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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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2
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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [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: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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3
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Huang J, Jin S, Guo R, Wu W, Yang C, Qin Y, Chen Q, He X, Qu J, Yang Z. Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis. RNA (NEW YORK, N.Y.) 2024; 30:435-447. [PMID: 38296629 PMCID: PMC10946434 DOI: 10.1261/rna.079865.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/21/2024] [Indexed: 02/02/2024]
Abstract
The histone lysine demethylase KDM5B is frequently up-regulated in various human cancer cells. However, its expression and functional role in human acute myeloid leukemia (AML) cells remain unclear. Here, we found that the expression level of KDM5B is high in primary human AML cells. We have demonstrated that knocking down KDM5B leads to apoptosis and impairs proliferation in primary human AML and some human AML cell lines. We further identified miR-140-3p as a downstream target gene of KDM5B. KDM5B expression was inversely correlated with the miR-140-3p level in primary human AML cells. Molecular studies showed that silencing KDM5B enhanced H3K4 trimethylation (H3K4me3) at the promoter of miR-140-3p, leading to high expression of miR-140-3p, which in turn inhibited B-cell CLL/lymphoma 2 (BCL2) expression. Finally, we demonstrate that the defective proliferation induced by KDM5B knockdown (KD) can be rescued with the miR-140-3p inhibitor or enhanced by combining KDM5B KD with a BCL2 inhibitor. Altogether, our data support the conclusion that KDM5B promotes tumorigenesis in human AML cells through the miR-140-3p/BCL2 axis. Targeting the KDM5B/miR-140-3p/BCL2 pathway may hold therapeutic promise for treating human AML.
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Affiliation(s)
- Jiaojuan Huang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiling Jin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Rongqun Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Wei Wu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chengxuan Yang
- Department of Galactophore, Xinxiang First People's Hospital, Xinxiang 453000, China
| | - Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingchuan Chen
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ximiao He
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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4
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Agrawal‐Singh S, Bagri J, Sakakini N, Huntly BJP. A guide to epigenetics in leukaemia stem cells. Mol Oncol 2023; 17:2493-2506. [PMID: 37872885 PMCID: PMC10701772 DOI: 10.1002/1878-0261.13544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
Leukaemia stem cells (LSCs) are the critical seed for the growth of haematological malignancies, driving the clonal expansion that enables disease initiation, relapse and often resistance. Specifically, they display inherent phenotypic and epigenetic plasticity resulting in complex heterogenic diseases. In this review, we discuss the key principles of deregulation of epigenetic processes that shape this disease evolution. We consider measures to define and quantify clonal heterogeneity, combining information from recent studies assessing mutational, transcriptional and epigenetic landscapes at single cell resolution in myeloid neoplasms (MN). We highlight the importance of integrating epigenetic and genetic information to better understand inter- and intra-patient heterogeneity and discuss how this understanding further informs evolution and progression trajectories and subsequent clinical response in MN. Under this topic, we also discuss efforts to identify mechanisms of resistance, by longitudinal analyses of patient samples. Finally, we highlight how we might target these aberrant epigenetic processes for better therapeutic outcomes and to potentially eradicate LSCs.
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Affiliation(s)
- Shuchi Agrawal‐Singh
- Department of Haematology, Jeffrey Cheah Biomedical CentreUniversity of CambridgeUK
- Cambridge Stem Cell InstituteUniversity of CambridgeUK
| | - Jaana Bagri
- Department of Haematology, Jeffrey Cheah Biomedical CentreUniversity of CambridgeUK
- Cambridge Stem Cell InstituteUniversity of CambridgeUK
| | - Nathalie Sakakini
- Department of Haematology, Jeffrey Cheah Biomedical CentreUniversity of CambridgeUK
- Cambridge Stem Cell InstituteUniversity of CambridgeUK
| | - Brian J. P. Huntly
- Department of Haematology, Jeffrey Cheah Biomedical CentreUniversity of CambridgeUK
- Cambridge Stem Cell InstituteUniversity of CambridgeUK
- Haematology ServiceCambridge University HospitalsUK
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5
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Zeng Z, Fu M, Hu Y, Wei Y, Wei X, Luo M. Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer. Mol Cancer 2023; 22:172. [PMID: 37853437 PMCID: PMC10583419 DOI: 10.1186/s12943-023-01877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
Cancer stem cells (CSCs), initially identified in leukemia in 1994, constitute a distinct subset of tumor cells characterized by surface markers such as CD133, CD44, and ALDH. Their behavior is regulated through a complex interplay of networks, including transcriptional, post-transcriptional, epigenetic, tumor microenvironment (TME), and epithelial-mesenchymal transition (EMT) factors. Numerous signaling pathways were found to be involved in the regulatory network of CSCs. The maintenance of CSC characteristics plays a pivotal role in driving CSC-associated tumor metastasis and conferring resistance to therapy. Consequently, CSCs have emerged as promising targets in cancer treatment. To date, researchers have developed several anticancer agents tailored to specifically target CSCs, with some of these treatment strategies currently undergoing preclinical or clinical trials. In this review, we outline the origin and biological characteristics of CSCs, explore the regulatory networks governing CSCs, discuss the signaling pathways implicated in these networks, and investigate the influential factors contributing to therapy resistance in CSCs. Finally, we offer insights into preclinical and clinical agents designed to eliminate CSCs.
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Affiliation(s)
- Zhen Zeng
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Minyang Fu
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuan Hu
- Department of Pediatric Nephrology Nursing, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Luo
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China.
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6
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González-Novo R, de Lope-Planelles A, Cruz Rodríguez MP, González-Murillo Á, Madrazo E, Acitores D, García de Lacoba M, Ramírez M, Redondo-Muñoz J. 3D environment controls H3K4 methylation and the mechanical response of the nucleus in acute lymphoblastic leukemia cells. Eur J Cell Biol 2023; 102:151343. [PMID: 37494871 DOI: 10.1016/j.ejcb.2023.151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, and the infiltration of leukemic cells is critical for disease progression and relapse. Nuclear deformability plays a critical role in cancer cell invasion through confined spaces; however, the direct impact of epigenetic changes on the nuclear deformability of leukemic cells remains unclear. Here, we characterized how 3D collagen matrix conditions induced H3K4 methylation in ALL cell lines and clinical samples. We used specific shRNA and chemical inhibitors to target WDR5 (a core subunit involved in H3K4 methylation) and determined that targeting WDR5 reduced the H3K4 methylation induced by the 3D environment and the invasiveness of ALL cells in vitro and in vivo. Intriguingly, targeting WDR5 did not reduce the adhesion or the chemotactic response of leukemia cells, suggesting a different mechanism by which H3K4 methylation might govern ALL cell invasiveness. Finally, we conducted biochemical, and biophysical experiments to determine that 3D environments promoted the alteration of the chromatin, the morphology, and the mechanical behavior of the nucleus in ALL cells. Collectively, our data suggest that 3D environments control an upregulation of H3K4 methylation in ALL cells, and targeting WDR5 might serve as a promising therapeutic target against ALL invasiveness in vivo.
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Affiliation(s)
- Raquel González-Novo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Ana de Lope-Planelles
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - María Pilar Cruz Rodríguez
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - África González-Murillo
- Oncolohematology Unit, Hospital Universitario Niño Jesús, Madrid, Spain; Health Research Institute La Princesa, Madrid, Spain
| | - Elena Madrazo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - David Acitores
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Mario García de Lacoba
- Bioinformatics and Biostatistics Unit, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Manuel Ramírez
- Oncolohematology Unit, Hospital Universitario Niño Jesús, Madrid, Spain; Health Research Institute La Princesa, Madrid, Spain
| | - Javier Redondo-Muñoz
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain.
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7
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Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers. Cancer Discov 2023; 13:1478-1497. [PMID: 36847506 PMCID: PMC10238656 DOI: 10.1158/2159-8290.cd-22-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate [(R)-2HG], an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers. SIGNIFICANCE Mutant IDH is known to induce histone hypermethylation. However, it is not known if this hypermethylation is functionally significant or is a bystander effect of (R)-2HG accumulation in IDH-mutant cells. Here, we provide evidence that KDM5 inhibition by (R)-2HG contributes to mutant IDH-mediated transformation in AML and glioma. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - John Z. Cao
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Manna Ahmed
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Bofu Huang
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Betty Rouaisnel
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bill H. Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael M. Levitt
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan Looper
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Harley I. Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cihangir Duy
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Lucy A. Godley
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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H3K27me3 Inactivates SFRP1 to Promote Cell Proliferation via Wnt/β-Catenin Signaling Pathway in Esophageal Squamous Cell Carcinoma. Dig Dis Sci 2023; 68:2463-2473. [PMID: 36933113 DOI: 10.1007/s10620-023-07892-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Histone methylations are generally considered to play an important role in multiple cancers by regulating cancer-related genes. AIMS This study aims to investigate the effects of H3K27me3-mediated inactivation of tumor suppressor gene SFRP1 and its function in esophageal squamous cell carcinoma (ESCC). METHODS We performed ChIP-seq on H3K27me3-enriched genomic DNA fragments in ESCC cells to screen out tumor suppressor genes that may be regulated by H3K27me3. ChIP-qPCR and Western blot were employed to explore the regulating mechanisms between H3K27me3 and SFRP1. Expression level of SFRP1 was assessed by quantitative real-time polymerase chain reaction (q-PCR) in 29 pairs of ESCC surgical samples. SFRP1 function in ESCC cells were detected by cell proliferation assay, colony formation assay and wound-healing assay. RESULTS Our results indicated that H3K27me3 was widely distributed in the genome of ESCC cells. Specifically, we found that H3K27me3 deposited on the upstream region of SFRP1 promoter and inactivated SFRP1 expression. Furthermore, we found SFRP1 was significantly down-regulated in ESCC tissues compared with the adjacent non-tumor tissues, and SFRP1 expression was significantly associated with TNM stage and lymph node metastasis. In vitro cell-based assay indicated that over-expression of SFRP1 significantly suppressed cell proliferation and negatively correlated with the expression of β-catenin in the nucleus. CONCLUSIONS Our study revealed a previously unrecognized finding that H3K27me3-mediated SFRP1 inhibit the cell proliferation of ESCC through inactivation of Wnt/β-catenin signaling pathway.
