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Ong JZL, Tan TK, Wang L, Tan SH, Sanda T. Regulatory mechanisms and context-dependent roles of TAL1 in T-cell acute lymphoblastic leukemia. Haematologica 2024; 109:1359-1372. [PMID: 37855064 PMCID: PMC11063860 DOI: 10.3324/haematol.2023.283450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy derived from thymic T-cell precursors. Approximately 40-60% of T-ALL cases exhibit aberrant overexpression of the TAL1 oncogenic transcription factor. Here, we provide a comprehensive view of the TAL1-induced transcriptional program in human T-ALL cells using a rapid protein degradation system coupled with integrative approaches. Our study demonstrates that TAL1 targets can be classified into several groups, each of which exhibits unique gene expression kinetics, chromatin features, and regulatory mechanisms. Group A genes are highly dependent on TAL1, many of which are not expressed in normal T cells or TAL1-negative T-ALL cells, representing an oncogenic TAL1 signature. The TAL1 complex predominantly activates group A genes. TAL1's effect is not replaceable with its regulatory partners GATA3 or RUNX1. In contrast, group B genes, many of which are generally expressed across different T-ALL subgroups, exhibit densely-connected chromatin-chromatin interactions and demonstrate the collaborative roles played by TAL1 with other transcription factors. Interestingly, TAL1 cooperates with NOTCH1 to regulate gene expression in TAL1-positive T-ALL cells, whereas it potentially antagonizes the NOTCH1-MYC pathway and leads to lethality in TAL1-negative/ TLX3-positive cells, demonstrating the context-dependent roles of TAL1.
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Affiliation(s)
- Jolynn Zu Lin Ong
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Lu Wang
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599; Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya.
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2
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Geng X, Wang C, Abdelrahman S, Perera T, Saed B, Hu YS, Wolfe A, Reneau J, Murga-Zamalloa C, Wilcox RA. GATA-3-dependent Gene Transcription is Impaired upon HDAC Inhibition. Clin Cancer Res 2024; 30:1054-1066. [PMID: 38165708 PMCID: PMC10922852 DOI: 10.1158/1078-0432.ccr-23-1699] [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: 06/06/2023] [Revised: 07/24/2023] [Accepted: 12/19/2023] [Indexed: 01/04/2024]
Abstract
PURPOSE Many peripheral and cutaneous T-cell lymphoma (CTCL) subtypes are poorly responsive to conventional chemotherapeutic agents and associated with dismal outcomes. The zinc finger transcription factor GATA-3 and the transcriptional program it instigates are oncogenic and highly expressed in various T-cell neoplasms. Posttranslational acetylation regulates GATA-3 DNA binding and target gene expression. Given the widespread use of histone deacetylase inhibitors (HDACi) in relapsed/refractory CTCL, we sought to examine the extent to which these agents attenuate the transcriptional landscape in these lymphomas. EXPERIMENTAL DESIGN Integrated GATA-3 chromatin immunoprecipitation sequencing and RNA sequencing analyses were performed in complementary cell line models and primary CTCL specimens treated with clinically available HDACi. RESULTS We observed that exposure to clinically available HDACi led to significant transcriptional reprogramming and increased GATA-3 acetylation. HDACi-dependent GATA-3 acetylation significantly impaired both its ability to bind DNA and transcriptionally regulate its target genes, thus leading to significant transcriptional reprogramming in HDACi-treated CTCL. CONCLUSIONS Beyond shedding new light on the mechanism of action associated with HDACi in CTCL, these findings have significant implications for their use, both as single agents and in combination with other novel agents, in GATA-3-driven lymphoproliferative neoplasms.
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Affiliation(s)
- Xiangrong Geng
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | - Chenguang Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | - Suhaib Abdelrahman
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL
| | - Ashley Wolfe
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | - John Reneau
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Ryan A. Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
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3
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Yang Y, Yang Y, Shen Y, Liu J, Zeng Y, Wei C, Liu C, Pan Y, Guo Q, Zhong F, Guo L, Liu W. Exploring the pharmacological mechanisms of Shuanghuanglian against T-cell acute lymphoblastic leukaemia through network pharmacology combined with molecular docking and experimental validation. PHARMACEUTICAL BIOLOGY 2023; 61:259-270. [PMID: 36656546 PMCID: PMC9858418 DOI: 10.1080/13880209.2023.2168703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 06/12/2023]
Abstract
CONTEXT Due to the poor prognosis of T-cell acute lymphoblastic leukaemia (T-ALL), there is an urgent need to identify safer and more cost-effective drugs. OBJECTIVE This study evaluated the antitumour activity of Shuanghuanglian (SHL) on T-ALL cells and elucidated the mechanism. MATERIALS AND METHODS Jurkat and Molt4 cells were treated with SHL (0.1, 0.2 and 0.4 mg/mL) for 24 and 48 h. The controls were treated with RPMI 1640 containing 10% foetal bovine serum. Cell viability was evaluated through Cell Counting Kit-8 assay. Patterns of death and signalling pathway alterations caused by SHL were identified by network pharmacology combined with GO enrichment analysis and then were verified by Hoechst 33342 staining, Annexin V-FITC/PI staining and Western blotting. Interactions of the active ingredients with targets were analysed by molecular docking. RESULTS The IC50 values of SHL in Jurkat and Molt4 cells were 0.30 ± 0.10 and 0.48 ± 0.07 mg/mL, respectively, at 24 h and 0.27 ± 0.05 and 0.30 ± 0.03 mg/mL at 48 h. In T-ALL, 117 target genes of SHL were mainly enriched in the apoptosis and NOTCH signalling pathways. SHL induced apoptosis was confirmed by Hoechst 33342 staining and flow cytometry. The protein levels of cleaved caspase-7 and cleaved PARP were significantly increased but those of cleaved NOTCH1 and MYC were reduced. The active ingredients of SHL can interact with γ-secretase.Discussion and conclusions: SHL induces apoptosis in T-ALL cells via the NOTCH1-MYC pathway and may be a potential drug for the treatment of T-ALL.
