1
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Katebi A, Chen X, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.29.551111. [PMID: 37577526 PMCID: PMC10418072 DOI: 10.1101/2023.07.29.551111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a novel optimization procedure to identify the optimal network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
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Affiliation(s)
- Ataur Katebi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Xiaowen Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
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2
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Li F, Xiong Y, Yang M, Chen P, Zhang J, Wang Q, Xu M, Wang Y, He Z, Zhao X, Huang J, Gu X, Zhang L, Sun R, Sun X, Li J, Ou J, Xu T, Huang X, Cao Y, Xu XR, Karakas D, Li J, Ni H, Zhang Q. c-Mpl-del, a c-Mpl alternative splicing isoform, promotes AMKL progression and chemoresistance. Cell Death Dis 2022; 13:869. [PMID: 36229456 PMCID: PMC9561678 DOI: 10.1038/s41419-022-05315-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Acute megakaryocytic leukemia (AMKL) is a clinically heterogeneous subtype of acute myeloid leukemia characterized by unrestricted megakaryoblast proliferation and poor prognosis. Thrombopoietin receptor c-Mpl is a primary regulator of megakaryopoeisis and a potent mitogenic receptor. Aberrant c-Mpl signaling has been implicated in a myriad of myeloid proliferative disorders, some of which can lead to AMKL, however, the role of c-Mpl in AMKL progression remains largely unexplored. Here, we identified increased expression of a c-Mpl alternative splicing isoform, c-Mpl-del, in AMKL patients. We found that c-Mpl-del expression was associated with enhanced AMKL cell proliferation and chemoresistance, and decreased survival in xenografted mice, while c-Mpl-del knockdown attenuated proliferation and restored apoptosis. Interestingly, we observed that c-Mpl-del exhibits preferential utilization of phosphorylated c-Mpl-del C-terminus Y607 and biased activation of PI3K/AKT pathway, which culminated in upregulation of GATA1 and downregulation of DDIT3-related apoptotic responses conducive to AMKL chemoresistance and proliferation. Thus, this study elucidates the critical roles of c-Mpl alternative splicing in AMKL progression and drug resistance, which may have important diagnostic and therapeutic implications for leukemia accelerated by c-Mpl-del overexpression.
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Affiliation(s)
- Fei Li
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyan Xiong
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Mo Yang
- grid.12981.330000 0001 2360 039XThe Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Peiling Chen
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jingkai Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiong Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China ,grid.12981.330000 0001 2360 039XInstitute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Miao Xu
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada
| | - Yiming Wang
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada ,Canadian Blood Services Centre for Innovation, Toronto, Canada
| | - Zuyong He
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Zhao
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junyu Huang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqiong Gu
- grid.410737.60000 0000 8653 1072Department of Blood Transfusion, Clinical Biological Resource Bank and Clinical Lab, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Zhang
- grid.410737.60000 0000 8653 1072Department of Blood Transfusion, Clinical Biological Resource Bank and Clinical Lab, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rui Sun
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xunsha Sun
- grid.12981.330000 0001 2360 039XNational Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingyao Li
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jinxin Ou
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ting Xu
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xueying Huang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yange Cao
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Ruby Xu
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada
| | - Danielle Karakas
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada
| | - June Li
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada ,Canadian Blood Services Centre for Innovation, Toronto, Canada
| | - Heyu Ni
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, and Toronto Platelet Immunobiology Group, University of Toronto, Toronto, Canada ,Canadian Blood Services Centre for Innovation, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Physiology, University of Toronto, Toronto, Canada
| | - Qing Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China ,grid.12981.330000 0001 2360 039XInstitute of Sun Yat-sen University in Shenzhen, Shenzhen, China
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3
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Koyunlar C, de Pater E. From Basic Biology to Patient Mutational Spectra of GATA2 Haploinsufficiencies: What Are the Mechanisms, Hurdles, and Prospects of Genome Editing for Treatment. Front Genome Ed 2021; 2:602182. [PMID: 34713225 PMCID: PMC8525360 DOI: 10.3389/fgeed.2020.602182] [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: 09/02/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are monogenetic disorders that result in a reduction of mature blood cell formation and predisposition to leukemia. In children with myeloid leukemia the gene most often mutated is Gata binding protein 2 (GATA2) and 80% of patients with GATA2 mutations develop myeloid malignancy before the age of forty. Although GATA2 is established as one of the key regulators of embryonic and adult hematopoiesis, the mechanisms behind the leukemia predisposition in GATA2 haploinsufficiencies is ambiguous. The only curative treatment option currently available is allogeneic hematopoietic stem cell transplantation (allo-SCT). However, allo-SCT can only be applied at a relatively late stage of the disease as its applicability is compromised by treatment related morbidity and mortality (TRM). Alternatively, autologous hematopoietic stem cell transplantation (auto-SCT), which is associated with significantly less TRM, might become a treatment option if repaired hematopoietic stem cells would be available. Here we discuss the recent literature on leukemia predisposition syndromes caused by GATA2 mutations, current knowledge on the function of GATA2 in the hematopoietic system and advantages and pitfalls of potential treatment options provided by genome editing.
