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Banerjee S, Sanyal S, Hodawadekar S, Naiyer S, Bano N, Banerjee A, Rhoades J, Dong D, Allman D, Atchison ML. Unusual lineage plasticity revealed by YY1 knockout in pro-B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586298. [PMID: 38586061 PMCID: PMC10996465 DOI: 10.1101/2024.03.22.586298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
During B cell development, cells progress through multiple developmental stages with the pro-B cell stage defining commitment to the B cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We find here that knockout of YY1 at the pro-B cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9- DL4 feeder system, as well as in vivo after injection into sub-lethally irradiated Rag1 -/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T cell lineage profile. Single cell-RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages indicating unusual lineage plasticity. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 likely regulates commitment in multiple cell lineages.
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2
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Shu X, Wang J, Zeng H, Shao L. Progression of Notch signaling regulation of B cells under radiation exposure. Front Immunol 2024; 15:1339977. [PMID: 38524139 PMCID: PMC10957566 DOI: 10.3389/fimmu.2024.1339977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
With the continuous development of nuclear technology, the radiation exposure caused by radiation therapy is a serious health hazard. It is of great significance to further develop effective radiation countermeasures. B cells easily succumb to irradiation exposure along with immunosuppressive response. The approach to ameliorate radiation-induced B cell damage is rarely studied, implying that the underlying mechanisms of B cell damage after exposure are eager to be revealed. Recent studies suggest that Notch signaling plays an important role in B cell-mediated immune response. Notch signaling is a critical regulator for B cells to maintain immune function. Although accumulating studies reported that Notch signaling contributes to the functionality of hematopoietic stem cells and T cells, its role in B cells is scarcely appreciated. Presently, we discussed the regulation of Notch signaling on B cells under radiation exposure to provide a scientific basis to prevent radiation-induced B cell damage.
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Affiliation(s)
- Xin Shu
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
| | - Jie Wang
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Interdisciplinary Science, Nanchang University, Nanchang, China
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Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
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Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
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Al-Zayan NR, Ashour MJ, Abuwarda HN, Sharif FA. ARID5B, IKZF1, GATA3, CEBPE, and CDKN2A germline polymorphisms and predisposition to childhood acute lymphoblastic leukemia. Pediatr Hematol Oncol 2023; 41:103-113. [PMID: 37578068 DOI: 10.1080/08880018.2023.2234946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/10/2023] [Accepted: 06/21/2023] [Indexed: 08/15/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent type of pediatric cancer. Germline single nucleotide polymorphisms (SNPs), including ARID5B (rs10821936 T/C), IKZF1 (rs4132601 T/G), GATA3 (rs3824662 G/T), CEBPE (rs2239633 G/A), and CDKN2A (rs3731217 A/C) have been linked to pediatric ALL in different populations. Hitherto, no previous studies have tested the relationship between these SNPs and pediatric ALL in Gaza strip. Therefore, we investigated the association between these polymorphisms and the occurrence of childhood ALL in this part of Palestine. This case-control study recruited 100 healthy controls and 78 ALL patients. Allele-specific PCR (AS-PCR) technique was used for SNPs genotyping. Relevant statistical tests were used and the multifactor dimensionality reduction (MDR) approach was applied in the analysis of gene-gene interactions. Minor alleles of ARID5B rs10821936 T/C (p = 0.007) and IKZF1 rs4132601 T/G (p = 0.045) were significantly higher in ALL patients. The homozygous (TT) genotype of GATA3 rs3824662 G/T (p = 0.038), (CC) of ARID5B rs10821936 T/C (p = 0.008), and (AC and CC) genotypes of CDKN2A rs3731217 A/C (p < 0.0001) were significantly higher in ALL cases. On MDR analysis, the best model for ALL risk was the five-factor model combination of the examined SNPs (CVC = 10/10; TBA = 0.632; p < 0.0001). This work demonstrates the association of ARID5B rs10821936 T/C, IKZF1 rs4132601 T/G, GATA3 rs3824662 G/T, and CDKN2A rs3731217 A/C polymorphisms with increased risk of pediatric ALL among a patient cohort from Gaza Strip. Further studies with a larger sample size are needed in order to confirm these findings and test the value of these SNPs in prognosis and treatment sensitivity.
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Affiliation(s)
| | | | | | - Fadel A Sharif
- Department of Medical Laboratory Sciences-IUG, Gaza, Palestine
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5
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Lian K, Shen Z, Yang R, Ye J, Shang B, Dong L, Li H, Wu J, Cheng Y, Xu X. Identification of Immune-Linked Hub Genes and Diagnostic Model Construction in Schizophrenia. J Mol Neurosci 2023; 73:635-648. [PMID: 37552420 PMCID: PMC10517044 DOI: 10.1007/s12031-023-02138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/17/2023] [Indexed: 08/09/2023]
Abstract
Schizophrenia (SCZ) is a prevalent, severe, and persistent mental disorder with an unknown etiology. Growing evidence indicates that immunological dysfunction is vital in the development of SCZ. Our study aims to uncover potential immune-linked hub genes and immune infiltration characteristics of SCZ, as well as to develop a diagnostic model based on immune-linked central genes. GSE38484 and GSE54913 chip expression data for patients with SCZ and healthy controls were retrieved. Weighted gene co-expression network analysis (WGCNA) was performed to identify major module genes and critical immune-linked genes. Functional enrichment analysis was conducted to elucidate the involvement of key genes in the immunological response to SCZ, along with the examination of their protein interactions. Moreover, 202 peripheral blood samples were examined using the single-sample gene set enrichment analysis (ssGSEA) method to detect distinct immune cell types. Hub immune-linked genes in SCZ were identified using the minimal absolute contraction and selection operator analysis. Receptor profiles of central immune-linked genes were analyzed to distinguish the two groups. Finally, the association between immune-linked hub genes and various types of immune cells was assessed. Our findings revealed ten immune cell types and nine key genes involved in SCZ, including effector memory CD4+ T cells, activated CD8+ T cells, mast cells, naive CD8+ T cells, PBMC, type 17 helper cells (Th17), central memory CD8+ T cells, CD56 bright NK cells, memory B cells, and regulatory T cells. Diagnostic models constructed using LASSO regression exhibited an average area under the curve (AUC) of 0.866. Our results indicate immunological dysfunction as a factor in the development of SCZ. ASGR2, ADRM1, AHANK, S100A8, FUCA1, AKNA, GATA3, AHCYL2, and PTRH2 are the key regulatory genes of immune cells, highlighting their potential as novel therapeutic targets for SCZ.
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Affiliation(s)
- Kun Lian
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
| | - Zonglin Shen
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
| | - Runxu Yang
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
| | - Jing Ye
- Sleep Medical Center, The First People’s Hospital of Yunnan, Kunming, 650101 Yunnan China
| | - Binli Shang
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
| | - Lei Dong
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
| | - Hongfang Li
- Lincang Psychiatric Hospital, Lincang, 677000 Yunnan China
| | - Jiabing Wu
- Lincang Psychiatric Hospital, Lincang, 677000 Yunnan China
| | - Yuqi Cheng
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
- Yunnan Clinical Research Center for Mental Disorders, Kunming, 650000 Yunnan China
| | - Xiufeng Xu
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, 650000 Yunnan China
- Yunnan Clinical Research Center for Mental Disorders, Kunming, 650000 Yunnan China
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Gurram RK, Wei D, Yu Q, Kamenyeva O, Chung H, Zheng M, Butcher MJ, Kabat J, Liu C, Khillan JS, Zhu J. Gata3 ZsG and Gata3 ZsG-fl: Novel murine Gata3 reporter alleles for identifying and studying Th2 cells and ILC2s in vivo. Front Immunol 2022; 13:975958. [PMID: 36466899 PMCID: PMC9709206 DOI: 10.3389/fimmu.2022.975958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/31/2022] [Indexed: 10/10/2023] Open
Abstract
T helper-2 (Th2) cells and type 2 innate lymphoid cells (ILC2s) play crucial roles during type 2 immune responses; the transcription factor GATA3 is essential for the differentiation and functions of these cell types. It has been demonstrated that GATA3 is critical for maintaining Th2 and ILC2 phenotype in vitro; GATA3 not only positively regulates type 2 lymphocyte-associated genes, it also negatively regulates many genes associated with other lineages. However, such functions cannot be easily verified in vivo because the expression of the markers for identifying Th2 and ILC2s depends on GATA3. Thus, whether Th2 cells and ILC2s disappear after Gata3 deletion or these Gata3-deleted "Th2 cells" or "ILC2s" acquire an alternative lineage fate is unknown. In this study, we generated novel GATA3 reporter mouse strains carrying the Gata3 ZsG or Gata3 ZsG-fl allele. This was achieved by inserting a ZsGreen-T2A cassette at the translation initiation site of either the wild type Gata3 allele or the modified Gata3 allele which carries two loxP sites flanking the exon 4. ZsGreen faithfully reflected the endogenous GATA3 protein expression in Th2 cells and ILC2s both in vitro and in vivo. These reporter mice also allowed us to visualize Th2 cells and ILC2s in vivo. An inducible Gata3 deletion system was created by crossing Gata3 ZsG-fl/fl mice with a tamoxifen-inducible Cre. Continuous expression of ZsGreen even after the Gata3 exon 4 deletion was noted, which allows us to isolate and monitor GATA3-deficient "Th2" cells and "ILC2s" during in vivo immune responses. Our results not only indicated that functional GATA3 is dispensable for regulating its own expression in mature type 2 lymphocytes, but also revealed that GATA3-deficient "ILC2s" might be much more stable in vivo than in vitro. Overall, the generation of these novel GATA3 reporters will provide valuable research tools to the scientific community in investigating type 2 immune responses in vivo.
