1
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Salafranca J, Ko JK, Mukherjee AK, Fritzsche M, van Grinsven E, Udalova IA. Neutrophil nucleus: shaping the past and the future. J Leukoc Biol 2023; 114:585-594. [PMID: 37480361 PMCID: PMC10673716 DOI: 10.1093/jleuko/qiad084] [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: 03/21/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
Neutrophils are innate immune cells that are key to protecting the host against infection and maintaining body homeostasis. However, if dysregulated, they can contribute to disease, such as in cancer or chronic autoinflammatory disorders. Recent studies have highlighted the heterogeneity in the neutrophil compartment and identified the presence of immature neutrophils and their precursors in these pathologies. Therefore, understanding neutrophil maturity and the mechanisms through which they contribute to disease is critical. Neutrophils were first characterized morphologically by Ehrlich in 1879 using microscopy, and since then, different technologies have been used to assess neutrophil maturity. The advances in the imaging field, including state-of-the-art microscopy and machine learning algorithms for image analysis, reinforce the use of neutrophil nuclear morphology as a fundamental marker of maturity, applicable for objective classification in clinical diagnostics. New emerging approaches, such as the capture of changes in chromatin topology, will provide mechanistic links between the nuclear shape, chromatin organization, and transcriptional regulation during neutrophil maturation.
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Affiliation(s)
- Julia Salafranca
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jacky Ka Ko
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Ananda K Mukherjee
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Marco Fritzsche
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Erinke van Grinsven
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
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2
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Batten DJ, Crofts JJ, Chuzhanova N. Towards In Silico Identification of Genes Contributing to Similarity of Patients' Multi-Omics Profiles: A Case Study of Acute Myeloid Leukemia. Genes (Basel) 2023; 14:1795. [PMID: 37761935 PMCID: PMC10531350 DOI: 10.3390/genes14091795] [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: 08/06/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
We propose a computational framework for selecting biologically plausible genes identified by clustering of multi-omics data that reveal patients' similarity, thus giving researchers a more comprehensive view on any given disease. We employ spectral clustering of a similarity network created by fusion of three similarity networks, based on mRNA expression of immune genes, miRNA expression and DNA methylation data, using SNF_v2.1 software. For each cluster, we rank multi-omics features, ensuring the best separation between clusters, and select the top-ranked features that preserve clustering. To find genes targeted by DNA methylation and miRNAs found in the top-ranked features, we use chromosome-conformation capture data and miRNet2.0 software, respectively. To identify informative genes, these combined sets of target genes are analyzed in terms of their enrichment in somatic/germline mutations, GO biological processes/pathways terms and known sets of genes considered to be important in relation to a given disease, as recorded in the Molecular Signature Database from GSEA. The protein-protein interaction (PPI) networks were analyzed to identify genes that are hubs of PPI networks. We used data recorded in The Cancer Genome Atlas for patients with acute myeloid leukemia to demonstrate our approach, and discuss our findings in the context of results in the literature.
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Affiliation(s)
| | | | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; (D.J.B.); (J.J.C.)
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3
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Yang L, Yan Y, Li J, Zhou C, Jin J, Zhang T, Wu H, Li X, Wang W, Yuan L, Zhang X, Gao J. (Tn5-)FISH-based imaging in the era of 3D/spatial genomics. BIOPHYSICS REPORTS 2023; 9:15-25. [PMID: 37426200 PMCID: PMC10323772 DOI: 10.52601/bpr.2023.220025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 07/11/2023] Open
Abstract
3D genomics mainly focuses on the 3D position of single genes at the cell level, while spatial genomics focuses more on the tissue level. In this exciting new era of 3D/spatial genomics, half-century old FISH and its derivative methods, including Tn5-FISH, play important roles. In this review, we introduce the Tn5-FISH we developed recently, and present six different applications published by our collaborators and us, based on (Tn5-)FISH, which can be either general BAC clone-based FISH or Tn5-FISH. In these interesting cases, (Tn5-)FISH demonstrated its vigorous ability of targeting sub-chromosomal structures across different diseases and cell lines (leukemia, mESCs (mouse embryonic stem cells), and differentiation cell lines). Serving as an effective tool to image genomic structures at the kilobase level, Tn5-FISH holds great potential to detect chromosomal structures in a high-throughput manner, thus bringing the dawn for new discoveries in the great era of 3D/spatial genomics.