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Characterization of bone marrow heterogeneity in NK-AML (M4/M5) based on single-cell RNA sequencing. Exp Hematol Oncol 2023; 12:25. [PMID: 36879313 PMCID: PMC9987113 DOI: 10.1186/s40164-023-00391-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
Normal karyotype acute myeloid leukemia (NK-AML) is a heterogeneous hematological malignancy that contains a minor population of self-renewing leukemia stem cells (LSCs), which complicate efforts to achieve long-term survival. We performed single-cell RNA sequencing to profile 39,288 cells from 6 bone marrow (BM) aspirates including 5 NK-AML (M4/M5) patients and 1 healthy donor. The single-cell transcriptome atlas and gene expression characteristics of each cell population in NK-AML (M4/M5) and healthy BM were obtained. In addition, we identified a distinct LSC-like cluster with possible biomarkers in NK-AML (M4/M5) and verified 6 genes using qRT‒PCR and bioinformatic analyses. In conclusion, we utilized single-cell technologies to provide an atlas of NK-AML (M4/M5) cell heterogeneity, composition, and biomarkers with implications for precision medicine and targeted therapies.
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10
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The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes. Leukemia 2023; 37:593-605. [PMID: 36631623 PMCID: PMC9991918 DOI: 10.1038/s41375-023-01810-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
Epigenetic regulators are frequently mutated in hematological malignancies including acute myeloid leukemia (AML). Thus, the identification and characterization of novel epigenetic drivers affecting AML biology holds potential to improve our basic understanding of AML and to uncover novel options for therapeutic intervention. To identify novel tumor suppressive epigenetic regulators in AML, we performed an in vivo short hairpin RNA (shRNA) screen in the context of CEBPA mutant AML. This identified the Histone 3 Lysine 4 (H3K4) demethylase KDM5C as a tumor suppressor, and we show that reduced Kdm5c/KDM5C expression results in accelerated growth both in human and murine AML cell lines, as well as in vivo in Cebpa mutant and inv(16) AML mouse models. Mechanistically, we show that KDM5C act as a transcriptional repressor through its demethylase activity at promoters. Specifically, KDM5C knockdown results in globally increased H3K4me3 levels associated with up-regulation of bivalently marked immature genes. This is accompanied by a de-differentiation phenotype that could be reversed by modulating levels of several direct and indirect downstream mediators. Finally, the association of KDM5C levels with long-term disease-free survival of female AML patients emphasizes the clinical relevance of our findings and identifies KDM5C as a novel female-biased tumor suppressor in AML.
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11
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Namitz KEW, Tan S, Cosgrove MS. Hierarchical assembly of the MLL1 core complex regulates H3K4 methylation and is dependent on temperature and component concentration. J Biol Chem 2023; 299:102874. [PMID: 36623730 PMCID: PMC9939731 DOI: 10.1016/j.jbc.2023.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023] Open
Abstract
Enzymes of the mixed lineage leukemia (MLL) family of histone H3 lysine 4 (H3K4) methyltransferases are critical for cellular differentiation and development and are regulated by interaction with a conserved subcomplex consisting of WDR5, RbBP5, Ash2L, and DPY30. While pairwise interactions between complex subunits have been determined, the mechanisms regulating holocomplex assembly are unknown. In this investigation, we systematically characterized the biophysical properties of a reconstituted human MLL1 core complex and found that the MLL1-WDR5 heterodimer interacts with the RbBP5-Ash2L-DPY30 subcomplex in a hierarchical assembly pathway that is highly dependent on concentration and temperature. Surprisingly, we found that the disassembled state is favored at physiological temperature, where the enzyme rapidly becomes irreversibly inactivated, likely because of complex components becoming trapped in nonproductive conformations. Increased protein concentration partially overcomes this thermodynamic barrier for complex assembly, suggesting a potential regulatory mechanism for spatiotemporal control of H3K4 methylation. Together, these results are consistent with the hypothesis that regulated assembly of the MLL1 core complex underlies an important mechanism for establishing different H3K4 methylation states in mammalian genomes.
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Affiliation(s)
- Kevin E W Namitz
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA
| | - Song Tan
- Penn State University, Department of Biochemistry and Molecular Biology, University Park, PA, USA
| | - Michael S Cosgrove
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA.
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12
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Rafeeinia A, Asadikaram G, Moazed V, Darabi MK. Organochlorine pesticides may induce leukemia by methylation of CDKN2B and MGMT promoters and histone modifications. Gene 2023; 851:146976. [DOI: 10.1016/j.gene.2022.146976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/25/2022] [Accepted: 10/11/2022] [Indexed: 11/27/2022]
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13
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He X, Xu Y, Huang D, Yu Z, Yu J, Xie L, Liu L, Yu Y, Chen C, Wan J, Zhang Y, Zheng J. P2X1 enhances leukemogenesis through PBX3-BCAT1 pathways. Leukemia 2023; 37:265-275. [PMID: 36418376 PMCID: PMC9898031 DOI: 10.1038/s41375-022-01759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
How bone marrow niches regulate leukemogenic activities of leukemia-initiating cells (LICs) is unclear. The present study revealed that the metabolic niche component, ATP, efficiently induced ion influx in LICs through its ligand-gated ion channel, P2X1. P2X1 deletion impaired LIC self-renewal capacities and resulted in an approximately 8-fold decrease in functional LIC numbers in a murine acute myeloid leukemia (AML) model without affecting normal hematopoiesis. P2X1 phosphorylation at specific sites of S387 and T389 was essential for sustaining its promoting effects on leukemia development. ATP-P2X1-mediated signaling upregulated the PBX3 level to transactivate BCAT1 to maintain LIC fates. P2X1 knockdown inhibited the proliferation of both human AML cell lines and primary cells. The P2X1 antagonist sufficiently suppressed AML cell proliferation. These results provided a unique perspective on how metabolic niche factor ATP fine-tunes LIC activities, which may benefit the development of strategies for targeting LICs or other cancer stem cells.
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Affiliation(s)
- Xiaoxiao He
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yilu Xu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Dan Huang
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Zhuo Yu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Jing Yu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Li Xie
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Ligen Liu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Ye Yu
- grid.254147.10000 0000 9776 7793School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Chiqi Chen
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jiangbo Wan
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Yaping Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China.
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14
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Egan G, Schimmer AD. Contribution of metabolic abnormalities to acute myeloid leukemia pathogenesis. Trends Cell Biol 2022; 33:455-462. [PMID: 36481232 DOI: 10.1016/j.tcb.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) is a malignant disease of myeloid precursors. Somatic mutations have long been accepted as drivers of this malignancy. Over the past decade, unique mitochondrial and metabolic dependencies of AML and AML stem cells have been identified, including a reliance on oxidative phosphorylation. More recently, metabolic enzymes have demonstrated noncanonical roles in regulating gene expression in AML, controlling cell differentiation and stemness. These mitochondrial and metabolic adaptations occur independent of underlying genomic abnormalities and contribute to chemoresistance and relapse. In this opinion article, we discuss the current understanding of AML pathogenesis and whether mitochondrial and metabolic abnormalities drive leukemogenesis or are a non-contributory phenotype.
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15
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Parallel functional annotation of cancer-associated missense mutations in histone methyltransferases. Sci Rep 2022; 12:18487. [PMID: 36323913 PMCID: PMC9630446 DOI: 10.1038/s41598-022-23229-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Abstract
Using exome sequencing for biomarker discovery and precision medicine requires connecting nucleotide-level variation with functional changes in encoded proteins. However, for functionally annotating the thousands of cancer-associated missense mutations, or variants of uncertain significance (VUS), purifying variant proteins for biochemical and functional analysis is cost-prohibitive and inefficient. We describe parallel functional annotation (PFA) of large numbers of VUS using small cultures and crude extracts in 96-well plates. Using members of a histone methyltransferase family, we demonstrate high-throughput structural and functional annotation of cancer-associated mutations. By combining functional annotation of paralogs, we discovered two phylogenetic and clustering parameters that improve the accuracy of sequence-based functional predictions to over 90%. Our results demonstrate the value of PFA for defining oncogenic/tumor suppressor functions of histone methyltransferases as well as enhancing the accuracy of sequence-based algorithms in predicting the effects of cancer-associated mutations.