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Affiliation(s)
- Rama K. Gurram
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Danping Wei
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Qiao Yu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
- Department of Gerontology and Respirology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Olena Kamenyeva
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Hyunwoo Chung
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mingzhu Zheng
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Matthew J. Butcher
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Juraj Kabat
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood institutes, National Institutes of Health, Bethesda, MD, United States
| | - Jaspal S. Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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7
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Bayer M, Boller S, Ramamoothy S, Zolotarev N, Cauchy P, Iwanami N, Mittler G, Boehm T, Grosschedl R. Tnpo3 enables EBF1 function in conditions of antagonistic Notch signaling. Genes Dev 2022; 36:901-915. [PMID: 36167471 PMCID: PMC9575695 DOI: 10.1101/gad.349696.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/02/2022] [Indexed: 02/03/2023]
Abstract
Transcription factor EBF1 (early B cell factor 1) acts as a key regulator of B cell specification. The transcriptional network in which EBF1 operates has been extensively studied; however, the regulation of EBF1 function remains poorly defined. By mass spectrometric analysis of proteins associated with endogenous EBF1 in pro-B cells, we identified the nuclear import receptor Transportin-3 (Tnpo3) and found that it interacts with the immunoglobulin-like fold domain of EBF1. We delineated glutamic acid 271 of EBF1 as a critical residue for the association with Tnpo3. EBF1E271A showed normal nuclear localization; however, it had an impaired B cell programming ability in conditions of Notch signaling, as determined by retroviral transduction of Ebf1 -/- progenitors. By RNA-seq analysis of EBF1E271A-expressing progenitors, we found an up-regulation of T lineage determinants and down-regulation of early B genes, although similar chromatin binding of EBF1E271A and EBF1wt was detected in pro-B cells expressing activated Notch1. B lineage-specific inactivation of Tnpo3 in mice resulted in a block of early B cell differentiation, accompanied by a down-regulation of B lineage genes and up-regulation of T and NK lineage genes. Taken together, our observations suggest that Tnpo3 ensures B cell programming by EBF1 in nonpermissive conditions.
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Affiliation(s)
- Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoothy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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8
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Oliveri F, Basler M, Rao TN, Fehling HJ, Groettrup M. Immunoproteasome Inhibition Reduces the T Helper 2 Response in Mouse Models of Allergic Airway Inflammation. Front Immunol 2022; 13:870720. [PMID: 35711460 PMCID: PMC9197384 DOI: 10.3389/fimmu.2022.870720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background Allergic asthma is a chronic disease and medical treatment often fails to fully control the disease in the long term, leading to a great need for new therapeutic approaches. Immunoproteasome inhibition impairs T helper cell function and is effective in many (auto-) inflammatory settings but its effect on allergic airway inflammation is unknown. Methods Immunoproteasome expression was analyzed in in vitro polarized T helper cell subsets. To study Th2 cells in vivo acute allergic airway inflammation was induced in GATIR (GATA-3-vYFP reporter) mice using ovalbumin and house dust mite extract. Mice were treated with the immunoproteasome inhibitor ONX 0914 or vehicle during the challenge phase and the induction of airway inflammation was analyzed. Results In vitro polarized T helper cell subsets (Th1, Th2, Th17, and Treg) express high levels of immunoproteasome subunits. GATIR mice proved to be a useful tool for identification of Th2 cells. Immunoproteasome inhibition reduced the Th2 response in both airway inflammation models. Furthermore, T cell activation and antigen-specific cytokine secretion was impaired and a reduced infiltration of eosinophils and professional antigen-presenting cells into the lung and the bronchoalveolar space was observed in the ovalbumin model. Conclusion These results show the importance of the immunoproteasome in Th2 cells and airway inflammation. Our data provides first insight into the potential of using immunoproteasome inhibition to target the aberrant Th2 response, e.g. in allergic airway inflammation.
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Affiliation(s)
- Franziska Oliveri
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Basler
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | | | | | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- *Correspondence: Marcus Groettrup,
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9
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Parriott G, Kee BL. E Protein Transcription Factors as Suppressors of T Lymphocyte Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:885144. [PMID: 35514954 PMCID: PMC9065262 DOI: 10.3389/fimmu.2022.885144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
T Lymphocyte Acute Lymphoblastic Leukemia (ALL) is an aggressive disease arising from transformation of T lymphocytes during their development. The mutation spectrum of T-ALL has revealed critical regulators of the growth and differentiation of normal and leukemic T lymphocytes. Approximately, 60% of T-ALLs show aberrant expression of the hematopoietic stem cell-associated helix-loop-helix transcription factors TAL1 and LYL1. TAL1 and LYL1 function in multiprotein complexes that regulate gene expression in T-ALL but they also antagonize the function of the E protein homodimers that are critical regulators of T cell development. Mice lacking E2A, or ectopically expressing TAL1, LYL1, or other inhibitors of E protein function in T cell progenitors, also succumb to an aggressive T-ALL-like disease highlighting that E proteins promote T cell development and suppress leukemogenesis. In this review, we discuss the role of E2A in T cell development and how alterations in E protein function underlie leukemogenesis. We focus on the role of TAL1 and LYL1 and the genes that are dysregulated in E2a-/- T cell progenitors that contribute to human T-ALL. These studies reveal novel mechanisms of transformation and provide insights into potential therapeutic targets for intervention in this disease.
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Affiliation(s)
- Geoffrey Parriott
- Committee on Immunology, University of Chicago, Chicago, IL, United States
| | - Barbara L Kee
- Committee on Immunology, University of Chicago, Chicago, IL, United States.,Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.,Department of Pathology, University of Chicago, Chicago, IL, United States
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10
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Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB. EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Mol Cell 2022; 82:1003-1020.e15. [PMID: 35182476 PMCID: PMC8897266 DOI: 10.1016/j.molcel.2022.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Chromatin misfolding has been implicated in cancer pathogenesis; yet, its role in therapy resistance remains unclear. Here, we systematically integrated sequencing and imaging data to examine the spatial and linear chromatin structures in targeted therapy-sensitive and -resistant human T cell acute lymphoblastic leukemia (T-ALL). We found widespread alterations in successive layers of chromatin organization including spatial compartments, contact domain boundaries, and enhancer positioning upon the emergence of targeted therapy resistance. The reorganization of genome folding structures closely coincides with the restructuring of chromatin activity and redistribution of architectural proteins. Mechanistically, the derepression and repositioning of the B-lineage-determining transcription factor EBF1 from the heterochromatic nuclear envelope to the euchromatic interior instructs widespread genome refolding and promotes therapy resistance in leukemic T cells. Together, our findings suggest that lineage-determining transcription factors can instruct changes in genome topology as a driving force for epigenetic adaptations in targeted therapy resistance.
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Affiliation(s)
- Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wu Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ashkan Bigdeli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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11
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Yang H, Zhang H, Luan Y, Liu T, Yang W, Roberts KG, Qian MX, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, Gastier-Foster J, Smith C, Pui CH, Evans WE, Hunger SP, Platanias LC, Relling MV, Mullighan CG, Loh ML, Yue F, Yang JJ. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Nat Genet 2022; 54:170-179. [PMID: 35115686 PMCID: PMC9794680 DOI: 10.1038/s41588-021-00993-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/29/2021] [Indexed: 12/31/2022]
Abstract
Inherited noncoding genetic variants confer significant disease susceptibility to childhood acute lymphoblastic leukemia (ALL) but the molecular processes linking germline polymorphisms with somatic lesions in this cancer are poorly understood. Through targeted sequencing in 5,008 patients, we identified a key regulatory germline variant in GATA3 associated with Philadelphia chromosome-like ALL (Ph-like ALL). Using CRISPR-Cas9 editing and samples from patients with Ph-like ALL, we showed that this variant activated a strong enhancer that upregulated GATA3 transcription. This, in turn, reshaped global chromatin accessibility and three-dimensional genome organization, including regions proximal to the ALL oncogene CRLF2. Finally, we showed that GATA3 directly regulated CRLF2 and potentiated the JAK-STAT oncogenic effects during leukemogenesis. Taken together, we provide evidence for a distinct mechanism by which a germline noncoding variant contributes to oncogene activation, epigenetic regulation and three-dimensional genome reprogramming.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao-Xiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, PA, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Internal Medicine Department, MountainView Hospital, University of Reno, Las Vegas, NV, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Da Kuang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Lena A Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Shalini C Reshmi
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Julie Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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12
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Strid T, Okuyama K, Tingvall-Gustafsson J, Kuruvilla J, Jensen CT, Lang S, Prasad M, Somasundaram R, Åhsberg J, Cristobal S, Soneji S, Ungerbäck J, Sigvardsson M. B Lymphocyte Specification Is Preceded by Extensive Epigenetic Priming in Multipotent Progenitors. THE JOURNAL OF IMMUNOLOGY 2021; 206:2700-2713. [PMID: 34021049 DOI: 10.4049/jimmunol.2100048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022]
Abstract
B lymphocyte development is dependent on the interplay between the chromatin landscape and lineage-specific transcription factors. It has been suggested that B lineage commitment is associated with major changes in the nuclear chromatin environment, proposing a critical role for lineage-specific transcription factors in the formation of the epigenetic landscape. In this report, we have used chromosome conformation capture in combination with assay for transposase-accessible chromatin sequencing analysis to enable highly efficient annotation of both proximal and distal transcriptional control elements to genes activated in B lineage specification in mice. A large majority of these genes were annotated to at least one regulatory element with an accessible chromatin configuration in multipotent progenitors. Furthermore, the majority of binding sites for the key regulators of B lineage specification, EBF1 and PAX5, occurred in already accessible regions. EBF1 did, however, cause a dynamic change in assay for transposase-accessible chromatin accessibility and was critical for an increase in distal promoter-enhancer interactions. Our data unravel an extensive epigenetic priming at regulatory elements annotated to lineage-restricted genes and provide insight into the interplay between the epigenetic landscape and transcription factors in cell specification.
