positive samples with upregulated genes involved in epigenetic modification.
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Affiliation(s)
- Mugdha Sharma
- Department of Medicine, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
| | - Chandra Bhavani
- St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, Karnataka 560034, India
| | - Srinag Bangalore Suresh
- Department of Medicine, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
| | - John Paul
- Department of Medicine, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
| | - Lokendra Yadav
- Department of Transfusion Medicine and Immunohematology, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
| | - Cecil Ross
- Department of Medicine, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
| | - Sweta Srivastava
- Department of Transfusion Medicine and Immunohematology, St. John's Medical College and Hospital, Bengaluru, Karnataka 560034, India
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Valiulienė G, Vitkevičienė A, Navakauskienė R. The epigenetic treatment remodel genome-wide histone H4 hyper-acetylation patterns and affect signaling pathways in acute promyelocytic leukemia cells. Eur J Pharmacol 2020; 889:173641. [PMID: 33045196 DOI: 10.1016/j.ejphar.2020.173641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 01/10/2023]
Abstract
Although majority of acute promyelocytic leukemia (APL) patients achieve complete remission after the standard treatment, 5-10% of patients are shown to relapse or develop resistance to treatment. In such cases, medications that target epigenetic processes could become an appealing supplementary approach. In this study, we tested the anti-leukemic activity of histone deacetylase inhibitor Belinostat (PXD101) and histone methyltransferase inhibitor 3-Deazaneplanocin A combined with all-trans retinoic acid in APL cells NB4, promyelocytes resembling HL-60 cells and APL patients' cells. After HL-60 and NB4 cell treatment, ChIP-sequencing was performed using antibodies against hyper-acetylated histone H4. Hyper-acetylated histone H4 distribution peaks were compared in treated vs untreated HL-60 and NB4 cells. Results demonstrated that in treated HL-60 cells, the majority of peaks were distributed within the regions of proximal promoters, whereas in treated NB4 cells, hyper-acetylated histone H4 peaks were mainly localized in gene body regions. Further ChIP-seq data analysis revealed the changes in histone H4 hyper-acetylation in promoter/gene body regions of genes involved in cancer signaling pathways. In addition, quantitative gene expression analysis proved changes in various cellular pathways important for carcinogenesis. Epigenetic treatment down-regulated the expression of MTOR, LAMTOR1, WNT2B, VEGFR3, FGF2, FGFR1, TGFA, TGFB1, TGFBR1, PDGFA, PDGFRA and PDGFRB genes in NB4, HL-60 and APL patients' cells. In addition, effect of epigenetic treatment on protein expression of aforementioned signaling pathways was confirmed with mass spectrometry analysis. Taken together, these results provide supplementary insights into molecular changes that occur during epigenetic therapy application in in vitro promyelocytic leukemia cell model.
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Affiliation(s)
- Giedrė Valiulienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania.
| | - Aida Vitkevičienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania.
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania.
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8
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Maimaitiyiming Y, Wang QQ, Hsu CH, Naranmandura H. Arsenic induced epigenetic changes and relevance to treatment of acute promyelocytic leukemia and beyond. Toxicol Appl Pharmacol 2020; 406:115212. [PMID: 32882258 DOI: 10.1016/j.taap.2020.115212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Epigenetic alterations regulate gene expression without changes in the DNA sequence. It is well-demonstrated that aberrant epigenetic changes contribute to the leukemogenesis of acute promyelocytic leukemia (APL). Arsenic trioxide (ATO) is one of the most common drugs used in the frontline treatment of APL that act through targeting and destabilizing the PML/RARα oncofusion protein. ATO together with all-trans retinoic acid (ATRA) lead to durable remission of more than 90% non-high-risk APL patients, turning APL treatment into a paradigm of oncoprotein targeted cure. Although relapse and drug resistance in APL are yet to be resolved in the clinic, epigenetic machineries might hold the key to address this issue. Further, ATO also showed promising anticancer activities against a variety of malignancies, but its application is particularly restricted due to limited understanding of the mechanism. Thus, a thorough understanding of epigenetic mechanism behind anti-leukemic effects of ATO would benefit the development of ATO-based anticancer strategy. Role of ATRA on APL associated epigenetic alterations has been extensively studied and reviewed. Recently, accumulating evidence suggest that ATO also induces some epigenetic changes that might favor APL eradication. In this article, we comprehensively discuss arsenic induced epigenetic changes and its relevance in APL treatment and beyond, so as to provide novel insights into overcoming arsenic resistance in APL and promote application of this drug to other malignancies.