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16
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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17
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Properties of Leukemic Stem Cells in Regulating Drug Resistance in Acute and Chronic Myeloid Leukemias. Biomedicines 2022; 10:biomedicines10081841. [PMID: 36009388 PMCID: PMC9405586 DOI: 10.3390/biomedicines10081841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Notoriously known for their capacity to reconstitute hematological malignancies in vivo, leukemic stem cells (LSCs) represent key drivers of therapeutic resistance and disease relapse, posing as a major medical dilemma. Despite having low abundance in the bulk leukemic population, LSCs have developed unique molecular dependencies and intricate signaling networks to enable self-renewal, quiescence, and drug resistance. To illustrate the multi-dimensional landscape of LSC-mediated leukemogenesis, in this review, we present phenotypical characteristics of LSCs, address the LSC-associated leukemic stromal microenvironment, highlight molecular aberrations that occur in the transcriptome, epigenome, proteome, and metabolome of LSCs, and showcase promising novel therapeutic strategies that potentially target the molecular vulnerabilities of LSCs.
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18
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Diverse Functions of KDM5 in Cancer: Transcriptional Repressor or Activator? Cancers (Basel) 2022; 14:cancers14133270. [PMID: 35805040 PMCID: PMC9265395 DOI: 10.3390/cancers14133270] [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: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic modifications are crucial for chromatin remodeling and transcriptional regulation. Post-translational modifications of histones are epigenetic processes that are fine-tuned by writer and eraser enzymes, and the disorganization of these enzymes alters the cellular state, resulting in human diseases. The KDM5 family is an enzymatic family that removes di- and tri-methyl groups (me2 and me3) from lysine 4 of histone H3 (H3K4), and its dysregulation has been implicated in cancer. Although H3K4me3 is an active chromatin marker, KDM5 proteins serve as not only transcriptional repressors but also transcriptional activators in a demethylase-dependent or -independent manner in different contexts. Notably, KDM5 proteins regulate the H3K4 methylation cycle required for active transcription. Here, we review the recent findings regarding the mechanisms of transcriptional regulation mediated by KDM5 in various contexts, with a focus on cancer, and further shed light on the potential of targeting KDM5 for cancer therapy.
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19
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Belhocine M, Simonin M, Abad Flores JD, Cieslak A, Manosalva I, Pradel L, Smith C, Mathieu EL, Charbonnier G, Martens JH, Stunnenberg HG, Maqbool MA, Mikulasova A, Russell LJ, Rico D, Puthier D, Ferrier P, Asnafi V, Spicuglia S. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes. Genome Res 2022; 32:1328-1342. [PMID: 34162697 PMCID: PMC9341507 DOI: 10.1101/gr.266924.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/05/2021] [Indexed: 01/03/2023]
Abstract
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain-associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain-associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain-associated genes in preleukemic cells. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extent and number of broad domains. Our results show that the regulation of broad H3K4me3 domains is associated with leukemogenesis, and suggest that the presence of these structures might be used for epigenetic prioritization of cancer-relevant genes, including long noncoding RNAs.
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Affiliation(s)
- Mohamed Belhocine
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France;,Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France;,Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - José David Abad Flores
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Iris Manosalva
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Lydie Pradel
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Joost H.A. Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Muhammad Ahmad Maqbool
- CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Aderley Park, Macclesfield SK104TG, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J. Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Denis Puthier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
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20
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Xiao L, Karsa M, Ronca E, Bongers A, Kosciolek A, El-Ayoubi A, Revalde JL, Seneviratne JA, Cheung BB, Cheung LC, Kotecha RS, Newbold A, Bjelosevic S, Arndt GM, Lock RB, Johnstone RW, Gudkov AV, Gurova KV, Haber M, Norris MD, Henderson MJ, Somers K. The Combination of Curaxin CBL0137 and Histone Deacetylase Inhibitor Panobinostat Delays KMT2A-Rearranged Leukemia Progression. Front Oncol 2022; 12:863329. [PMID: 35677155 PMCID: PMC9168530 DOI: 10.3389/fonc.2022.863329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Rearrangements of the Mixed Lineage Leukemia (MLL/KMT2A) gene are present in approximately 10% of acute leukemias and characteristically define disease with poor outcome. Driven by the unmet need to develop better therapies for KMT2A-rearranged leukemia, we previously discovered that the novel anti-cancer agent, curaxin CBL0137, induces decondensation of chromatin in cancer cells, delays leukemia progression and potentiates standard of care chemotherapies in preclinical KMT2A-rearranged leukemia models. Based on the promising potential of histone deacetylase (HDAC) inhibitors as targeted anti-cancer agents for KMT2A-rearranged leukemia and the fact that HDAC inhibitors also decondense chromatin via an alternate mechanism, we investigated whether CBL0137 could potentiate the efficacy of the HDAC inhibitor panobinostat in KMT2A-rearranged leukemia models. The combination of CBL0137 and panobinostat rapidly killed KMT2A-rearranged leukemia cells by apoptosis and significantly delayed leukemia progression and extended survival in an aggressive model of MLL-AF9 (KMT2A:MLLT3) driven murine acute myeloid leukemia. The drug combination also exerted a strong anti-leukemia response in a rapidly progressing xenograft model derived from an infant with KMT2A-rearranged acute lymphoblastic leukemia, significantly extending survival compared to either monotherapy. The therapeutic enhancement between CBL0137 and panobinostat in KMT2A-r leukemia cells does not appear to be mediated through cooperative effects of the drugs on KMT2A rearrangement-associated histone modifications. Our data has identified the CBL0137/panobinostat combination as a potential novel targeted therapeutic approach to improve outcome for KMT2A-rearranged leukemia.
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Affiliation(s)
- Lin Xiao
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Mawar Karsa
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Emma Ronca
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia
| | - Angelika Bongers
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia
| | - Angelika Kosciolek
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia
| | - Ali El-Ayoubi
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia
| | - Jezrael L Revalde
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia.,Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.,Division of Paediatrics, School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Andrea Newbold
- Gene Regulation Laboratory, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stefan Bjelosevic
- Gene Regulation Laboratory, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Greg M Arndt
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia.,Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrei V Gudkov
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, United States
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, United States
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, Sydney, NSW, Australia
| | - Michelle J Henderson
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Klaartje Somers
- Children's Cancer Institute, Lowy Cancer Research Institute, University of New South Wales, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
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21
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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22
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Chan LH, Yan Q. Awakening KDM5B to defeat leukemia. Proc Natl Acad Sci U S A 2022; 119:e2202245119. [PMID: 35312367 PMCID: PMC9060505 DOI: 10.1073/pnas.2202245119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lok Hei Chan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT 06520
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23
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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24
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A PRC2-Kdm5b axis sustains tumorigenicity of acute myeloid leukemia. Proc Natl Acad Sci U S A 2022; 119:2122940119. [PMID: 35217626 PMCID: PMC8892512 DOI: 10.1073/pnas.2122940119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemias (AMLs) with the NUP98-NSD1 or mixed lineage leukemia (MLL) rearrangement (MLL-r) share transcriptomic profiles associated with stemness-related gene signatures and display poor prognosis. The molecular underpinnings of AML aggressiveness and stemness remain far from clear. Studies with EZH2 enzymatic inhibitors show that polycomb repressive complex 2 (PRC2) is crucial for tumorigenicity in NUP98-NSD1+ AML, whereas transcriptomic analysis reveal that Kdm5b, a lysine demethylase gene carrying "bivalent" chromatin domains, is directly repressed by PRC2. While ectopic expression of Kdm5b suppressed AML growth, its depletion not only promoted tumorigenicity but also attenuated anti-AML effects of PRC2 inhibitors, demonstrating a PRC2-|Kdm5b axis for AML oncogenesis. Integrated RNA sequencing (RNA-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq), and Cleavage Under Targets & Release Using Nuclease (CUT&RUN) profiling also showed that Kdm5b directly binds and represses AML stemness genes. The anti-AML effect of Kdm5b relies on its chromatin association and/or scaffold functions rather than its demethylase activity. Collectively, this study describes a molecular axis that involves histone modifiers (PRC2-|Kdm5b) for sustaining AML oncogenesis.