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Affiliation(s)
- Liheng Yang
- Seaver College, Pepperdine University, CA 90263, USA
| | - Yan Yan
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, BNRist, Department of Automation, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Beijing 100084, China
| | - JunLin Li
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100084, China
| | - Cheng Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jinlan Jin
- Department of Critical Care Medicine, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518034, China
| | - Tongmei Zhang
- Medical Oncology, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Haokaifeng Wu
- Centre for Regenerative Medicine and Health, HongKong Institute of Science & Innovation, Chinese Academy of Sciences, HongKong SAR, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, China
| | - Xingang Li
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Wei Wang
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Li Yuan
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100084, China
| | - Xu Zhang
- Beijing Institute of Collaborative Innovation, Beijing 100094, China
| | - Juntao Gao
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, BNRist, Department of Automation, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Beijing 100084, China
- Institute for TCM-X, Beijing 100084, China
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4
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Gong H, Li M, Ji M, Zhang X, Yuan Z, Zhang S, Yang Y, Li C, Chen Y. MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network. CELL REPORTS METHODS 2023; 3:100386. [PMID: 36814847 PMCID: PMC9939382 DOI: 10.1016/j.crmeth.2022.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/15/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Chromatin interactions play essential roles in chromatin conformation and gene expression. However, few tools exist to analyze the spatial density of regulatory chromatin interactions (SD-RCI). Here, we present the multi-modal network (MINE) toolkit, including MINE-Loop, MINE-Density, and MINE-Viewer. The MINE-Loop network aims to enhance the detection of RCIs, MINE-Density quantifies the SD--RCI, and MINE-Viewer facilitates 3D visualization of the density of chromatin interactions and participating regulatory factors (e.g., transcription factors). We applied MINE to investigate the relationship between the SD-RCI and chromatin volume change in HeLa cells before and after liquid-liquid phase separation. Changes in SD-RCI before and after treating the HeLa cells with 1,6-hexanediol suggest that changes in chromatin organization was related to the degree of activation or repression of genes. Together, the MINE toolkit enables quantitative studies on different aspects of chromatin conformation and regulatory activity.
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Affiliation(s)
- Haiyan Gong
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Minghong Li
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Mengdie Ji
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Xiaotong Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan 528399, China
| | - Zan Yuan
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Sichen Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yi Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Chun Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
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5
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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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6
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Elrakaybi A, Ruess DA, Lübbert M, Quante M, Becker H. Epigenetics in Pancreatic Ductal Adenocarcinoma: Impact on Biology and Utilization in Diagnostics and Treatment. Cancers (Basel) 2022; 14:cancers14235926. [PMID: 36497404 PMCID: PMC9738647 DOI: 10.3390/cancers14235926] [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: 10/01/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignancies with high potential of metastases and therapeutic resistance. Although genetic mutations drive PDAC initiation, they alone do not explain its aggressive nature. Epigenetic mechanisms, including aberrant DNA methylation and histone modifications, significantly contribute to inter- and intratumoral heterogeneity, disease progression and metastasis. Thus, increased understanding of the epigenetic landscape in PDAC could offer new potential biomarkers and tailored therapeutic approaches. In this review, we shed light on the role of epigenetic modifications in PDAC biology and on the potential clinical applications of epigenetic biomarkers in liquid biopsy. In addition, we provide an overview of clinical trials assessing epigenetically targeted treatments alone or in combination with other anticancer therapies to improve outcomes of patients with PDAC.