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Affiliation(s)
- Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Qian Wang
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China.
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9
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HDAC and HMT Inhibitors in Combination with Conventional Therapy: A Novel Treatment Option for Acute Promyelocytic Leukemia. JOURNAL OF ONCOLOGY 2019; 2019:6179573. [PMID: 31396278 PMCID: PMC6668531 DOI: 10.1155/2019/6179573] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/23/2022]
Abstract
Acute promyelocytic leukemia (APL) is characterized by PML-RARA translocation, which causes the blockage of promyelocyte differentiation. Conventional treatment with Retinoic acid and chemotherapeutics is quite satisfactory. However, there are still patients who relapse or develop resistance to conventional treatment. To propose new possibilities for acute leukemia treatment, we studied the potential of histone deacetylase (HDAC) inhibitor and histone methyl transferase (HMT) inhibitor to enhance conventional therapy in vitro and ex vivo. NB4 and HL60 cell lines were used as an in vitro model; APL patient bone marrow mononuclear cells were used as an ex vivo model. Cell samples were treated with Belinostat (HDAC inhibitor) and 3-Deazaneplanocin A (HMT inhibitor) in combination with conventional treatment (Retinoic acid and Idarubicin). We demonstrated that the combined treatment used in the study had slightly higher effect on cell proliferation inhibition than conventional treatment. Also, enhanced treatment showed stronger effect on induction of apoptosis and on suppression of metabolism. Moreover, the treatment accelerated granulocytic cell differentiation and caused chromatin remodelling (increased H3K14 and H4 acetylation levels). In vitro and ex vivo models showed similar response to the treatment with different combinations of 3-Deazaneplanocin A, Belinostat, Retinoic acid, and Idarubicin. In conclusion, we suggest that 3-Deazaneplanocin A and Belinostat enhanced conventional acute promyelocytic leukemia treatment and could be considered for further investigations for clinical use.
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Huynh TT, Sultan M, Vidovic D, Dean CA, Cruickshank BM, Lee K, Loung CY, Holloway RW, Hoskin DW, Waisman DM, Weaver ICG, Marcato P. Retinoic acid and arsenic trioxide induce lasting differentiation and demethylation of target genes in APL cells. Sci Rep 2019; 9:9414. [PMID: 31263158 PMCID: PMC6602962 DOI: 10.1038/s41598-019-45982-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/19/2019] [Indexed: 12/11/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is characterized by arrested differentiation of promyelocytes. Patients treated with all-trans retinoic acid (ATRA) alone experience relapse, while patients treated with ATRA and arsenic trioxide (ATO) are often relapse-free. This suggests sustained changes have been elicited by the combination therapy. To understand the lasting effects of the combination therapy, we compared the effects of ATRA and ATO on NB4 and ATRA-resistant NB4-MR2 APL cells during treatment versus post treatment termination. After treatment termination, NB4 cells treated with ATRA or ATO reverted to non-differentiated cells, while combination-treated cells remained terminally differentiated. This effect was diminished in NB4-MR2 cells. This suggests combination treatment induced more permanent changes. Combination treatment induced higher expression of target genes (e.g., transglutaminase 2 and retinoic acid receptor beta), which in NB4 cells was sustained post treatment termination. To determine whether sustained epigenetic changes were responsible, we quantified the enrichment of histone modifications by chromatin immunoprecipitation, and CpG methylation by bisulfite-pyrosequencing. While ATRA and combination treatment induced similar histone acetylation enrichment, combination treatment induced greater demethylation of target genes, which was sustained. Therefore, sustained demethylation of target genes by ATRA and ATO combination treatment is associated with lasting differentiation and gene expression changes.