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Affiliation(s)
- Cansu Koyunlar
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Emma de Pater
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
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4
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Liu X, Shi H, Shen J, Li Y, Yan W, Sun Y, Liao A, Tan Y, Yang W, Wang H. Dual Growth Factor (rhTPO + G-CSF) and Chemotherapy Combination Regimen for Elderly Patients with Acute Myeloid Leukemia: A Phase II Single-Arm Multicenter Study. Int J Gen Med 2021; 14:6093-6099. [PMID: 34611424 PMCID: PMC8485918 DOI: 10.2147/ijgm.s323699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/20/2021] [Indexed: 12/03/2022] Open
Abstract
Acute myeloid leukemia (AML) is a disease affecting older adults, although optimal strategies for treating such patients remain unclear. This prospective phase II, open-label, multicenter study was designed to assess the efficacy and safety of two hematologic growth factors, recombinant human thrombopoietin (rhTPO) and granulocyte colony-stimulating factor (G-CSF), in combination with decitabine, cytarabine, and aclarubicin (D-CTAG regimen) to treat older adults with newly diagnosed AML (Identifier: NCT04168138). The above agents were administered as follows: decitabine (15 mg/m2 daily, days 1–5); low-dose cytarabine (10 mg/m2 q12 h, days 3–9); rhTPO (15,000 U daily, days 2, 4, 6, 8, 10–24 or until >50×109/L platelets); aclarubicin (14 mg/m2 daily, days 3–6); and G-CSF (300 μg daily, days 2–9). We concurrently monitored historic controls treated with decitabine followed by cytarabine, aclarubicin, and G-CSF (D-CAG) only. After the first D-CTAG cycle, the overall response rate (ORR) was 84.2% (16/19), including 13 (73.7%) complete remissions (CRs) and three (15.8%) partial remissions. This CR rate surpassed that of the D-CAG treatment (p < 0.05). Median overall survival (OS) time in the D-CTAG group was 20.2 months (range, 4–31 months), compared with 14 months in the D-CAG group, and 1-year OS was 78%. The proportion of those experiencing grade III–IV thrombocytopenia was significantly lower for D-CTAG (57.9%) than for D-CAG (88.4%; p < 0.05). Ultimately, the curative effect of adding rhTPO was not inferior to that of D-CAG, and D-CTAG proved safer for elderly patients, especially in terms of hematologic toxicity. A prospective phase III randomized study is warranted to confirm these observations.
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Affiliation(s)
- Xiaoyu Liu
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Hua Shi
- Haematology Department of Sun Yat-sen Memorial Hospital, Sun Yat-sen University Shen Shan Central Hospital, Guangzhou, People's Republic of China
| | - Jing Shen
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yang Li
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Wei Yan
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Ying Sun
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Aijun Liao
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yehui Tan
- Haematology Department of The First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Wei Yang
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Huihan Wang
- Haematology Department of Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
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5
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Chung HY, Lin BA, Lin YX, Chang CW, Tzou WS, Pei TW, Hu CH. Meis1, Hi1α, and GATA1 are integrated into a hierarchical regulatory network to mediate primitive erythropoiesis. FASEB J 2021; 35:e21915. [PMID: 34496088 DOI: 10.1096/fj.202001044rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 12/16/2022]
Abstract
During development, erythroid cells are generated by two waves of hematopoiesis. In zebrafish, primitive erythropoiesis takes place in the intermediate cell mass region, and definitive erythropoiesis arises from the aorta-gonad mesonephros. TALE-homeoproteins Meis1 and Pbx1 function upstream of GATA1 to specify the erythroid lineage. Embryos lacking Meis1 or Pbx1 have weak gata1 expression and fail to produce primitive erythrocytes. Nevertheless, the underlying mechanism of how Meis1 and Pbx1 mediate gata1 transcription in erythrocytes remains unclear. Here we show that Hif1α acts downstream of Meis1 to mediate gata1 expression in zebrafish embryos. Inhibition of Meis1 expression resulted in suppression of hif1a expression and abrogated primitive erythropoiesis, while injection with in vitro-synthesized hif1α mRNA rescued gata1 transcription in Meis1 morphants and recovered their erythropoiesis. Ablation of Hif1α expression either by morpholino knockdown or Crispr-Cas9 knockout suppressed gata1 transcription and abrogated primitive erythropoiesis. Results of chromatin immunoprecipitation assays showed that Hif1α associates with hypoxia-response elements located in the 3'-flanking region of gata1 during development, suggesting that Hif1α regulates gata1 expression in vivo. Together, our results indicate that Meis1, Hif1α, and GATA1 indeed comprise a hierarchical regulatory network in which Hif1α acts downstream of Meis1 to activate gata1 transcription through direct interactions with its cis-acting elements in primitive erythrocytes.