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Affiliation(s)
- Tobias Strid
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden; and.,Department of Clinical Pathology, Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Kazuki Okuyama
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jacob Kuruvilla
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | | | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mahadesh Prasad
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rajesh Somasundaram
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Josefine Åhsberg
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Susana Cristobal
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mikael Sigvardsson
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden; .,Division of Molecular Hematology, Lund University, Lund, Sweden; and
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13
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Zhang H, Liu APY, Devidas M, Lee S, Cao X, Pei D, Borowitz M, Wood B, Gastier-Foster JM, Dai Y, Raetz E, Larsen E, Winick N, Bowman WP, Karol S, Yang W, Martin PL, Carroll WL, Pui CH, Mullighan CG, Evans WE, Cheng C, Hunger SP, Relling MV, Loh ML, Yang JJ. Association of GATA3 Polymorphisms With Minimal Residual Disease and Relapse Risk in Childhood Acute Lymphoblastic Leukemia. J Natl Cancer Inst 2021; 113:408-417. [PMID: 32894760 PMCID: PMC8680540 DOI: 10.1093/jnci/djaa138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/17/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Minimal residual disease (MRD) after induction therapy is one of the strongest prognostic factors in childhood acute lymphoblastic leukemia (ALL), and MRD-directed treatment intensification improves survival. Little is known about the effects of inherited genetic variants on interpatient variability in MRD. METHODS A genome-wide association study was performed on 2597 children on the Children's Oncology Group AALL0232 trial for high-risk B-cell ALL. Association between genotype and end-of-induction MRD levels was evaluated for 863 370 single nucleotide polymorphisms (SNPs), adjusting for genetic ancestry and treatment strata. Top variants were further evaluated in a validation cohort of 491 patients from the Children's Oncology Group P9905 and 6 ALL trials. The independent prognostic value of single nucleotide polymorphisms was determined in multivariable analyses. All statistical tests were 2-sided. RESULTS In the discovery genome-wide association study, we identified a genome-wide significant association at the GATA3 locus (rs3824662, odds ratio [OR] = 1.58, 95% confidence interval [CI] = 1.35 to 1.84; P = 1.15 × 10-8 as a dichotomous variable). This association was replicated in the validation cohort (P = .003, MRD as a dichotomous variable). The rs3824662 risk allele independently predicted ALL relapse after adjusting for age, white blood cell count, and leukemia DNA index (P = .04 and .007 in the discovery and validation cohort, respectively) and remained prognostic when the analyses were restricted to MRD-negative patients (P = .04 and .03 for the discovery and validation cohorts, respectively). CONCLUSION Inherited GATA3 variant rs3824662 strongly influences ALL response to remission induction therapy and is associated with relapse. This work highlights the potential utility of germline variants in upfront risk stratification in ALL.
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Affiliation(s)
- Hui Zhang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Department of Hematology & Oncology,
Guangzhou Women and Children’s Medical Center, Guangzhou,
China
| | - Anthony Pak-Yin Liu
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Department of Biostatistics, University of
Florida, Gainesville, FL, USA
| | - Shawn HR Lee
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Division of Paediatric Hematology-Oncology, Khoo
Teck Puat-National University Children’s Medical Institute, National
University Health System, Singapore
| | - Xueyuan Cao
- Preventive Medicine, University of Tennessee Health
Science Center, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Michael Borowitz
- Division of Hematologic Pathology, Department of
Pathology, Johns Hopkins Medical Institute, Baltimore, MD,
USA
| | - Brent Wood
- Department of Laboratory Medicine, University of
Washington, Seattle, WA, USA
| | | | - Yunfeng Dai
- Department of Biostatistics, University of
Florida, Gainesville, FL, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology,
Department of Pediatrics, Stephen D. Hassenfeld Children’s Center for
Cancer & Blood Disorders, New York, NY, USA
| | - Eric Larsen
- Maine Children’s Cancer
Program, Scarborough, ME, USA
| | - Naomi Winick
- Department of Pediatrics, University of Texas
Southwestern Medical Center, Dallas, TX, USA
| | - W Paul Bowman
- Department of Pediatrics, Cook Children’s
Medical Center, Fort Worth, TX, USA
| | - Seth Karol
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Paul L Martin
- Department of Pediatrics, Duke
University, Durham, NC, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology,
Department of Pediatrics, Stephen D. Hassenfeld Children’s Center for
Cancer & Blood Disorders, New York, NY, USA
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood
Cancer Research, Department of Pediatrics, Children’s Hospital of
Philadelphia and the Perelman School of Medicine at the University of
Pennsylvania, Philadelphia, PA, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Division of Hematology Oncology, Department of
Pediatrics, Benioff Children’s Hospital and University of
California, San Francisco, San Francisco, CA, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
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14
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany,International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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15
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
- International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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16
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Wei C, Yu P, Cheng L. Hematopoietic Reprogramming Entangles with Hematopoiesis. Trends Cell Biol 2020; 30:752-763. [PMID: 32861580 DOI: 10.1016/j.tcb.2020.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
Hematopoiesis generally refers to hematopoietic development in fetuses and adults, as well as to hematopoietic stem cell differentiation into progeny lineages. The multiple processes that generate diverse hematopoietic cells have been considered to be unidirectional. However, many reports have recently demonstrated that these processes are not only reversible but also interconvertible via cell reprogramming. The cell reprogramming that occurs in hematopoietic cells is termed hematopoietic reprogramming. We focus on both autogenous and artificial hematopoietic reprogramming under physiological and pathological conditions that is mainly directed by the actions of transcription factors (TFs), chemical compounds, or extracellular cytokines. A comprehensive understanding of hematopoietic reprogramming will help us not only to generate desirable cells for cell therapy but also to further analyze normal and malignant hematopoiesis.
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Affiliation(s)
- Chuijin Wei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Pei Yu
- Department of Orthopaedics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lin Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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17
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Son MJ, Oh KJ, Park A, Kwon MG, Suh JM, Kim IC, Kim S, Lee SC, Kim WK, Bae KH. GATA3 induces the upregulation of UCP-1 by directly binding to PGC-1α during adipose tissue browning. Metabolism 2020; 109:154280. [PMID: 32473155 DOI: 10.1016/j.metabol.2020.154280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Obesity is recognized as the cause of multiple metabolic diseases and is rapidly increasing worldwide. As obesity is due to an imbalance in energy homeostasis, the promotion of energy consumption through browning of white adipose tissue (WAT) has emerged as a promising therapeutic strategy to counter the obesity epidemic. However, the molecular mechanisms of the browning process are not well understood. In this study, we investigated the effects of the GATA family of transcription factors on the browning process. METHODS We used qPCR to analyze the expression of GATA family members during WAT browning. In order to investigate the function of GATA3 in the browning process, we used the lentivirus system for the ectopic expression and knockdown of GATA3. Western blot and real-time qPCR analyses revealed the regulation of thermogenic genes upon ectopic expression and knockdown of GATA3. Luciferase reporter assays, co-immunoprecipitation, and chromatin immunoprecipitation were performed to demonstrate that GATA3 interacts with proliferator-activated receptor-γ co-activator-1α (PGC-1α) to regulate the promoter activity of uncoupling protein-1 (UCP-1). Enhanced energy expenditure by GATA3 was confirmed using oxygen consumption assays, and the mitochondrial content was assessed using MitoTracker. Furthermore, we examined the in vivo effects of lentiviral GATA3 overexpression and knockdown in inguinal adipose tissue of mice. RESULTS Gata3 expression levels were significantly elevated in the inguinal adipose tissue of mice exposed to cold conditions. Ectopic expression of GATA3 enhanced the expression of UCP-1 and thermogenic genes upon treatment with norepinephrine whereas GATA3 knockdown had the opposite effect. Luciferase reporter assays using the UCP-1 promoter region showed that UCP-1 expression was increased in a dose-dependent manner by GATA3 regardless of norepinephrine treatment. GATA3 was found to directly bind to the promoter region of UCP-1. Furthermore, our results indicated that GATA3 interacts with the transcriptional coactivator PGC-1α to increase the expression of UCP-1. Taken together, we demonstrate that GATA3 has an important role in enhancing energy expenditure by increasing the expression of thermogenic genes both in vitro and in vivo. CONCLUSION GATA3 may represent a promising target for the prevention and treatment of obesity by regulating thermogenic capacity.