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25
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Zhu B, Zhong W, Cao X, Pan G, Xu M, Zheng J, Chen H, Feng X, Luo C, Lu C, Xiao J, Lin W, Lai C, Li M, Du X, Yi Q, Yan D. Loss of miR-31-5p drives hematopoietic stem cell malignant transformation and restoration eliminates leukemia stem cells in mice. Sci Transl Med 2022; 14:eabh2548. [PMID: 35080912 DOI: 10.1126/scitranslmed.abh2548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Leukemia stem cells (LSCs) propagate leukemia and are responsible for the high frequency of relapse of treated patients. The ability to target LSCs remains elusive, indicating a need to understand the underlying mechanism of LSC formation. Here, we report that miR-31-5p is reduced or undetectable in human LSCs compared to hematopoietic stem progenitor cells (HSPCs). Inhibition of miR-31-5p in HSPCs promotes the expression of its target gene FIH, encoding FIH [factor inhibiting hypoxia-inducing factor 1α (HIF-1α)], to suppress HIF-1α signaling. Increased FIH resulted in a switch from glycolysis to oxidative phosphorylation (OXPHOS) as the predominant mode of energy metabolism and increased the abundance of the oncometabolite fumarate. Increased fumarate promoted the conversion of HSPCs to LSCs and initiated myeloid leukemia-like disease in NOD-Prkdcscid IL2rgtm1/Bcgen (B-NDG) mice. We further demonstrated that miR-31-5p inhibited long- and short-term hematopoietic stem cells with a high frequency of LSCs. In combination with the chemotherapeutic agent Ara-C (cytosine arabinoside), restoration of miR-31-5p using G7 poly (amidoamine) nanosized dendriplex encapsulating miR-31-5p eliminated LSCs and inhibited acute myeloid leukemia (AML) progression in patient-derived xenograft mouse models. These results demonstrated a mechanism of HSC malignant transformation through altered energy metabolism and provided a potential therapeutic strategy to treat patients with AML.
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Affiliation(s)
- Biying Zhu
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Wenbin Zhong
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Xiuye Cao
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Guoping Pan
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Mengyang Xu
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Jie Zheng
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Huanzhao Chen
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Xiaoqin Feng
- Hematology and Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chengwei Luo
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, China
| | - Chen Lu
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Jie Xiao
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Weize Lin
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Chaofeng Lai
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Mingchuan Li
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Xin Du
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, China
| | - Qing Yi
- Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daoguang Yan
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
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26
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Staehle HF, Pahl HL, Jutzi JS. The Cross Marks the Spot: The Emerging Role of JmjC Domain-Containing Proteins in Myeloid Malignancies. Biomolecules 2021; 11:biom11121911. [PMID: 34944554 PMCID: PMC8699298 DOI: 10.3390/biom11121911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Histone methylation tightly regulates chromatin accessibility, transcription, proliferation, and cell differentiation, and its perturbation contributes to oncogenic reprogramming of cells. In particular, many myeloid malignancies show evidence of epigenetic dysregulation. Jumonji C (JmjC) domain-containing proteins comprise a large and diverse group of histone demethylases (KDMs), which remove methyl groups from lysines in histone tails and other proteins. Cumulating evidence suggests an emerging role for these demethylases in myeloid malignancies, rendering them attractive targets for drug interventions. In this review, we summarize the known functions of Jumonji C (JmjC) domain-containing proteins in myeloid malignancies. We highlight challenges in understanding the context-dependent mechanisms of these proteins and explore potential future pharmacological targeting.
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Affiliation(s)
- Hans Felix Staehle
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Heike Luise Pahl
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Jonas Samuel Jutzi
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, MA, USA
- Correspondence:
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27
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KDM5A suppresses PML-RARα target gene expression and APL differentiation through repressing H3K4me2. Blood Adv 2021; 5:3241-3253. [PMID: 34448811 DOI: 10.1182/bloodadvances.2020002819] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/29/2021] [Indexed: 11/20/2022] Open
Abstract
Epigenetic abnormalities are frequently involved in the initiation and progression of cancers, including acute myeloid leukemia (AML). A subtype of AML, acute promyelocytic leukemia (APL), is mainly driven by a specific oncogenic fusion event of promyelocytic leukemia-RA receptor fusion oncoprotein (PML-RARα). PML-RARα was reported as a transcription repressor through the interaction with nuclear receptor corepressor and histone deacetylase complexes leading to the mis-suppression of its target genes and differentiation blockage. Although previous studies were mainly focused on the connection of histone acetylation, it is still largely unknown whether alternative epigenetics mechanisms are involved in APL progression. KDM5A is a demethylase of histone H3 lysine 4 di- and tri-methylations (H3K4me2/3) and a transcription corepressor. Here, we found that the loss of KDM5A led to APL NB4 cell differentiation and retarded growth. Mechanistically, through epigenomics and transcriptomics analyses, KDM5A binding was detected in 1889 genes, with the majority of the binding events at promoter regions. KDM5A suppressed the expression of 621 genes, including 42 PML-RARα target genes, primarily by controlling the H3K4me2 in the promoters and 5' end intragenic regions. In addition, a recently reported pan-KDM5 inhibitor, CPI-455, on its own could phenocopy the differentiation effects as KDM5A loss in NB4 cells. CPI-455 treatment or KDM5A knockout could greatly sensitize NB4 cells to all-trans retinoic acid-induced differentiation. Our findings indicate that KDM5A contributed to the differentiation blockage in the APL cell line NB4, and inhibition of KDM5A could greatly potentiate NB4 differentiation.
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28
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Deregulation of Transcriptional Enhancers in Cancer. Cancers (Basel) 2021; 13:cancers13143532. [PMID: 34298745 PMCID: PMC8303223 DOI: 10.3390/cancers13143532] [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: 06/03/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary One of the major challenges in cancer treatments is the dynamic adaptation of tumor cells to cancer therapies. In this regard, tumor cells can modify their response to environmental cues without altering their DNA sequence. This cell plasticity enables cells to undergo morphological and functional changes, for example, during the process of tumour metastasis or when acquiring resistance to cancer therapies. Central to cell plasticity, are the dynamic changes in gene expression that are controlled by a set of molecular switches called enhancers. Enhancers are DNA elements that determine when, where and to what extent genes should be switched on and off. Thus, defects in enhancer function can disrupt the gene expression program and can lead to tumour formation. Here, we review how enhancers control the activity of cancer-associated genes and how defects in these regulatory elements contribute to cell plasticity in cancer. Understanding enhancer (de)regulation can provide new strategies for modulating cell plasticity in tumour cells and can open new research avenues for cancer therapy. Abstract Epigenetic regulations can shape a cell’s identity by reversible modifications of the chromatin that ultimately control gene expression in response to internal and external cues. In this review, we first discuss the concept of cell plasticity in cancer, a process that is directly controlled by epigenetic mechanisms, with a particular focus on transcriptional enhancers as the cornerstone of epigenetic regulation. In the second part, we discuss mechanisms of enhancer deregulation in adult stem cells and epithelial-to-mesenchymal transition (EMT), as two paradigms of cell plasticity that are dependent on epigenetic regulation and serve as major sources of tumour heterogeneity. Finally, we review how genetic variations at enhancers and their epigenetic modifiers contribute to tumourigenesis, and we highlight examples of cancer drugs that target epigenetic modifications at enhancers.
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29
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Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
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Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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30
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Lin CH, Vu JP, Yang CY, Sirisawad M, Chen CT, Dao H, Liu J, Ma X, Pan C, Cefalu J, Tse C, Jackson E, Kuo HP. Glutamate-cysteine ligase catalytic subunit as a therapeutic target in acute myeloid leukemia and solid tumors. Am J Cancer Res 2021; 11:2911-2927. [PMID: 34249435 PMCID: PMC8263632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogenous and aggressive disease with a poor prognosis, necessitating further improvements in treatment therapies. Recently, several targeted therapies have become available for specific AML populations. To identify potential new therapeutic targets for AML, we analyzed published genome wide CRISPR-based screens to generate a gene essentiality dataset across a panel of 14 human AML cell lines while eliminating common essential genes through integration analysis with core fitness genes among 324 human cancer cell lines and DepMap databases. The key glutathione metabolic enzyme, glutamate-cysteine ligase catalytic subunit (GCLC), met the selection threshold. Using CRISPR knockout, GCLC was confirmed to be essential for the cell growth, survival, clonogenicity, and leukemogenesis in AML cells but was comparatively dispensable for normal hematopoietic stem and progenitor cells (HSPCs), indicating that GCLC is a potential therapeutic target for AML. In addition, we evaluated the essentiality of GCLC in solid tumors and demonstrated that GCLC represents a synthetic lethal target for ARID1A-deficient ovarian and gastric cancers.
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Affiliation(s)
| | - John P Vu
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | | | | | - Chun-Te Chen
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | - Hung Dao
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | - Jing Liu
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | - Xuan Ma
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | - Chin Pan
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
| | | | - Chris Tse
- AbbVie Oncology DiscoveryNorth Chicago, IL 60064, USA
| | | | - Hsu-Ping Kuo
- AbbVie Oncology DiscoverySunnyvale, CA 94085, USA
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31
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Sterling J, Menezes SV, Abbassi RH, Munoz L. Histone lysine demethylases and their functions in cancer. Int J Cancer 2021; 148:2375-2388. [PMID: 33128779 DOI: 10.1002/ijc.33375] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022]
Abstract
Histone lysine demethylases (KDMs) are enzymes that remove the methylation marks on lysines in nucleosomes' histone tails. These changes in methylation marks regulate gene transcription during both development and malignant transformation. Depending on which lysine residue is targeted, the effect of a given KDM on gene transcription can be either activating or repressing, and KDMs can regulate the expression of both oncogenes and tumour suppressors. Thus, the functions of KDMs can be regarded as both oncogenic and tumour suppressive, contingent on cell context and the enzyme isoform. Finally, KDMs also demethylate nonhistone proteins and have a variety of demethylase-independent functions. These epigenetic and other mechanisms that KDMs control make them important regulators of malignant tumours. Here, we present an overview of eight KDM subfamilies, their most-studied lysine targets and selected recent data on their roles in cancer stem cells, tumour aggressiveness and drug tolerance.