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Affiliation(s)
- Hsin-Yu Chung
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Bo-An Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yi-Xuan Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chen-Wei Chang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Wen-Shyong Tzou
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pei
- Department of Computer Science and Information Engineering, National Taipei University of Technology
| | - Chin-Hwa Hu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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6
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Falconi G, Fabiani E, Criscuolo M, Fianchi L, Finelli C, Cerqui E, Pelosi E, Screnci M, Gurnari C, Zangrilli I, Postorino M, Laurenti L, Piciocchi A, Testa U, Lo-Coco F, Voso MT. Transcription factors implicated in late megakaryopoiesis as markers of outcome after azacitidine and allogeneic stem cell transplantation in myelodysplastic syndrome. Leuk Res 2019; 84:106191. [DOI: 10.1016/j.leukres.2019.106191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 07/14/2019] [Indexed: 01/07/2023]
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7
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GATA2 mutations and overexpression in pediatric acute myeloid leukemia. PEDIATRIC HEMATOLOGY ONCOLOGY JOURNAL 2019. [DOI: 10.1016/j.phoj.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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8
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Li H, Zhao N, Li Y, Xing H, Chen S, Xu Y, Tang K, Tian Z, Wang M, Rao Q, Wang J. c-MPL Is a Candidate Surface Marker and Confers Self-Renewal, Quiescence, Chemotherapy Resistance, and Leukemia Initiation Potential in Leukemia Stem Cells. Stem Cells 2018; 36:1685-1696. [PMID: 30106501 DOI: 10.1002/stem.2897] [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] [Received: 03/12/2018] [Revised: 06/29/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) is initiated and maintained by a unique, small subset of leukemia cells known as leukemia stem cells (LSCs). Self-renewal, quiescence, and chemotherapy resistance are key stemness properties of LSCs that are essential for poor clinical responses to conventional therapies. Identifying LSC surface markers and targeting LSCs are important for the development of potential therapies. In this study, application of chemotherapy treatment in AML-ETO9a (AE9a) leukemia mice led to the enrichment of a chemotherapy-resistant cell population identified as Lin- c-Kit+ c-MPL+ . In addition, this c-MPL-positive cell population within Lin- c-Kit+ leukemia cells included a high percentage of cells in a quiescent state, enhanced colony formation ability, and increased homing efficiency. Serial transplantation demonstrated that Lin- c-Kit+ c-MPL+ cells displayed a significantly high potential for leukemia initiation. Furthermore, it was demonstrated that in AML patients, c-MPL was expressed on the majority of CD34+ leukemia cells and that the proportion of c-MPL+ cells in CD34+ leukemia cells is associated with poor prognosis. Finally, AMM2, an inhibitor of c-MPL, was shown to significantly enhance the survival of AE9a leukemia mice when combined with chemotherapeutic agent. These results indicate that c-MPL is a candidate LSC surface marker that may serve as a therapeutic target for the elimination of LSCs. Stem Cells 2018;36:1685-1696.
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Affiliation(s)
- Huan Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Na Zhao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Yihui Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Haiyan Xing
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Shuying Chen
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Yingxi Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Kejing Tang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Zheng Tian
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Min Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Qing Rao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
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9
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Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, Graña-Castro O, Pisano DG, Barrero MJ. CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. Epigenetics Chromatin 2018; 11:30. [PMID: 29884215 PMCID: PMC5992658 DOI: 10.1186/s13072-018-0197-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/27/2018] [Indexed: 02/06/2023] Open
Abstract
Background The reported antitumor activity of the BET family bromodomain inhibitors has prompted the development of inhibitors against other bromodomains. However, the human genome encodes more than 60 different bromodomains and most of them remain unexplored. Results We report that the bromodomains of the histone acetyltransferases CREBBP/EP300 are critical to sustain the proliferation of human leukemia and lymphoma cell lines. EP300 is very abundant at super-enhancers in K562 and is coincident with sites of GATA1 and MYC occupancy. In accordance, CREBBP/EP300 bromodomain inhibitors interfere with GATA1- and MYC-driven transcription, causing the accumulation of cells in the G0/G1 phase of the cell cycle. The CREBBP/CBP30 bromodomain inhibitor CBP30 displaces CREBBP and EP300 from GATA1 and MYC binding sites at enhancers, resulting in a decrease in the levels of histone acetylation at these regulatory regions and consequently reduced gene expression of critical genes controlled by these transcription factors. Conclusions Our data shows that inhibition of CREBBP/EP300 bromodomains can interfere with oncogene-driven transcriptional programs in cancer cells and consequently hold therapeutic potential. Electronic supplementary material The online version of this article (10.1186/s13072-018-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Veronica Garcia-Carpizo
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Sergio Ruiz-Llorente
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Jacinto Sarmentero
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - David G Pisano
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Maria J Barrero
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain.