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Affiliation(s)
- Asmaa Elrakaybi
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Clinical Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Dietrich A. Ruess
- Department of General and Visceral Surgery, Center of Surgery, Medical Center University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Quante
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Department of Gastroenterology and Hepatology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Heiko Becker
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Correspondence: ; Tel.: +49-761-270-36000
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7
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Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
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Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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8
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Li B, Lin D, Zhai X, Fan G, Zhao Z, Cao X, Yang H, Che T, Yuan Z, Liu T. Conformational Changes in Three-Dimensional Chromatin Structure in Paulownia fortunei After Phytoplasma Infection. PHYTOPATHOLOGY 2022; 112:373-386. [PMID: 34124940 DOI: 10.1094/phyto-01-21-0030-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Higher-order chromatin structures play important roles in regulating multiple biological processes such as growth and development as well as biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia or about whole-genome chromatin conformational changes that occur in response to Paulownia witches' broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in both healthy and phytoplasma-infected Paulownia fortunei genome. The heat map results indicated that the strongest interactions between chromosomes were in the telomeres. We confirmed that the main structural characteristics of A/B compartments, topologically associated domains, and chromatin loops were prominent in the Paulownia genome and were clearly altered in phytoplasma-infected plants. By combining chromatin immunoprecipitation sequencing, Hi-C signals, and RNA sequencing data, we inferred that the chromatin structure changed and the modification levels of three histones (H3K4me3/K9ac/K36me3) increased in phytoplasma-infected P. fortunei, which was associated with changes of transcriptional activity. We concluded that for epigenetic modifications, transcriptional activity might function in combination to shape chromatin packing in healthy and phytoplasm-infected Paulownia. Finally, 11 genes (e.g., RPN6, Sec61 subunit-α) that were commonly located at specific topologically associated domain boundaries, A/B compartment switching and specific loops, and had been associated with histone marks were identified and considered as closely related to PaWB stress. Our results provide new insights into the nexus between gene regulation and chromatin conformational alterations in nonmodel plants upon phytopathogen infection and plant disease resistance.
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Affiliation(s)
- Bingbing Li
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Dan Lin
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Xiaoqiao Zhai
- Forestry Academy of Henan, Zhengzhou, Henan 450002, People's Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Xibing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Haibo Yang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Tiandong Che
- Annoroad Gene Technology Co., Ltd., Beijing 100176, People's Republic of China
| | - Zan Yuan
- Annoroad Gene Technology Co., Ltd., Beijing 100176, People's Republic of China
| | - Tao Liu
- Annoroad Gene Technology Co., Ltd., Beijing 100176, People's Republic of China
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9
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van der Kouwe E, Heller G, Czibere A, Pulikkan JA, Agreiter C, Castilla LH, Delwel R, Di Ruscio A, Ebralidze AK, Forte M, Grebien F, Heyes E, Kazianka L, Klinger J, Kornauth C, Le T, Lind K, Barbosa IAM, Pemovska T, Pichler A, Schmolke AS, Schweicker CM, Sill H, Sperr WR, Spittler A, Surapally S, Trinh BQ, Valent P, Vanura K, Welner RS, Zuber J, Tenen DG, Staber PB. Core-binding factor leukemia hijacks the T-cell-prone PU.1 antisense promoter. Blood 2021; 138:1345-1358. [PMID: 34010414 PMCID: PMC8525333 DOI: 10.1182/blood.2020008971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022] Open
Abstract
The blood system serves as a key model for cell differentiation and cancer. It is orchestrated by precise spatiotemporal expression of crucial transcription factors. One of the key master regulators in the hematopoietic systems is PU.1. Reduced levels of PU.1 are characteristic for human acute myeloid leukemia (AML) and are known to induce AML in mouse models. Here, we show that transcriptional downregulation of PU.1 is an active process involving an alternative promoter in intron 3 that is induced by RUNX transcription factors driving noncoding antisense transcription. Core-binding factor (CBF) fusions RUNX1-ETO and CBFβ-MYH11 in t(8;21) and inv(16) AML, respectively, activate the PU.1 antisense promoter that results in a shift from sense toward antisense transcription and myeloid differentiation blockade. In patients with CBF-AML, we found that an elevated antisense/sense transcript and promoter accessibility ratio represents a hallmark compared with normal karyotype AML or healthy CD34+ cells. Competitive interaction of an enhancer with the proximal or the antisense promoter forms a binary on/off switch for either myeloid or T-cell development. Leukemic CBF fusions thus use a physiological mechanism used by T cells to decrease sense transcription. Our study is the first example of a sense/antisense promoter competition as a crucial functional switch for gene expression perturbation by oncogenes. Hence, this disease mechanism reveals a previously unknown Achilles heel for future precise therapeutic targeting of oncogene-induced chromatin remodeling.