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Affiliation(s)
- You Yang
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yan Yang
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yunfu Shen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jing Liu
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yan Zeng
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Chengming Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Chunyan Liu
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yansha Pan
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Fangfang Zhong
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Ling Guo
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
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4
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Bernabé-Rubio M, Ali S, Bhosale PG, Goss G, Mobasseri SA, Tapia-Rojo R, Zhu T, Hiratsuka T, Battilocchi M, Tomás IM, Ganier C, Garcia-Manyes S, Watt FM. Myc-dependent dedifferentiation of Gata6 + epidermal cells resembles reversal of terminal differentiation. Nat Cell Biol 2023; 25:1426-1438. [PMID: 37735598 PMCID: PMC10567550 DOI: 10.1038/s41556-023-01234-5] [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: 01/12/2022] [Accepted: 08/16/2023] [Indexed: 09/23/2023]
Abstract
Dedifferentiation is the process by which terminally differentiated cells acquire the properties of stem cells. During mouse skin wound healing, the differentiated Gata6-lineage positive cells of the sebaceous duct are able to dedifferentiate. Here we have integrated lineage tracing and single-cell mRNA sequencing to uncover the underlying mechanism. Gata6-lineage positive and negative epidermal stem cells in wounds are transcriptionally indistinguishable. Furthermore, in contrast to reprogramming of induced pluripotent stem cells, the same genes are expressed in the epidermal dedifferentiation and differentiation trajectories, indicating that dedifferentiation does not involve adoption of a new cell state. We demonstrate that dedifferentiation is not only induced by wounding, but also by retinoic acid treatment or mechanical expansion of the epidermis. In all three cases, dedifferentiation is dependent on the master transcription factor c-Myc. Mechanotransduction and actin-cytoskeleton remodelling are key features of dedifferentiation. Our study elucidates the molecular basis of epidermal dedifferentiation, which may be generally applicable to adult tissues.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Shahnawaz Ali
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Priyanka G Bhosale
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Georgina Goss
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | | | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Tong Zhu
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Toru Hiratsuka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
- Department of Oncogenesis and Growth Regulation, Research Center, Osaka International Cancer Institute, Chuoku, Japan
| | - Matteo Battilocchi
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Inês M Tomás
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK.
- Directors' Unit, EMBL Heidelberg, Heidelberg, Germany.
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5
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Oh S, Parikh D, Xiao J, Liu X, Gu K, Chong MMW. Mapping the two distinct proliferative bursts early in T-cell development. Immunol Cell Biol 2023; 101:766-774. [PMID: 37465975 PMCID: PMC10952215 DOI: 10.1111/imcb.12670] [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: 03/23/2023] [Revised: 05/17/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
Abstract
T-cell development occurs in the thymus and is tightly regulated to produce a diverse enough repertoire of mature T cells that can recognize any potential pathogen. The development of T cells is dependent on small numbers of uncommitted precursors that continually seed the thymus from the bone marrow. As they progress along the developmental pathway, there is a massive expansion in cell number to generate the necessary diversity in T-cell receptor chain usage. It is recognized that there are two proliferative bursts that occur early in T-cell development, one prior to β-selection and one after, and these are responsible for the expansion. While the proliferation following β-selection is well-characterized, the earlier proliferative burst has yet to be precisely defined. In this study, we employ single-cell RNA sequencing coupled to trajectory inference methods to pinpoint when in T-cell development thymocytes are induced into cell cycle. We show that the first proliferative burst is initiated in the double-negative (DN) 2a stage before T lineage commitment occurs, with cell cycling downregulated by the DN3a stage. A second burst is then initiated at the DN3b stage, immediately after β-selection. We subsequently employ fluorescence-activated cell sorting-based analysis for DNA content to confirm these two proliferative bursts.
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Affiliation(s)
- Seungyoul Oh
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
- Department of Medicine (St Vincent's)University of MelbourneFitzroyVICAustralia
| | - Dhruti Parikh
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
- Department of Medicine (St Vincent's)University of MelbourneFitzroyVICAustralia
| | - Jiyao Xiao
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
- Faculty of ScienceUniversity of MelbourneParkvilleVICAustralia
| | - Xin Liu
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
| | - Karen Gu
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
| | - Mark MW Chong
- St Vincent's Institute of Medical ResearchFitzroyVICAustralia
- Department of Medicine (St Vincent's)University of MelbourneFitzroyVICAustralia
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6
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Toribio ML, González-García S. Notch Partners in the Long Journey of T-ALL Pathogenesis. Int J Mol Sci 2023; 24:ijms24021383. [PMID: 36674902 PMCID: PMC9866461 DOI: 10.3390/ijms24021383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological disease that arises from the oncogenic transformation of developing T cells during T-lymphopoiesis. Although T-ALL prognosis has improved markedly in recent years, relapsing and refractory patients with dismal outcomes still represent a major clinical issue. Consequently, understanding the pathological mechanisms that lead to the appearance of this malignancy and developing novel and more effective targeted therapies is an urgent need. Since the discovery in 2004 that a major proportion of T-ALL patients carry activating mutations that turn NOTCH1 into an oncogene, great efforts have been made to decipher the mechanisms underlying constitutive NOTCH1 activation, with the aim of understanding how NOTCH1 dysregulation converts the physiological NOTCH1-dependent T-cell developmental program into a pathological T-cell transformation process. Several molecular players have so far been shown to cooperate with NOTCH1 in this oncogenic process, and different therapeutic strategies have been developed to specifically target NOTCH1-dependent T-ALLs. Here, we comprehensively analyze the molecular bases of the cross-talk between NOTCH1 and cooperating partners critically involved in the generation and/or maintenance and progression of T-ALL and discuss novel opportunities and therapeutic approaches that current knowledge may open for future treatment of T-ALL patients.