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10
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Wang X, Lin P, Ho JWK. Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest. BMC Genomics 2018; 19:929. [PMID: 29363433 PMCID: PMC5780765 DOI: 10.1186/s12864-017-4340-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same core motif in different cell types. How a TF can bind to the genome in such a highly cell-type specific manner, is a critical research question. One hypothesis is that a TF requires co-binding of different TFs in different cell types. If this is the case, it may be possible to observe different combinations of TF motifs – a motif grammar – located at the TF binding sites in different cell types. In this study, we develop a bioinformatics method to systematically identify DNA motifs in TF binding sites across multiple cell types based on published ChIP-seq data, and address two questions: (1) can we build a machine learning classifier to predict cell-type specificity based on motif combinations alone, and (2) can we extract meaningful cell-type specific motif grammars from this classifier model. Results We present a Random Forest (RF) based approach to build a multi-class classifier to predict the cell-type specificity of a TF binding site given its motif content. We applied this RF classifier to two published ChIP-seq datasets of TF (TCF7L2 and MAX) across multiple cell types. Using cross-validation, we show that motif combinations alone are indeed predictive of cell types. Furthermore, we present a rule mining approach to extract the most discriminatory rules in the RF classifier, thus allowing us to discover the underlying cell-type specific motif grammar. Conclusions Our bioinformatics analysis supports the hypothesis that combinatorial TF motif patterns are cell-type specific. Electronic supplementary material The online version of this article (10.1186/s12864-017-4340-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Wang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Peijie Lin
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia. .,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia.
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11
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Wang L, Cai W, Zhang W, Chen X, Dong W, Tang D, Zhang Y, Ji C, Zhang M. Inhibition of poly(ADP-ribose) polymerase 1 protects against acute myeloid leukemia by suppressing the myeloproliferative leukemia virus oncogene. Oncotarget 2016; 6:27490-504. [PMID: 26314963 PMCID: PMC4695004 DOI: 10.18632/oncotarget.4748] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/13/2015] [Indexed: 01/08/2023] Open
Abstract
An abnormal expression of poly(ADP-ribose) polymerase 1 (PARP-1) has been described in many tumors. PARP-1 promotes tumorigenesis and cancer progression by acting on different molecular pathways. PARP-1 inhibitors can be used with radiotherapy or chemotherapy to enhance the susceptibility of tumor cells to the treatment. However, the specific mechanism of PARP-1 in acute myeloid leukemia (AML) remains unknown. Our study showed that expression of PARP-1 was upregulated in AML patients. PARP-1 inhibition slowed AML cell proliferation, arrested the cell cycle, induced apoptosis in vitro and improved AML prognosis in vivo. Mechanistically, microarray assay of AML cells with loss of PARP-1 function revealed that the myeloproliferative leukemia virus oncogene (MPL) was significantly downregulated. In human AML samples, MPL expression was increased, and gain-of-function and loss-of-function analysis demonstrated that MPL promoted cell growth. Moreover, PARP-1 and MPL expression were positively correlated in AML samples, and their overexpression was associated with an unfavorable prognosis. Furthermore, PARP-1 and MPL consistently acted on Akt and ERK1/2 pathways, and the anti-proliferative and pro-apoptotic function observed with PARP-1 inhibition were reversed in part via MPL activation upon thrombopoietin stimulation or gene overexpression. These data highlight the important function of PARP-1 in the progression of AML, which suggest PARP-1 as a potential target for AML treatment.
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Affiliation(s)
- Lingbo Wang
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, China.,The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Weili Cai
- Department of Cardiology, The Third Hospital of Jinan, Jinan, China
| | - Wei Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Xueying Chen
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Wenqian Dong
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Dongqi Tang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, China
| | - Mingxiang Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, China
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12
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Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation. Mol Cell Biol 2015; 35:2059-72. [PMID: 25848090 DOI: 10.1128/mcb.01413-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/27/2015] [Indexed: 11/20/2022] Open
Abstract
Setd8 is the sole histone methyltransferase in mammals capable of monomethylating histone H4 lysine 20 (H4K20me1). Setd8 is expressed at significantly higher levels in erythroid cells than any other cell or tissue type, suggesting that Setd8 has an erythroid-cell-specific function. To test this hypothesis, stable Setd8 knockdown was established in extensively self-renewing erythroblasts (ESREs), a well-characterized, nontransformed model of erythroid maturation. Knockdown of Setd8 resulted in impaired erythroid maturation characterized by a delay in hemoglobin accumulation, larger mean cell area, persistent ckit expression, incomplete nuclear condensation, and lower rates of enucleation. Setd8 knockdown did not alter ESRE proliferation or viability or result in accumulation of DNA damage. Global gene expression analyses following Setd8 knockdown demonstrated that in erythroid cells, Setd8 functions primarily as a repressor. Most notably, Gata2 expression was significantly higher in knockdown cells than in control cells and Gata2 knockdown rescued some of the maturation impairments associated with Setd8 disruption. Setd8 occupies critical regulatory elements in the Gata2 locus, and knockdown of Setd8 resulted in loss of H4K20me1 and gain of H4 acetylation at the Gata2 1S promoter. These results suggest that Setd8 is an important regulator of erythroid maturation that works in part through repression of Gata2 expression.