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Affiliation(s)
- Jayden Sterling
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharleen V Menezes
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ramzi H Abbassi
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Lenka Munoz
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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32
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van Gils N, Denkers F, Smit L. Escape From Treatment; the Different Faces of Leukemic Stem Cells and Therapy Resistance in Acute Myeloid Leukemia. Front Oncol 2021; 11:659253. [PMID: 34012921 PMCID: PMC8126717 DOI: 10.3389/fonc.2021.659253] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/08/2021] [Indexed: 12/26/2022] Open
Abstract
Standard induction chemotherapy, consisting of an anthracycline and cytarabine, has been the first-line therapy for many years to treat acute myeloid leukemia (AML). Although this treatment induces complete remissions in the majority of patients, many face a relapse (adaptive resistance) or have refractory disease (primary resistance). Moreover, older patients are often unfit for cytotoxic-based treatment. AML relapse is due to the survival of therapy-resistant leukemia cells (minimal residual disease, MRD). Leukemia cells with stem cell features, named leukemic stem cells (LSCs), residing within MRD are thought to be at the origin of relapse initiation. It is increasingly recognized that leukemia "persisters" are caused by intra-leukemic heterogeneity and non-genetic factors leading to plasticity in therapy response. The BCL2 inhibitor venetoclax, combined with hypomethylating agents or low dose cytarabine, represents an important new therapy especially for older AML patients. However, often there is also a small population of AML cells refractory to venetoclax treatment. As AML MRD reflects the sum of therapy resistance mechanisms, the different faces of treatment "persisters" and LSCs might be exploited to reach an optimal therapy response and prevent the initiation of relapse. Here, we describe the different epigenetic, transcriptional, and metabolic states of therapy sensitive and resistant AML (stem) cell populations and LSCs, how these cell states are influenced by the microenvironment and affect treatment outcome of AML. Moreover, we discuss potential strategies to target dynamic treatment resistance and LSCs.
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Affiliation(s)
- Noortje van Gils
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Fedor Denkers
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Linda Smit
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
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33
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Mosquera Orgueira A, Peleteiro Raíndo A, Cid López M, Díaz Arias JÁ, González Pérez MS, Antelo Rodríguez B, Alonso Vence N, Bao Pérez L, Ferreiro Ferro R, Albors Ferreiro M, Abuín Blanco A, Fontanes Trabazo E, Cerchione C, Martinnelli G, Montesinos Fernández P, Mateo Pérez Encinas M, Luis Bello López J. Personalized Survival Prediction of Patients With Acute Myeloblastic Leukemia Using Gene Expression Profiling. Front Oncol 2021; 11:657191. [PMID: 33854980 PMCID: PMC8040929 DOI: 10.3389/fonc.2021.657191] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is a heterogeneous neoplasm characterized by cytogenetic and molecular alterations that drive patient prognosis. Currently established risk stratification guidelines show a moderate predictive accuracy, and newer tools that integrate multiple molecular variables have proven to provide better results. In this report, we aimed to create a new machine learning model of AML survival using gene expression data. We used gene expression data from two publicly available cohorts in order to create and validate a random forest predictor of survival, which we named ST-123. The most important variables in the model were age and the expression of KDM5B and LAPTM4B, two genes previously associated with the biology and prognostication of myeloid neoplasms. This classifier achieved high concordance indexes in the training and validation sets (0.7228 and 0.6988, respectively), and predictions were particularly accurate in patients at the highest risk of death. Additionally, ST-123 provided significant prognostic improvements in patients with high-risk mutations. Our results indicate that survival of patients with AML can be predicted to a great extent by applying machine learning tools to transcriptomic data, and that such predictions are particularly precise among patients with high-risk mutations.
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Affiliation(s)
- Adrián Mosquera Orgueira
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrés Peleteiro Raíndo
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Cid López
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - José Ángel Díaz Arias
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Marta Sonia González Pérez
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Beatriz Antelo Rodríguez
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Natalia Alonso Vence
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Bao Pérez
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Roi Ferreiro Ferro
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Manuel Albors Ferreiro
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Aitor Abuín Blanco
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Emilia Fontanes Trabazo
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain
| | - Claudio Cerchione
- Hematology Unit, Istituto Tumori della Romagna IRST IRCCS, Meldola, Italy
| | | | | | - Manuel Mateo Pérez Encinas
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - José Luis Bello López
- University Hospital of Santiago de Compostela (SERGAS), Department of Hematology, Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Grupo de Investigación en Síndromes Linfoproliferativos, Santiago de Compostela, Spain.,Departamento de Medicina, University of Santiago de Compostela, Santiago de Compostela, Spain
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Das AB, Smith-Díaz CC, Vissers MCM. Emerging epigenetic therapeutics for myeloid leukemia: modulating demethylase activity with ascorbate. Haematologica 2021; 106:14-25. [PMID: 33099992 PMCID: PMC7776339 DOI: 10.3324/haematol.2020.259283] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
The past decade has seen a proliferation of drugs that target epigenetic pathways. Many of these drugs were developed to treat acute myeloid leukemia, a condition in which dysregulation of the epigenetic landscape is well established. While these drugs have shown promise, critical issues persist. Specifically, patients with the same mutations respond quite differently to treatment. This is true even with highly specific drugs that are designed to target the underlying oncogenic driver mutations. Furthermore, patients who do respond may eventually develop resistance. There is now evidence that epigenetic heterogeneity contributes, in part, to these issues. Cancer cells also have a remarkable capacity to ‘rewire’ themselves at the epigenetic level in response to drug treatment, and thereby maintain expression of key oncogenes. This epigenetic plasticity is a promising new target for drug development. It is therefore important to consider combination therapy in cases in which both driver mutations and epigenetic plasticity are targeted. Using ascorbate as an example of an emerging epigenetic therapeutic, we review the evidence for its potential use in both of these modes. We provide an overview of 2-oxoglutarate dependent dioxygenases with DNA, histone and RNA demethylase activity, focusing on those which require ascorbate as a cofactor. We also evaluate their role in the development and maintenance of acute myeloid leukemia. Using this information, we highlight situations in which the use of ascorbate to restore 2-oxoglutarate dependent dioxygenase activity could prove beneficial, in contrast to contexts in which targeted inhibition of specific enzymes might be preferred. Finally, we discuss how these insights could be incorporated into the rational design of future clinical trials.
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Affiliation(s)
- Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, Christchurch.
| | - Carlos C Smith-Díaz
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
| | - Margreet C M Vissers
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
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Zheng Y, Tang L, Chen G, Liu Z. Comprehensive Bioinformatics Analysis of Key Methyltransferases and Demethylases for Histone Lysines in Hepatocellular Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820983284. [PMID: 33355042 PMCID: PMC7871294 DOI: 10.1177/1533033820983284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background & Aims: Methylation of lysines on histones, controlled by various methyltransferases and demethylases, is an important component of epigenetic modifications, and abnormal regulation of such enzymes serves as common events in hepatocellular carcinoma. We determined to identify important methyltransferases and demethylases that might regulate the development of hepatocellular carcinoma by bioinformatics. Methods: The Oncomine and UALCAN databases were used to retrieve mRNA expression levels of histone lysine methyltransferases and demethylases in hepatocellular carcinoma. Data analyses of genetic alterations, mainly mutations and copy number alterations, were performed on the cBioportal platform. Protein-protein interactions were established in the STRING database. Results: mRNA expression of 8 genes correlated with clinical staging and grading, whereas 4 genes indicated a role in the prognosis, all co-expressed with SEDB1 and WHSC1. Genetically, 12 genes showing an alteration rate higher than 5% were identified, and only 3 were indicative of prognosis. Copy number gains in ASH1L, SETDB1, and KDM5B might partially contribute to the upregulation of their mRNA expression. The close relationship of mutations in MLL2/MLL3 with driver gene mutations in hepatocellular carcinoma provided a rationale for further investigation. Conclusions: We identified 11 methyltransferases and demethylases for major histone lysines that might be promising research targets in the pathogenesis, development, and prediction of prognosis in hepatocellular carcinoma using bioinformatics.