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7
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Al-Khreisat MJ, Hussain FA, Abdelfattah AM, Almotiri A, Al-Sanabra OM, Johan MF. The Role of NOTCH1, GATA3, and c-MYC in T Cell Non-Hodgkin Lymphomas. Cancers (Basel) 2022; 14:cancers14112799. [PMID: 35681778 PMCID: PMC9179380 DOI: 10.3390/cancers14112799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Lymphomas are heterogeneous malignant tumours of white blood cells characterised by the aberrant proliferation of mature lymphoid cells or their precursors. Lymphomas are classified into main types depending on the histopathologic evidence of biopsy taken from an enlarged lymph node, progress stages, treatment strategies, and outcomes: Hodgkin and non-Hodgkin lymphoma (NHL). Moreover, lymphomas can be further divided into subtypes depending on the cell origin, and immunophenotypic and genetic aberrations. Many factors play vital roles in the progression, pathogenicity, incidence, and mortality rate of lymphomas. Among NHLs, peripheral T cell lymphomas (PTCLs) are rare lymphoid malignancies, that have various cellular morphology and genetic mutations. The clinical presentations are usually observed at the advanced stage of the disease. Many recent studies have reported that the expressions of NOTCH1, GATA3, and c-MYC are associated with poorer prognosis in PTCL and are involved in downstream activities. However, questions have been raised about the pathological relationship between these factors in PTCLs. Therefore, in this review, we investigate the role and relationship of the NOTCH1 pathway, transcriptional factor GATA3 and proto-oncogene c-MYC in normal T cell development and malignant PTCL subtypes.
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Affiliation(s)
- Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Ali Mahmoud Abdelfattah
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Alhomidi Almotiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences—Dawadmi, Shaqra University, Dawadmi 17464, Saudi Arabia;
| | - Ola Mohammed Al-Sanabra
- Department of Medical Laboratory Sciences, Faculty of Science, Al-Balqa Applied University, Al-Salt 19117, Jordan;
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Correspondence: ; Tel.: +60-97-67-62-00
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8
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Parriott G, Kee BL. E Protein Transcription Factors as Suppressors of T Lymphocyte Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:885144. [PMID: 35514954 PMCID: PMC9065262 DOI: 10.3389/fimmu.2022.885144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
T Lymphocyte Acute Lymphoblastic Leukemia (ALL) is an aggressive disease arising from transformation of T lymphocytes during their development. The mutation spectrum of T-ALL has revealed critical regulators of the growth and differentiation of normal and leukemic T lymphocytes. Approximately, 60% of T-ALLs show aberrant expression of the hematopoietic stem cell-associated helix-loop-helix transcription factors TAL1 and LYL1. TAL1 and LYL1 function in multiprotein complexes that regulate gene expression in T-ALL but they also antagonize the function of the E protein homodimers that are critical regulators of T cell development. Mice lacking E2A, or ectopically expressing TAL1, LYL1, or other inhibitors of E protein function in T cell progenitors, also succumb to an aggressive T-ALL-like disease highlighting that E proteins promote T cell development and suppress leukemogenesis. In this review, we discuss the role of E2A in T cell development and how alterations in E protein function underlie leukemogenesis. We focus on the role of TAL1 and LYL1 and the genes that are dysregulated in E2a-/- T cell progenitors that contribute to human T-ALL. These studies reveal novel mechanisms of transformation and provide insights into potential therapeutic targets for intervention in this disease.
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Affiliation(s)
- Geoffrey Parriott
- Committee on Immunology, University of Chicago, Chicago, IL, United States
| | - Barbara L Kee
- Committee on Immunology, University of Chicago, Chicago, IL, United States.,Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.,Department of Pathology, University of Chicago, Chicago, IL, United States
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9
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Antoszewski M, Fournier N, Ruiz Buendía GA, Lourenco J, Liu Y, Sugrue T, Dubey C, Nkosi M, Pritchard CE, Huijbers IJ, Segat GC, Alonso-Moreno S, Serracanta E, Belver L, Ferrando AA, Ciriello G, Weng AP, Koch U, Radtke F. Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL. Blood 2022; 139:2483-2498. [PMID: 35020836 PMCID: PMC9710489 DOI: 10.1182/blood.2021012077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape during T-ALL initiation is unknown. Here we demonstrate an essential role for the high-mobility-group transcription factor Tcf1 in orchestrating chromatin accessibility and topology, allowing aberrant Notch1 signaling to convey its oncogenic function. Although essential, Tcf1 is not sufficient to initiate leukemia. The formation of a leukemia-prone epigenetic landscape at the distal Notch1-regulated Myc enhancer, which is fundamental to this disease, is Tcf1-dependent and occurs within the earliest progenitor stage even before cells adopt a T lymphocyte or leukemic fate. Moreover, we discovered a unique evolutionarily conserved Tcf1-regulated enhancer element in the distal Myc-enhancer, which is important for the transition of preleukemic cells to full-blown disease.