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13
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Mir MA, Kochuparambil ST, Abraham RS, Rodriguez V, Howard M, Hsu AP, Jackson AE, Holland SM, Patnaik MM. Spectrum of myeloid neoplasms and immune deficiency associated with germline GATA2 mutations. Cancer Med 2015; 4:490-9. [PMID: 25619630 PMCID: PMC4402062 DOI: 10.1002/cam4.384] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 01/25/2023] Open
Abstract
Guanine-adenine-thymine-adenine 2 (GATA2) mutated disorders include the recently described MonoMAC syndrome (Monocytopenia and Mycobacterium avium complex infections), DCML (dendritic cell, monocyte, and lymphocyte deficiency), familial MDS/AML (myelodysplastic syndrome/acute myeloid leukemia) (myeloid neoplasms), congenital neutropenia, congenital lymphedema (Emberger's syndrome), sensorineural deafness, viral warts, and a spectrum of aggressive infections seen across all age groups. While considerable efforts have been made to identify the mutations that characterize this disorder, pathogenesis remains a work in progress with less than 100 patients described in current literature. Varying clinical presentations offer diagnostic challenges. Allogeneic stem cell transplant remains the treatment of choice. Morbidity, mortality, and social costs due to the familial nature of the disease are considerable. We describe our experience with the disorder in three affected families and a comprehensive review of current literature.
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Affiliation(s)
- Muhammad A Mir
- Penn State Milton S. Hershey Cancer Institute, Hershey, Pennsylvania
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14
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Li LJ, Tao JL, Fu R, Wang HQ, Jiang HJ, Yue LZ, Zhang W, Liu H, Shao ZH. Increased CD34+CD38−CD123+ cells in myelodysplastic syndrome displaying malignant features similar to those in AML. Int J Hematol 2014; 100:60-9. [DOI: 10.1007/s12185-014-1590-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/29/2023]
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15
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Xavier AC, Ge Y, Taub J. Unique clinical and biological features of leukemia in Down syndrome children. Expert Rev Hematol 2014; 3:175-86. [DOI: 10.1586/ehm.10.14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Niscola P, Tendas A, Minelli M, Perrotti A, Fabritiis PD, Poeta GD. Pure erythroid leukemia in advanced breast cancer. Blood Res 2014; 49:69-72. [PMID: 24724072 PMCID: PMC3974964 DOI: 10.5045/br.2014.49.1.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/06/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Andrea Tendas
- Hematology Division, S. Eugenio Hospital, Rome, Italy
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17
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Caldwell JT, Edwards H, Dombkowski AA, Buck SA, Matherly LH, Ge Y, Taub JW. Overexpression of GATA1 confers resistance to chemotherapy in acute megakaryocytic Leukemia. PLoS One 2013; 8:e68601. [PMID: 23874683 PMCID: PMC3707876 DOI: 10.1371/journal.pone.0068601] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 05/31/2013] [Indexed: 12/29/2022] Open
Abstract
It has been previously shown that acute myeloid leukemia (AML) patients with higher levels of GATA1 expression have poorer outcomes. Furthermore, pediatric Down syndrome (DS) patients with acute megakaryocytic leukemia (AMKL), whose blast cells almost universally harbor somatic mutations in exon 2 of the transcription factor gene GATA1, demonstrate increased overall survival relative to non-DS pediatric patients, suggesting a potential role for GATA1 in chemotherapy response. In this study, we confirmed that amongst non-DS patients, GATA1 transcripts were significantly higher in AMKL blasts compared to blasts from other AML subgroups. Further, GATA1 transcript levels significantly correlated with transcript levels for the anti-apoptotic protein Bcl-xL in our patient cohort. ShRNA knockdown of GATA1 in the megakaryocytic cell line Meg-01 resulted in significantly increased cytarabine (ara-C) and daunorubicin anti-proliferative sensitivities and decreased Bcl-xL transcript and protein levels. Chromatin immunoprecipitation (ChIP) and reporter gene assays demonstrated that the Bcl-x gene (which transcribes the Bcl-xL transcripts) is a bona fide GATA1 target gene in AMKL cells. Treatment of the Meg-01 cells with the histone deacetylase inhibitor valproic acid resulted in down-regulation of both GATA1 and Bcl-xL and significantly enhanced ara-C sensitivity. Furthermore, additional GATA1 target genes were identified by oligonucleotide microarray and ChIP-on-Chip analyses. Our findings demonstrate a role for GATA1 in chemotherapy resistance in non-DS AMKL cells, and identified additional GATA1 target genes for future studies.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Cells, Cultured
- Child
- Child, Preschool
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- GATA1 Transcription Factor/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/physiology
- Humans
- Leukemia, Megakaryoblastic, Acute/drug therapy
- Leukemia, Megakaryoblastic, Acute/genetics
- Microarray Analysis
- Up-Regulation/drug effects
- Up-Regulation/genetics
- Valproic Acid/pharmacology
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Affiliation(s)
- John Timothy Caldwell
- MD/PhD Program, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Cancer Biology Program, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Holly Edwards
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Alan A. Dombkowski
- Division of Pharmacology and Toxicology, Children’s Hospital of Michigan, Detroit, Michigan, United States of America
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Steven A. Buck
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Division of Pediatric Hematology/Oncology, Children’s Hospital of Michigan, Detroit, Michigan, United States of America
