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Zhang S, Audiger C, Chopin M, Nutt SL. Transcriptional regulation of dendritic cell development and function. Front Immunol 2023; 14:1182553. [PMID: 37520521 PMCID: PMC10382230 DOI: 10.3389/fimmu.2023.1182553] [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: 03/08/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Dendritic cells (DCs) are sentinel immune cells that form a critical bridge linking the innate and adaptive immune systems. Extensive research addressing the cellular origin and heterogeneity of the DC network has revealed the essential role played by the spatiotemporal activity of key transcription factors. In response to environmental signals DC mature but it is only following the sensing of environmental signals that DC can induce an antigen specific T cell response. Thus, whilst the coordinate action of transcription factors governs DC differentiation, sensing of environmental signals by DC is instrumental in shaping their functional properties. In this review, we provide an overview that focuses on recent advances in understanding the transcriptional networks that regulate the development of the reported DC subsets, shedding light on the function of different DC subsets. Specifically, we discuss the emerging knowledge on the heterogeneity of cDC2s, the ontogeny of pDCs, and the newly described DC subset, DC3. Additionally, we examine critical transcription factors such as IRF8, PU.1, and E2-2 and their regulatory mechanisms and downstream targets. We highlight the complex interplay between these transcription factors, which shape the DC transcriptome and influence their function in response to environmental stimuli. The information presented in this review provides essential insights into the regulation of DC development and function, which might have implications for developing novel therapeutic strategies for immune-related diseases.
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Affiliation(s)
- Shengbo Zhang
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cindy Audiger
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Michaël Chopin
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stephen L. Nutt
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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2
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Fang Y, Chen W, Li Z, Chen Y, Wu X, Zhu X, Wang H, Chen X, Liang Q, Huang J, Han X, Hong W, Wang X, Wei W, Yu Z, Tu J. The role of a key transcription factor PU.1 in autoimmune diseases. Front Immunol 2022; 13:1001201. [PMID: 36248862 PMCID: PMC9557192 DOI: 10.3389/fimmu.2022.1001201] [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: 07/23/2022] [Accepted: 09/12/2022] [Indexed: 12/03/2022] Open
Abstract
PU.1, a transcription factor member of the E26 transformation-specific family, affects the function of a variety of immune cells in several physiological and pathological conditions. Previous studies studying the role of PU.1 in pathological conditions have mainly focused on immune system-related cancers, and a series of articles have confirmed that PU.1 mutation can induce a variety of immune cell-related malignancies. The underlying mechanism has also been extensively validated. However, the role of PU.1 in other major immune system-related diseases, namely, systemic autoimmune diseases, is still unclear. It was only in recent years that researchers began to gradually realize that PU.1 also played an important role in a variety of autoimmune diseases, such as rheumatoid arthritis (RA), experimental autoimmune encephalomyelitis (EAE) and systemic lupus erythematosus (SLE). This review article summarizes the findings of recent studies that investigated the role of PU.1 in various autoimmune diseases and the related underlying mechanisms. Furthermore, it presents new ideas and provides insight into the role of PU.1 as a potential treatment target for autoimmune diseases and highlights existing research problems and future research directions in related fields.
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Affiliation(s)
- Yilong Fang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Weile Chen
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Zhe Li
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Yu Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Xuming Wu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Xiangling Zhu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Huihui Wang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Xiaochun Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Qiuni Liang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jinghua Huang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Xintong Han
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Wenming Hong
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xinming Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
| | - Zhiying Yu
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
| | - Jiajie Tu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
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3
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Giannopoulou AI, Kanakoglou DS, Papavassiliou AG, Piperi C. Insights into the multi-faceted role of Pioneer transcription factors in glioma formation and progression with targeting options. Biochim Biophys Acta Rev Cancer 2022; 1877:188801. [PMID: 36113627 DOI: 10.1016/j.bbcan.2022.188801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Pioneer transcription factors (TFs) present an important subtype of transcription factors which are vital for cell programming during embryonic development and cellular memory during mitotic growth, as well as cell fate reprogramming. Pioneer TFs can engage specific target binding sites on nucleosomal DNA to attract chromatin remodeling complexes, cofactors, and other transcription factors, ultimately controlling gene expression by shaping locally the epigenome. The priority of binding that they exhibit in contrast to other transcription factors and their involvement in crucial events regarding cell fate, has implicated their aberrant function in the pathogenesis of several disorders including carcinogenesis. Emerging experimental data indicate that certain Pioneer TFs are highly implicated in gliomas development, in neoplastic cell proliferation, angiogenic processes, resistance to therapy, and patient survival. Herein, we describe the main structural characteristics and functional mechanisms of pioneer TFs, focusing on their central role in the pathogenesis and progression of gliomas. We further highlight the current treatment options ranging from natural agents (oleanolic acid) to a variety of chemical compounds (APR-246, COTI-2) and discuss potential delivery systems, including nanoparticles, viral vectors, and intracellular protein delivery techniques.
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Affiliation(s)
- Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Dimitrios S Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
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4
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Zheng L, Zhang Z, Song K, Xu X, Tong Y, Wei J, Jiang L. Potential biomarkers for inflammatory response in acute lung injury. Open Med (Wars) 2022; 17:1066-1076. [PMID: 35795000 PMCID: PMC9186513 DOI: 10.1515/med-2022-0491] [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: 04/23/2021] [Revised: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 11/15/2022] Open
Abstract
Acute lung injury (ALI) is a severe respiratory disorder occurring in critical care medicine, with high rates of mortality and morbidity. This study aims to screen the potential biomarkers for ALI. Microarray data of lung tissues from lung-specific geranylgeranyl pyrophosphate synthase large subunit 1 knockout and wild-type mice treated with lipopolysaccharide were downloaded. Differentially expressed genes (DEGs) between ALI and wild-type mice were screened. Functional analysis and the protein-protein interaction (PPI) modules were analyzed. Finally, a miRNA-transcription factor (TF)-target regulation network was constructed. Totally, 421 DEGs between ALI and wild-type mice were identified. The upregulated DEGs were mainly enriched in the peroxisome proliferator-activated receptor signaling pathway, and fatty acid metabolic process, while downregulated DEGs were related to cytokine-cytokine receptor interaction and regulation of cytokine production. Cxcl5, Cxcl9, Ccr5, and Cxcr4 were key nodes in the PPI network. In addition, three miRNAs (miR505, miR23A, and miR23B) and three TFs (PU1, CEBPA, and CEBPB) were key molecules in the miRNA-TF-target network. Nine genes including ADRA2A, P2RY12, ADORA1, CXCR1, and CXCR4 were predicted as potential druggable genes. As a conclusion, ADRA2A, P2RY12, ADORA1, CXCL5, CXCL9, CXCR1, and CXCR4 might be novel markers and potential druggable genes in ALI by regulating inflammatory response.
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Affiliation(s)
- Lanzhi Zheng
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
| | - Zhuoyi Zhang
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Youdian Road 54#, Shangcheng District, Hangzhou City, 310006 Zhejiang Province, China
| | - Kang Song
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
| | - Xiaoyang Xu
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
| | - Yixin Tong
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
| | - Jinling Wei
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
| | - Lu Jiang
- Emergency Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou City, 310006 Zhejiang Province, China
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5
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Gerber JP, Russ J, Chandrasekar V, Offermann N, Lee HM, Spear S, Guzzi N, Maida S, Pattabiraman S, Zhang R, Kayvanjoo AH, Datta P, Kasturiarachchi J, Sposito T, Izotova N, Händler K, Adams PD, Marafioti T, Enver T, Wenzel J, Beyer M, Mass E, Bellodi C, Schultze JL, Capasso M, Nimmo R, Salomoni P. Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation. Nat Cell Biol 2021; 23:1224-1239. [PMID: 34876685 PMCID: PMC8683376 DOI: 10.1038/s41556-021-00774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/14/2021] [Indexed: 12/25/2022]
Abstract
Defective silencing of retrotransposable elements has been linked to inflammageing, cancer and autoimmune diseases. However, the underlying mechanisms are only partially understood. Here we implicate the histone H3.3 chaperone Daxx, a retrotransposable element repressor inactivated in myeloid leukaemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx alters the chromatin landscape, H3.3 distribution and histone marks of haematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional programme for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to develop an autoinflammatory skin disease. While these molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx, haematopoietic progenitors in these mice show unique chromatin and transcriptome alterations, suggesting an interaction between these two pathways. Overall, our findings implicate retrotransposable element silencing in haematopoiesis and suggest a cross-talk between the H3.3 loading machinery and the pioneer transcription factor Pu.1.