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Affiliation(s)
- Mateusz Antoszewski
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Nadine Fournier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Gustavo A. Ruiz Buendía
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Joao Lourenco
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yuanlong Liu
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Tara Sugrue
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Botnar Research Centre for Child Health, University of Basel & ETH Zürich, Basel, Switzerland
| | - Christelle Dubey
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- INSELSPITAL, Universitätsspital Bern, Universitätsklinik für Thoraxchirurgie, Forschungsabteilung Thoraxchirurgie, Bern, Switzerland
| | - Marianne Nkosi
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Colin E.J. Pritchard
- Mouse Clinic for Cancer & Aging (MCCA)/Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivo J. Huijbers
- Mouse Clinic for Cancer & Aging (MCCA)/Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Laura Belver
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Catalan Institute of Oncology-Immuno Procure, Barcelona, Spain
| | - Adolfo A. Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Giovanni Ciriello
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Ute Koch
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Freddy Radtke
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
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10
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Firing up chromatin to forge T-ALL. Blood 2022; 139:2418-2420. [PMID: 35446377 DOI: 10.1182/blood.2021015364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
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11
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Date Y, Taniuchi I, Ito K. Oncogenic Runx1-Myc axis in p53-deficient thymic lymphoma. Gene 2022; 819:146234. [PMID: 35114276 DOI: 10.1016/j.gene.2022.146234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 11/04/2022]
Abstract
p53 deficiency and Myc dysregulation are frequently associated with cancer. However, the molecular mechanisms linking these two major oncogenic events are poorly understood. Using an osteosarcoma model caused by p53 loss, we have recently shown that Runx3 aberrantly upregulates Myc via mR1, a Runx consensus site in the Myc promoter. Here, we focus on thymic lymphoma, a major tumour type caused by germline p53 deletion in mice, and examine whether the oncogenic Runx-Myc axis plays a notable role in the development of p53-deficient lymphoma. Mice lacking p53 specifically in thymocytes (LP mice) mostly succumbed to thymic lymphoma. Runx1 and Myc were upregulated in LP mouse lymphoma compared with the normal thymus. Depletion of Runx1 or Myc prolonged the lifespan of LP mice and suppressed lymphoma development. In lymphoma cells isolated from LP mice, knockdown of Runx1 led to Myc suppression, weakening their tumour forming ability in immunocompromised mice. The mR1 locus was enriched by both Runx1 and H3K27ac, an active chromatin marker. LP mice with mutated mR1 had a longer lifespan and a lower incidence of lymphoma. Treatment with AI-10-104, a Runx inhibitor, improved the survival of LP mice. These results suggest that Myc upregulation by Runx1 is a key event in p53-deficient thymic lymphoma development and provide a clinical rationale for targeting the Runx family in p53-deficient malignancies.
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Affiliation(s)
- Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
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12
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Myc-Interacting Zinc Finger Protein 1 (Miz-1) Is Essential to Maintain Homeostasis and Immunocompetence of the B Cell Lineage. BIOLOGY 2022; 11:biology11040504. [PMID: 35453704 PMCID: PMC9027237 DOI: 10.3390/biology11040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022]
Abstract
Aging of the immune system is described as a progressive loss of the ability to respond to immunologic stimuli and is commonly referred to as immunosenescence. B cell immunosenescence is characterized by a decreased differentiation rate in the bone marrow and accumulation of antigen-experienced and age-associated B cells in secondary lymphoid organs (SLOs). A specific deletion of the POZ-domain of the transcription factor Miz-1 in pro-B cells, which is known to be involved in bone marrow hematopoiesis, leads to premature aging of the B cell lineage. In mice, this causes a severe reduction in bone marrow-derived B cells with a drastic decrease from the pre-B cell stage on. Further, mature, naïve cells in SLOs are reduced at an early age, while post-activation-associated subpopulations increase prematurely. We propose that Miz-1 interferes at several key regulatory checkpoints, critical during B cell aging, and counteracts a premature loss of immunocompetence. This enables the use of our mouse model to gain further insights into mechanisms of B cell aging and it can significantly contribute to understand molecular causes of impaired adaptive immune responses to counteract loss of immunocompetence and restore a functional immune response in the elderly.
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13
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Benbarche S, Lopez CK, Salataj E, Aid Z, Thirant C, Laiguillon MC, Lecourt S, Belloucif Y, Vaganay C, Antonini M, Hu J, da Silva Babinet A, Ndiaye-Lobry D, Pardieu B, Petit A, Puissant A, Chaumeil J, Mercher T, Lobry C. Screening of ETO2-GLIS2-induced Super Enhancers identifies targetable cooperative dependencies in acute megakaryoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabg9455. [PMID: 35138899 PMCID: PMC8827662 DOI: 10.1126/sciadv.abg9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Super Enhancers (SEs) are clusters of regulatory elements associated with cell identity and disease. However, whether these elements are induced by oncogenes and can regulate gene modules cooperating for cancer cell transformation or maintenance remains elusive. To address this question, we conducted a genome-wide CRISPRi-based screening of SEs in ETO2-GLIS2+ acute megakaryoblastic leukemia. This approach revealed SEs essential for leukemic cell growth and survival that are induced by ETO2-GLIS2 expression. In particular, we identified a de novo SE specific of this leukemia subtype and regulating expression of tyrosine kinase-associated receptors KIT and PDGFRA. Combined expression of these two receptors was required for leukemic cell growth, and CRISPRi-mediated inhibition of this SE or treatment with tyrosine kinase inhibitors impaired progression of leukemia in vivo in patient-derived xenografts experiments. Our results show that fusion oncogenes, such as ETO2-GLIS2, can induce activation of SEs regulating essential gene modules synergizing for leukemia progression.
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Affiliation(s)
- Salima Benbarche
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Cécile K. Lopez
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Eralda Salataj
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Zakia Aid
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Cécile Thirant
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | | | - Séverine Lecourt
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Yannis Belloucif
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Camille Vaganay
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Marion Antonini
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Jiang Hu
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | | | | | - Bryann Pardieu
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Arnaud Petit
- Hôpital Trousseau, Sorbonne Université, Assistance Publique - Hôpitaux de Paris CONECT-AML, Paris F-75012, France
| | - Alexandre Puissant
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Julie Chaumeil
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
- Corresponding author. (C.L.); (T.M.)
| | - Camille Lobry
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
- Corresponding author. (C.L.); (T.M.)