| | - Larry H. Matherly
- Cancer Biology Program, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Yubin Ge
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Jeffrey W. Taub
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Division of Pediatric Hematology/Oncology, Children’s Hospital of Michigan, Detroit, Michigan, United States of America
- * E-mail:
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18
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Bai Y, Qiu GR, Zhou F, Gong LY, Gao F, Sun KL. Overexpression of DICER1 induced by the upregulation of GATA1 contributes to the proliferation and apoptosis of leukemia cells. Int J Oncol 2013; 42:1317-24. [PMID: 23426981 DOI: 10.3892/ijo.2013.1831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/17/2013] [Indexed: 11/06/2022] Open
Abstract
Dicer, a member of the RNase III family, is the key enzyme required for the biogenesis of microRNAs and small interfering RNAs. Recent evidence indicates that DICER1 expression levels vary among different solid tumors and decreased or increased DICER1 expression has been associated with aggressive cancers. In this study, we assessed DICER1 expression levels in acute myeloid leukemia (AML) and investigated its biological effects and transcriptional regulation in leukemia cell lines. We demonstrated that DICER1 was overexpressed in AML patients and leukemia cell lines by real-time quantitative PCR and western blot analysis. A functional assay demonstrated that the silencing of DICER1 inhibited cell proliferation and promoted apoptosis in leukemia cell lines. We also demonstrated that DICER1 was upregulated by the hematopoietic transcription factor, GATA1, through luciferase, electrophoretic mobility shift and chromatin immunoprecipitation assays. These data suggest that DICER1 plays an important role in AML and the finding that the upregulation of DICER1 is induced by GATA1 may provide a framework for the understanding of differential DICER1 expression levels in multiple types of cancer.
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Affiliation(s)
- Ying Bai
- Department of Medical Genetics, China Medical University, Shenyang, P.R. China.
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19
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Abstract
In acute myeloid leukemia (AML), aberrant expression and mutations of transcription factors have been correlated with disease outcome. In the present study, we performed expression and mutation screening of GATA2, which is an essential transcription factor for regulation of myeloid lineage determination, in de novo pediatric AML patients. GATA2 mutations were detected in 5 of 230 patients, representing a frequency of 2.2% overall and 9.8% in cytogenetically normal AML. GATA2 expression analysis demonstrated that in 155 of 237 diagnostic samples (65%), GATA2 expression was higher than in normal BM. In complete remission, normalization of GATA2 expression was observed, whereas GATA2 expression levels stayed high in patients with resistant disease. High GATA2 expression at diagnosis was an independent poor prognostic factor for overall survival (hazard ratio [HR] = 1.7, P = .045), event-free survival (HR = 2.1, P = .002), and disease-free survival (HR = 2.3, P = .004). The prognostic impact of GATA2 was particularly evident in specific AML subgroups. In patients with French-American-British M5 morphology, inv(16), or high WT1 expression, significant differences in survival were observed between patients with high versus normal GATA2 expression. We conclude that high GATA2 expression is a novel poor prognostic marker in pediatric AML, which may contribute to better risk-group stratification and risk-adapted therapy in the future.
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20
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Ayala R, Martínez-López J, Gilsanz F. Acute myeloid leukemia and transcription factors: role of erythroid Krüppel-like factor (EKLF). Cancer Cell Int 2012; 12:25. [PMID: 22676581 PMCID: PMC3407786 DOI: 10.1186/1475-2867-12-25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 06/07/2012] [Indexed: 11/10/2022] Open
Abstract
We have investigated the role of erythroid transcription factors mRNA expression in patients with acute myeloid leukemia (AML) in the context of cytogenetic and other prognostic molecular markers, such as FMS-like Tyrosine Kinase 3 (FLT3), Nucleophosmin 1 (NPM1), and CCAAT/enhance-binding protein α (CEBPA) mutations. Further validation of Erythroid Krüppel-like Factor (EKLF) mRNA expression as a prognostic factor was assessed.We evaluated GATA binding protein 1 (GATA1), GATA binding protein 2 (GATA2), EKLF and Myeloproliferative Leukemia virus oncogen homology (cMPL) gene mRNA expression in the bone marrow of 65 AML patients at diagnosis, and assessed any correlation with NPM1, FLT3 and CEBPA mutations. EKLF-positive AML was associated with lower WBC in peripheral blood (P = 0.049), a higher percentage of erythroblasts in bone marrow (p = 0.057), and secondary AMLs (P = 0.036). High expression levels of EKLF showed a trend to association with T-cell antigen expression, such as CD7 (P = 0.057). Patients expressing EKLF had longer Overall Survival (OS) and Event Free Survival (EFS) than those patients not expressing EKLF (median OS was 35.61 months and 19.31 months, respectively, P = 0.0241; median EFS was 19.80 months and 8.03 months, respectively, P = 0.0140). No correlation of GATA1, GATA2, EKLF and cMPL levels was observed with FLT-3 or NPM1 mutation status. Four of four CEBPA mutated AMLs were EKLF positive versus 10 of 29 CEBPA wild-type AMLs; three of the CEBPA mutated, EKLF-positive AMLs were also GATA2 positive. There were no cases of CEBPA mutations in the EKLF-negative AML group. In conclusion, we have validated EKLF mRNA expression as an independent predictor of outcome in AML, and its expression is not associated with FLT3-ITD and NPM1 mutations. EKLF mRNA expression in AML patients may correlate with dysregulated CEBPA.