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Grants
- P01 AG031862 NIA NIH HHS
- C416/A25145 Cancer Research UK
- C16420/A18066 Cancer Research UK
- MC_U132670601 Medical Research Council
- C33499/A20265 Cancer Research UK
- Deutsches Zentrum für Neurodegenerative Erkrankungen (German Center for Neurodegenerative Diseases)
- Worldwide Cancer Research
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme People Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster Immunosensation2
- Aging and Metabolic Programming (AMPro) Consortium from Helmholtz
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster Immunosensation2ImmunoSensation2
- Cancer Research UK (CRUK)
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster ImmunoSensation2
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: Ideas Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Wilhelm Sander-Stiftung (Wilhelm Sander Foundation)
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster ImmunoSensation2 Aging and Metabolic Programming (AMPro) Consortium from Helmholtz
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Affiliation(s)
- Julia P Gerber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jenny Russ
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Nina Offermann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Hang-Mao Lee
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sarah Spear
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Simona Maida
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Ruoyu Zhang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Amir H Kayvanjoo
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Preeta Datta
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | | | - Teresa Sposito
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Natalia Izotova
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Teresa Marafioti
- Department of Cancer Biology, UCL Cancer Institute, London, UK
- Department of Pathology, University College London, London, UK
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jörg Wenzel
- Department of Dermatology and Allergy, University Medical Center, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Elvira Mass
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Melania Capasso
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachael Nimmo
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Department of Cancer Biology, UCL Cancer Institute, London, UK.
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6
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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7
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Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. EBioMedicine 2021; 71:103559. [PMID: 34461601 PMCID: PMC8403728 DOI: 10.1016/j.ebiom.2021.103559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping “cell-of-origin”. Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. Methods We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naïve and memory B-cells) from 36 donor tonsils using >325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). Findings From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. Interpretation Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. Funding National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation.
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8
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Hosokawa H, Koizumi M, Masuhara K, Romero-Wolf M, Tanaka T, Nakayama T, Rothenberg EV. Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells. J Exp Med 2021; 218:e20202648. [PMID: 34180951 PMCID: PMC8241539 DOI: 10.1084/jem.20202648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/01/2021] [Accepted: 06/10/2021] [Indexed: 12/16/2022] Open
Abstract
PU.1 (encoded by Spi1), an ETS-family transcription factor with many hematopoietic roles, is highly expressed in the earliest intrathymic T cell progenitors but must be down-regulated during T lineage commitment. The transcription factors Runx1 and GATA3 have been implicated in this Spi1 repression, but the basis of the timing was unknown. We show that increasing Runx1 and/or GATA3 down-regulates Spi1 expression in pro-T cells, while deletion of these factors after Spi1 down-regulation reactivates its expression. Leveraging the stage specificities of repression and transcription factor binding revealed an unconventional but functional site in Spi1 intron 2. Acute Cas9-mediated deletion or disruption of the Runx and GATA motifs in this element reactivates silenced Spi1 expression in a pro-T cell line, substantially more than disruption of other candidate elements, and counteracts the repression of Spi1 in primary pro-T cells during commitment. Thus, Runx1 and GATA3 work stage specifically through an intronic silencing element in mouse Spi1 to control strength and maintenance of Spi1 repression during T lineage commitment.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
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9
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Liang F, Zhang C, Guo H, Gao SH, Yang FY, Zhou GB, Wang GZ. Comprehensive analysis of BTN3A1 in cancers: mining of omics data and validation in patient samples and cellular models. FEBS Open Bio 2021; 11:2586-2599. [PMID: 34293829 PMCID: PMC8409294 DOI: 10.1002/2211-5463.13256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/21/2021] [Indexed: 11/11/2022] Open
Abstract
Butyrophilin 3A1 (BTN3A1), a major histocompatibility complex‐associated gene that encodes a membrane protein with two extracellular immunoglobulin domains and an intracellular B30.2 domain, is critical in T‐cell activation and adaptive immune response. Here, the expression of BTN3A1 in cancers was analyzed in eight databases comprising 86 733 patients of 33 cancers, and the findings were validated in patient samples and cell models. We showed that BTN3A1 was expressed in most cancers, and its expression level was strongly correlated with clinical outcome of 13 cancers. Mutations of BTN3A1 were detected, and the mutations were distributed throughout the entire gene. Gene set enrichment analysis showed that BTN3A1 co‐expression genes and interacting proteins were enriched in immune regulation‐related pathways. BTN3A1 was associated with tumor‐infiltrating immune cells and was co‐expressed with multiple immune checkpoints in patients with breast cancer (BRCA) and non‐small cell lung cancer (NSCLC). We reported that BTN3A1 was downregulated in 46 of 65 (70.8%) NSCLCs, and its expression level was inversely associated with clinical outcome of the patients. BTN3A1 in tumor samples was lower than in counterpart normal tissues in 31 of 38 (81.6%) BRCAs. Bioinformatics analyses showed that BTN3A1 could be a target gene of transcription factor Spi‐1 proto‐oncogene (SPI1), and our ‘wet’ experiments showed that ectopic expression of SPI1 upregulated, whereas silencing of SPI1 downregulated, BTN3A1 expression in cells. These results suggest that BTN3A1 may function as a tumor suppressor and may serve as a potential prognostic biomarker in NSCLCs and BRCAs.
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Affiliation(s)
- Fan Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Guo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - San-Hui Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fu-Ying Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guang-Biao Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gui-Zhen Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Lv L, Wei Q, Wang Z, Zhao Y, Chen N, Yi Q. Clinical and Molecular Correlates of NLRC5 Expression in Patients With Melanoma. Front Bioeng Biotechnol 2021; 9:690186. [PMID: 34307322 PMCID: PMC8299757 DOI: 10.3389/fbioe.2021.690186] [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: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
NLRC5 is an important regulator in antigen presentation and inflammation, and its dysregulation promotes tumor progression. In melanoma, the impact of NLRC5 expression on molecular phenotype, clinical characteristics, and tumor features is largely unknown. In the present study, public datasets from the Cancer Cell Line Encyclopedia (CCLE), Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and cBioPortal were used to address these issues. We identify that NLRC5 is expressed in both immune cells and melanoma cells in melanoma samples and its expression is regulated by SPI1 and DNA methylation. NLRC5 expression is closely associated with Breslow thickness, Clark level, recurrence, pathologic T stage, and ulceration status in melanoma. Truncating/splice mutations rather than missense mutations in NLRC5 could compromise the expression of downstream genes. Low expression of NLRC5 is associated with poor prognosis, low activity of immune-related signatures, low infiltrating level of immune cells, and low cytotoxic score in melanoma. Additionally, NLRC5 expression correlates with immunotherapy efficacy in melanoma. In summary, these findings suggest that NLRC5 acts as a tumor suppressor in melanoma via modulating the tumor immune microenvironment. Targeting the NLRC5 related pathway might improve efficacy of immunotherapy for melanoma patients.
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Affiliation(s)
- Lei Lv
- Anhui Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qinqin Wei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhiwen Wang
- Anhui Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yujia Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Ni Chen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Qiyi Yi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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11
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Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol 2021; 22:197. [PMID: 34225769 PMCID: PMC8258993 DOI: 10.1186/s13059-021-02414-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. RESULTS Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. CONCLUSIONS By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
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Affiliation(s)
- Melania Barile
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Isabella Inzani
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Cambridge, CB2 0QQ UK
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1SD UK
| | - Carolina Guibentif
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
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12
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Raghav PK, Gangenahalli G. PU.1 Mimic Synthetic Peptides Selectively Bind with GATA-1 and Allow c-Jun PU.1 Binding to Enhance Myelopoiesis. Int J Nanomedicine 2021; 16:3833-3859. [PMID: 34113102 PMCID: PMC8187006 DOI: 10.2147/ijn.s303235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hematopoietic stem cells' commitment to myelopoiesis builds immunity to prevent infection. This process is controlled through transcription factor, especially Purine rich box 1 (PU.1) protein, which plays a central role in regulating myelopoiesis. The β3/β4 region of PU.1 accommodates a coactivator transcription factor, c-Jun, to activate myelopoiesis. However, an erythroid transcription factor, GATA-1, competes with c-Jun for the β3/β4 region, abolishing myelopoiesis and promoting erythropoiesis. This competitive regulation decides the hematopoietic stem cells' commitment towards either erythroid or myeloid lineage. METHODS Therefore, this study investigated the in vitro and in vivo effect of novel synthetic PU.1 β3/β4 mimic peptide analogs and peptide-loaded hydrophilic poly(D,L-lactide-co-glycolide) (PLGA) nanoparticles. RESULTS The designed peptides significantly increase the expression of corresponding myeloid markers, specifically CD33 in vitro. However, the in vivo delivery of peptide-loaded PLGA nanoparticles, which have sustained release effect of peptides, increases 10.8% of granulocytes as compared to control. CONCLUSION The observations showed that the fabricated nanoparticles protected the loaded peptides from the harsh intracellular environment for a longer duration without causing any toxicity. These findings highlight the possibility to use these peptides and peptide-loaded nanoparticles to increase hematopoietic stem cell commitment to myeloid cells in case of opportunistic infection.