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14
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Yang H, Zhang H, Luan Y, Liu T, Yang W, Roberts KG, Qian MX, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, Gastier-Foster J, Smith C, Pui CH, Evans WE, Hunger SP, Platanias LC, Relling MV, Mullighan CG, Loh ML, Yue F, Yang JJ. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Nat Genet 2022; 54:170-179. [PMID: 35115686 PMCID: PMC9794680 DOI: 10.1038/s41588-021-00993-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/29/2021] [Indexed: 12/31/2022]
Abstract
Inherited noncoding genetic variants confer significant disease susceptibility to childhood acute lymphoblastic leukemia (ALL) but the molecular processes linking germline polymorphisms with somatic lesions in this cancer are poorly understood. Through targeted sequencing in 5,008 patients, we identified a key regulatory germline variant in GATA3 associated with Philadelphia chromosome-like ALL (Ph-like ALL). Using CRISPR-Cas9 editing and samples from patients with Ph-like ALL, we showed that this variant activated a strong enhancer that upregulated GATA3 transcription. This, in turn, reshaped global chromatin accessibility and three-dimensional genome organization, including regions proximal to the ALL oncogene CRLF2. Finally, we showed that GATA3 directly regulated CRLF2 and potentiated the JAK-STAT oncogenic effects during leukemogenesis. Taken together, we provide evidence for a distinct mechanism by which a germline noncoding variant contributes to oncogene activation, epigenetic regulation and three-dimensional genome reprogramming.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao-Xiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, PA, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Internal Medicine Department, MountainView Hospital, University of Reno, Las Vegas, NV, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Da Kuang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Lena A Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Shalini C Reshmi
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Julie Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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Ma Y, Guo G, Li T, Wen F, Yang J, Chen B, Wang X, Chen JL. A novel imatinib-upregulated long noncoding RNA plays a critical role in inhibition of tumor growth induced by Abl oncogenes. Mol Cancer 2022; 21:5. [PMID: 34980123 PMCID: PMC8722111 DOI: 10.1186/s12943-021-01478-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dysregulation of long noncoding RNAs (lncRNAs) has been linked to various human cancers. Bcr-Abl oncogene that results from a reciprocal translocation between human chromosome 9 and 22, is associated with several hematological malignancies. However, the role of lncRNAs in Bcr-Abl-induced leukemia remains largely unexplored. METHODS LncRNA cDNA microarray was employed to identify key lncRNAs involved in Bcr-Abl-mediated cellular transformation. Abl-transformed cell survival and xenografted tumor growth in mice were evaluated to dissect the role of imatinib-upregulated lncRNA 1 (IUR1) in Abl-induced tumorigenesis. Primary bone marrow transformation and in vivo leukemia transplant using lncRNA-IUR1 knockout (KO) mice were further conducted to address the functional relevance of lncRNA-IUR1 in Abl-mediated leukemia. Transcriptome RNA-seq and Western blotting were performed to determine the mechanisms by which lncRNA-IUR1 regulates Bcr-Abl-induced tumorigenesis. RESULTS We identified lncRNA-IUR1 as a critical negative regulator of Bcr-Abl-induced tumorigenesis. LncRNA-IUR1 expressed in a very low level in Bcr-Abl-positive cells from chronic myeloid leukemia patients. Interestingly, it was significantly induced in Abl-positive leukemic cells treated by imatinib. Depletion of lncRNA-IUR1 promoted survival of Abl-transformed human leukemic cells in experiments in vitro and xenografted tumor growth in mice, whereas ectopic expression of lncRNA-IUR1 sensitized the cells to apoptosis and suppressed tumor growth. In concert, silencing murine lncRNA-IUR1 in Abl-transformed cells accelerated cell survival and the development of leukemia in mice. Furthermore, lncRNA-IUR1 deficient mice were generated, and we observed that knockout of murine lncRNA-IUR1 facilitated Bcr-Abl-mediated primary bone marrow transformation. Moreover, animal leukemia model revealed that lncRNA-IUR1 deficiency promoted Abl-transformed cell survival and development of leukemia in mice. Mechanistically, we demonstrated that lncRNA-IUR1 suppressed Bcr-Abl-induced tumorigenesis through negatively regulating STAT5-mediated GATA3 expression. CONCLUSIONS These findings unveil an inhibitory role of lncRNA-IUR1 in Abl-mediated cellular transformation, and provide new insights into molecular mechanisms underlying Abl-induced leukemogenesis.
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Affiliation(s)
- Yun Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guijie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tingting Li
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Faxin Wen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianling Yang
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, 100191, China
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefei Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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16
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Chu X, Qian M, Yang J, Wu D, Gao J, Cao L, Fang F, Pan J, Zhang H, Hu S. Effect of GATA3 rs3824662 gene polymorphism in Han Chinese children with pre-B-cell acute lymphoblastic leukemia with 10 years follow-up. Front Pediatr 2022; 10:1044866. [PMID: 36714653 PMCID: PMC9875006 DOI: 10.3389/fped.2022.1044866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
PURPOSE To evaluate the influence of GATA3 rs3824662 on pre-B-cell acute lymphoblastic leukemia (pre-B-cell ALL) susceptibility and long-term prognosis in Han Chinese children with pre-B-cell ALL treated with the CCLG-2008 protocol at the Children's Hospital of Soochow University. METHODS A total of 256 patients with childhood pre-B-cell ALL under the CCLG-2008 protocol were enrolled in this study, and 174 healthy children were used as case controls. GATA3 rs3824662 genotyping was performed using a polymerase chain reaction, followed by Sanger sequencing. The association of genotype with clinical characteristics, treatment response, adverse events, and outcomes were analyzed. RESULTS The A allele frequency of GATA3 rs3824662 in patients with pre-B cell ALL was significantly higher than that in healthy children (OR = 1.41, 95% CI = 1.042-1.908; P = 0.026). Among patients with pre-B-cell ALL, the GATA3 rs3824662 AA genotype was associated with poor prednisolone response and high blast cell burden on day 15 of the induction therapy (P = 0.011 and 0.007, respectively). Patients with the rs3824662 AA variant suffered more episodes of sepsis than those with the CC or CA variants (P = 0.021). The GATA3 rs3824662 AA genotype was significantly associated with sepsis [hazard ratio (HR) = 3.375; P = 0.01]. No significant differences were found in the cumulative incidence of relapse, overall survival, and event-free survival among all genotypes. CONCLUSION GATA3 rs3824662 was associated with susceptibility in Han Chinese children with pre-B-cell ALL and could be a possible risk factor for poor early treatment response and treatment-related sepsis.