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Affiliation(s)
- Min Jeong Son
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Anna Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Min-Gi Kwon
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Jae Myoung Suh
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Il-Chul Kim
- Department of Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
| | - Won Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
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18
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Rao TN, Kumar S, Pulikkottil AJ, Oliveri F, Hendriks RW, Beckel F, Fehling HJ. Novel, Non-Gene-Destructive Knock-In Reporter Mice Refute the Concept of Monoallelic Gata3 Expression. THE JOURNAL OF IMMUNOLOGY 2020; 204:2600-2611. [PMID: 32213568 DOI: 10.4049/jimmunol.2000025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/26/2020] [Indexed: 02/04/2023]
Abstract
Accurately tuned expression levels of the transcription factor GATA-3 are crucial at several stages of T cell and innate lymphoid cell development and differentiation. Moreover, several lines of evidence suggest that Gata3 expression might provide a reliable molecular marker for the identification of elusive progenitor cell subsets at the earliest stages of T lineage commitment. To be able to faithfully monitor Gata3 expression noninvasively at the single-cell level, we have generated a novel strain of knock-in reporter mice, termed GATIR, by inserting an expression cassette encoding a bright fluorescent marker into the 3'-untranslated region of the endogenous Gata3 locus. Importantly, in contrast to three previously published strains of Gata3 reporter mice, GATIR mice preserve physiological Gata3 expression on the targeted allele. In this study, we show that GATIR mice faithfully reflect endogenous Gata3 expression without disturbing the development of GATA-3-dependent lymphoid cell populations. We further show that GATIR mice provide an ideal tool for noninvasive monitoring of Th2 polarization and straightforward identification of innate lymphoid cell 2 progenitor populations. Finally, as our reporter is non-gene-destructive, GATIR mice can be bred to homozygosity, not feasible with previously published strains of Gata3 reporter mice harboring disrupted alleles. The availability of hetero- and homozygous Gata3 reporter mice with an exceptionally bright fluorescent marker, allowed us to visualize allelic Gata3 expression in individual cells simply by flow cytometry. The unambiguous results obtained provide compelling evidence against previously postulated monoallelic Gata3 expression in early T lineage and hematopoietic stem cell subsets.
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Affiliation(s)
| | - Suresh Kumar
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
| | | | - Franziska Oliveri
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus Medical Center, NL-3000 CA Rotterdam, the Netherlands
| | - Franziska Beckel
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
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19
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Jacobsen JA, Bartom ET, Sigvardsson M, Kee BL. Ezh2 Represses Transcription of Innate Lymphoid Genes in B Lymphocyte Progenitors and Maintains the B-2 Cell Fate. THE JOURNAL OF IMMUNOLOGY 2020; 204:1760-1769. [PMID: 32094206 DOI: 10.4049/jimmunol.1901188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/28/2020] [Indexed: 02/05/2023]
Abstract
Lymphocyte lineage specification and commitment requires the activation of lineage-specific genes and repression of alternative lineage genes, respectively. The mechanisms governing alternative lineage gene repression and commitment in lymphocytes are largely unknown. In this study, we demonstrate that Ezh2, which represses gene expression through methylation of histone 3 lysine 27, was essential for repression of numerous genes, including genes encoding innate lymphocyte transcription factors, specifically in murine B lymphocyte progenitors, but these cells maintained their B lymphocyte identity. However, adult Ezh2-deficient B lymphocytes expressed Lin28b, which encodes an RNA-binding protein associated with fetal hematopoietic gene expression programs, and these cells acquired a fetal B-1 lymphocyte phenotype in vitro and in vivo. Therefore, Ezh2 coordinates the repression of multiple gene programs in B lymphocytes and maintains the adult B-2 cell fate.
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Affiliation(s)
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, Lund SE-221 00, Sweden; and
| | - Barbara L Kee
- Committee on Immunology, The University of Chicago, Chicago, IL 60657; .,Department of Pathology, The University of Chicago, Chicago, IL 60657
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20
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Ohki K, Kiyokawa N, Saito Y, Hirabayashi S, Nakabayashi K, Ichikawa H, Momozawa Y, Okamura K, Yoshimi A, Ogata-Kawata H, Sakamoto H, Kato M, Fukushima K, Hasegawa D, Fukushima H, Imai M, Kajiwara R, Koike T, Komori I, Matsui A, Mori M, Moriwaki K, Noguchi Y, Park MJ, Ueda T, Yamamoto S, Matsuda K, Yoshida T, Matsumoto K, Hata K, Kubo M, Matsubara Y, Takahashi H, Fukushima T, Hayashi Y, Koh K, Manabe A, Ohara A. Clinical and molecular characteristics of MEF2D fusion-positive B-cell precursor acute lymphoblastic leukemia in childhood, including a novel translocation resulting in MEF2D-HNRNPH1 gene fusion. Haematologica 2019; 104:128-137. [PMID: 30171027 PMCID: PMC6312004 DOI: 10.3324/haematol.2017.186320] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Fusion genes involving MEF2D have recently been identified in precursor B-cell acute lymphoblastic leukemia, mutually exclusive of the common risk stratifying genetic abnormalities, although their true incidence and associated clinical characteristics remain unknown. We identified 16 cases of acute lymphoblastic leukemia and 1 of lymphoma harboring MEF2D fusions, including MEF2D-BCL9 (n=10), MEF2D-HNRNPUL1 (n=6), and one novel MEF2D-HNRNPH1 fusion. The incidence of MEF2D fusions overall was 2.4% among consecutive precursor B-cell acute lymphoblastic leukemia patients enrolled onto a single clinical trial. They frequently showed a cytoplasmic μ chain-positive pre-B immunophenotype, and often expressed an aberrant CD5 antigen. Besides up- and down-regulation of HDAC9 and MEF2C, elevated GATA3 expression was also a characteristic feature of MEF2D fusion-positive patients. Mutations of PHF6, recurrent in T-cell acute lymphoblastic leukemia, also showed an unexpectedly high frequency (50%) in these patients. MEF2D fusion-positive patients were older (median age 9 years) with elevated WBC counts (median: 27,300/ml) at presentation and, as a result, were mostly classified as NCI high risk. Although they responded well to steroid treatment, MEF2D fusion-positive patients showed a significantly worse outcome, with 53.3% relapse and subsequent death. Stem cell transplantation was ineffective as salvage therapy. Interestingly, relapse was frequently associated with the presence of CDKN2A/CDKN2B gene deletions. Our observations indicate that MEF2D fusions comprise a distinct subgroup of precursor B-cell acute lymphoblastic leukemia with a characteristic immunophenotype and gene expression signature, associated with distinct clinical features.
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Affiliation(s)
- Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Fuchu-shi
| | - Shinsuke Hirabayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hitoshi Ichikawa
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Ai Yoshimi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito-shi
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Hiroko Fukushima
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki
| | - Masako Imai
- Department of Pediatrics, Japanese Red Cross Musashino Hospital, Tokyo
| | - Ryosuke Kajiwara
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa
| | - Takashi Koike
- Department of Pediatrics, Tokai University School of Medicine, Kanagawa
| | - Isao Komori
- Department of Pediatrics, Matsudo City Hospital, Chiba
| | - Atsushi Matsui
- Department of Pediatrics, Japanese Red Cross Maebashi Hospital, Gunma
| | - Makiko Mori
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba
| | - Myoung-Ja Park
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa-shi
| | - Takahiro Ueda
- Department of Pediatrics, Nippon Medical School, Bunkyo-ku, Tokyo
| | - Shohei Yamamoto
- Department of Pediatrics, Showa University Fujigaoka Hospital, Yokohama-shi, Kanagawa
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Yoichi Matsubara
- Director, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Takashi Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki-shi, Gunma, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Akira Ohara
- Department of Pediatrics, Toho University Omori Medical Center, Tokyo
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21
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Sud A, Thomsen H, Orlando G, Försti A, Law PJ, Broderick P, Cooke R, Hariri F, Pastinen T, Easton DF, Pharoah PDP, Dunning AM, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Campa D, Hoffmann P, Nöthen MM, Jöckel KH, von Strandmann EP, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma. Blood 2018; 132:2040-2052. [PMID: 30194254 PMCID: PMC6236462 DOI: 10.1182/blood-2018-06-855296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/19/2018] [Indexed: 02/08/2023] Open
Abstract
To further our understanding of inherited susceptibility to Hodgkin lymphoma (HL), we performed a meta-analysis of 7 genome-wide association studies totaling 5325 HL cases and 22 423 control patients. We identify 5 new HL risk loci at 6p21.31 (rs649775; P = 2.11 × 10-10), 6q23.3 (rs1002658; P = 2.97 × 10-8), 11q23.1 (rs7111520; P = 1.44 × 10-11), 16p11.2 (rs6565176; P = 4.00 × 10-8), and 20q13.12 (rs2425752; P = 2.01 × 10-8). Integration of gene expression, histone modification, and in situ promoter capture Hi-C data at the 5 new and 13 known risk loci implicates dysfunction of the germinal center reaction, disrupted T-cell differentiation and function, and constitutive NF-κB activation as mechanisms of predisposition. These data provide further insights into the genetic susceptibility and biology of HL.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Fadi Hariri
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, United Kingdom
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Per Hoffmann
- Human Genomic Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics and
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics and
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | | | - Elke Pogge von Strandmann
- Experimental Tumor Research, Center for Tumor Biology and Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University, Marburg, Germany
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom; and
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Nick Orr
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom; and
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
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22
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Jensen CT, Åhsberg J, Sommarin MNE, Strid T, Somasundaram R, Okuyama K, Ungerbäck J, Kupari J, Airaksinen MS, Lang S, Bryder D, Soneji S, Karlsson G, Sigvardsson M. Dissection of progenitor compartments resolves developmental trajectories in B-lymphopoiesis. J Exp Med 2018; 215:1947-1963. [PMID: 29899037 PMCID: PMC6028518 DOI: 10.1084/jem.20171384] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 03/12/2018] [Accepted: 05/18/2018] [Indexed: 01/22/2023] Open
Abstract
Jensen et al. report the identification and characterization of novel lymphoid progenitor populations in the mouse bone marrow. The work resolves the complexity of the BLP/pre-pro–B/Fraction A compartments and provides a developmental trajectory for early B cell development. To understand the developmental trajectories in early lymphocyte differentiation, we identified differentially expressed surface markers on lineage-negative lymphoid progenitors (LPs). Single-cell polymerase chain reaction experiments allowed us to link surface marker expression to that of lineage-associated transcription factors (TFs) and identify GFRA2 and BST1 as markers of early B cells. Functional analyses in vitro and in vivo as well as single-cell gene expression analyses supported that surface expression of these proteins defined distinct subpopulations that include cells from both the classical common LPs (CLPs) and Fraction A compartments. The formation of the GFRA2-expressing stages of development depended on the TF EBF1, critical both for the activation of stage-specific target genes and modulation of the epigenetic landscape. Our data show that consecutive expression of Ly6D, GFRA2, and BST1 defines a developmental trajectory linking the CLP to the CD19+ progenitor compartment.