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Affiliation(s)
- Pawan Kumar Raghav
- Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, 110054, India
| | - Gurudutta Gangenahalli
- Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, 110054, India
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13
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Xie B, Khoyratty TE, Abu-Shah E, F Cespedes P, MacLean AJ, Pirgova G, Hu Z, Ahmed AA, Dustin ML, Udalova IA, Arnon TI. The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:1515-1527. [PMID: 33608456 PMCID: PMC7980533 DOI: 10.4049/jimmunol.2000367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/31/2021] [Indexed: 11/24/2022]
Abstract
The PI3K pathway plays a key role in B cell activation and is important for the differentiation of Ab producing plasma cells (PCs). Although much is known about the molecular mechanisms that modulate PI3K signaling in B cells, the transcriptional regulation of PI3K expression is poorly understood. In this study, we identify the zinc finger protein Zbtb18 as a transcriptional repressor that directly binds enhancer/promoter regions of genes encoding class I PI3K regulatory subunits, subsequently limiting their expression, dampening PI3K signaling and suppressing PC responses. Following activation, dividing B cells progressively downregulated Zbtb18, allowing gradual amplification of PI3K signals and enhanced development of PCs. Human Zbtb18 displayed similar expression patterns and function in human B cells, acting to inhibit development of PCs. Furthermore, a number of Zbtb18 mutants identified in cancer patients showed loss of suppressor activity, which was also accompanied by impaired regulation of PI3K genes. Taken together, our study identifies Zbtb18 as a repressor of PC differentiation and reveals its previously unappreciated function as a transcription modulator of the PI3K signaling pathway.
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Affiliation(s)
- Bin Xie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Tariq E Khoyratty
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Enas Abu-Shah
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Pablo F Cespedes
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Andrew J MacLean
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Gabriela Pirgova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Tal I Arnon
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
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14
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Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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15
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Rothenberg EV, Göttgens B. How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson. Curr Opin Hematol 2021; 28:1-10. [PMID: 33229891 PMCID: PMC7755131 DOI: 10.1097/moh.0000000000000628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This historical perspective reviews how work of Eric H. Davidson was a catalyst and exemplar for explaining haematopoietic cell fate determination through gene regulation. RECENT FINDINGS Researchers studying blood and immune cells pioneered many of the early mechanistic investigations of mammalian gene regulatory processes. These efforts included the characterization of complex gene regulatory sequences exemplified by the globin and T-cell/B-cell receptor gene loci, as well as the identification of many key regulatory transcription factors through the fine mapping of chromosome translocation breakpoints in leukaemia patients. As the repertoire of known regulators expanded, assembly into gene regulatory network models became increasingly important, not only to account for the truism that regulatory genes do not function in isolation but also to devise new ways of extracting biologically meaningful insights from even more complex information. Here we explore how Eric H. Davidson's pioneering studies of gene regulatory network control in nonvertebrate model organisms have had an important and lasting impact on research into blood and immune cell development. SUMMARY The intellectual framework developed by Davidson continues to contribute to haematopoietic research, and his insistence on demonstrating logic and causality still challenges the frontier of research today.
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Affiliation(s)
- Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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16
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McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA. Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia. Cell Stem Cell 2020; 25:258-272.e9. [PMID: 31374198 DOI: 10.1016/j.stem.2019.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/28/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Tumors are composed of phenotypically heterogeneous cancer cells that often resemble various differentiation states of their lineage of origin. Within this hierarchy, it is thought that an immature subpopulation of tumor-propagating cancer stem cells (CSCs) differentiates into non-tumorigenic progeny, providing a rationale for therapeutic strategies that specifically eradicate CSCs or induce their differentiation. The clinical success of these approaches depends on CSC differentiation being unidirectional rather than reversible, yet this question remains unresolved even in prototypically hierarchical malignancies, such as acute myeloid leukemia (AML). Here, we show in murine and human models of AML that, upon perturbation of endogenous expression of the lineage-determining transcription factor PU.1 or withdrawal of established differentiation therapies, some mature leukemia cells can de-differentiate and reacquire clonogenic and leukemogenic properties. Our results reveal plasticity of CSC maturation in AML, highlighting the need to therapeutically eradicate cancer cells across a range of differentiation states.
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Affiliation(s)
- Mark D McKenzie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Margherita Ghisi
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Steven Ngo
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Luisa Cimmino
- Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA
| | - Cécile Esnault
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Ruijie Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Jessica M Salmon
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Michael Erlichster
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew T Witkowski
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Grace J Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Chopin
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandar Dakic
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Emilia Simankowicz
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Giovanna Pomilio
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Tina Vu
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Pavle Krsmanovic
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Shian Su
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Luyi Tian
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tracey M Baldwin
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Daniela A Zalcenstein
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ladina DiRago
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Shu Wang
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Donald Metcalf
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ben A Croker
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Graeme I Lancaster
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Andrew J Murphy
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Stephen L Nutt
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Vitek Pospisil
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Meaghan Wall
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, VIC 3065, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew H Wei
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Hugues de Thé
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Matthew E Ritchie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Campus Vienna Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia.
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17
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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18
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Yashiro T, Takeuchi H, Kasakura K, Nishiyama C. PU.1 regulates Ccr7 gene expression by binding to its promoter in naïve CD4 + T cells. FEBS Open Bio 2020; 10:1115-1121. [PMID: 32297481 PMCID: PMC7262917 DOI: 10.1002/2211-5463.12861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 01/06/2023] Open
Abstract
C‐C chemokine receptor type 7 (CCR7) is expressed on naïve T cells, B cells, and activated dendritic cells (DCs). We previously demonstrated that the transcription factor PU.1/Spi1 positively regulates the expression of CCR7 in DCs. In the present study, we investigated the role of PU.1 in CCR7 expression in T cells. To confirm whether PU.1 is involved in the expression of CCR7, we conducted a ChIP assay in various T cells purified from splenocytes and thymocytes and found that PU.1 binds to the Ccr7 promoter‐proximal region in spleen naïve CD4+ T cells, but not in thymocytes. Small interfering RNA‐mediated PU.1 knockdown resulted in decreased CCR7 expression in spleen naïve CD4+ T cells. Compared to naïve CD4+ T cells, Spi1 and Ccr7 mRNA levels decreased in Th1 and Th2 cells, in which PU.1 did not bind to the Ccr7 promoter, suggesting that CCR7 expression decreases due to the dissociation of PU.1 from the Ccr7 promoter during the development of effector T cells from naïve T cells. Collectively, we concluded that CCR7 expression level correlates with the binding level of PU.1 to the Ccr7 promoter and PU.1 acts as a transcriptional activator of the Ccr7 gene in naïve CD4+ T cells.
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Affiliation(s)
- Takuya Yashiro
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Japan
| | - Hiromi Takeuchi
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Japan
| | - Kazumi Kasakura
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Japan
| | - Chiharu Nishiyama
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Japan
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19
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Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia 2019; 33:2720-2731. [PMID: 31073152 PMCID: PMC6842075 DOI: 10.1038/s41375-019-0474-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Ikaros encodes a transcription factor that functions as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells resulted in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic, global, epigenomic and gene expression analyses to determine the mechanisms of Ikaros tumor suppressor activity. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effects of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Our results establish that Ikaros’ tumor suppressor function occurs via global regulation of the enhancer and super-enhancer landscape and through pioneering activity. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.
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Affiliation(s)
- Yali Ding
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chunhua Song
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital Southeast University, Institute of Hematology Southeast University, 210009, Nanjing, China
| | - Chandrika Gowda
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Glenn Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Mark E Reeves
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Dhimant Desai
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suming Huang
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kimberly J Payne
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Sinisa Dovat
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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20
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Rothenberg EV, Hosokawa H, Ungerbäck J. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development. Front Immunol 2019; 10:228. [PMID: 30842770 PMCID: PMC6391351 DOI: 10.3389/fimmu.2019.00228] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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21
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Nurminen V, Neme A, Seuter S, Carlberg C. Modulation of vitamin D signaling by the pioneer factor CEBPA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:96-106. [PMID: 30550771 DOI: 10.1016/j.bbagrm.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 01/31/2023]
Abstract
The myeloid master regulator CCAAT enhancer-binding protein alpha (CEBPA) is known as a pioneer factor. In this study, we report the CEBPA cistrome of THP-1 human monocytes after stimulation with the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) for 2, 8 and 24 h. About a third of the genomic VDR binding sites co-located with those of CEBPA. In parallel, the binding strength of 5% of the CEBPA cistrome, i.e. some 1500 sites, is significantly (p < 0.001) affected by 1,25(OH)2D3. Transcriptome-wide analysis after CEBPA silencing indicated that the pioneer factor enhances both the basal expression and ligand inducibility of 70 vitamin D target genes largely involved in lipid signaling and metabolism. In contrast, CEBPA suppresses 82 vitamin D target genes many of which are related to the modulation of T cell activity by monocytes. The inducibility of the promoter-specific histone marker H3K4me3 distinguishes the former class of genes from the latter. Moreover, prominent occupancy of the myeloid pioneer factor PU.1 on 1,25(OH)2D3-sensitive CEBPA enhancers mechanistically explains the dichotomy of vitamin D target genes. In conclusion, CEBPA supports vitamin D signaling concerning actions of the innate immune system, but uses the antagonism with PU.1 for suppressing possible overreactions of adaptive immunity.