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Affiliation(s)
- E van der Kouwe
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - G Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | | | | | - C Agreiter
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - L H Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - R Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Di Ruscio
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - A K Ebralidze
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - M Forte
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - F Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Kazianka
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - J Klinger
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C Kornauth
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - T Le
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - K Lind
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - I A M Barbosa
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - T Pemovska
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Pichler
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A-S Schmolke
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C M Schweicker
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - H Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - W R Sperr
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, and
| | - S Surapally
- Versiti Blood Research Institute, Milwaukee, WI
| | - B Q Trinh
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - P Valent
- Department of Medicine I, Division of Hematology and Hemostaseology, and
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - K Vanura
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - R S Welner
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL; and
| | - J Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - D G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
- Cancer Science Institute, National University of Singapore, Singapore
| | - P B Staber
- Department of Medicine I, Division of Hematology and Hemostaseology, and
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10
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Shareef SJ, Bevill SM, Raman AT, Aryee MJ, van Galen P, Hovestadt V, Bernstein BE. Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nat Biotechnol 2021; 39:1086-1094. [PMID: 33958785 PMCID: PMC8434949 DOI: 10.1038/s41587-021-00910-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Barcoded DNA fragments are pooled before bisulfite conversion, allowing multiplex processing and technical consistency in low-input samples. Application of XRBS to single leukemia cells enabled us to evaluate genetic copy number variations and methylation variability across individual cells. Our analysis highlights heterochromatic H3K9me3 regions as having the highest cell-to-cell variability in their methylation, likely reflecting inherent epigenetic instability of these late-replicating regions, compounded by differences in cell cycle stages among sampled cells.
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Affiliation(s)
- Sarah J. Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samantha M. Bevill
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ayush T. Raman
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin J. Aryee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peter van Galen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Division of Hematology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA.,Co-corresponding (, )
| | - Bradley E. Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Co-corresponding (, )
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11
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Danieli A, Papantonis A. Spatial genome architecture and the emergence of malignancy. Hum Mol Genet 2021; 29:R197-R204. [PMID: 32619215 DOI: 10.1093/hmg/ddaa128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter-enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.
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Affiliation(s)
- Adi Danieli
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
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12
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Tian L, Ku L, Yuan Z, Wang C, Su H, Wang S, Song X, Dou D, Ren Z, Lai J, Liu T, Du C, Chen Y. Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3582-3596. [PMID: 33677565 DOI: 10.1093/jxb/erab087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.