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Affiliation(s)
- Thomas T Huynh
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Mohammad Sultan
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Dejan Vidovic
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Cheryl A Dean
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | | | - Kristen Lee
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Chao-Yu Loung
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Ryan W Holloway
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - David W Hoskin
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - David M Waisman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Ian C G Weaver
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada.
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada.
- Brain Repair Centre, Dalhousie University, Halifax, NS, Canada.
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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11
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Celano M, Mio C, Sponziello M, Verrienti A, Bulotta S, Durante C, Damante G, Russo D. Targeting post-translational histone modifications for the treatment of non-medullary thyroid cancer. Mol Cell Endocrinol 2018; 469:38-47. [PMID: 28579118 DOI: 10.1016/j.mce.2017.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/25/2017] [Accepted: 05/30/2017] [Indexed: 02/07/2023]
Abstract
Genomic and epigenetic alterations are now being exploited as molecular targets in cancer treatment. Abnormalities involving the post-translational modification of histones have been demonstrated in thyroid cancer, and they are regarded as promising molecular targets for novel drug treatment of tumors that are resistant to conventional therapies. After a brief overview of the histone modifications most commonly associated with human malignancies, we will review recently published preclinical and clinical findings regarding the use of histone-activity modulators in thyroid cancers. Particular attention will be focused on their use as re-differentiating or anti-proliferating agents, the differential effects observed when they are used alone and in combination with other targeted drugs, and current prospects for their use in the treatment of thyroid cancer.
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Affiliation(s)
- Marilena Celano
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy
| | - Marialuisa Sponziello
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Antonella Verrienti
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Cosimo Durante
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
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12
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Wefers C, Schreibelt G, Massuger LFAG, de Vries IJM, Torensma R. Immune Curbing of Cancer Stem Cells by CTLs Directed to NANOG. Front Immunol 2018; 9:1412. [PMID: 29971070 PMCID: PMC6018198 DOI: 10.3389/fimmu.2018.01412] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 12/15/2022] Open
Abstract
Cancer stem cells (CSCs) have been identified as the source of tumor growth and disease recurrence. Eradication of CSCs is thus essential to achieve durable responses, but CSCs are resistant to current anti-tumor therapies. Novel therapeutic approaches that specifically target CSCs will, therefore, be crucial to improve patient outcome. Immunotherapies, which boost the body's own immune system to eliminate cancerous cells, could be an alternative approach to target CSCs. Vaccines of dendritic cells (DCs) loaded with tumor antigens can evoke highly specific anti-tumor T cell responses. Importantly, DC vaccination also promotes immunological memory formation, paving the way for long-term cancer control. Here, we propose a DC vaccination that specifically targets CSCs. DCs loaded with NANOG peptides, a protein required for maintaining stem cell properties, could evoke a potent anti-tumor immune response against CSCs. We hypothesize that the resulting immunological memory will also control newly formed CSCs, thereby preventing disease recurrence.