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Affiliation(s)
- Veijo Nurminen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Antonio Neme
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
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22
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Pang SHM, de Graaf CA, Hilton DJ, Huntington ND, Carotta S, Wu L, Nutt SL. PU.1 Is Required for the Developmental Progression of Multipotent Progenitors to Common Lymphoid Progenitors. Front Immunol 2018; 9:1264. [PMID: 29942304 PMCID: PMC6005176 DOI: 10.3389/fimmu.2018.01264] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/22/2018] [Indexed: 01/27/2023] Open
Abstract
The transcription factor PU.1 is required for the development of mature myeloid and lymphoid cells. Due to this essential role and the importance of PU.1 in regulating several signature markers of lymphoid progenitors, its precise function in early lymphopoiesis has been difficult to define. Here, we demonstrate that PU.1 was required for efficient generation of lymphoid-primed multipotent progenitors (LMPPs) from hematopoietic stem cells and was essential for the subsequent formation of common lymphoid progenitors (CLPs). By contrast, further differentiation into the B-cell lineage was independent of PU.1. Examination of the transcriptional changes in conditional progenitors revealed that PU.1 activates lymphoid genes in LMPPs, while repressing genes normally expressed in neutrophils. These data identify PU.1 as a critical regulator of lymphoid priming and the transition between LMPPs and CLPs.
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Affiliation(s)
- Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Carolyn A de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Oncology Research, Boehringer Ingelheim, Vienna, Austria
| | - Li Wu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Institute for Immunology, Tsinghua University School of Medicine, Beijing, China
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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23
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Hosokawa H, Rothenberg EV. Cytokines, Transcription Factors, and the Initiation of T-Cell Development. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028621. [PMID: 28716889 DOI: 10.1101/cshperspect.a028621] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multipotent blood progenitor cells migrate into the thymus and initiate the T-cell differentiation program. T-cell progenitor cells gradually acquire T-cell characteristics while shedding their multipotentiality for alternative fates. This process is supported by extracellular signaling molecules, including Notch ligands and cytokines, provided by the thymic microenvironment. T-cell development is associated with dynamic change of gene regulatory networks of transcription factors, which interact with these environmental signals. Together with Notch or pre-T-cell-receptor (TCR) signaling, cytokines always control proliferation, survival, and differentiation of early T cells, but little is known regarding their cross talk with transcription factors. However, recent results suggest ways that cytokines expressed in distinct intrathymic niches can specifically modulate key transcription factors. This review discusses how stage-specific roles of cytokines and transcription factors can jointly guide development of early T cells.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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24
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Abstract
Pioneer transcription factors have the unique and important role of unmasking chromatin domains during development to allow the implementation of new cellular programs. Compared with those of other transcription factors, this activity implies that pioneer factors can recognize their target DNA sequences in so-called compacted or "closed" heterochromatin and can trigger remodeling of the adjoining chromatin landscape to provide accessibility to nonpioneer transcription factors. Recent studies identified several steps of pioneer action, namely rapid but weak initial binding to heterochromatin and stabilization of binding followed by chromatin opening and loss of cytosine-phosphate-guanine (CpG) methylation that provides epigenetic memory. Whereas CpG demethylation depends on replication, chromatin opening does not. In this Minireview, we highlight the unique properties of this transcription factor class and the challenges of understanding their mechanism of action.
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Affiliation(s)
- Alexandre Mayran
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
| | - Jacques Drouin
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
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25
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Liu Z, Feng Q, Sun P, Lu Y, Yang M, Zhang X, Jin X, Li Y, Lu SJ, Quan C. Genome-wide DNA methylation drives human embryonic stem cell erythropoiesis by remodeling gene expression dynamics. Epigenomics 2017; 9:1543-1558. [PMID: 29135282 DOI: 10.2217/epi-2017-0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body. Moreover, erythropoietic genes with differentially methylated CpG sites that were primarily enriched in nonisland regions were upregulated, and demethylation of their gene bodies was associated with the presence of enhancers and DNase I hypersensitive sites. Finally, the components of JAK-STAT-NF-κB signaling were DNA hypomethylated and upregulated, which targets the key genes for erythropoiesis. CONCLUSION Erythroid lineage commitment by hESCs requires genome-wide DNA methylation modifications to remodel gene expression dynamics.
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Affiliation(s)
- Zhijing Liu
- Department of Pathology, Qingdao Municipal Hospital, Affiliated with Qingdao University, 1 Jiaozhou Road, Qingdao 266000, Shandong, China
| | - Qiang Feng
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Pengpeng Sun
- Department of Critical Care Medicine, Qingdao Center Medical Group, Affiliated with Qingdao University, 127 Siliunan Road, Qingdao 266042, Shandong, China
| | - Yan Lu
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Minlan Yang
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Xiaowei Zhang
- Center for Translational Medicine, Central Hospital of Zibo, Affiliated with Shandong University, 54 Gongqingtuan Road, Zibo 255000, Shandong, China
| | - Xiangshu Jin
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Yulin Li
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Shi-Jiang Lu
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Chengshi Quan
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
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26
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Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS Pathog 2017; 13:e1006664. [PMID: 28968461 PMCID: PMC5638620 DOI: 10.1371/journal.ppat.1006664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 10/12/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infection converts resting human B cells into permanently proliferating lymphoblastoid cell lines (LCLs). The Epstein-Barr virus nuclear antigen 2 (EBNA2) plays a key role in this process. It preferentially binds to B cell enhancers and establishes a specific viral and cellular gene expression program in LCLs. The cellular DNA binding factor CBF1/CSL serves as a sequence specific chromatin anchor for EBNA2. The ubiquitous expression of this highly conserved protein raises the question whether additional cellular factors might determine EBNA2 chromatin binding selectively in B cells. Here we used CBF1 deficient B cells to identify cellular genes up or downregulated by EBNA2 as well as CBF1 independent EBNA2 chromatin binding sites. Apparently, CBF1 independent EBNA2 target genes and chromatin binding sites can be identified but are less frequent than CBF1 dependent EBNA2 functions. CBF1 independent EBNA2 binding sites are highly enriched for EBF1 binding motifs. We show that EBNA2 binds to EBF1 via its N-terminal domain. CBF1 proficient and deficient B cells require EBF1 to bind to CBF1 independent binding sites. Our results identify EBF1 as a co-factor of EBNA2 which conveys B cell specificity to EBNA2. Epstein-Barr virus (EBV) infection is closely linked to cancer development. At particular risk are immunocompromised individuals like post-transplant patients which can develop B cell lymphomas. In healthy individuals EBV preferentially infects B cells and establishes a latent infection without causing apparent clinical symptoms in most cases. Upon infection, Epstein-Barr virus nuclear antigen 2 (EBNA2) initiates a B cell specific gene expression program that causes activation and proliferation of the infected cells. EBNA2 is a transcription factor well known to use a cellular protein, CBF1/CSL, as a DNA adaptor. CBF1/CSL is a sequence specific DNA binding protein robustly expressed in all tissues. Here we show that EBNA2 can form complexes with early B cell factor 1 (EBF1), a B cell specific DNA binding transcription factor, and EBF1 stabilizes EBNA2 chromatin binding. This EBNA2/EBF1 complex might serve as a novel target to develop future small molecule strategies that act as antivirals in latent B cell infection.
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Affiliation(s)
- Laura V Glaser
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Simone Rieger
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sybille Thumann
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sophie Beer
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | | | | | | | | | - Björn Grüning
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Stefan Krebs
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Blum
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Ralf Zimmer
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Florian Erhard
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
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27
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Seki M, Kimura S, Isobe T, Yoshida K, Ueno H, Nakajima-Takagi Y, Wang C, Lin L, Kon A, Suzuki H, Shiozawa Y, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J. Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia. Nat Genet 2017; 49:1274-1281. [PMID: 28671687 DOI: 10.1038/ng.3900] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/24/2017] [Indexed: 12/12/2022]
Abstract
The outcome of treatment-refractory and/or relapsed pediatric T cell acute lymphoblastic leukemia (T-ALL) is extremely poor, and the genetic basis for this is not well understood. Here we report comprehensive profiling of 121 cases of pediatric T-ALL using transcriptome and/or targeted capture sequencing, through which we identified new recurrent gene fusions involving SPI1 (STMN1-SPI1 and TCF7-SPI1). Cases positive for fusions involving SPI1 (encoding PU.1), accounting for 3.9% (7/181) of the examined pediatric T-ALL cases, showed a double-negative (DN; CD4-CD8-) or CD8+ single-positive (SP) phenotype and had uniformly poor overall survival. These cases represent a subset of pediatric T-ALL distinguishable from the known T-ALL subsets in terms of expression of genes involved in T cell precommitment, establishment of T cell identity, and post-β-selection maturation and with respect to mutational profile. PU.1 fusion proteins retained transcriptional activity and, when constitutively expressed in mouse stem/progenitor cells, induced cell proliferation and resulted in a maturation block. Our findings highlight a unique role of SPI1 fusions in high-risk pediatric T-ALL.