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Affiliation(s)
- Yang Zheng
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
| | - Lili Tang
- Institute of Military Cognition and Brain Sciences, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Guojiang Chen
- Institute of Pharmacology and Toxicology, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Ziling Liu
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
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Wong CC, Xu J, Bian X, Wu JL, Kang W, Qian Y, Li W, Chen H, Gou H, Liu D, Yat Luk ST, Zhou Q, Ji F, Chan LS, Shirasawa S, Sung JJ, Yu J. In Colorectal Cancer Cells With Mutant KRAS, SLC25A22-Mediated Glutaminolysis Reduces DNA Demethylation to Increase WNT Signaling, Stemness, and Drug Resistance. Gastroenterology 2020; 159:2163-2180.e6. [PMID: 32814111 DOI: 10.1053/j.gastro.2020.08.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/03/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Mutant KRAS promotes glutaminolysis, a process that uses steps from the tricarboxylic cycle to convert glutamine to α-ketoglutarate and other molecules via glutaminase and SLC25A22. This results in inhibition of demethylases and epigenetic alterations in cells that increase proliferation and stem cell features. We investigated whether mutant KRAS-mediated glutaminolysis affects the epigenomes and activities of colorectal cancer (CRC) cells. METHODS We created ApcminKrasG12D mice with intestine-specific knockout of SLC25A22 (ApcminKrasG12DSLC25A22fl/fl mice). Intestine tissues were collected and analyzed by histology, immunohistochemistry, and DNA methylation assays; organoids were derived and studied for stem cell features, along with organoids derived from 2 human colorectal tumor specimens. Colon epithelial cells (1CT) and CRC cells (DLD1, DKS8, HKE3, and HCT116) that expressed mutant KRAS, with or without knockdown of SLC25A22 or other proteins, were deprived of glutamine or glucose and assayed for proliferation, colony formation, glucose or glutamine consumption, and apoptosis; gene expression patterns were analyzed by RNA sequencing, proteins by immunoblots, and metabolites by liquid chromatography-mass spectrometry, with [U-13C5]-glutamine as a tracer. Cells and organoids with knocked down, knocked out, or overexpressed proteins were analyzed for DNA methylation at CpG sites using arrays. We performed immunohistochemical analyses of colorectal tumor samples from 130 patients in Hong Kong (57 with KRAS mutations) and Kaplan-Meier analyses of survival. We analyzed gene expression levels of colorectal tumor samples in The Cancer Genome Atlas. RESULTS CRC cells that express activated KRAS required glutamine for survival, and rapidly incorporated it into the tricarboxylic cycle (glutaminolysis); this process required SLC25A22. Cells incubated with succinate and non-essential amino acids could proliferate under glutamine-free conditions. Mutant KRAS cells maintained a low ratio of α-ketoglutarate to succinate, resulting in reduced 5-hydroxymethylcytosine-a marker of DNA demethylation, and hypermethylation at CpG sites. Many of the hypermethylated genes were in the WNT signaling pathway and at the protocadherin gene cluster on chromosome 5q31. CRC cells without mutant KRAS, or with mutant KRAS and knockout of SLC25A22, expressed protocadherin genes (PCDHAC2, PCDHB7, PCDHB15, PCDHGA1, and PCDHGA6)-DNA was not methylated at these loci. Expression of the protocadherin genes reduced WNT signaling to β-catenin and expression of the stem cell marker LGR5. ApcminKrasG12DSLC25A22fl/fl mice developed fewer colon tumors than ApcminKrasG12D mice (P < .01). Organoids from ApcminKrasG12DSLC25A22fl/fl mice had reduced expression of LGR5 and other markers of stemness compared with organoids derived from ApcminKrasG12D mice. Knockdown of SLC25A22 in human colorectal tumor organoids reduced clonogenicity. Knockdown of lysine demethylases, or succinate supplementation, restored expression of LGR5 to SLC25A22-knockout CRC cells. Knockout of SLC25A22 in CRC cells that express mutant KRAS increased their sensitivity to 5-fluorouacil. Level of SLC25A22 correlated with levels of LGR5, nuclear β-catenin, and a stem cell-associated gene expression pattern in human colorectal tumors with mutations in KRAS and reduced survival times of patients. CONCLUSIONS In CRC cells that express activated KRAS, SLC25A22 promotes accumulation of succinate, resulting in increased DNA methylation, activation of WNT signaling to β-catenin, increased expression of LGR5, proliferation, stem cell features, and resistance to 5-fluorouacil. Strategies to disrupt this pathway might be developed for treatment of CRC.
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Affiliation(s)
- Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China.
| | - Jiaying Xu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Xiqing Bian
- State Key Laboratory for Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Jian-Lin Wu
- State Key Laboratory for Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Wei Kang
- Department of Anatomical and Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Yun Qian
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China; Department of Surgery, Chinese University of Hong Kong, Hong Kong, China
| | - Huarong Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Hongyan Gou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Dabin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Simson Tsz Yat Luk
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Qiming Zhou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Fenfen Ji
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Lam-Shing Chan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Joseph Jy Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong, China.
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Abstract
2-Oxoglutarate-dependent dioxygenases (2OGDDs) are a superfamily of enzymes that play diverse roles in many biological processes, including regulation of hypoxia-inducible factor-mediated adaptation to hypoxia, extracellular matrix formation, epigenetic regulation of gene transcription and the reprogramming of cellular metabolism. 2OGDDs all require oxygen, reduced iron and 2-oxoglutarate (also known as α-ketoglutarate) to function, although their affinities for each of these co-substrates, and hence their sensitivity to depletion of specific co-substrates, varies widely. Numerous 2OGDDs are recurrently dysregulated in cancer. Moreover, cancer-specific metabolic changes, such as those that occur subsequent to mutations in the genes encoding succinate dehydrogenase, fumarate hydratase or isocitrate dehydrogenase, can dysregulate specific 2OGDDs. This latter observation suggests that the role of 2OGDDs in cancer extends beyond cancers that harbour mutations in the genes encoding members of the 2OGDD superfamily. Herein, we review the regulation of 2OGDDs in normal cells and how that regulation is corrupted in cancer.
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Affiliation(s)
- Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA.
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Mehtonen J, Teppo S, Lahnalampi M, Kokko A, Kaukonen R, Oksa L, Bouvy-Liivrand M, Malyukova A, Mäkinen A, Laukkanen S, Mäkinen PI, Rounioja S, Ruusuvuori P, Sangfelt O, Lund R, Lönnberg T, Lohi O, Heinäniemi M. Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities. Genome Med 2020; 12:99. [PMID: 33218352 PMCID: PMC7679990 DOI: 10.1186/s13073-020-00799-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. METHODS We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. RESULTS We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment resistance, we show that inhibition of ETS-transcription factors reduced cell viability and resolved pathways contributing to this using scRNA-seq. CONCLUSIONS Our data provide a detailed picture of the transcription factor activities characterizing both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.
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Affiliation(s)
- Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Susanna Teppo
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Aleksi Kokko
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Riina Kaukonen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Laura Oksa
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Maria Bouvy-Liivrand
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Alena Malyukova
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Artturi Mäkinen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Saara Laukkanen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Petri I Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | | | - Pekka Ruusuvuori
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Olli Lohi
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
- Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland.
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Liu B, Kumar R, Chao HP, Mehmood R, Ji Y, Tracz A, Tang DG. Evidence for context-dependent functions of KDM5B in prostate development and prostate cancer. Oncotarget 2020; 11:4243-4252. [PMID: 33245716 PMCID: PMC7679033 DOI: 10.18632/oncotarget.27818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PCa) is one of the leading causes of cancer-related deaths worldwide. Prostate tumorigenesis and PCa progression involve numerous genetic as well as epigenetic perturbations. Histone modification represents a fundamental epigenetic mechanism that regulates diverse cellular processes, and H3K4 methylation, one such histone modification associated with active transcription, can be reversed by dedicated histone demethylase KDM5B (JARID1B). Abnormal expression and functions of KDM5B have been implicated in several cancer types including PCa. Consistently, our bioinformatics analysis reveals that the KDM5B mRNA levels are upregulated in PCa compared to benign prostate tissues, and correlate with increased tumor grade and poor patient survival, supporting an oncogenic function of KDM5B in PCa. Surprisingly, however, when we generated prostate-specific conditional Kdm5b knockout mice using probasin (Pb) promoter-driven Cre: loxP system, we observed that Kdm5b deletion did not affect normal prostate development but instead induced mild hyperplasia. These results suggest that KDM5B may possess context-dependent roles in normal prostate development vs. PCa development and progression.
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Affiliation(s)
- Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D Anderson Cancer Center, Science Park, Smithville, TX, USA.,These authors contributed equally to this work
| | - Rahul Kumar
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,These authors contributed equally to this work
| | - Hseuh-Ping Chao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D Anderson Cancer Center, Science Park, Smithville, TX, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Rashid Mehmood
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Life Sciences, College of Science and General Studies, Alfaisal University, Takhasusi Street, Riyadh, Saudi Arabia
| | - Yibing Ji
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Amanda Tracz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Dean G Tang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D Anderson Cancer Center, Science Park, Smithville, TX, USA.,Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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SUV39H1 regulates the progression of MLL-AF9-induced acute myeloid leukemia. Oncogene 2020; 39:7239-7252. [PMID: 33037410 PMCID: PMC7728597 DOI: 10.1038/s41388-020-01495-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/11/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic regulations play crucial roles in leukemogenesis and leukemia progression. SUV39H1 is the dominant H3K9 methyltransferase in the hematopoietic system, and its expression declines with aging. However, the role of SUV39H1 via its-mediated repressive modification H3K9me3 in leukemogenesis/leukemia progression remains to be explored. We found that SUV39H1 was down-regulated in a variety of leukemias, including MLL-r AML, as compared with normal individuals. Decreased levels of Suv39h1 expression and genomic H3K9me3 occupancy were observed in LSCs from MLL-r-induced AML mouse models in comparison with that of hematopoietic stem/progenitor cells. Suv39h1 overexpression increased leukemia latency and decreased the frequency of LSCs in MLL-r AML mouse models, while Suv39h1 knockdown accelerated disease progression with increased number of LSCs. Increased Suv39h1 expression led to the inactivation of Hoxb13 and Six1, as well as reversion of Hoxa9/Meis1 downstream target genes, which in turn decelerated leukemia progression. Interestingly, Hoxb13 expression is up-regulated in MLL-AF9-induced AML cells, while knockdown of Hoxb13 in MLL-AF9 leukemic cells significantly prolonged the survival of leukemic mice with reduced LSC frequencies. Our data revealed that SUV39H1 functions as a tumor suppressor in MLL-AF9-induced AML progression. These findings provide the direct link of SUV39H1 to AML development and progression.