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Affiliation(s)
- Lei Tian
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
- Henan Institute of Science and Technology for Development, Zhengzhou, China
| | - Lixia Ku
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Zan Yuan
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Cuiling Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Huihui Su
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Shunxi Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Xiaoheng Song
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Dandan Dou
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Zhenzhen Ren
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Tao Liu
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ, USA
| | - Yanhui Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
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13
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Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021; 14:14. [PMID: 33741028 PMCID: PMC7980343 DOI: 10.1186/s13072-021-00390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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14
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Regulation of MYB by distal enhancer elements in human myeloid leukemia. Cell Death Dis 2021; 12:223. [PMID: 33637692 PMCID: PMC7910426 DOI: 10.1038/s41419-021-03515-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/31/2022]
Abstract
MYB plays vital roles in regulating proliferation and differentiation of hematopoietic progenitor cells, dysregulation of MYB has been implicated in the pathogenesis of leukemia. Although the transcription of MYB has been well studied, its detailed underlying regulatory mechanisms still remain elusive. Here, we detected the long-range interaction between the upstream regions, −34k and −88k, and the MYB promoter in K562, U937, and HL-60 cells using circularized chromosome conformation capture (4C) assay, which declined when MYB was downregulated during chemical-induced differentiation. The enrichment of enhancer markers, H3K4me1 and H3K27ac, and enhancer activity at the −34k and −88k regions were confirmed by ChIP-qPCR and luciferase assay respectively. ChIP-qPCR showed the dynamic binding of GATA1, TAL1, and CCAAT/enhancer-binding protein (C/EBPβ) at −34k and −88k during differentiation of K562 cells. Epigenome editing by a CRISPR-Cas9-based method showed that H3K27ac at −34k enhanced TF binding and MYB expression, while DNA methylation inhibited MYB expression. Taken together, our data revealed that enhancer elements at −34k are required for MYB expression, TF binding, and epigenetic modification are closely involved in this process in human myeloid leukemia cells.
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15
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Buschner G, Feuerecker B, Spinner S, Seidl C, Essler M. Differentiation of acute myeloid leukemia (AML) cells with ATRA reduces 18F-FDG uptake and increases sensitivity towards ABT-737-induced apoptosis. Leuk Lymphoma 2020; 62:630-639. [PMID: 33140666 DOI: 10.1080/10428194.2020.1839648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Acute myeloid leukemia (AML) is a malignant disease of the bone marrow, comprising various subtypes. We have investigated seven different AML cell lines that showed different sensitivities toward the inducer of apoptosis ABT-737, with IC50 concentrations ranging from 9.9 nM to 1.8 µM. Besides, the AML cell lines revealed distinct differences in 18F-FDG uptake ranging from 4.1 to 11.0%. Moreover, the Pearson coefficient (0.363) suggests a moderate correlation between 18F-FDG uptake and the IC50 values of ABT-737. Differentiation of the AML cell lines NB-4 and AML-193 with all-trans-retinoic-acid (ATRA) induced a significant increase in sensitivity towards ABT-737 along with a reduced uptake of 18F-FDG. Therefore, 18F-FDG uptake could be predictive on sensitivity to treatment with ABT-737. Furthermore, because differentiation treatment of AML cells using ATRA reduced 18F-FDG uptake and increased sensitivity towards ABT-737, a combined treatment regimen with ATRA and ABT-737 might be a promising therapeutic option in the future.
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Affiliation(s)
- Gabriel Buschner
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Benedikt Feuerecker
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sabine Spinner
- Department of Hematology and Oncology, Internal Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christof Seidl
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Markus Essler
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,Department of Nuclear Medicine, Universitätsklinikum Bonn, Bonn, Germany
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16
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Jiang S, Li H, Hong H, Du G, Huang X, Sun Y, Wang J, Tao H, Xu K, Li C, Chen Y, Chen H, Bo X. Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. Brief Bioinform 2020; 22:5912562. [PMID: 32987404 PMCID: PMC8138881 DOI: 10.1093/bib/bbaa210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Abstract
Topologically associated domains (TADs) are spatial and functional units of metazoan chromatin structure. Interpretation of the interplay between regulatory factors and chromatin structure within TADs is crucial to understand the spatial and temporal regulation of gene expression. However, a computational metric for the sensitive characterization of TAD regulatory landscape is lacking. Here, we present the spatial density of open chromatin (SDOC) metric as a quantitative measurement of intra-TAD chromatin state and structure. SDOC sensitively reflects epigenetic properties and gene transcriptional activity in TADs. During mouse T-cell development, we found that TADs with decreased SDOC are enriched in repressed developmental genes, and the joint effect of SDOC-decreasing and TAD clustering corresponds to the highest level of gene repression. In addition, we revealed a pervasive preference for TADs with similar SDOC to interact with each other, which may reflect the principle of chromatin organization.