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Affiliation(s)
| | | | | | - Tobias Strid
- Division of Molecular Hematology, Lund University, Lund, Sweden.,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Rajesh Somasundaram
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Kazuki Okuyama
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jonas Ungerbäck
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jussi Kupari
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Göran Karlsson
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, Lund, Sweden .,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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23
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Liu S, Chan HL, Bai F, Ma J, Scott A, Robbins DJ, Capobianco AJ, Zhu P, Pei XH. Gata3 restrains B cell proliferation and cooperates with p18INK4c to repress B cell lymphomagenesis. Oncotarget 2018; 7:64007-64020. [PMID: 27588406 PMCID: PMC5325421 DOI: 10.18632/oncotarget.11746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
GATA3, a lineage specifier, controls lymphoid cell differentiation and its function in T cell commitment and development has been extensively studied. GATA3 promotes T cell specification by repressing B cell potential in pro T cells and decreased GATA3 expression is essential for early B cell commitment. Inherited genetic variation in GATA3 has been associated with lymphoma susceptibility. However, it remains elusive how the loss of function of GATA3 promotes B cell development and induces B cell lymphomas. In this study, we found that haploid loss of Gata3 by heterozygous germline deletion increased B cell populations in the bone marrow (BM) and spleen, and decreased CD4 T cell populations in the thymus, confirming that Gata3 promotes T and suppresses B cell development. We discovered that haploid loss of Gata3 reduced thymocyte proliferation with induction of p18Ink4c (p18), an inhibitor of CDK4 and CDK6, but enhanced B cell proliferation in the BM and spleen independent of p18. Loss of p18 partially restored Gata3 deficient thymocyte proliferation, but further stimulated Gata3 deficient B cell proliferation in the BM and spleen. Furthermore, we discovered that haploid loss of Gata3 in p18 deficient mice led to the development of B cell lymphomas that were capable of rapidly regenerating tumors when transplanted into immunocompromised mice. These results indicate that Gata3 deficiency promotes B cell differentiation and proliferation, and cooperates with p18 loss to induce B cell lymphomas. This study, for the first time, reveals that Gata3 is a tumor suppressor specifically in B cell lymphomagenesis.
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Affiliation(s)
- Shiqin Liu
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China.,Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - Ho Lam Chan
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - Feng Bai
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - Jinshan Ma
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami.,Xinjiang Uigur Autonomous Region People's Hospital, Xinjiang, 830001, China
| | - Alexandria Scott
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami.,The Sheila and David Fuente Graduate Program in Cancer Biology, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - David J Robbins
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami.,Sylvester Cancer Center, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - Anthony J Capobianco
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami.,Sylvester Cancer Center, Miller School of Medicine, University of Miami, FL 33136, Miami
| | - Ping Zhu
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Xin-Hai Pei
- Molecular Oncology Program, Division of Surgical Oncology, Department of Surgery, Miller School of Medicine, University of Miami, FL 33136, Miami.,The Sheila and David Fuente Graduate Program in Cancer Biology, Miller School of Medicine, University of Miami, FL 33136, Miami.,Sylvester Cancer Center, Miller School of Medicine, University of Miami, FL 33136, Miami
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24
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Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc Natl Acad Sci U S A 2018; 114:5800-5807. [PMID: 28584128 DOI: 10.1073/pnas.1610617114] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.
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25
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Hou Q, Liao F, Zhang S, Zhang D, Zhang Y, Zhou X, Xia X, Ye Y, Yang H, Li Z, Wang L, Wang X, Ma Z, Zhu Y, Ouyang L, Wang Y, Zhang H, Yang L, Xu H, Shu Y. Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia. Oncotarget 2018; 8:36040-36053. [PMID: 28415601 PMCID: PMC5482637 DOI: 10.18632/oncotarget.16424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/11/2017] [Indexed: 02/05/2023] Open
Abstract
GATA3 polymorphisms were reported to be significantly associated with susceptibility of pediatric B-lineage acute lymphoblastic leukemia (ALL), by impacting on GATA3 expression. We noticed that ALL-related GATA3 polymorphism located around in the tissue-specific enhancer, and significantly associated with GATA3 expression. Although the regulatory network of GATA3 has been well reported in T cells, the functional status of GATA3 is poorly understood in B-ALL. We thus conducted genome-wide gene expression association analyses to reveal expression associated genes and pathways in nine independent B-ALL patient cohorts. In B-ALL patients, 173 candidates were identified to be significantly associated with GATA3 expression, including some reported GATA3-related genes (e.g., ITM2A) and well-known tumor-related genes (e.g., STAT4). Some of the candidates exhibit tissue-specific and subtype-specific association with GATA3. Through overexpression and down-regulation of GATA3 in leukemia cell lines, several reported and novel GATA3 regulated genes were validated. Moreover, association of GATA3 expression and its targets can be impacted by SNPs (e.g., rs4894953), which locate in the potential GATA3 binding motif. Our findings suggest that GATA3 may be involved in multiple tumor-related pathways (e.g., STAT/JAK pathway) in B-ALL to impact leukemogenesis through epigenetic regulation.
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Affiliation(s)
- Qianqian Hou
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Fei Liao
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shouyue Zhang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Duyu Zhang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyan Zhou
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Xuyang Xia
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yuanxin Ye
- Department of Laboratory Medicine, Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hanshuo Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Zhaozhi Li
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Leiming Wang
- Department of Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Xi Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angles, Los Angles, California, USA
| | - Zhigui Ma
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiping Zhu
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yuelan Wang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Heng Xu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China.,Department of Laboratory Medicine, Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Shu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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26
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Li R, Cauchy P, Ramamoorthy S, Boller S, Chavez L, Grosschedl R. Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming. Genes Dev 2018; 32:96-111. [PMID: 29440261 PMCID: PMC5830932 DOI: 10.1101/gad.309583.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/20/2017] [Indexed: 01/07/2023]
Abstract
B-cell fate determination requires the action of transcription factors that operate in a regulatory network to activate B-lineage genes and repress lineage-inappropriate genes. However, the dynamics and hierarchy of events in B-cell programming remain obscure. To uncouple the dynamics of transcription factor expression from functional consequences, we generated induction systems in developmentally arrested Ebf1-/- pre-pro-B cells to allow precise experimental control of EBF1 expression in the genomic context of progenitor cells. Consistent with the described role of EBF1 as a pioneer transcription factor, we show in a time-resolved analysis that EBF1 occupancy coincides with EBF1 expression and precedes the formation of chromatin accessibility. We observed dynamic patterns of EBF1 target gene expression and sequential up-regulation of transcription factors that expand the regulatory network at the pro-B-cell stage. A continuous EBF1 function was found to be required for Cd79a promoter activity and for the maintenance of an accessible chromatin domain that is permissive for binding of other transcription factors. Notably, transient EBF1 occupancy was detected at lineage-inappropriate genes prior to their silencing in pro-B cells. Thus, persistent and transient functions of EBF1 allow for an ordered sequence of epigenetic and transcriptional events in B-cell programming.
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Affiliation(s)
- Rui Li
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center, 69120 Heidelberg, Germany
- Department of Medicine, Division of Medial Genetics, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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Boller S, Li R, Grosschedl R. Defining B Cell Chromatin: Lessons from EBF1. Trends Genet 2018; 34:257-269. [PMID: 29336845 DOI: 10.1016/j.tig.2017.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/11/2022]
Abstract
Hematopoiesis is regulated by signals from the microenvironment, transcription factor networks, and changes of the epigenetic landscape. Transcription factors interact with and shape chromatin to allow for lineage- and cell type-specific changes in gene expression. During B lymphopoiesis, epigenetic regulation is observed in multilineage progenitors in which a specific chromatin context is established, at the onset of the B cell differentiation when early B cell factor 1 (EBF1) induces lineage-specific changes in chromatin, during V(D)J recombination and after antigen-driven activation of B cells and terminal differentiation. In this review, we discuss the epigenetic changes underlying B cell differentiation, focusing on the role of transcription factor EBF1 in B cell lineage priming.