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Affiliation(s)
- Xinran Chu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Maoxiang Qian
- Department of Hematology and Oncology, Institute of Biomedical Sciences, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Yang
- Department of Pediatrics, Subei People's Hospital of Jiangsu Province, Yangzhou, China
| | - Dong Wu
- Department of Pediatrics, Yiyuan People's Hospital, Zibo, China
| | - Jing Gao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Lu Cao
- Department of Emergency, Children's Hospital of Soochow University, Suzhou, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Hui Zhang
- Department of Hematology and Oncology, Fujian Branch of Shanghai Children's Medical Center, Fujian Children's Hospital, Fuzhou, China.,Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
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17
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Rashkovan M, Albero R, Gianni F, Perez-Duran P, Miller HI, Mackey AL, Paietta EM, Tallman MS, Rowe JM, Litzow MR, Wiernik PH, Luger S, Sulis ML, Soni RK, Ferrando AA. Intracellular cholesterol pools regulate oncogenic signaling and epigenetic circuitries in Early T-cell Precursor Acute Lymphoblastic Leukemia. Cancer Discov 2021; 12:856-871. [PMID: 34711640 DOI: 10.1158/2159-8290.cd-21-0551] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022]
Abstract
Early T-cell acute lymphoblastic leukemia (ETP-ALL) is an aggressive hematologic malignancy associated with early relapse and poor prognosis that is genetically, immunophenotypically and transcriptionally distinct from more mature T-cell acute lymphoblastic (T-ALL) tumors. Here, we leveraged global metabolomic and transcriptomic profiling of primary ETP and T-ALL leukemia samples to identify specific metabolic circuitries differentially active in this high-risk leukemia group. ETP-ALLs showed increased biosynthesis of phospholipids and sphingolipids, and were specifically sensitive to inhibition of 3-hydroxy-3-methylglutaryl-CoA Reductase (HMGCR), the rate-limiting enzyme in the mevalonate pathway. Mechanistically, inhibition of cholesterol synthesis inhibited oncogenic AKT1 signaling and suppressed MYC expression via loss of chromatin accessibility at a leukemia stem cell-specific long range MYC enhancer. In all, these results identify the mevalonate pathway as a druggable novel vulnerability in high-risk ETP-ALL cells and uncover an unanticipated critical role for cholesterol biosynthesis in signal transduction and epigenetic circuitries driving leukemia cell growth and survival.
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Affiliation(s)
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University Medical Center
| | - Francesca Gianni
- Institute for Cancer Genetics, Columbia University Medical Center
| | | | - Hannah I Miller
- Institute for Cancer Genetics, Columbia University Medical Center
| | - Adam L Mackey
- Institute for Cancer Genetics, Columbia University Medical Center
| | - Elisabeth M Paietta
- Montefiore Medical Center-North Division, Albert Einstein College of Medicine
| | - Martin S Tallman
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center
| | - Jacob M Rowe
- Department of Hematology and Bone Marrow Transplantation, Rambam Medical Center and Technion
| | - Mark R Litzow
- Division of Hematology and Department of Internal Medicine, Mayo Clinic
| | | | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania
| | | | - Rajesh K Soni
- Proteomics Core Facility, Columbia University Medical Center
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18
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MYC in T-cell acute lymphoblastic leukemia: functional implications and targeted strategies. BLOOD SCIENCE 2021; 3:65-70. [PMID: 35402840 PMCID: PMC8974894 DOI: 10.1097/bs9.0000000000000073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/03/2021] [Indexed: 01/12/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer that frequently occurs in children and adolescents, which results from the transformation of immature T-cell progenitors. Aberrant cell growth and proliferation of T-ALL lymphoblasts are sustained by activation of strong oncogenic drivers. Mounting evidence highlights the critical role of the NOTCH1-MYC highway toward the initiation and progression of T-ALL. MYC has been emphasized as a primary NOTCH1 transcriptional target impinging in leukemia-initiating cell activity particularly responsible for disease onset and relapse. These findings lay a foundation of T-ALL as an ideal disease model for studying MYC-mediated cancer. The biology of MYC deregulation in T-ALL supports innovative strategies for therapeutic targeting of MYC. To summarize the relevant literature and data in recent years, we here provide a comprehensive overview of the functional importance of MYC in T-ALL development, and the molecular mechanisms underlying MYC deregulation in T-ALL. Finally, we illustrate the innovative MYC-targeted approaches that have been evaluated in pre-clinical models and shown significant efficacy. Given the complexity of T-ALL molecular pathogenesis, we propose that a combination of anti-MYC strategies with conventional chemotherapies or other targeted/immunotherapies may provide the most durable response, especially for those patients with relapsed and refractory T-ALL.
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19
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EBF1 and PAX5 control pro-B cell expansion via opposing regulation of the Myc gene. Blood 2021; 137:3037-3049. [PMID: 33619557 DOI: 10.1182/blood.2020009564] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Genes encoding B lineage-restricted transcription factors are frequently mutated in B-lymphoid leukemias, suggesting a close link between normal and malignant B-cell development. One of these transcription factors is early B-cell factor 1 (EBF1), a protein of critical importance for lineage specification and survival of B-lymphoid progenitors. Here, we report that impaired EBF1 function in mouse B-cell progenitors results in reduced expression of Myc. Ectopic expression of MYC partially rescued B-cell expansion in the absence of EBF1 both in vivo and in vitro. Using chromosome conformation analysis in combination with ATAC-sequencing, chromatin immunoprecipitation-sequencing, and reporter gene assays, six EBF1-responsive enhancer elements were identified within the Myc locus. CRISPR-Cas9-mediated targeting of EBF1-binding sites identified one element of key importance for Myc expression and pro-B cell expansion. These data provide evidence that Myc is a direct target of EBF1. Furthermore, chromatin immunoprecipitation-sequencing analysis revealed that several regulatory elements in the Myc locus are targets of PAX5. However, ectopic expression of PAX5 in EBF1-deficient cells inhibits the cell cycle and reduces Myc expression, suggesting that EBF1 and PAX5 act in an opposing manner to regulate Myc levels. This hypothesis is further substantiated by the finding that Pax5 inactivation reduces requirements for EBF1 in pro-B-cell expansion. The binding of EBF1 and PAX5 to regulatory elements in the human MYC gene in a B-cell acute lymphoblastic leukemia cell line indicates that the EBF1:PAX5:MYC regulatory loop is conserved and may control both normal and malignant B-cell development.