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Affiliation(s)
- Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Changshan Wang
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Lin Lin
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Ryoji Hanada
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Hiroshi Moritake
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Takao Deguchi
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Yoshiko Hashii
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital, Sendai, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | | | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University, Tokyo, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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28
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Saelee P, Kearly A, Nutt SL, Garrett-Sinha LA. Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1. Front Immunol 2017; 8:383. [PMID: 28439269 PMCID: PMC5383717 DOI: 10.3389/fimmu.2017.00383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/17/2017] [Indexed: 12/16/2022] Open
Abstract
Background The transcription factor Ets1 is highly expressed in B lymphocytes. Loss of Ets1 leads to premature B cell differentiation into antibody-secreting cells (ASCs), secretion of autoantibodies, and development of autoimmune disease. Despite the importance of Ets1 in B cell biology, few Ets1 target genes are known in these cells. Results To obtain a more complete picture of the function of Ets1 in regulating B cell differentiation, we performed Ets1 ChIP-seq in primary mouse B cells to identify >10,000-binding sites, many of which were localized near genes that play important roles in B cell activation and differentiation. Although Ets1 bound to many sites in the genome, it was required for regulation of less than 5% of them as evidenced by gene expression changes in B cells lacking Ets1. The cohort of genes whose expression was altered included numerous genes that have been associated with autoimmune disease susceptibility. We focused our attention on four such Ets1 target genes Ptpn22, Stat4, Egr1, and Prdm1 to assess how they might contribute to Ets1 function in limiting ASC formation. We found that dysregulation of these particular targets cannot explain altered ASC differentiation in the absence of Ets1. Conclusion We have identified genome-wide binding targets for Ets1 in B cells and determined that a relatively small number of these putative target genes require Ets1 for their normal expression. Interestingly, a cohort of genes associated with autoimmune disease susceptibility is among those that are regulated by Ets1. Identification of the target genes of Ets1 in B cells will help provide a clearer picture of how Ets1 regulates B cell responses and how its loss promotes autoantibody secretion.
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Affiliation(s)
- Prontip Saelee
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Alyssa Kearly
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
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29
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Kumar D, Puan KJ, Andiappan AK, Lee B, Westerlaken GHA, Haase D, Melchiotti R, Li Z, Yusof N, Lum J, Koh G, Foo S, Yeong J, Alves AC, Pekkanen J, Sun LD, Irwanto A, Fairfax BP, Naranbhai V, Common JEA, Tang M, Chuang CK, Jarvelin MR, Knight JC, Zhang X, Chew FT, Prabhakar S, Jianjun L, Wang DY, Zolezzi F, Poidinger M, Lane EB, Meyaard L, Rötzschke O. A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus. Genome Med 2017; 9:18. [PMID: 28219444 PMCID: PMC5319034 DOI: 10.1186/s13073-017-0404-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/11/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals. The underlying mechanism of regulation, its genetic control as well as potential clinical implications had not been explored yet. METHODS Whole blood eQTL data of a Chinese cohort was used to identify SNPs regulating the expression of VSTM1, the gene encoding SIRL-1. The genotype effect was validated by flow cytometry (cell surface expression), correlated with electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP) and bisulfite sequencing (C-methylation) and its functional impact studied the inhibition of reactive oxygen species (ROS). RESULTS We found a significant association of a single CpG-SNP, rs612529T/C, located in the promoter of VSTM1. Through flow cytometry analysis we confirmed that primarily in the monocytes the protein level of SIRL-1 is strongly associated with genotype of this SNP. In monocytes, the T allele of this SNP facilitates binding of the transcription factors YY1 and PU.1, of which the latter has been recently shown to act as docking site for modifiers of DNA methylation. In line with this notion rs612529T associates with a complete demethylation of the VSTM1 promoter correlating with the allele-specific upregulation of SIRL-1 expression. In monocytes, this upregulation strongly impacts the IgA-induced production of ROS by these cells. Through targeted association analysis we found a significant Meta P value of 1.14 × 10-6 for rs612529 for association to atopic dermatitis (AD). CONCLUSION Low expression of SIRL-1 on monocytes is associated with an increased risk for the manifestation of an inflammatory skin disease. It thus underlines the role of both the cell subset and this inhibitory immune receptor in maintaining immune homeostasis in the skin. Notably, the genetic regulation is achieved by a single CpG-SNP, which controls the overall methylation state of the promoter gene segment.
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Affiliation(s)
- Dilip Kumar
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Kia Joo Puan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Anand Kumar Andiappan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Geertje H A Westerlaken
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, P.O. box 85090, Utrecht, 3508 AB, The Netherlands
| | - Doreen Haase
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Rossella Melchiotti
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Zhuang Li
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Nurhashikin Yusof
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Geraldine Koh
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Shihui Foo
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Joe Yeong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore.,Department of Pathology, Singapore General Hospital, Singapore, Republic of Singapore
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Juha Pekkanen
- Department of Environmental Health, National Institute for Health and Welfare, Kuopio, Finland
| | - Liang Dan Sun
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Astrid Irwanto
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research of Singapore (A*STAR), Singapore, Republic of Singapore
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, Oxford, UK.,Department of Oncology, Cancer and Haematology Centre, Churchill Hospital, Oxford, UK
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, Oxford, UK.,Department of Oncology, Cancer and Haematology Centre, Churchill Hospital, Oxford, UK
| | - John E A Common
- Institute of Medical Biology (IMB), A*STAR (Agency for Science, Technology and Research), Singapore, Republic of Singapore
| | - Mark Tang
- National Skin Center, Singapore, Republic of Singapore
| | - Chin Keh Chuang
- Institute of Molecular & Cellular Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Republic of Singapore.,Department of Physiology, NUS Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Center for Life Course Epidemiology, Faculty of Medicine, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, P.O. Box 5000, Aapistie 5A, 90014, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, 90029 OYS, P.O. Box 20, 90220, Oulu, Finland
| | | | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Shyam Prabhakar
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research of Singapore (A*STAR), Singapore, Republic of Singapore
| | - Liu Jianjun
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research of Singapore (A*STAR), Singapore, Republic of Singapore
| | - De Yun Wang
- Department of Otolaryngology, National University of Singapore, Singapore, Republic of Singapore.,Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore
| | - E Birgitte Lane
- Institute of Medical Biology (IMB), A*STAR (Agency for Science, Technology and Research), Singapore, Republic of Singapore
| | - Linde Meyaard
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, P.O. box 85090, Utrecht, 3508 AB, The Netherlands.
| | - Olaf Rötzschke
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore.
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30
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Seuter S, Neme A, Carlberg C. Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:405-415. [PMID: 28232093 DOI: 10.1016/j.bbagrm.2017.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/07/2017] [Accepted: 02/12/2017] [Indexed: 01/15/2023]
Abstract
The ETS-domain transcription factor PU.1 acts as a pioneer factor for other transcription factors including nuclear receptors. In this study, we report that in THP-1 human monocytes the PU.1 cistrome comprises 122,319 genomic sites. Interestingly, at 6498 (5.3%) of these loci PU.1 binding was significantly modulated by the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). In most cases 1,25(OH)2D3 increased PU.1 association, which correlated strongly with VDR co-location and overlap ratios for canonical DR3-type VDR binding sites. Genome-wide 6488 sites associating both with PU.1 and VDR as well as 5649 non-VDR overlapping, 1,25(OH)2D3-sensitive PU.1 loci represent the PU.1-VDR crosstalk and can be described by four gene regulatory scenarios, each. Chromatin accessibility was the major discriminator between these models. The location of the PU.1 binding loci in open chromatin coincided with a significantly smaller mean distance to the closest 1,25(OH)2D3 target gene. PU.1 knockdown indicated that the pioneer factor is relevant for the transcriptional activation of 1,25(OH)2D3 target genes but its impact differed in magnitude and orientation. In conclusion, PU.1 is an important modulator of VDR signaling in monocytes, including but also exceeding its role as a pioneer factor, but we found no evidence for a direct interaction of both proteins.
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Affiliation(s)
- Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Antonio Neme
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
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31
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Corradin O, Cohen AJ, Luppino JM, Bayles IM, Schumacher FR, Scacheri PC. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet 2016; 48:1313-1320. [PMID: 27643537 PMCID: PMC5083135 DOI: 10.1038/ng.3674] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022]
Abstract
SNPs associated with disease susceptibility often reside in enhancer clusters, or super-enhancers. Constituents of these enhancer clusters cooperate to regulate target genes and often extend beyond the linkage disequilibrium (LD) blocks containing risk SNPs identified in genome-wide association studies (GWAS). We identified 'outside variants', defined as SNPs in weak LD with GWAS risk SNPs that physically interact with risk SNPs as part of a target gene's regulatory circuitry. These outside variants further explain variation in target gene expression beyond that explained by GWAS-associated SNPs. Additionally, the clinical risk associated with GWAS SNPs is considerably modified by the genotype of outside variants. Collectively, these findings suggest a potential model in which outside variants and GWAS SNPs that physically interact in 3D chromatin collude to influence target transcript levels as well as clinical risk. This model offers an additional hypothesis for the source of missing heritability for complex traits.