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Affiliation(s)
- Rosa Ayala
- Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain.
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21
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Bresnick EH, Katsumura KR, Lee HY, Johnson KD, Perkins AS. Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies. Nucleic Acids Res 2012; 40:5819-31. [PMID: 22492510 PMCID: PMC3401466 DOI: 10.1093/nar/gks281] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hematopoiesis. While certain GATA-2 target genes are implicated in leukemogenesis, only recently have definitive insights emerged linking GATA-2 to human hematologic pathophysiologies. These pathophysiologies include myelodysplastic syndrome, acute myeloid leukemia and an immunodeficiency syndrome with complex phenotypes including leukemia. As GATA-2 has a pivotal role in the etiology of human cancer, it is instructive to consider mechanisms underlying normal GATA factor function/regulation and how dissecting such mechanisms may reveal unique opportunities for thwarting GATA-2-dependent processes in a therapeutic context. This article highlights GATA factor mechanistic principles, with a heavy emphasis on GATA-1 and GATA-2 functions in the hematopoietic system, and new links between GATA-2 dysregulation and human pathophysiologies.
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Affiliation(s)
- Emery H Bresnick
- Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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22
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Chakraborty S, Datta S, Datta S. Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies. ACTA ACUST UNITED AC 2012; 28:799-806. [PMID: 22238271 DOI: 10.1093/bioinformatics/bts022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
MOTIVATION In a typical gene expression profiling study, our prime objective is to identify the genes that are differentially expressed between the samples from two different tissue types. Commonly, standard analysis of variance (ANOVA)/regression is implemented to identify the relative effects of these genes over the two types of samples from their respective arrays of expression levels. But, this technique becomes fundamentally flawed when there are unaccounted sources of variability in these arrays (latent variables attributable to different biological, environmental or other factors relevant in the context). These factors distort the true picture of differential gene expression between the two tissue types and introduce spurious signals of expression heterogeneity. As a result, many genes which are actually differentially expressed are not detected, whereas many others are falsely identified as positives. Moreover, these distortions can be different for different genes. Thus, it is also not possible to get rid of these variations by simple array normalizations. This both-way error can lead to a serious loss in sensitivity and specificity, thereby causing a severe inefficiency in the underlying multiple testing problem. In this work, we attempt to identify the hidden effects of the underlying latent factors in a gene expression profiling study by partial least squares (PLS) and apply ANCOVA technique with the PLS-identified signatures of these hidden effects as covariates, in order to identify the genes that are truly differentially expressed between the two concerned tissue types. RESULTS We compare the performance of our method SVA-PLS with standard ANOVA and a relatively recent technique of surrogate variable analysis (SVA), on a wide variety of simulation settings (incorporating different effects of the hidden variable, under situations with varying signal intensities and gene groupings). In all settings, our method yields the highest sensitivity while maintaining relatively reasonable values for the specificity, false discovery rate and false non-discovery rate. Application of our method to gene expression profiling for acute megakaryoblastic leukemia shows that our method detects an additional six genes, that are missed by both the standard ANOVA method as well as SVA, but may be relevant to this disease, as can be seen from mining the existing literature.
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Affiliation(s)
- Sutirtha Chakraborty
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
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23
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Overexpression of GATA2 predicts an adverse prognosis for patients with acute myeloid leukemia and it is associated with distinct molecular abnormalities. Leukemia 2011; 26:550-4. [PMID: 21904383 DOI: 10.1038/leu.2011.235] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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24
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The role of the GATA2 transcription factor in normal and malignant hematopoiesis. Crit Rev Oncol Hematol 2011; 82:1-17. [PMID: 21605981 DOI: 10.1016/j.critrevonc.2011.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/18/2011] [Accepted: 04/21/2011] [Indexed: 11/23/2022] Open
Abstract
Hematopoiesis involves an elaborate regulatory network of transcription factors that coordinates the expression of multiple downstream genes, and maintains homeostasis within the hematopoietic system through the accurate orchestration of cellular proliferation, differentiation and survival. As a result, defects in the expression levels or the activity of these transcription factors are intimately linked to hematopoietic disorders, including leukemia. The GATA family of nuclear regulatory proteins serves as a prototype for the action of lineage-restricted transcription factors. GATA1 and GATA2 are expressed principally in hematopoietic lineages, and have essential roles in the development of multiple hematopoietic cells, including erythrocytes and megakaryocytes. Moreover, GATA2 is crucial for the proliferation and maintenance of hematopoietic stem cells and multipotential progenitors. In this review, we summarize the current knowledge regarding the biological properties and functions of the GATA2 transcription factor in normal and malignant hematopoiesis.