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20
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Belver L, Albero R, Ferrando AA. Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia. Trends Immunol 2021; 42:418-431. [PMID: 33858773 PMCID: PMC8091164 DOI: 10.1016/j.it.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
Enhancers control dynamic changes in gene expression and orchestrate the tightly controlled transcriptional circuitries that direct and coordinate cell growth, proliferation, survival, lineage commitment, and differentiation during lymphoid development. Enhancer hijacking and neoenhancer formation at oncogene loci, as well as aberrant activation of oncogene-associated enhancers, can induce constitutive activation of self-perpetuating oncogenic transcriptional circuitries, and contribute to the malignant transformation of immature lymphoid progenitors in acute lymphoblastic leukemia (ALL). In this review, we present recent discoveries of the role of enhancer dynamics in mouse and human lymphoid development, and discuss how genetic and epigenetic alterations of enhancer function can promote leukemogenesis, and potential strategies for targeting the enhancer machinery in the treatment of ALL.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, 08916, Spain
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Department of Systems Biology, Columbia University, New York, NY, 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA.
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21
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Clinical Applications of Genomic Alterations in ATLL: Predictive Markers and Therapeutic Targets. Cancers (Basel) 2021; 13:cancers13081801. [PMID: 33918793 PMCID: PMC8068906 DOI: 10.3390/cancers13081801] [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: 03/05/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary In this review paper, we aim to summarize recent findings of genomic alterations found in adult T-cell leukemia/lymphoma (ATLL), which is an incurable disease induced by a virus; human T-cell leukemia virus type 1 (HTLV-1). Genomic alterations of ATLL have been comprehensively analyzed and the identified alterations and HTLV-1 infection synergistically act for ATLL development. As HTLV-1 is an endemic disease, ATLL frequently occurs in the endemic areas. Current clinicogenomic analyses suggest the existence of regional difference in ATLL pathophysiology. From a clinical perspective, several studies identified alterations that act as predictive markers and that a part of the alterations can be targetable in ATLL. The alterations can be leveraged to improve ATLL prognosis. Abstract Adult T-cell leukemia/lymphoma (ATLL) is a peripheral T-cell lymphoma (PTCL) caused by human T-cell leukemia virus type 1 (HTLV-1). Recent comprehensive genomic analyses have revealed the genomic landscape. One of the important findings of genomic alterations in ATLL is that almost all alterations are subclonal, suggesting that therapeutic strategies targeting a genomic alteration will result in partial effects. Among the identified alterations, genes involved in T-cell receptor signaling and immune escape mechanisms, such as PLCG1, CARD11, and PD-L1 (also known as CD274), are characteristic of ATLL alterations. From a geographic perspective, ATLL patients in Caribbean islands tend to be younger than those in Japan and the landscape differs between the two areas. Additionally, young Japanese ATLL patients frequently have CD28 fusions, compared with unselected Japanese cases. From a clinical perspective, PD-L1 amplification is an independent prognostic factor among every subtype of ATLL case. Recently, genomic analysis using deep sequencing identified a pre-ATLL clone with ATLL-common mutations in HTLV-1 carriers before development, indicating that genomic analysis can stratify cases based on the risks of development and mortality. In addition to genomic alterations, targetable super-enhancers have been identified in ATLL. These data can be leveraged to improve the prognosis of ATLL.
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22
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Tottone L, Lancho O, Loh JW, Singh A, Kimura S, Roels J, Kuchmiy A, Strubbe S, Lawlor MA, da Silva-Diz V, Luo S, Gachet S, García-Prieto CA, Hagelaar R, Esteller M, Meijerink JPP, Soulier J, Taghon T, Van Vlierberghe P, Mullighan CG, Khiabanian H, Rocha PP, Herranz D. A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Blood Cancer Discov 2020; 2:92-109. [PMID: 33458694 DOI: 10.1158/2643-3230.bcd-20-0201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the PTEN promoter in multiple hematopoietic populations, including T-cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced PTEN levels in T-ALL cells. Moreover, PE-null mice show reduced Pten levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by Pten loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased PTEN levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.
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Affiliation(s)
- Luca Tottone
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Olga Lancho
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Jui-Wan Loh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Amartya Singh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Matthew A Lawlor
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Victoria da Silva-Diz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shirley Luo
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Stéphanie Gachet
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | | | - Jean Soulier
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey.
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
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23
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Rovirosa L, Ramos-Morales A, Javierre BM. The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer. Front Immunol 2020; 11:592087. [PMID: 33117405 PMCID: PMC7575776 DOI: 10.3389/fimmu.2020.592087] [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: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Associations between blood cancer and genetic predisposition, including both inherited variants and acquired mutations and epimutations, have been well characterized. However, the majority of these variants affect noncoding regions, making their mechanisms difficult to hypothesize and hindering the translation of these insights into patient benefits. Fueled by unprecedented progress in next-generation sequencing and computational integrative analysis, studies have started applying combinations of epigenetic, genome architecture, and functional assays to bridge the gap between noncoding variants and blood cancer. These complementary tools have not only allowed us to understand the potential malignant role of these variants but also to differentiate key variants, cell-types, and conditions from misleading ones. Here, we briefly review recent studies that have provided fundamental insights into our understanding of how noncoding mutations at enhancers predispose and promote blood malignancies in the context of spatial genome architecture.