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Affiliation(s)
- Christina Wefers
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
- Department of Obstetrics and Gynecology, Radboudumc, Nijmegen, Netherlands
| | - Gerty Schreibelt
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | | | - I. Jolanda M. de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Ruurd Torensma
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
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13
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De Nicola M, Bruni E, Traversa E, Ghibelli L. Slow release of etoposide from dextran conjugation shifts etoposide activity from cytotoxicity to differentiation: A promising tool for dosage control in anticancer metronomic therapy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:2005-2014. [PMID: 28535989 DOI: 10.1016/j.nano.2017.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/30/2017] [Accepted: 05/08/2017] [Indexed: 11/27/2022]
Abstract
Drug conjugation, improving drug stability, solubility and body permanence, allows achieving impressive results in tumor control. Here, we show that conjugation may provide a straightforward method to administer drugs by the emerging anticancer metronomic approach, presently consisting of low, repeated doses of cytotoxic drugs used in traditional chemotherapy, thus reducing toxicity without reducing efficiency; however, low dose maintenance in tumor sites is difficult. We show that conjugating the antitumor drug etoposide to dextran via pH-sensitive bond produces slow releasing, apoptosis-proficient conjugates rapidly internalized into acidic lysosomes; importantly, release of active etoposide requires cell internalization and acidic pH. Conjugation, without impairing etoposide-induced complete elimination of tumor cells, shifted the mode of apoptosis from cytotoxicity- to differentiation-related; interestingly, high conjugate doses acted as low doses of free etoposide, thus mimicking the effect of metronomic therapy. This indicates slow release as a promising novel strategy for stabilizing low drug levels in metronomic regimens.
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Affiliation(s)
- Milena De Nicola
- Dipartimento di Biologia, Università di Roma Tor Vergata, Roma, Italy; Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Roma, Italy.
| | - Emanuele Bruni
- Dipartimento di Biologia, Università di Roma Tor Vergata, Roma, Italy.
| | - Enrico Traversa
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Roma, Italy; International Research Center for Renewable Energy (IRCRE), Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Lina Ghibelli
- Dipartimento di Biologia, Università di Roma Tor Vergata, Roma, Italy.
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14
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All-trans retinoic acid and arsenic trioxide fail to derepress the monocytic differentiation driver Irf8 in acute promyelocytic leukemia cells. Cell Death Dis 2017; 8:e2782. [PMID: 28492552 PMCID: PMC5520717 DOI: 10.1038/cddis.2017.197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/13/2022]
Abstract
All-trans retinoic acid (ATRA) and/or arsenic trioxide (ATO) administration leads to granulocytic maturation and/or apoptosis of acute promyelocytic leukemia (APL) cells mainly by targeting promyelocytic leukemia/retinoic acid receptor alpha (PML/RARα). Yet, ~10–15% of APL patients are not cured by ATRA- and ATO-based therapies, and a potential failure of ATRA and ATO in completely reversing PML/RARα-driven oncogenic alterations has not been comprehensively examined. Here we characterized the in vivo primary responses of dysregulated genes in APL cells treated with ATRA and ATO using a GFP-labeled APL model. Although induced granulocytic differentiation of APL cells was evident after ATRA or ATO administration, the expression of the majority of dysregulated genes in the c-Kit+ APL progenitors was not consistently corrected. Irf8, whose expression increased along with spontaneous differentiation of the APL progenitors in vivo, represented such a PML/RARα-dysregulated gene that was refractory to ATRA/ATO signaling. Interestingly, Irf8 induction, but not its knockdown, decreased APL leukemogenic potential through driving monocytic maturation. Thus, we reveal that certain PML/RARα-dysregulated genes that are refractory to ATRA/ATO signaling are potentially crucial regulators of the immature status and leukemogenic potential of APL cells, which can be exploited for the development of new therapeutic strategies for ATRA/ATO-resistant APL cases.