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Affiliation(s)
- Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rui Li
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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28
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Musa YR, Boller S, Puchalska M, Grosschedl R, Mittler G. Comprehensive Proteomic Investigation of Ebf1 Heterozygosity in Pro-B Lymphocytes Utilizing Data Independent Acquisition. J Proteome Res 2017; 17:76-85. [DOI: 10.1021/acs.jproteome.7b00369] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yaarub R. Musa
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Sören Boller
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Monika Puchalska
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Gerhard Mittler
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
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29
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Sud A, Thomsen H, Law PJ, Försti A, Filho MIDS, Holroyd A, Broderick P, Orlando G, Lenive O, Wright L, Cooke R, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Hoffmann P, Nöthen MM, Jöckel KH, Strandmann EPV, Lightfoot T, Kane E, Roman E, Lake A, Montgomery D, Jarrett RF, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility. Nat Commun 2017; 8:1892. [PMID: 29196614 PMCID: PMC5711884 DOI: 10.1038/s41467-017-00320-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023] Open
Abstract
Several susceptibility loci for classical Hodgkin lymphoma have been reported. However, much of the heritable risk is unknown. Here, we perform a meta-analysis of two existing genome-wide association studies, a new genome-wide association study, and replication totalling 5,314 cases and 16,749 controls. We identify risk loci for all classical Hodgkin lymphoma at 6q22.33 (rs9482849, P = 1.52 × 10-8) and for nodular sclerosis Hodgkin lymphoma at 3q28 (rs4459895, P = 9.43 × 10-17), 6q23.3 (rs6928977, P = 4.62 × 10-11), 10p14 (rs3781093, P = 9.49 × 10-13), 13q34 (rs112998813, P = 4.58 × 10-8) and 16p13.13 (rs34972832, P = 2.12 × 10-8). Additionally, independent loci within the HLA region are observed for nodular sclerosis Hodgkin lymphoma (rs9269081, HLA-DPB1*03:01, Val86 in HLA-DRB1) and mixed cellularity Hodgkin lymphoma (rs1633096, rs13196329, Val86 in HLA-DRB1). The new and established risk loci localise to areas of active chromatin and show an over-representation of transcription factor binding for determinants of B-cell development and immune response.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Lauren Wright
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M1 3BB, UK
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Per Hoffmann
- Department of Biomedicine, Division of Medical Genetics, University of Basel, Basel, 4031, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | | | | | - Tracy Lightfoot
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Annette Lake
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Dorothy Montgomery
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Ruth F Jarrett
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, 50937, Germany
| | - Nick Orr
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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30
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Yaguchi A, Ishibashi T, Terada K, Ueno-Yokohata H, Saito Y, Fujimura J, Shimizu T, Ohki K, Manabe A, Kiyokawa N. EP300-ZNF384 fusion gene product up-regulates GATA3 gene expression and induces hematopoietic stem cell gene expression signature in B-cell precursor acute lymphoblastic leukemia cells. Int J Hematol 2017; 106:269-281. [PMID: 28378055 DOI: 10.1007/s12185-017-2220-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 01/08/2023]
Abstract
ZNF384-related fusion genes are associated with a distinct subgroup of B-cell precursor acute lymphoblastic leukemias in childhood, with a frequency of approximately 3-4%. We previously identified a novel EP300-ZNF384 fusion gene. Patients with the ZNF384-related fusion gene exhibit a hematopoietic stem cell (HSC) gene expression signature and characteristic immunophenotype with negative or low expression of CD10 and aberrant expression of myeloid antigens, such as CD33 and CD13. However, the molecular basis of this pathogenesis remains completely unknown. In the present study, we examined the biological effects of EP300-ZNF384 expression induced by retrovirus-mediated gene transduction in an REH B-cell precursor acute lymphoblastic leukemia cell line, and observed the acquisition of the HSC gene expression signature and an up-regulation of GATA3 gene expression, as assessed by microarray analysis. In contrast, the gene expression profile induced by wild-type ZNF384 in REH cells was significantly different from that by EP300-ZNF384 expression. Together with the results of reporter assays, which revealed the enhancement of GATA3-promoter activity by EP300-ZNF384 expression, these findings suggest that EP300-ZNF384 mediates GATA3 gene expression and may be involved in the acquisition of the HSC gene expression signature and characteristic immunophenotype in B-cell precursor acute lymphoblastic leukemia cells.
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Affiliation(s)
- Akinori Yaguchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takeshi Ishibashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Hitomi Ueno-Yokohata
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, 9-1 Akashi-cho, Chuo-ku, Tokyo, 104-8560, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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31
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Law PJ, Sud A, Mitchell JS, Henrion M, Orlando G, Lenive O, Broderick P, Speedy HE, Johnson DC, Kaiser M, Weinhold N, Cooke R, Sunter NJ, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Carmichael J, Bailey JR, Pratt G, Rahman T, Pepper C, Fegan C, von Strandmann EP, Engert A, Försti A, Chen B, Filho MIDS, Thomsen H, Hoffmann P, Noethen MM, Eisele L, Jöckel KH, Allan JM, Swerdlow AJ, Goldschmidt H, Catovsky D, Morgan GJ, Hemminki K, Houlston RS. Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. Sci Rep 2017; 7:41071. [PMID: 28112199 PMCID: PMC5253627 DOI: 10.1038/srep41071] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/14/2016] [Indexed: 02/08/2023] Open
Abstract
B-cell malignancies (BCM) originate from the same cell of origin, but at different maturation stages and have distinct clinical phenotypes. Although genetic risk variants for individual BCMs have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. We explored genome-wide association studies of chronic lymphocytic leukaemia (CLL, N = 1,842), Hodgkin lymphoma (HL, N = 1,465) and multiple myeloma (MM, N = 3,790). We identified a novel pleiotropic risk locus at 3q22.2 (NCK1, rs11715604, P = 1.60 × 10-9) with opposing effects between CLL (P = 1.97 × 10-8) and HL (P = 3.31 × 10-3). Eight established non-HLA risk loci showed pleiotropic associations. Within the HLA region, Ser37 + Phe37 in HLA-DRB1 (P = 1.84 × 10-12) was associated with increased CLL and HL risk (P = 4.68 × 10-12), and reduced MM risk (P = 1.12 × 10-2), and Gly70 in HLA-DQB1 (P = 3.15 × 10-10) showed opposing effects between CLL (P = 3.52 × 10-3) and HL (P = 3.41 × 10-9). By integrating eQTL, Hi-C and ChIP-seq data, we show that the pleiotropic risk loci are enriched for B-cell regulatory elements, as well as an over-representation of binding of key B-cell transcription factors. These data identify shared biological pathways influencing the development of CLL, HL and MM. The identification of these risk loci furthers our understanding of the aetiological basis of BCMs.
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Affiliation(s)
- Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nicola J. Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Graham H. Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Geoffrey Summerfield
- Department of Haematology, Queen Elizabeth Hospital, Gateshead, Newcastle upon Tyne, UK
| | - Robert J. Harris
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - David J. Allsup
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Jonathan Carmichael
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - James R. Bailey
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Thahira Rahman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | | | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland
| | - Markus M. Noethen
- Institute of Human Genetics, University of Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Germany
| | | | | | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center of Tumor Diseases, Heidelberg, Germany
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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32
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Yang CY, Ramamoorthy S, Boller S, Rosenbaum M, Rodriguez Gil A, Mittler G, Imai Y, Kuba K, Grosschedl R. Interaction of CCR4-NOT with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis. Genes Dev 2016; 30:2310-2324. [PMID: 27807034 PMCID: PMC5110997 DOI: 10.1101/gad.285452.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023]
Abstract
Yang et al. used SILAC-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells and identified most components of the multifunctional CCR4–NOT complex, which regulates transcription and mRNA degradation. The interaction of the CCR4–NOT complex with EBF1 diversifies the function of EBF1 in a context-dependent manner and may coordinate transcriptional and post-transcriptional gene regulation. Transcription factor EBF1 (early B-cell factor 1) regulates early B-cell differentiation by poising or activating lineage-specific genes and repressing genes associated with alternative cell fates. To identify proteins that regulate the diverse functions of EBF1, we used SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells. This analysis identified most components of the multifunctional CCR4–NOT complex, which regulates transcription and mRNA degradation. CNOT3 interacts with EBF1, and we identified histidine 240 in EBF1 as a critical residue for this interaction. Complementation of Ebf1−/− progenitors with EBF1H240A revealed a partial block of pro-B-cell differentiation and altered expression of specific EBF1 target genes that show either reduced transcription or increased mRNA stability. Most deregulated EBF1 target genes show normal occupancy by EBF1H240A, but we also detected genes with altered occupancy, suggesting that the CCR4–NOT complex affects multiple activities of EBF1. Mice with conditional Cnot3 inactivation recapitulate the block of early B-cell differentiation, which we found to be associated with an impaired autoregulation of Ebf1 and reduced expression of pre-B-cell receptor components. Thus, the interaction of the CCR4–NOT complex with EBF1 diversifies the function of EBF1 in a context-dependent manner and may coordinate transcriptional and post-transcriptional gene regulation.
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Affiliation(s)
- Cheng-Yuan Yang
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Marc Rosenbaum
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Alfonso Rodriguez Gil
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Yumiko Imai
- Department of Biochemistry and Metabolic Sciences, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Sciences, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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33
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Sen R. A Pioneer's Tail. Immunity 2016; 44:516-518. [PMID: 26982358 DOI: 10.1016/j.immuni.2016.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this issue of Immunity, Boller et al. (2016) show that a C-terminal domain of EBF1 is required for chromatin binding and induction of DNase I hypersensitive sites. These properties mark EBF1 as a pioneer factor in B cell development and demonstrate a role for non-DNA binding domains in this process.
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Affiliation(s)
- Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA.