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Affiliation(s)
- Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Andrea J Cohen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer M Luppino
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ian M Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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32
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Bouttier M, Laperriere D, Memari B, Mangiapane J, Fiore A, Mitchell E, Verway M, Behr MA, Sladek R, Barreiro LB, Mader S, White JH. Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection. Nucleic Acids Res 2016; 44:10571-10587. [PMID: 27604870 PMCID: PMC5159539 DOI: 10.1093/nar/gkw782] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/19/2022] Open
Abstract
To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated in host defenses and apoptosis. Our analysis revealed that 40% of de novo regions contained human/primate-specific Alu transposable elements, enriched in the AluJ and S subtypes. These contained several transcription factor binding sites, including those for members of the MEF2 and ATF families, and LXR and RAR nuclear receptors, all of which have been implicated in macrophage differentiation, survival, and responses to stress and infection. Combining bioinformatics, molecular genetics, and biochemical approaches, we linked genes adjacent to H3K4me1-associated Alu repeats to macrophage metabolic responses against Mtb infection. In particular, we show that LXRα signaling, which reduced Mtb viability 18-fold by altering cholesterol metabolism and enhancing macrophage apoptosis, can be initiated at response elements present in Alu repeats. These studies decipher the mechanism of early macrophage transcriptional responses to Mtb, highlighting the role of Alu element transposition in shaping human transcription programs during innate immunity.
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Affiliation(s)
- Manuella Bouttier
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada
| | - David Laperriere
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - Babak Memari
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Joseph Mangiapane
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Amanda Fiore
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Eric Mitchell
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Mark Verway
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Marcel A Behr
- McGill University, Montréal, Québec, Canada.,Division of Infectious Diseases and Medical Microbiology, Montréal, Québec, Canada.,McGill International TB Centre, Montréal, Québec, Canada
| | - Robert Sladek
- McGill University, Montréal, Québec, Canada.,School of Computer Science, Montréal, Québec, Canada.,Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | - Luis B Barreiro
- Université de Montréal, Montréal, Québec, Canada.,Department of Pediatrics, Montréal, Québec, Canada
| | - Sylvie Mader
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - John H White
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada.,Department of Medecine, Montréal, Québec, Canada
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33
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Kao CY, He Z, Zannas AS, Hahn O, Kühne C, Reichel JM, Binder EB, Wotjak CT, Khaitovich P, Turck CW. Fluoxetine treatment prevents the inflammatory response in a mouse model of posttraumatic stress disorder. J Psychiatr Res 2016; 76:74-83. [PMID: 26897419 DOI: 10.1016/j.jpsychires.2016.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 01/17/2023]
Abstract
Despite intense research efforts the molecular mechanisms affecting stress-vulnerable brain regions in posttraumatic stress disorder (PTSD) remain elusive. In the current study we have applied global transcriptomic profiling to a PTSD mouse model induced by foot shock fear conditioning. We compared the transcriptomes of prelimbic cortex, anterior cingulate cortex (ACC), basolateral amygdala, central nucleus of amygdala, nucleus accumbens (NAc) and CA1 of the dorsal hippocampus between shocked and non-shocked (control) mice, with and without fluoxetine treatment by RNA sequencing. Differentially expressed (DE) genes were identified and clustered for in silico pathway analysis. Findings in relevant brain regions were further validated with immunohistochemistry. DE genes belonging to 11 clusters were identified including increased inflammatory response in ACC in shocked mice. In line with this finding, we noted higher microglial activation in ACC of shocked mice. Chronic fluoxetine treatment initiated in the aftermath of the trauma prevented inflammatory gene expression alterations in ACC and ameliorated PTSD-like symptoms, implying an important role of the immune response in PTSD pathobiology. Our results provide novel insights into molecular mechanisms affected in PTSD and suggest therapeutic applications with anti-inflammatory agents.
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Affiliation(s)
- Chi-Ya Kao
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstrasse 2-10, 80804 Munich, Germany; Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshadernerstr. 2, 82152 Planegg-Martinsried, Germany
| | - Zhisong He
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, People's Republic of China
| | - Anthony S Zannas
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstrasse 2-10, 80804 Munich, Germany; Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, 27710 Durham, NC, USA
| | - Oliver Hahn
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, People's Republic of China
| | - Claudia Kühne
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstrasse 2-10, 80804 Munich, Germany
| | - Judith M Reichel
- Max Planck Institute of Psychiatry, Department of Stress Neurobiology and Neurogenetics, Kraepelinstrasse 2-10, 80804 Munich, Germany
| | - Elisabeth B Binder
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstrasse 2-10, 80804 Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University Medical School, 30307 Atlanta, GA, USA
| | - Carsten T Wotjak
- Max Planck Institute of Psychiatry, Department of Stress Neurobiology and Neurogenetics, Kraepelinstrasse 2-10, 80804 Munich, Germany
| | - Philipp Khaitovich
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, People's Republic of China.
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstrasse 2-10, 80804 Munich, Germany.
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34
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Geiger TL, Sun JC. Development and maturation of natural killer cells. Curr Opin Immunol 2016; 39:82-9. [PMID: 26845614 PMCID: PMC4801705 DOI: 10.1016/j.coi.2016.01.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 12/21/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that are critical for host protection against pathogens and cancer due to their ability to rapidly release inflammatory cytokines and kill infected or transformed cells. In the 40 years since their initial discovery, much has been learned about how this important cellular lineage develops and functions. We now know that NK cells are the founding members of an expanded family of lymphocyte known as innate lymphoid cells (ILC). Furthermore, we have recently discovered that NK cells can possess features of adaptive immunity such as antigen specificity and long-lived memory responses. Here we will review our current understanding of the molecular mechanisms driving development of NK cells from the common lymphoid progenitor (CLP) to mature NK cells, and from activated effectors to long-lived memory NK cells.
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Affiliation(s)
- Theresa L Geiger
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, New York, NY 10065, United States; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Joseph C Sun
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, New York, NY 10065, United States; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, United States.
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Puhr S, Lee J, Zvezdova E, Zhou YJ, Liu K. Dendritic cell development-History, advances, and open questions. Semin Immunol 2016; 27:388-96. [PMID: 27040276 DOI: 10.1016/j.smim.2016.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/16/2016] [Indexed: 01/22/2023]
Abstract
Dendritic cells (DCs) are uniquely potent in orchestrating T cell immune response, thus they are indispensable immune sentinels. They originate from progenitors in the bone marrow through hematopoiesis, a highly regulated developmental process involving multiple cellular and molecular events. This review highlights studies of DC development-from the discovery of DCs as glass-adherent antigen presenting cells to the debate and resolution of their origin and lineage map. In particular, we summarize the roles of lineage-specific cytokines, the placement of distinct hematopoietic progenitors within the DC lineage and transcriptional programs governing DC development, which together have allowed us to diagram the current view of DC hematopoiesis. Important open questions and debates on the DC development and relevant models are also discussed.
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Affiliation(s)
- Sarah Puhr
- Columbia University Medical Center, Department of Microbiology and Immunology, New York, NY 10032, USA.
| | - Jaeyop Lee
- Columbia University Medical Center, Department of Microbiology and Immunology, New York, NY 10032, USA.
| | - Ekaterina Zvezdova
- Columbia University Medical Center, Department of Microbiology and Immunology, New York, NY 10032, USA.
| | - Yu J Zhou
- Columbia University Medical Center, Department of Microbiology and Immunology, New York, NY 10032, USA
| | - Kang Liu
- Columbia University Medical Center, Department of Microbiology and Immunology, New York, NY 10032, USA.
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Weber C, Telerman SB, Reimer AS, Sequeira I, Liakath-Ali K, Arwert EN, Watt FM. Macrophage Infiltration and Alternative Activation during Wound Healing Promote MEK1-Induced Skin Carcinogenesis. Cancer Res 2016; 76:805-817. [PMID: 26754935 PMCID: PMC4757739 DOI: 10.1158/0008-5472.can-14-3676] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 11/09/2015] [Indexed: 12/26/2022]
Abstract
Macrophages are essential for the progression and maintenance of many cancers, but their role during the earliest stages of tumor formation is unclear. To test this, we used a previously described transgenic mouse model of wound-induced skin tumorigenesis, in which expression of constitutively active MEK1 in differentiating epidermal cells results in chronic inflammation (InvEE mice). Upon wounding, the number of epidermal and dermal monocytes and macrophages increased in wild-type and InvEE skin, but the increase was greater, more rapid, and more sustained in InvEE skin. Macrophage ablation reduced tumor incidence. Furthermore, bioluminescent imaging in live mice to monitor macrophage flux at wound sites revealed that macrophage accumulation was predictive of tumor formation; wounds with the greatest number of macrophages at day 5 went on to develop tumors. Gene expression profiling of flow-sorted monocytes, macrophages, and T cells from InvEE and wild-type skin showed that as wound healing progressed, InvEE macrophages altered their phenotype. Throughout wound healing and after wound closure, InvEE macrophages demonstrated sustained upregulation of several markers implicated in alternative macrophage activation including arginase-1 (ARG1) and mannose receptor (CD206). Notably, inhibition of ARG1 activity significantly reduced tumor formation and epidermal proliferation in vivo, whereas addition of L-arginase to cultured keratinocytes stimulated proliferation. We conclude that macrophages play a key role in early, inflammation-mediated skin tumorigenesis, with mechanistic evidence suggesting that ARG1 secretion drives tumor development by stimulating epidermal cell proliferation. These findings highlight the importance of cancer immunotherapies aiming to polarize tumor-associated macrophages toward an antitumor phenotype.