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41
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Evolving insights on histone methylome regulation in human acute myeloid leukemia pathogenesis and targeted therapy. Exp Hematol 2020; 92:19-31. [PMID: 32950598 DOI: 10.1016/j.exphem.2020.09.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive, disseminated hematological malignancy associated with clonal selection of aberrant self-renewing hematopoietic stem cells and progenitors and poorly differentiated myeloid blasts. The most prevalent form of leukemia in adults, AML is predominantly an age-related disorder and accounts for more than 10,000 deaths per year in the United States alone. In comparison to solid tumors, AML has an overall low mutational burden, albeit more than 70% of AML patients harbor somatic mutations in genes encoding epigenetic modifiers and chromatin regulators. In the past decade, discoveries highlighting the role of DNA and histone modifications in determining cellular plasticity and lineage commitment have attested to the importance of epigenetic contributions to tumor cell de-differentiation and heterogeneity, tumor initiation, maintenance, and relapse. Orchestration in histone methylation levels regulates pluripotency and multicellular development. The increasing number of reversible methylation regulators being identified, including histone methylation writer, reader, and eraser enzymes, and their implications in AML pathogenesis have widened the scope of epigenetic reprogramming, with multiple drugs currently in various stages of preclinical and clinical trials. AML methylome also determines response to conventional chemotherapy, as well as AML cell interaction within a tumor-immune microenvironment ecosystem. Here we summarize the latest developments focusing on molecular derangements in histone methyltransferases (HMTs) and histone demethylases (HDMs) in AML pathogenesis. AML-associated HMTs and HDMs, through intricate crosstalk mechanisms, maintain an altered histone methylation code conducive to disease progression. We further discuss their importance in governing response to therapy, which can be used as a biomarker for treatment efficacy. Finally we deliberate on the therapeutic potential of targeting aberrant histone methylome in AML, examine available small molecule inhibitors in combination with immunomodulating therapeutic approaches and caveats, and discuss how future studies can enable posited epigenome-based targeted therapy to become a mainstay for AML treatment.
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Fu YD, Huang MJ, Guo JW, You YZ, Liu HM, Huang LH, Yu B. Targeting histone demethylase KDM5B for cancer treatment. Eur J Med Chem 2020; 208:112760. [PMID: 32883639 DOI: 10.1016/j.ejmech.2020.112760] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
KDM5B (Lysine-Specific Demethylase 5B) erases the methyl group from H3K4me2/3, which performs wide regulatory effects on chromatin structure, and represses the transcriptional function of genes. KDM5B functions as an oncogene and associates with human cancers closely. Targeting KDM5B has been a promising direction for curing cancer since the emergence of potent KDM5B inhibitor CPI-455. In this area, most reported KDM5B inhibitors are Fe (Ⅱ) chelators, which also compete with the cofactor 2-OG in the active pockets. Besides, Some KDM5B inhibitors have been identified through high throughput screening or biochemical screening. In this reviewing article, we summarized the pioneering progress in KDM5B to provide a comprehensive realization, including crystal structure, transcriptional regulation function, cancer-related functions, development of inhibitors, and SAR studies. We hope to provide a comprehensive overview of KDM5B and the development of KDM5B inhibitors.
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Affiliation(s)
- Yun-Dong Fu
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ming-Jie Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Jia-Wen Guo
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ya-Zhen You
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-Hua Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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Secker KA, Bruns L, Keppeler H, Jeong J, Hentrich T, Schulze-Hentrich JM, Mankel B, Fend F, Schneidawind D, Schneidawind C. Only Hematopoietic Stem and Progenitor Cells from Cord Blood Are Susceptible to Malignant Transformation by MLL-AF4 Translocations. Cancers (Basel) 2020; 12:cancers12061487. [PMID: 32517300 PMCID: PMC7352867 DOI: 10.3390/cancers12061487] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/18/2023] Open
Abstract
Mixed lineage leukemia (MLL) (KMT2A) rearrangements (KMT2Ar) play a crucial role in leukemogenesis. Dependent on age, major differences exist regarding disease frequency, main fusion partners and prognosis. In infants, up to 80% of acute lymphoid leukemia (ALL) bear a MLL translocation and half of them are t(4;11), resulting in a poor prognosis. In contrast, in adults only 10% of acute myeloid leukemia (AML) bear t(9;11) with an intermediate prognosis. The reasons for these differences are poorly understood. Recently, we established an efficient CRISPR/Cas9-based KMT2Ar model in hematopoietic stem and progenitor cells (HSPCs) derived from human cord blood (huCB) and faithfully mimicked the underlying biology of the disease. Here, we applied this model to HSPCs from adult bone marrow (huBM) to investigate the impact of the cell of origin and fusion partner on disease development. Both genome-edited infant and adult KMT2Ar cells showed monoclonal outgrowth with an immature morphology, myelomonocytic phenotype and elevated KMT2Ar target gene expression comparable to patient cells. Strikingly, all KMT2Ar cells presented with indefinite growth potential except for MLL-AF4 huBM cells ceasing proliferation after 80 days. We uncovered FFAR2, an epigenetic tumor suppressor, as potentially responsible for the inability of MLL-AF4 to immortalize adult cells under myeloid conditions.
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Affiliation(s)
- Kathy-Ann Secker
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, 72076 Tuebingen, Germany; (K.-A.S.); (L.B.); (H.K.); (D.S.)
| | - Lukas Bruns
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, 72076 Tuebingen, Germany; (K.-A.S.); (L.B.); (H.K.); (D.S.)
| | - Hildegard Keppeler
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, 72076 Tuebingen, Germany; (K.-A.S.); (L.B.); (H.K.); (D.S.)
| | - Johan Jeong
- Synthego Corporation, Menlo Park, CA 94025, USA;
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tuebingen, Germany; (T.H.); (J.M.S.-H.)
| | - Julia M. Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tuebingen, Germany; (T.H.); (J.M.S.-H.)
| | - Barbara Mankel
- Institute of Pathology and Neuropathology, University of Tuebingen, 72076 Tuebingen, Germany; (B.M.); (F.F.)
| | - Falko Fend
- Institute of Pathology and Neuropathology, University of Tuebingen, 72076 Tuebingen, Germany; (B.M.); (F.F.)
| | - Dominik Schneidawind
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, 72076 Tuebingen, Germany; (K.-A.S.); (L.B.); (H.K.); (D.S.)
| | - Corina Schneidawind
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, 72076 Tuebingen, Germany; (K.-A.S.); (L.B.); (H.K.); (D.S.)
- Correspondence: ; Tel.: +49-7071-29-84319
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Tan Y, Wu Q, Zhou F. Targeting acute myeloid leukemia stem cells: Current therapies in development and potential strategies with new dimensions. Crit Rev Oncol Hematol 2020; 152:102993. [PMID: 32502928 DOI: 10.1016/j.critrevonc.2020.102993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
High relapse rate of acute myeloid leukemia (AML) is still a crucial problem despite considerable advances in anti-cancer therapies. One crucial cause of relapse is the existence of leukemia stem cells (LSCs) with self-renewal ability, which contribute to repeated treatment resistance and recurrence. Treatments targeting LSCs, especially in combination with existing chemotherapy regimens or hematopoietic stem cell transplantation might help achieve a higher complete remission rate and improve overall survival. Many novel agents of different therapeutic strategies that aim to modulate LSCs self-renewal, proliferation, apoptosis, and differentiation are under investigation. In this review, we summarize the latest advances of different therapies in development based on the biological characteristics of LSCs, with particular attention on natural products, synthetic compounds, antibody therapies, and adoptive cell therapies that promote the LSC eradication. We also explore the causes of AML recurrence and proposed potential strategies with new dimensions for targeting LSCs in the future.
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Affiliation(s)
- Yuxin Tan
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People's Republic of China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People's Republic of China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People's Republic of China.