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Boller S, Ramamoorthy S, Akbas D, Nechanitzky R, Burger L, Murr R, Schübeler D, Grosschedl R. Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming. Immunity 2016; 44:527-541. [PMID: 26982363 DOI: 10.1016/j.immuni.2016.02.021] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 11/03/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022]
Abstract
Lymphopoiesis requires the activation of lineage-specific genes embedded in naive, inaccessible chromatin or in primed, accessible chromatin. The mechanisms responsible for de novo gain of chromatin accessibility, known as "pioneer" function, remain poorly defined. Here, we showed that the EBF1 C-terminal domain (CTD) is required for the regulation of a specific gene set involved in B cell fate decision and differentiation, independently of activation and repression functions. Using genome-wide analysis of DNaseI hypersensitivity and DNA methylation in multipotent Ebf1(-/-) progenitors and derivative EBF1wt- or EBF1ΔC-expressing cells, we found that the CTD promoted chromatin accessibility and DNA demethylation in previously naive chromatin. The CTD allowed EBF1 to bind at inaccessible genomic regions that offer limited co-occupancy by other transcription factors, whereas the CTD was dispensable for EBF1 binding at regions that are occupied by multiple transcription factors. Thus, the CTD enables EBF1 to confer permissive lineage-specific changes in progenitor chromatin landscape.
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Affiliation(s)
- Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Duygu Akbas
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Robert Nechanitzky
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Rabih Murr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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Jensen CT, Strid T, Sigvardsson M. Exploring the multifaceted nature of the common lymphoid progenitor compartment. Curr Opin Immunol 2016; 39:121-6. [PMID: 26871596 DOI: 10.1016/j.coi.2016.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 01/03/2023]
Abstract
While the common lymphoid progenitor compartment was originally thought to be a rather homogenous cell population, it has become increasingly clear that this compartment is highly heterogeneous both with regard to phenotypic and functional features. The exploration of this cellular complexity has generated novel molecular insights into regulatory events in lymphoid lineage restriction and provided support for the idea that multiple lineage restriction events occur at this developmental stage. Furthermore, the identification of multiple lineage-restricted progenitors with mixed lineage potential challenges a strictly hierarchical model for lymphoid development. Instead we propose a model based on competence windows during which cell fates are established through the action of lineage determining factors.
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Affiliation(s)
| | - Tobias Strid
- Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, Sweden; Department of Clinical and Experimental Medicine, Linköping University, Sweden.
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Ohmura S, Mizuno S, Oishi H, Ku CJ, Hermann M, Hosoya T, Takahashi S, Engel JD. Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs. J Clin Invest 2016; 126:865-78. [PMID: 26808502 DOI: 10.1172/jci83894] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023] Open
Abstract
The transcription factor GATA3 is essential for the genesis and maturation of the T cell lineage, and GATA3 dysregulation has pathological consequences. Previous studies have shown that GATA3 function in T cell development is regulated by multiple signaling pathways and that the Notch nuclear effector, RBP-J, binds specifically to the Gata3 promoter. We previously identified a T cell-specific Gata3 enhancer (Tce1) lying 280 kb downstream from the structural gene and demonstrated in transgenic mice that Tce1 promoted T lymphocyte-specific transcription of reporter genes throughout T cell development; however, it was not clear if Tce1 is required for Gata3 transcription in vivo. Here, we determined that the canonical Gata3 promoter is insufficient for Gata3 transcriptional activation in T cells in vivo, precluding the possibility that promoter binding by a host of previously implicated transcription factors alone is responsible for Gata3 expression in T cells. Instead, we demonstrated that multiple lineage-affiliated transcription factors bind to Tce1 and that this enhancer confers T lymphocyte-specific Gata3 activation in vivo, as targeted deletion of Tce1 in a mouse model abrogated critical functions of this T cell-regulatory element. Together, our data show that Tce1 is both necessary and sufficient for critical aspects of Gata3 T cell-specific transcriptional activity.
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Naradikian MS, Hao Y, Cancro MP. Age-associated B cells: key mediators of both protective and autoreactive humoral responses. Immunol Rev 2015; 269:118-29. [DOI: 10.1111/imr.12380] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Martin S. Naradikian
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia PA USA
| | - Yi Hao
- Department of Microbiology; Tongji Medical College; Huazhong University of Science and Technology, Wuhan, China
| | - Michael P. Cancro
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia PA USA
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Flores Saiffe Farías A, Jaime Herrera López E, Moreno Vázquez CJ, Li W, Prado Montes de Oca E. Predicting functional regulatory SNPs in the human antimicrobial peptide genes DEFB1 and CAMP in tuberculosis and HIV/AIDS. Comput Biol Chem 2015; 59 Pt A:117-25. [PMID: 26447748 DOI: 10.1016/j.compbiolchem.2015.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/04/2023]
Abstract
Single nucleotide polymorphisms (SNPs) in transcription factor binding sites (TFBSs) within gene promoter region or enhancers can modify the transcription rate of genes related to complex diseases. These SNPs can be called regulatory SNPs (rSNPs). Data compiled from recent projects, such as the 1000 Genomes Project and ENCODE, has revealed essential information used to perform in silico prediction of the molecular and biological repercussions of SNPs within TFBS. However, most of these studies are very limited, as they only analyze SNPs in coding regions or when applied to promoters, and do not integrate essential biological data like TFBSs, expression profiles, pathway analysis, homotypic redundancy (number of TFBSs for the same TF in a region), chromatin accessibility and others, which could lead to a more accurate prediction. Our aim was to integrate different data in a biologically coherent method to analyze the proximal promoter regions of two antimicrobial peptide genes, DEFB1 and CAMP, that are associated with tuberculosis (TB) and HIV/AIDS. We predicted SNPs within the promoter regions that are more likely to interact with transcription factors (TFs). We also assessed the impact of homotypic redundancy using a novel approach called the homotypic redundancy weight factor (HWF). Our results identified 10 SNPs, which putatively modify the binding affinity of 24 TFs previously identified as related to TB and HIV/AIDS expression profiles (e.g. KLF5, CEBPA and NFKB1 for TB; FOXP2, BRCA1, CEBPB, CREB1, EBF1 and ZNF354C for HIV/AIDS; and RUNX2, HIF1A, JUN/AP-1, NR4A2, EGR1 for both diseases). Validating with the OregAnno database and cell-specific functional/non functional SNPs from additional 13 genes, our algorithm performed 53% sensitivity and 84.6% specificity to detect functional rSNPs using the DNAseI-HUP database. We are proposing our algorithm as a novel in silico method to detect true functional rSNPs in antimicrobial peptide genes. With further improvement, this novel method could be applied to other promoters in order to design probes and to discover new drug targets for complex diseases.
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Affiliation(s)
- Adolfo Flores Saiffe Farías
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
| | - Enrique Jaime Herrera López
- Industrial Biotechnology, CIATEJ AC, Zapopan Unit, CONACYT, Camino Arenero 1227, Col. El Bajío del Arenal, CP 45019 Zapopan, Jalisco, Mexico.
| | - Cristopher Jorge Moreno Vázquez
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
| | - Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, 350 Community Dr. Manhasset, NY 11030, USA.
| | - Ernesto Prado Montes de Oca
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico; Molecular Biology Laboratory, Biosafety Area, Medical and Pharmaceutical Biotechnology, Guadalajara Unit, CIATEJ AC, CONACYT, Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
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Ungerbäck J, Åhsberg J, Strid T, Somasundaram R, Sigvardsson M. Combined heterozygous loss of Ebf1 and Pax5 allows for T-lineage conversion of B cell progenitors. ACTA ACUST UNITED AC 2015; 212:1109-23. [PMID: 26056231 PMCID: PMC4493409 DOI: 10.1084/jem.20132100] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 05/11/2015] [Indexed: 01/07/2023]
Abstract
Ungerbäck et al. show that transcription factors Ebf1 and Pax5 act in a coordinated, dose-dependent manner to preserve B-lineage cell fate. Combined heterozygous loss of both transcription factors results in increased T cell lineage skewing in B cell progenitors. To investigate how transcription factor levels impact B-lymphocyte development, we generated mice carrying transheterozygous mutations in the Pax5 and Ebf1 genes. Whereas combined reduction of Pax5 and Ebf1 had minimal impact on the development of the earliest CD19+ progenitors, these cells displayed an increased T cell potential in vivo and in vitro. The alteration in lineage fate depended on a Notch1-mediated conversion process, whereas no signs of de-differentiation could be detected. The differences in functional response to Notch signaling in Wt and Pax5+/−Ebf1+/− pro–B cells were reflected in the transcriptional response. Both genotypes responded by the generation of intracellular Notch1 and activation of a set of target genes, but only the Pax5+/−Ebf1+/− pro–B cells down-regulated genes central for the preservation of stable B cell identity. This report stresses the importance of the levels of transcription factor expression during lymphocyte development, and suggests that Pax5 and Ebf1 collaborate to modulate the transcriptional response to Notch signaling. This provides an insight on how transcription factors like Ebf1 and Pax5 preserve cellular identity during differentiation.