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Affiliation(s)
- Christine Weber
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB12 0RE, UK
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Stephanie B. Telerman
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Andreas S. Reimer
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Ines Sequeira
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Kifayathullah Liakath-Ali
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB12 0RE, UK
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Esther N. Arwert
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Fiona M. Watt
- King’s College London Centre for Stem Cells & Regenerative Medicine, 28 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
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Schmidt SV, Krebs W, Ulas T, Xue J, Baßler K, Günther P, Hardt AL, Schultze H, Sander J, Klee K, Theis H, Kraut M, Beyer M, Schultze JL. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res 2016; 26:151-70. [PMID: 26729620 PMCID: PMC4746609 DOI: 10.1038/cr.2016.1] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022] Open
Abstract
Differentiation of inflammatory macrophages from monocytes is characterized by an orderly integration of epigenetic and transcriptional regulatory mechanisms guided by lineage-determining transcription factors such as PU.1. Further activation of macrophages leads to a stimulus- or microenvironment-specific signal integration with subsequent transcriptional control established by the action of tissue- or signal-associated transcription factors. Here, we assess four histone modifications during human macrophage activation and integrate this information with the gene expression data from 28 different macrophage activation conditions in combination with GM-CSF. Bioinformatically, for inflammatory macrophages we define a unique network of transcriptional and epigenetic regulators (TRs), which was characterized by accessible promoters independent of the activation signal. In contrast to the general accessibility of promoters of TRs, mRNA expression of central TRs belonging to the TR network displayed stimulus-specific expression patterns, indicating a second level of transcriptional regulation beyond epigenetic chromatin changes. In contrast, stringent integration of epigenetic and transcriptional regulation was observed in networks of TRs established from somatic tissues and tissue macrophages. In these networks, clusters of TRs with permissive histone marks were associated with high gene expression whereas clusters with repressive chromatin marks were associated with absent gene expression. Collectively, these results support that macrophage activation during inflammation in contrast to lineage determination is mainly regulated transcriptionally by a pre-defined TR network.
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Affiliation(s)
- Susanne V Schmidt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Jia Xue
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Patrick Günther
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Anna-Lena Hardt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Hartmut Schultze
- Schultze Know How Beteiligungsgesellschaft mbH, Kirschblütenweg 2, 53639 Königswinter, Germany
| | - Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
- German Center for Neurodegenerative Diseases, 53175 Bonn, Germany
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Johansen LH, Thim HL, Jørgensen SM, Afanasyev S, Strandskog G, Taksdal T, Fremmerlid K, McLoughlin M, Jørgensen JB, Krasnov A. Comparison of transcriptomic responses to pancreas disease (PD) and heart and skeletal muscle inflammation (HSMI) in heart of Atlantic salmon (Salmo salar L). FISH & SHELLFISH IMMUNOLOGY 2015; 46:612-23. [PMID: 26232631 DOI: 10.1016/j.fsi.2015.07.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 05/13/2023]
Abstract
Pancreas disease (PD) and heart and skeletal muscle inflammation (HSMI) are viral diseases associated with SAV (salmonid alphavirus) and PRV (piscine reovirus), which induce systemic infections and pathologies in cardiac and skeletal muscle tissue of farmed Atlantic salmon (Salmo salar L), resulting in severe morbidity and mortality. While general features of the clinical symptoms and pathogenesis of salmonid viral diseases are relatively well studied, much less is known about molecular mechanisms associated with immunity and disease-specific changes. In this study, transcriptomic analyses of heart tissue from PD and HSMI challenged Atlantic salmon were done, focusing on the mature phases of both diseases at respectively 28-35 and 42-77 days post infection. A large number of immune genes was activated in both trials with prevalence of genes associated with early innate antiviral responses, their expression levels being slightly higher in PD challenged fish. Activation of the IFN axis was in parallel with inflammatory changes that involved diverse humoral and cellular factors. Adaptive immune response genes were more pronounced in fish with HSMI, as suggested by increased expression of a large number of genes associated with differentiation and maturation of B lymphocytes and cytotoxic T cells. A similar down-regulation of non-immune genes such as myofiber and mitochondrial proteins between diseases was most likely reflecting myocardial pathology. A suite of genes important for cardiac function including B-type natriuretic peptide and four neuropeptides displayed differential expression between PD and HSMI. Comparison of results revealed common and distinct features and added to the understanding of both diseases at their mature phases with typical clinical pictures. A number of genes that showed disease-specific changes can be of interest for diagnostics.
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Affiliation(s)
| | - Hanna L Thim
- Norwegian College of Fisheries Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | | | - Sergey Afanasyev
- Nofima AS, P.O. Box 6122, N-9291 Tromsø, Norway; Sechenov Institute of Evolutionary Physiology and Biochemistry, M. Toreza Av. 44, Saint Petersburg 194223, Russia
| | - Guro Strandskog
- Norwegian College of Fisheries Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Torunn Taksdal
- Norwegian Veterinary Institute, P.O. Box 750, N-0106 Oslo, Norway
| | - Kjersti Fremmerlid
- Norwegian College of Fisheries Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | | | - Jorunn B Jørgensen
- Norwegian College of Fisheries Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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40
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Hoppmann N, Graetz C, Paterka M, Poisa-Beiro L, Larochelle C, Hasan M, Lill CM, Zipp F, Siffrin V. New candidates for CD4 T cell pathogenicity in experimental neuroinflammation and multiple sclerosis. Brain 2015; 138:902-17. [DOI: 10.1093/brain/awu408] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Abstract
Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. This review by Iwafuchi-Doi and Zaret focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatin-binding properties, and facilitators and impediments to chromatin binding. A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in “closed” chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Lu D, Nakagawa R, Lazzaro S, Staudacher P, Abreu-Goodger C, Henley T, Boiani S, Leyland R, Galloway A, Andrews S, Butcher G, Nutt SL, Turner M, Vigorito E. The miR-155-PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation. ACTA ACUST UNITED AC 2014; 211:2183-98. [PMID: 25288398 PMCID: PMC4203942 DOI: 10.1084/jem.20140338] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A single microRNA (miRNA) can regulate the expression of many genes, though the level of repression imparted on any given target is generally low. How then is the selective pressure for a single miRNA/target interaction maintained across long evolutionary distances? We addressed this problem by disrupting in vivo the interaction between miR-155 and PU.1 in mice. Remarkably, this interaction proved to be key to promoting optimal T cell-dependent B cell responses, a previously unrecognized role for PU.1. Mechanistically, miR-155 inhibits PU.1 expression, leading to Pax5 down-regulation and the initiation of the plasma cell differentiation pathway. Additional PU.1 targets include a network of genes whose products are involved in adhesion, with direct links to B-T cell interactions. We conclude that the evolutionary adaptive selection of the miR-155-PU.1 interaction is exercised through the effectiveness of terminal B cell differentiation.
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Affiliation(s)
- Dong Lu
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Rinako Nakagawa
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Sandra Lazzaro
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Philipp Staudacher
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Cei Abreu-Goodger
- National Laboratory of Genomics for Biodiversity (Langbio), Cinvestav, Irapuato, 36821 Guanajuato, Mexico
| | - Tom Henley
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Sara Boiani
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Rebecca Leyland
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Alison Galloway
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Simon Andrews
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Geoffrey Butcher
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia 3010, Australia Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Martin Turner
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
| | - Elena Vigorito
- Lymphocyte Signaling and Development and The Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire CB22 3AT, England, UK
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Boller S, Grosschedl R. The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function. Immunol Rev 2014; 261:102-15. [PMID: 25123279 PMCID: PMC4312928 DOI: 10.1111/imr.12206] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During the last decades, many studies have investigated the transcriptional and epigenetic regulation of lineage decision in the hematopoietic system. These efforts led to a model in which extrinsic signals and intrinsic cues establish a permissive chromatin context upon which a regulatory network of transcription factors and epigenetic modifiers act to guide the differentiation of hematopoietic lineages. These networks include lineage-specific factors that further modify the epigenetic landscape and promote the generation of specific cell types. The process of B lymphopoiesis requires a set of transcription factors, including Ikaros, PU.1, E2A, and FoxO1 to 'prime' cis-regulatory regions for subsequent activation by the B-lineage-specific transcription factors EBF1 and Pax-5. The expression of EBF1 is initiated by the combined action of E2A and FoxO1, and it is further enhanced and maintained by several positive feedback loops that include Pax-5 and IL-7 signaling. EBF1 acts in concert with Ikaros, PU.1, Runx1, E2A, FoxO1, and Pax-5 to establish the B cell-specific transcription profile. EBF1 and Pax-5 also collaborate to repress alternative cell fates and lock cells into the B-lineage fate. In addition to the functions of EBF1 in establishing and maintaining B-cell identity, EBF1 is required to coordinate differentiation with cell proliferation and survival.