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45
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Leukemogenic Chromatin Alterations Promote AML Leukemia Stem Cells via a KDM4C-ALKBH5-AXL Signaling Axis. Cell Stem Cell 2020; 27:81-97.e8. [PMID: 32402251 DOI: 10.1016/j.stem.2020.04.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/13/2020] [Accepted: 03/31/2020] [Indexed: 12/19/2022]
Abstract
N6-methyladenosine (m6A) is a commonly present modification of mammalian mRNAs and plays key roles in various cellular processes. m6A modifiers catalyze this reversible modification. However, the underlying mechanisms by which these m6A modifiers are regulated remain elusive. Here we show that expression of m6A demethylase ALKBH5 is regulated by chromatin state alteration during leukemogenesis of human acute myeloid leukemia (AML), and ALKBH5 is required for maintaining leukemia stem cell (LSC) function but is dispensable for normal hematopoiesis. Mechanistically, KDM4C regulates ALKBH5 expression via increasing chromatin accessibility of ALKBH5 locus, by reducing H3K9me3 levels and promoting recruitment of MYB and Pol II. Moreover, ALKBH5 affects mRNA stability of receptor tyrosine kinase AXL in an m6A-dependent way. Thus, our findings link chromatin state dynamics with expression regulation of m6A modifiers and uncover a selective and critical role of ALKBH5 in AML that might act as a therapeutic target of specific targeting LSCs.
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46
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Vetrie D, Helgason GV, Copland M. The leukaemia stem cell: similarities, differences and clinical prospects in CML and AML. Nat Rev Cancer 2020; 20:158-173. [PMID: 31907378 DOI: 10.1038/s41568-019-0230-9] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 01/21/2023]
Abstract
For two decades, leukaemia stem cells (LSCs) in chronic myeloid leukaemia (CML) and acute myeloid leukaemia (AML) have been advanced paradigms for the cancer stem cell field. In CML, the acquisition of the fusion tyrosine kinase BCR-ABL1 in a haematopoietic stem cell drives its transformation to become a LSC. In AML, LSCs can arise from multiple cell types through the activity of a number of oncogenic drivers and pre-leukaemic events, adding further layers of context and genetic and cellular heterogeneity to AML LSCs not observed in most cases of CML. Furthermore, LSCs from both AML and CML can be refractory to standard-of-care therapies and persist in patients, diversify clonally and serve as reservoirs to drive relapse, recurrence or progression to more aggressive forms. Despite these complexities, LSCs in both diseases share biological features, making them distinct from other CML or AML progenitor cells and from normal haematopoietic stem cells. These features may represent Achilles' heels against which novel therapies can be developed. Here, we review many of the similarities and differences that exist between LSCs in CML and AML and examine the therapeutic strategies that could be used to eradicate them.
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MESH Headings
- Animals
- Biomarkers, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Disease Management
- Disease Susceptibility
- Drug Development
- History, 20th Century
- History, 21st Century
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/etiology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Molecular Targeted Therapy
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Research/history
- Research/trends
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Affiliation(s)
- David Vetrie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - G Vignir Helgason
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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Zhu Q, Fang L, Heuberger J, Kranz A, Schipper J, Scheckenbach K, Vidal RO, Sunaga-Franze DY, Müller M, Wulf-Goldenberg A, Sauer S, Birchmeier W. The Wnt-Driven Mll1 Epigenome Regulates Salivary Gland and Head and Neck Cancer. Cell Rep 2020; 26:415-428.e5. [PMID: 30625324 DOI: 10.1016/j.celrep.2018.12.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/13/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022] Open
Abstract
We identified a regulatory system that acts downstream of Wnt/β-catenin signaling in salivary gland and head and neck carcinomas. We show in a mouse tumor model of K14-Cre-induced Wnt/β-catenin gain-of-function and Bmpr1a loss-of-function mutations that tumor-propagating cells exhibit increased Mll1 activity and genome-wide increased H3K4 tri-methylation at promoters. Null mutations of Mll1 in tumor mice and in xenotransplanted human head and neck tumors resulted in loss of self-renewal of tumor-propagating cells and in block of tumor formation but did not alter normal tissue homeostasis. CRISPR/Cas9 mutagenesis and pharmacological interference of Mll1 at sequences that inhibit essential protein-protein interactions or the SET enzyme active site also blocked the self-renewal of mouse and human tumor-propagating cells. Our work provides strong genetic evidence for a crucial role of Mll1 in solid tumors. Moreover, inhibitors targeting specific Mll1 interactions might offer additional directions for therapies to treat these aggressive tumors.
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Affiliation(s)
- Qionghua Zhu
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Liang Fang
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany; Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Julian Heuberger
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Andrea Kranz
- Biotechnology Center, Technical University, 01307 Dresden, Germany
| | - Jörg Schipper
- Department of Head and Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Kathrin Scheckenbach
- Department of Head and Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Ramon Oliveira Vidal
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Daniele Yumi Sunaga-Franze
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Marion Müller
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | | | - Sascha Sauer
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Walter Birchmeier
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany.
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Microbial enzymes for deprivation of amino acid metabolism in malignant cells: biological strategy for cancer treatment. Appl Microbiol Biotechnol 2020; 104:2857-2869. [PMID: 32037468 DOI: 10.1007/s00253-020-10432-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Amino acid deprivation therapy (AADT) is emerging as a promising strategy for the development of novel therapeutics against cancer. This biological therapy relies upon the differences in the metabolism of cancer and normal cells. The rapid growth of tumors results in decreased expression of certain enzymes leading to auxotrophy for some specific amino acids. These auxotrophic tumors are targeted by amino acid-depleting enzymes. The depletion of amino acid selectively inhibits tumor growth as the normal cells can synthesize amino acids by their usual machinery. The enzymes used in AADT are mostly obtained from microbes for their easy availability. Microbial L-asparaginase is already approved by FDA for the treatment of acute lymphoblastic leukemia. Arginine deiminase and methionase are under clinical trials and the therapeutic potential of lysine oxidase, glutaminase and phenylalanine ammonia lyase is also being explored. The present review provides an overview of microbial amino acid depriving enzymes. Various attributes of these enzymes like structure, mode of action, production, formulations, and targeted cancers are discussed. The challenges faced and the combat strategies to establish AADT in standard cancer armamentarium are also reviewed.Key Points • Amino acid deprivation therapy is a potential therapy for auxotrophic tumors. • Microbial enzymes are used due to their ease of manipulation and high productivity. • Enzyme properties are improved by PEGylation, encapsulation, and genetic engineering. • AADT can be employed as combinational therapy for better containment of cancer.
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49
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Park S, Kim GW, Kwon SH, Lee JS. Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease. FEBS J 2020; 287:2891-2902. [PMID: 31967712 DOI: 10.1111/febs.15219] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/23/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Histone modifications affect transcription by changing the chromatin structure. In particular, histone H3 lysine 4 trimethylation (H3K4me3) is one of the most recognized epigenetic marks of active transcription. While many studies have provided evidence of the correlation between H3K4me3 and active transcription, details regarding the mechanism involved remain unclear. The first study on the broad H3K4me3 domain was reported in 2014; subsequently, the function of this domain has been studied in various cell types. In this review, we summarized the recent studies on the role of the broad H3K4me3 domain in transcription, development, memory formation, and several diseases, including cancer and autoimmune diseases. The broadest H3K4me3 domains are associated with increased transcriptional precision of cell-type-specific genes related to cell identity and other essential functions. The broad H3K4me3 domain regulates maternal zygotic activation in early mammalian development. In systemic autoimmune diseases, high expression of immune-responsive genes requires the presence of the broad H3K4me3 domain in the promoter-proximal regions. Transcriptional repression of tumor-suppressor genes is associated with the shortening of the broad H3K4me3 domains in cancer cells. Additionally, the broad H3K4me3 domain interacts with the super-enhancer to regulate cancer-associated genes. During memory formation, H3K4me3 breadth is regulated in the hippocampus CA1 neurons. Taken together, these findings indicate that H3K4me3 breadth is essential for the regulation of the transcriptional output across multiple cell types.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
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50
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Histone lysine demethylase KDM5B maintains chronic myeloid leukemia via multiple epigenetic actions. Exp Hematol 2020; 82:53-65. [PMID: 32007477 DOI: 10.1016/j.exphem.2020.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 11/23/2022]
Abstract
The histone lysine demethylase KDM5 family is implicated in normal development and stem cell maintenance by epigenetic modulation of histone methylation status. Deregulation of the KDM5 family has been reported in various types of cancers, including hematological malignancies. However, their transcriptional regulatory roles in the context of leukemia remain unclear. Here, we find that KDM5B is strongly expressed in normal CD34+ hematopoietic stem/progenitor cells and chronic myeloid leukemia (CML) cells. Knockdown of KDM5B in K562 CML cells reduced leukemia colony-forming potential. Transcriptome profiling of KDM5B knockdown K562 cells revealed the deregulation of genes involved in myeloid differentiation and Toll-like receptor signaling. Through the integration of transcriptome and ChIP-seq profiling data, we show that KDM5B is enriched at the binding sites of the GATA and AP-1 transcription factor families, suggesting their collaborations in the regulation of transcription. Even though the binding of KDM5B substantially overlapped with H3K4me1 or H3K4me3 mark at gene promoters, only a small subset of the KDM5B targets showed differential expression in association with the histone demethylation activity. By characterizing the interacting proteins in K562 cells, we discovered that KDM5B recruits protein complexes involved in the mRNA processing machinery, implying an alternative epigenetic action mediated by KDM5B in gene regulation. Our study highlights the oncogenic functions of KDM5B in CML cells and suggests that KDM5B is vital to the transcriptional regulation via multiple epigenetic mechanisms.
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