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Affiliation(s)
- Jonas Ungerbäck
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linköping, Sweden
| | - Josefine Åhsberg
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linköping, Sweden
| | - Tobias Strid
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linköping, Sweden
| | - Rajesh Somasundaram
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linköping, Sweden
| | - Mikael Sigvardsson
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linköping, Sweden
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40
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Transcription factor networks in B-cell differentiation link development to acute lymphoid leukemia. Blood 2015; 126:144-52. [PMID: 25990863 DOI: 10.1182/blood-2014-12-575688] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 05/12/2015] [Indexed: 12/26/2022] Open
Abstract
B-lymphocyte development in the bone marrow is controlled by the coordinated action of transcription factors creating regulatory networks ensuring activation of the B-lymphoid program and silencing of alternative cell fates. This process is tightly connected to malignant transformation because B-lineage acute lymphoblastic leukemia cells display a pronounced block in differentiation resulting in the expansion of immature progenitor cells. Over the last few years, high-resolution analysis of genetic changes in leukemia has revealed that several key regulators of normal B-cell development, including IKZF1, TCF3, EBF1, and PAX5, are genetically altered in a large portion of the human B-lineage acute leukemias. This opens the possibility of directly linking the disrupted development as well as aberrant gene expression patterns in leukemic cells to molecular functions of defined transcription factors in normal cell differentiation. This review article focuses on the roles of transcription factors in early B-cell development and their involvement in the formation of human leukemia.
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41
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Abstract
The immune system can be divided into innate and adaptive components that differ in their rate and mode of cellular activation, with innate immune cells being the first responders to invading pathogens. Recent advances in the identification and characterization of innate lymphoid cells have revealed reiterative developmental programs that result in cells with effector fates that parallel those of adaptive lymphoid cells and are tailored to effectively eliminate a broad spectrum of pathogenic challenges. However, activation of these cells can also be associated with pathologies such as autoimmune disease. One major distinction between innate and adaptive immune system cells is the constitutive expression of ID proteins in the former and inducible expression in the latter. ID proteins function as antagonists of the E protein transcription factors that play critical roles in lymphoid specification as well as B- and T-lymphocyte development. In this review, we examine the transcriptional mechanisms controlling the development of innate lymphocytes, including natural killer cells and the recently identified innate lymphoid cells (ILC1, ILC2, and ILC3), and innate-like lymphocytes, including natural killer T cells, with an emphasis on the known requirements for the ID proteins.
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Affiliation(s)
- Mihalis Verykokakis
- Committee on Immunology and Department of Pathology, The University of Chicago, Chicago, IL, USA
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42
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Abstract
The lymphocyte family has expanded significantly in recent years to include not only the adaptive lymphocytes (T cells, B cells) and NK cells, but also several additional innate lymphoid cell (ILC) types. ILCs lack clonally distributed antigen receptors characteristic of adaptive lymphocytes and instead respond exclusively to signaling via germline-encoded receptors. ILCs resemble T cells more closely than any other leukocyte lineage at the transcriptome level and express many elements of the core T cell transcriptional program, including Notch, Gata3, Tcf7, and Bcl11b. We present our current understanding of the shared and distinct transcriptional regulatory mechanisms involved in the development of adaptive T lymphocytes and closely related ILCs. We discuss the possibility that a core set of transcriptional regulators common to ILCs and T cells establish enhancers that enable implementation of closely aligned effector pathways. Studies of the transcriptional regulation of lymphopoiesis will support the development of novel therapeutic approaches to correct early lymphoid developmental defects and aberrant lymphocyte function.
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Affiliation(s)
- Maria Elena De Obaldia
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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43
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de Almeida CR, Hendriks RW, Stadhouders R. Dynamic Control of Long-Range Genomic Interactions at the Immunoglobulin κ Light-Chain Locus. Adv Immunol 2015; 128:183-271. [DOI: 10.1016/bs.ai.2015.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Tindemans I, Serafini N, Di Santo JP, Hendriks RW. GATA-3 function in innate and adaptive immunity. Immunity 2014; 41:191-206. [PMID: 25148023 DOI: 10.1016/j.immuni.2014.06.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023]
Abstract
The zinc-finger transcription factor GATA-3 has received much attention as a master regulator of T helper 2 (Th2) cell differentiation, during which it controls interleukin-4 (IL-4), IL-5, and IL-13 expression. More recently, GATA-3 was shown to contribute to type 2 immunity through regulation of group 2 innate lymphoid cell (ILC2) development and function. Furthermore, during thymopoiesis, GATA-3 represses B cell potential in early T cell precursors, activates TCR signaling in pre-T cells, and promotes the CD4(+) T cell lineage after positive selection. GATA-3 also functions outside the thymus in hematopoietic stem cells, regulatory T cells, CD8(+) T cells, thymic natural killer cells, and ILC precursors. Here we discuss the varied functions of GATA-3 in innate and adaptive immune cells, with emphasis on its activity in T cells and ILCs, and examine the mechanistic basis for the dose-dependent, developmental-stage- and cell-lineage-specific activity of this transcription factor.
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Affiliation(s)
- Irma Tindemans
- Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U668, 75724 Paris, France
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U668, 75724 Paris, France
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands.
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45
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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: 94] [Impact Index Per Article: 9.4] [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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46
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Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends Immunol 2014; 35:211-8. [DOI: 10.1016/j.it.2014.03.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/28/2014] [Accepted: 03/28/2014] [Indexed: 01/09/2023]
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47
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Wan YY. GATA3: a master of many trades in immune regulation. Trends Immunol 2014; 35:233-42. [PMID: 24786134 DOI: 10.1016/j.it.2014.04.002] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/28/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
GATA3 has conventionally been regarded as a transcription factor that drives the differentiation of T helper (Th) 2 cells. Increasing evidence points to a function for GATA3 beyond controlling Th2 differentiation. GATA3 regulates T cell development, proliferation, and maintenance. Furthermore, recent studies have demonstrated important roles for GATA3 in innate lymphoid cells. Thus, GATA3 emerges as a factor with diverse functions in immune regulation, which are in some cases cell-type specific and in others shared by multiple cell types. Here, I discuss recent discoveries and the current understanding of the functions of GATA3 in immune regulation.
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Affiliation(s)
- Yisong Y Wan
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA.
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48
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Serafini N, Klein Wolterink RG, Satoh-Takayama N, Xu W, Vosshenrich CA, Hendriks RW, Di Santo JP. Gata3 drives development of RORγt+ group 3 innate lymphoid cells. J Exp Med 2014; 211:199-208. [PMID: 24419270 PMCID: PMC3920560 DOI: 10.1084/jem.20131038] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 12/24/2013] [Indexed: 12/12/2022] Open
Abstract
Group 3 innate lymphoid cells (ILC3) include IL-22-producing NKp46(+) cells and IL-17A/IL-22-producing CD4(+) lymphoid tissue inducerlike cells that express RORγt and are implicated in protective immunity at mucosal surfaces. Whereas the transcription factor Gata3 is essential for T cell and ILC2 development from hematopoietic stem cells (HSCs) and for IL-5 and IL-13 production by T cells and ILC2, the role for Gata3 in the generation or function of other ILC subsets is not known. We found that abundant GATA-3 protein is expressed in mucosa-associated ILC3 subsets with levels intermediate between mature B cells and ILC2. Chimeric mice generated with Gata3-deficient fetal liver hematopoietic precursors lack all intestinal RORγt(+) ILC3 subsets, and these mice show defective production of IL-22 early after infection with the intestinal pathogen Citrobacter rodentium, leading to impaired survival. Further analyses demonstrated that ILC3 development requires cell-intrinsic Gata3 expression in fetal liver hematopoietic precursors. Our results demonstrate that Gata3 plays a generalized role in ILC lineage determination and is critical for the development of gut RORγt(+) ILC3 subsets that maintain mucosal barrier homeostasis. These results further extend the paradigm of Gata3-dependent regulation of diversified innate ILC and adaptive T cell subsets.
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Affiliation(s)
- Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
| | - Roel G.J. Klein Wolterink
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, 3000CA Rotterdam, Netherlands
| | - Naoko Satoh-Takayama
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
| | - Wei Xu
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
| | - Christian A.J. Vosshenrich
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
| | - Rudi W. Hendriks
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, 3000CA Rotterdam, Netherlands
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
- INSERM U668, 75724 Paris, France
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49
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Abstract
T and B cells share a common somatic gene rearrangement mechanism for assembling the genes that code for their antigen receptors; they also have developmental pathways with many parallels. Shared usage of basic helix-loop-helix E proteins as transcriptional drivers underlies these common features. However, the transcription factor networks in which these E proteins are embedded are different both in membership and in architecture for T and B cell gene regulatory programs. These differences permit lineage commitment decisions to be made in different hierarchical orders. Furthermore, in contrast to B cell gene networks, the T cell gene network architecture for effector differentiation is sufficiently modular so that E protein inputs can be removed. Complete T cell-like effector differentiation can proceed without T cell receptor rearrangement or selection when E proteins are neutralized, yielding natural killer and other innate lymphoid cells.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology, California Institute of Technology, Pasadena, California 91125;
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50
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Pang SHM, Carotta S, Nutt SL. Transcriptional control of pre-B cell development and leukemia prevention. Curr Top Microbiol Immunol 2014; 381:189-213. [PMID: 24831348 DOI: 10.1007/82_2014_377] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The differentiation of early B cell progenitors is controlled by multiple transcriptional regulators and growth-factor receptors. The triad of DNA-binding proteins, E2A, EBF1, and PAX5 is critical for both the early specification and commitment of B cell progenitors, while a larger number of secondary determinants, such as members of the Ikaros, ETS, Runx, and IRF families have more direct roles in promoting stage-specific pre-B gene-expression program. Importantly, it is now apparent that mutations in many of these transcription factors are associated with the progression to acute lymphoblastic leukemia. In this review, we focus on recent studies that have shed light on the transcriptional hierarchy that controls efficient B cell commitment and differentiation as well as focus on the oncogenic consequences of the loss of many of the same factors.
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Affiliation(s)
- Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
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