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25
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KLFs and ATRA-induced differentiation: new pathways for exploitation. Leuk Res 2011; 35:846-7. [PMID: 21543117 DOI: 10.1016/j.leukres.2011.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 04/02/2011] [Accepted: 04/03/2011] [Indexed: 12/30/2022]
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26
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Bonadies N, Foster SD, Chan WI, Kvinlaug BT, Spensberger D, Dawson MA, Spooncer E, Whetton AD, Bannister AJ, Huntly BJ, Göttgens B. Genome-wide analysis of transcriptional reprogramming in mouse models of acute myeloid leukaemia. PLoS One 2011; 6:e16330. [PMID: 21297973 PMCID: PMC3030562 DOI: 10.1371/journal.pone.0016330] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 12/12/2010] [Indexed: 11/27/2022] Open
Abstract
Acute leukaemias are commonly caused by mutations that corrupt the transcriptional circuitry of haematopoietic stem/progenitor cells. However, the mechanisms underlying large-scale transcriptional reprogramming remain largely unknown. Here we investigated transcriptional reprogramming at genome-scale in mouse retroviral transplant models of acute myeloid leukaemia (AML) using both gene-expression profiling and ChIP-sequencing. We identified several thousand candidate regulatory regions with altered levels of histone acetylation that were characterised by differential distribution of consensus motifs for key haematopoietic transcription factors including Gata2, Gfi1 and Sfpi1/Pu.1. In particular, downregulation of Gata2 expression was mirrored by abundant GATA motifs in regions of reduced histone acetylation suggesting an important role in leukaemogenic transcriptional reprogramming. Forced re-expression of Gata2 was not compatible with sustained growth of leukaemic cells thus suggesting a previously unrecognised role for Gata2 in downregulation during the development of AML. Additionally, large scale human AML datasets revealed significantly higher expression of GATA2 in CD34+ cells from healthy controls compared with AML blast cells. The integrated genome-scale analysis applied in this study represents a valuable and widely applicable approach to study the transcriptional control of both normal and aberrant haematopoiesis and to identify critical factors responsible for transcriptional reprogramming in human cancer.
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Affiliation(s)
- Nicolas Bonadies
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Samuel D. Foster
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Wai-In Chan
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Brynn T. Kvinlaug
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Dominik Spensberger
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Mark A. Dawson
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Elaine Spooncer
- School of Cancer and Imaging Sciences, University of Manchester, Manchester, United Kingdom
| | - Anthony D. Whetton
- School of Cancer and Imaging Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew J. Bannister
- Gurdon Institute and Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Brian J. Huntly
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
- * E-mail:
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27
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GATA factors in human neuroblastoma: distinctive expression patterns in clinical subtypes. Br J Cancer 2009; 101:1481-9. [PMID: 19707195 PMCID: PMC2768442 DOI: 10.1038/sj.bjc.6605276] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background: The aim of this study is to elucidate the expression patterns of GATA transcription factors in neuroblastoma and the developing sympathetic nervous system (SNS). Methods: GATA-2, -3 and -4 and their cofactor friend-of-GATA (FOG)-2 were investigated in primary neuroblastoma by immunohistochemistry, real-time RT-PCR (n=73) and microarray analysis (n=251). In addition, GATA-2, -3 and FOG-2 expression was determined by northern-blot hybridisation. In the developing murine SNS, Gata-4 and Fog-2 were examined by immunohistochemistry. Results: Although Gata-2, -3 and Fog-2 are expressed in the developing nervous system, Gata-4 was not detected. In contrast, protein expression of all factors was observed in human neuroblastoma. Northern-blot hybridisation and real-time RT-PCR suggested specific expression patterns of the four genes in primary neuroblastoma, but did not show unequivocal results. In the large cohort examined by microarrays, a significant association of GATA-2, -3 and FOG-2 expression with low-risk features was observed, whereas GATA-4 mRNA levels correlated with MYCN-amplification. Conclusion: The transcription factors GATA-2 and -3, which are essential for normal SNS development, and their cofactor FOG-2 are downregulated in aggressive but not in favourable neuroblastoma. In contrast, upregulation of GATA-4 appears to be a common feature of this malignancy and might contribute to neuroblastoma pathogenesis.
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