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15
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A novel PAD4/SOX4/PU.1 signaling pathway is involved in the committed differentiation of acute promyelocytic leukemia cells into granulocytic cells. Oncotarget 2016; 7:3144-57. [PMID: 26673819 PMCID: PMC4823096 DOI: 10.18632/oncotarget.6551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/20/2015] [Indexed: 12/31/2022] Open
Abstract
All-trans retinoic acid (ATRA) treatment yields cure rates > 80% through proteasomal degradation of the PML-RARα fusion protein that typically promotes acute promyelocytic leukemia (APL). However, recent evidence indicates that ATRA can also promote differentiation of leukemia cells that are PML-RARα negative, such as HL-60 cells. Here, gene expression profiling of HL-60 cells was used to investigate the alternative mechanism of impaired differentiation in APL. The expression of peptidylarginine deiminase 4 (PADI4), encoding PAD4, a protein that post-translationally converts arginine into citrulline, was restored during ATRA-induced differentiation. We further identified that hypermethylation in the PADI4 promoter was associated with its transcriptional repression in HL-60 and NB4 (PML-RARα positive) cells. Functionally, PAD4 translocated into the nucleus upon ATRA exposure and promoted ATRA-mediated differentiation. Mechanistic studies using RNAi knockdown or electroporation-mediated delivery of PADI4, along with chromatin immunoprecipitation, helped identify PU.1 as an indirect target and SOX4 as a direct target of PAD4 regulation. Indeed, PAD4 regulates SOX4-mediated PU.1 expression, and thereby the differentiation process, in a SOX4-dependent manner. Taken together, our results highlight an association between PAD4 and DNA hypermethylation in APL and demonstrate that targeting PAD4 or regulating its downstream effectors may be a promising strategy to control differentiation in the clinic.
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16
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Keeshan K, Vieugué P, Chaudhury S, Rishi L, Gaillard C, Liang L, Garcia E, Nakamura T, Omidvar N, Kogan SC. Co-operative leukemogenesis in acute myeloid leukemia and acute promyelocytic leukemia reveals C/EBPα as a common target of TRIB1 and PML/RARA. Haematologica 2016; 101:1228-1236. [PMID: 27390356 DOI: 10.3324/haematol.2015.138503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 06/24/2016] [Indexed: 12/22/2022] Open
Abstract
The PML/RARA fusion protein occurs as a result of the t(15;17) translocation in the acute promyelocytic leukemia subtype of human acute myeloid leukemia. Gain of chromosome 8 is the most common chromosomal gain in human acute myeloid leukemia, including acute promyelocytic leukemia. We previously demonstrated that gain of chromosome 8-containing MYC is of central importance in trisomy 8, but the role of the nearby TRIB1 gene has not been experimentally addressed in this context. We have now tested the hypothesis that both MYC and TRIB1 have functional roles underlying leukemogenesis of trisomy 8 by using retroviral vectors to express MYC and TRIB1 in wild-type bone marrow and in marrow that expressed a PML/RARA transgene. Interestingly, although MYC and TRIB1 readily co-operated in leukemogenesis for wild-type bone marrow, TRIB1 provided no selective advantage to cells expressing PML/RARA. We hypothesized that this lack of co-operation between PML/RARA and TRIB1 reflected a common pathway for their effect: both proteins targeting the myeloid transcription factor C/EBPα. In support of this idea, TRIB1 expression abrogated the all-trans retinoic acid response of acute promyelocytic leukemia cells in vitro and in vivo Our data delineate the common and redundant inhibitory effects of TRIB1 and PML/RARA on C/EBPα providing a potential explanation for the lack of selection of TRIB1 in human acute promyelocytic leukemia, and highlighting the key role of C/EBPs in acute promyelocytic leukemia pathogenesis and therapeutic response. In addition, the co-operativity we observed between MYC and TRIB1 in the absence of PML/RARA show that, outside of acute promyelocytic leukemia, gain of both genes may drive selection for trisomy 8.