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Affiliation(s)
- Shuai Jiang
- Beijing Institute of Ratiation Medicine, Department of Biotechnology
| | - Hao Li
- Beijing Institute of Radiation Medicine
| | - Hao Hong
- Beijing Institute of Ratiation Medicine, Department of Biotechnology
| | - Guifang Du
- Beijing Institute of Ratiation Medicine, Department of Biotechnology
| | - Xin Huang
- Beijing Institute of Ratiation Medicine, Department of Biotechnology
| | - Yu Sun
- Beijing Institute of Ratiation Medicine, Department of Biotechnology
| | | | - Huan Tao
- Beijing Institute of Radiation Medicine
| | - Kang Xu
- Beijing Institute of Radiation Medicine
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University. He is also a Professor at the Center for Statistical Science and the Center for Bioinformatics in Peking University
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine and Department of Automation in Tsinghua University
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17
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Jin Z, Lu Y, Wu Y, Che J, Dong X. Development of differentiation modulators and targeted agents for treating neuroblastoma. Eur J Med Chem 2020; 207:112818. [PMID: 32937281 DOI: 10.1016/j.ejmech.2020.112818] [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: 06/07/2020] [Revised: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Neuroblastoma (NB) is one of the most common pediatric malignancies. Easy metastasis, poor prognosis, and a high degree of heterogeneity of NB hinder its successful treatment. Several different therapeutic strategies have been developed to overcome these problems, including differentiation and targeted therapy. In this review, we summarize the recent development of differentiation modulators and targeted agents for treating NB. Several promising targets of NB were also discussed.
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Affiliation(s)
- Zegao Jin
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yang Lu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yizhe Wu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310058, PR China; Cancer Center of Zhejiang University, Hangzhou, 310058, PR China.
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18
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Zhang S, Zhou L, Zhang M, Wang Y, Wang M, Du J, Gu W, Kui F, Li J, Geng S, Du G. Berberine Maintains the Neutrophil N1 Phenotype to Reverse Cancer Cell Resistance to Doxorubicin. Front Pharmacol 2020; 10:1658. [PMID: 32063859 PMCID: PMC7000449 DOI: 10.3389/fphar.2019.01658] [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: 11/06/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
This study explores the contributions of neutrophils to chemotherapeutic resistance and berberine-regulated cancer cell sensitivity to doxorubicin (DOX). In vitro experiments, continuous DOX treatment led to the shift of HL-60 cells to N2 neutrophils and thus induced chemotherapeutic resistance. The combination treatment with DOX and 2 µM berberine resulted in the differentiation of HL-60 cells toward N1 and therefore stimulated HL-60 cell immune clearance. Berberine increased reactive oxygen species (ROS) and decreased autophagy and therefore induced apoptosis in HL-60-N2 cells with morphological changes, but had no effect on cell viability in HL-60-N1 cells. The neutrophil-regulating efficacy of berberine was confirmed in the urethane-induced lung carcinogenic model and H22 liver cancer allograft model. Furthermore, we found that DOX-derived neutrophils had high levels of CD133 and CD309 surface expression, which prevented both chemotherapeutic sensitivity and immune rejection by self-expression of PD-L1 and surface expression of PD-1 receptor on T cells, whereas berberine could downregulate CD133 and CD309 surface expression. Finally, berberine-relevant targets and pathways were evaluated. This study first suggests an important role of berberine in regulating neutrophil phenotypes to maintain cancer cell sensitivity to DOX.
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Affiliation(s)
- Shuhui Zhang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Lin Zhou
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Mengdi Zhang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Yuehua Wang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Mengqi Wang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Jincheng Du
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
- Chinese Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Wenwen Gu
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Fuguang Kui
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Jiahuan Li
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
| | - Shengnan Geng
- School of Pharmacy and Chemical Engineering, Zhengzhou University of Industry Technology, Xinzheng, China
| | - Gangjun Du
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng, China
- School of Pharmacy and Chemical Engineering, Zhengzhou University of Industry Technology, Xinzheng, China
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