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Affiliation(s)
- Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and EpigeneticsFreiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and EpigeneticsFreiburg, Germany
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Raeven RHM, Brummelman J, Pennings JLA, Nijst OEM, Kuipers B, Blok LER, Helm K, van Riet E, Jiskoot W, van Els CACM, Han WGH, Kersten GFA, Metz B. Molecular signatures of the evolving immune response in mice following a Bordetella pertussis infection. PLoS One 2014; 9:e104548. [PMID: 25137043 PMCID: PMC4138111 DOI: 10.1371/journal.pone.0104548] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/14/2014] [Indexed: 12/21/2022] Open
Abstract
Worldwide resurgence of pertussis necessitates the need for improvement of pertussis vaccines and vaccination strategies. Since natural infections induce a longer-lasting immunity than vaccinations, detailed knowledge of the immune responses following natural infection can provide important clues for such improvement. The purpose was to elucidate the kinetics of the protective immune response evolving after experimental Bordetella pertussis (B. pertussis) infection in mice. Data were collected from (i) individual analyses, i.e. microarray, flow cytometry, multiplex immunoassays, and bacterial clearance; (ii) twelve time points during the infection; and (iii) different tissues involved in the immune responses, i.e. lungs, spleen and blood. Combined data revealed detailed insight in molecular and cellular sequence of events connecting different phases (innate, bridging and adaptive) of the immune response following the infection. We detected a prolonged acute phase response, broad pathogen recognition, and early gene signatures of subsequent T-cell recruitment in the lungs. Activation of particular transcription factors and specific cell markers provided insight into the time course of the transition from innate towards adaptive immune responses, which resulted in a broad spectrum of systemic antibody subclasses and splenic Th1/Th17 memory cells against B. pertussis. In addition, signatures preceding the local generation of Th1 and Th17 cells as well as IgA in the lungs, considered key elements in protection against B. pertussis, were established. In conclusion, molecular and cellular immunological processes in response to live B. pertussis infection were unraveled, which may provide guidance in selecting new vaccine candidates that should evoke local and prolonged protective immune responses.
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Affiliation(s)
- René H. M. Raeven
- Intravacc, Bilthoven, The Netherlands
- Division of Drug Delivery Technology, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Jolanda Brummelman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen L. A. Pennings
- Centre for Health Protection (GZB), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Betsy Kuipers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Kina Helm
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Wim Jiskoot
- Division of Drug Delivery Technology, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Cecile A. C. M. van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Wanda G. H. Han
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gideon F. A. Kersten
- Intravacc, Bilthoven, The Netherlands
- Division of Drug Delivery Technology, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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Yui MA, Rothenberg EV. Developmental gene networks: a triathlon on the course to T cell identity. Nat Rev Immunol 2014; 14:529-45. [PMID: 25060579 PMCID: PMC4153685 DOI: 10.1038/nri3702] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells acquire their ultimate identities by activating combinations of transcription factors that initiate and sustain expression of the appropriate cell type-specific genes. T cell development depends on the progression of progenitor cells through three major phases, each of which is associated with distinct transcription factor ensembles that control the recruitment of these cells to the thymus, their proliferation, lineage commitment and responsiveness to T cell receptor signals, all before the allocation of cells to particular effector programmes. All three phases are essential for proper T cell development, as are the mechanisms that determine the boundaries between each phase. Cells that fail to shut off one set of regulators before the next gene network phase is activated are predisposed to leukaemic transformation.
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Affiliation(s)
- Mary A Yui
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Ellen V Rothenberg
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
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46
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Abstract
The plasmacytoid dendritic cell (pDC) is vital to the coordinated action of innate and adaptive immunity. pDC development has not been unequivocally traced, nor has its transcriptional regulatory network been fully clarified. Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and demonstrate this lineage-specific requirement in the adult organism. Furthermore, we identify BCL11A gene targets and provide a molecular mechanism for its action in pDC commitment. Embryonic germ-line deletion of Bcl11a revealed an absolute cellular, molecular, and functional absence of pDCs in fetal mice. In adults, deletion of Bcl11a in hematopoietic stem cells resulted in perturbed yet continued generation of progenitors, loss of downstream pDC and B-cell lineages, and persisting myeloid, conventional dendritic, and T-cell lineages. Challenge with virus resulted in a marked reduction of antiviral response in conditionally deleted adults. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators, including ID2 and MTG16. Our results identify BCL11A as an essential, lineage-specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed "default" pathway for common dendritic cell progenitors.
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47
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Abstract
Dendritic cells (DCs) are professional antigen presenting cells involved critically not only in provoking innate immune responses but also in establishing adaptive immune responses. Dendritic cells are heterogenous and divided into several subsets, including plasmactyoid DCs (pDCs) and several types of conventional DCs (cDCs), which show subset-specific functions. Plasmactyoid DCs are featured by their ability to produce large amounts of type I interferons (IFNs) in response to nucleic acid sensors, TLR7 and TLR9 and involved in anti-viral immunity and pathogenesis of certain autoimmune disorders such as psoriasis. Conventional DCs include the DC subsets with high crosspresentation activity, which contributes to anti-viral and anti-tumor immunity. These subsets are generated from hematopoietic stem cells (HSCs) via several intermediate progenitors and the development is regulated by the transcriptional mechanisms in which subset-specific transcription factors play major roles. We have recently found that an Ets family transcription factor, SPI-B, which is abundantly expressed in pDCs among DC subsets, plays critical roles in functions and late stage development of pDCs. SPI-B functions in cooperation with other transcription factors, especially, interferon regulatory factor (IRF) family members. Here we review the transcription factor-based molecular mechanisms for generation and functions of DCs, mainly by focusing on the roles of SPI-B and its relatives.
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48
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Huber R, Pietsch D, Günther J, Welz B, Vogt N, Brand K. Regulation of monocyte differentiation by specific signaling modules and associated transcription factor networks. Cell Mol Life Sci 2014; 71:63-92. [PMID: 23525665 PMCID: PMC11113479 DOI: 10.1007/s00018-013-1322-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 02/12/2013] [Accepted: 03/07/2013] [Indexed: 12/26/2022]
Abstract
Monocyte/macrophages are important players in orchestrating the immune response as well as connecting innate and adaptive immunity. Myelopoiesis and monopoiesis are characterized by the interplay between expansion of stem/progenitor cells and progression towards further developed (myelo)monocytic phenotypes. In response to a variety of differentiation-inducing stimuli, various prominent signaling pathways are activated. Subsequently, specific transcription factors are induced, regulating cell proliferation and maturation. This review article focuses on the integration of signaling modules and transcriptional networks involved in the determination of monocytic differentiation.
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Affiliation(s)
- René Huber
- Institute of Clinical Chemistry, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany,
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Ciau-Uitz A, Wang L, Patient R, Liu F. ETS transcription factors in hematopoietic stem cell development. Blood Cells Mol Dis 2013; 51:248-55. [DOI: 10.1016/j.bcmd.2013.07.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/04/2013] [Indexed: 01/08/2023]
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Rothenberg EV, Champhekar A, Damle S, Del Real MM, Kueh HY, Li L, Yui MA. Transcriptional establishment of cell-type identity: dynamics and causal mechanisms of T-cell lineage commitment. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 78:31-41. [PMID: 24135716 DOI: 10.1101/sqb.2013.78.020271] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Precursor cell entry into the T-cell developmental pathway can be divided into two phases by the closure of T-lineage commitment. As cells decide against the last alternative options to the T-cell fate, they turn on the transcription factor Bcl11b and silence expression of a group of multipotent progenitor regulatory factors that include hematopoietic transcription factor PU.1. Functional perturbation tests show that Bcl11b is needed for commitment while PU.1 actively participates in keeping open access to alternative fates, until it is silenced; however, PU.1 and Bcl11b both contribute positively to T-cell development. Our recent work reviewed here sheds light on the transcriptional regulatory network that determines the timing and irreversibility of Bcl11b activation, the ways that Notch signaling from the thymic microenvironment restricts the action of PU.1 to prevent it from diverting cells to non-T fates, and the target genes that PU.1 still regulates under the influence of Notch signaling to contribute to T-cell generation. We argue that T-cell development depends on the sequential operation of two interlaced, but mutually antagonistic, gene regulatory networks, one initially supporting expansion before commitment and the other imposing a "terminal" differentiation process on committed cells.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
| | - Ameya Champhekar
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
| | - Sagar Damle
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
| | | | - Hao Yuan Kueh
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
| | - Long Li
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
| | - Mary A Yui
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125
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