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Affiliation(s)
- Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| | - Pauline Vieugué
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Shahzya Chaudhury
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| | - Loveena Rishi
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| | - Coline Gaillard
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Lu Liang
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| | - Elaine Garcia
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Takuro Nakamura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Nader Omidvar
- Department of Haematology, School of Medicine, Cardiff University, UK
| | - Scott C Kogan
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
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17
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Cheung N, Fung TK, Zeisig BB, Holmes K, Rane JK, Mowen KA, Finn MG, Lenhard B, Chan LC, So CWE. Targeting Aberrant Epigenetic Networks Mediated by PRMT1 and KDM4C in Acute Myeloid Leukemia. Cancer Cell 2016; 29:32-48. [PMID: 26766589 PMCID: PMC4712026 DOI: 10.1016/j.ccell.2015.12.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/31/2015] [Accepted: 12/15/2015] [Indexed: 02/07/2023]
Abstract
Transcriptional deregulation plays a major role in acute myeloid leukemia, and therefore identification of epigenetic modifying enzymes essential for the maintenance of oncogenic transcription programs holds the key to better understanding of the biology and designing effective therapeutic strategies for the disease. Here we provide experimental evidence for the functional involvement and therapeutic potential of targeting PRMT1, an H4R3 methyltransferase, in various MLL and non-MLL leukemias. PRMT1 is necessary but not sufficient for leukemic transformation, which requires co-recruitment of KDM4C, an H3K9 demethylase, by chimeric transcription factors to mediate epigenetic reprogramming. Pharmacological inhibition of KDM4C/PRMT1 suppresses transcription and transformation ability of MLL fusions and MOZ-TIF2, revealing a tractable aberrant epigenetic circuitry mediated by KDM4C and PRMT1 in acute leukemia.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Epigenesis, Genetic/genetics
- Gene Expression Regulation, Leukemic/genetics
- Humans
- Jumonji Domain-Containing Histone Demethylases/genetics
- Jumonji Domain-Containing Histone Demethylases/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Protein-Arginine N-Methyltransferases/genetics
- Protein-Arginine N-Methyltransferases/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Transcription Factors/genetics
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Affiliation(s)
- Ngai Cheung
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK
| | - Tsz Kan Fung
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK
| | - Bernd B Zeisig
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK
| | - Katie Holmes
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK
| | - Jayant K Rane
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK
| | - Kerri A Mowen
- Department of Chemical Physiology and Immunology & Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Boris Lenhard
- Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Du Cane Road, London W12 0NN, UK
| | - Li Chong Chan
- Department of Pathology, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Chi Wai Eric So
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK.
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18
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Lozano-Santos C, Amigo-Jiménez I, Nova-Gurumeta S, Pérez-Sanz N, García-Pardo A, García-Marco JA. Arsenic trioxide synergistically potentiates the cytotoxic effect of fludarabine in chronic lymphocytic leukemia cells by further inactivating the Akt and ERK signaling pathways. Biochem Biophys Res Commun 2015; 461:243-8. [PMID: 25869069 DOI: 10.1016/j.bbrc.2015.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 04/02/2015] [Indexed: 11/25/2022]
Abstract
CLL remains an incurable disease, making it crucial to continue searching for new therapies efficient in all CLL cases. We have studied the effect of combining arsenic trioxide (ATO) with fludarabine, a frontline drug in CLL. We have found a synergistic interaction between 1 μM ATO and 5 μM fludarabine that significantly enhanced the cytotoxic effect of the individual drugs. Importantly, ATO sensitized fludarabine-resistant cells to the action of this drug. The mechanism behind this effect included the downregulation of phospho-Akt, phospho-ERK, and the Mcl-1/Bim and Bcl-2/Bax ratios. The combination of ATO and fludarabine partially overcame the survival effect induced by co-culturing CLL cells with stromal cells. Therefore, low concentrations of ATO combined with fludarabine may be an efficient therapeutic strategy in CLL patients.
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Affiliation(s)
- Carol Lozano-Santos
- Molecular Cytogenetics Unit, Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and IDIPHIM, Madrid, Spain
| | - Irene Amigo-Jiménez
- Cellular and Molecular Medicine Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sara Nova-Gurumeta
- Molecular Cytogenetics Unit, Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and IDIPHIM, Madrid, Spain
| | - Nuria Pérez-Sanz
- Molecular Cytogenetics Unit, Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and IDIPHIM, Madrid, Spain
| | - Angeles García-Pardo
- Cellular and Molecular Medicine Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - José A García-Marco
- Molecular Cytogenetics Unit, Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and IDIPHIM, Madrid, Spain.
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