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Affiliation(s)
- Llorenç Rovirosa
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Alberto Ramos-Morales
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain.,Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
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24
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Fang C, Rao S, Crispino JD, Ntziachristos P. Determinants and role of chromatin organization in acute leukemia. Leukemia 2020; 34:2561-2575. [PMID: 32690881 PMCID: PMC7999176 DOI: 10.1038/s41375-020-0981-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
DNA is compacted into higher order structures that have major implications in gene regulation. These structures allow for long-range interactions of DNA elements, such as the association of promoters with their cognate enhancers. In recent years, mutations in genes that control these structures, including the cohesin-complex and the insulator-binding protein CTCF, have been found in a spectrum of hematologic disorders, and especially in acute leukemias. Cohesin and CTCF are critical for mediating looping and establishing boundaries within chromatin. Cells that harbor mutations in these genes display aberrant chromatin architecture and resulting differences in gene expression that contribute to leukemia initiation and progression. Here, we provide detailed discussion of the nature of 3D interactions and the way that they are disrupted in acute leukemia. Continued research in this area will provide new insights into the mechanisms of leukemogenesis and may shed light on novel treatment strategies.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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25
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McCarter AC, Gatta GD, Melnick A, Kim E, Sha C, Wang Q, Nalamolu JK, Liu Y, Keeley TM, Yan R, Sun M, Kodgule R, Kunnath N, Ambesi-Impiombato A, Kuick R, Rao A, Ryan RJH, Kee BL, Samuelson LC, Ostrowski MC, Ferrando AA, Chiang MY. Combinatorial ETS1-dependent control of oncogenic NOTCH1 enhancers in T-cell leukemia. Blood Cancer Discov 2020; 1:178-197. [PMID: 32924017 DOI: 10.1158/2643-3230.bcd-20-0026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Notch activation is highly prevalent among cancers, in particular T-cell acute lymphoblastic leukemia (T-ALL). However, the use of pan-Notch inhibitors to treat cancers has been hampered by adverse effects, particularly intestinal toxicities. To circumvent this barrier in T-ALL, we aimed to inhibit ETS1, a developmentally important T-cell transcription factor previously shown to co-bind Notch response elements. Using complementary genetic approaches in mouse models, we show that ablation of Ets1 leads to strong Notch-mediated suppressive effects on T-cell development and leukemogenesis, but milder intestinal effects than pan-Notch inhibitors. Mechanistically, genome-wide chromatin profiling studies demonstrate that Ets1 inactivation impairs recruitment of multiple Notch-associated factors and Notch-dependent activation of transcriptional elements controlling major Notch-driven oncogenic effector pathways. These results uncover previously unrecognized hierarchical heterogeneity of Notch-controlled genes and points to Ets1-mediated enucleation of Notch-Rbpj transcriptional complexes as a target for developing specific anti-Notch therapies in T-ALL that circumvent the barriers of pan-Notch inhibition.
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Affiliation(s)
- Anna C McCarter
- Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI.,These authors contributed equally
| | - Giusy Della Gatta
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally
| | - Ashley Melnick
- Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI
| | - Erin Kim
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Cher Sha
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Qing Wang
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Jahnavi K Nalamolu
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | - Theresa M Keeley
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Ran Yan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Mengxi Sun
- Department of Pathology, University of Chicago
| | - Rohan Kodgule
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Nicholas Kunnath
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Rork Kuick
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | | | - Linda C Samuelson
- Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY.,Department of Pediatrics, Columbia University Medical Center, New York, NY.,Department of Systems Biology, Columbia University, New York, NY
| | - Mark Y Chiang
- Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI.,Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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26
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Benetatos L, Benetatou A, Vartholomatos G. Enhancers and MYC interplay in hematopoiesis. J Mol Med (Berl) 2020; 98:471-481. [PMID: 32144465 DOI: 10.1007/s00109-020-01891-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/16/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022]
Abstract
Transcription requires the fine interplay between enhancers and transcription factors. Enhancers are able to activate transcription of genes involved in normal cell biology, whereas aberrant enhancer activity leads to oncogenesis. MYC is a well-established proto-oncogene involved in half of human cancers amplifying the output of its targets. The crosstalk between MYC and enhancers is known for many years since the discovery of IgH enhancer juxtaposition with MYC in high-grade lymphomas. Here, we focus mainly in the enhancers surrounding MYC in the 8q24 locus. That region comprises several enhancers that associate with other transcription factors, transmembrane receptors, and fusion genes composing complex regulatory networks aberrantly expressed in almost all types of hematological malignancies. Understanding the nature of these interactions in normal blood cells and in leukemias/lymphomas will expand MYC targeting options in the armamentarium against hematological cancers.
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Affiliation(s)
| | - Agapi Benetatou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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27
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Abstract
The search for oncogenic mutations in haematological malignancies has largely focused on coding sequence variants. These variants have been critical in understanding these complex cancers in greater detail, ultimately leading to better disease monitoring, subtyping and prognostication. In contrast, the search for oncogenic variants in the noncoding genome has proven to be challenging given the vastness of the search space, the intrinsic difficulty in assessing the impact of variants that do not code for functional proteins, and our still primitive understanding of the function harboured by large parts of the noncoding genome. Recent studies have broken ground on this quest, identifying somatically acquired and recurrent mutations in the noncoding genome that activate the expression of proto-oncogenes. In this Review, we explore some of the best-characterised examples of noncoding mutations in haematological malignancies, and highlight how a significant majority of these variants impinge on gene regulation through the formation of aberrant enhancers and promoters. We delve into the challenges faced by those that embark on a search for noncoding driver mutations, and provide a framework distilled from studies that have successfully identified such variants to overcome some of the most salient hurdles. Finally, we discuss the current therapeutic strategies being explored to target the oncogenic mechanism supported by recurrent noncoding variants. We postulate that the continued discovery and functional characterisation of somatic variants in the noncoding genome will not only advance our understanding of haematological malignancies, but offer novel therapeutic avenues and provide important insights into transcriptional regulation on a broader scale. Summary: This Review highlights the challenging but rewarding search for somatic mutations in the noncoding genome, and how such variants nucleate aberrant enhancers and promoters that drive the expression of proto-oncogenes.
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Affiliation(s)
- Sunniyat Rahman
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Marc R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
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