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Sigvardsson M. Early B-Cell Factor 1: An Archetype for a Lineage-Restricted Transcription Factor Linking Development to Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:143-156. [PMID: 39017843 DOI: 10.1007/978-3-031-62731-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The development of highly specialized blood cells from hematopoietic stem cells (HSCs) in the bone marrow (BM) is dependent upon a stringently orchestrated network of stage- and lineage-restricted transcription factors (TFs). Thus, the same stem cell can give rise to various types of differentiated blood cells. One of the key regulators of B-lymphocyte development is early B-cell factor 1 (EBF1). This TF belongs to a small, but evolutionary conserved, family of proteins that harbor a Zn-coordinating motif and an IPT/TIG (immunoglobulin-like, plexins, transcription factors/transcription factor immunoglobulin) domain, creating a unique DNA-binding domain (DBD). EBF proteins play critical roles in diverse developmental processes, including body segmentation in the Drosophila melanogaster embryo, and retina formation in mice. While several EBF family members are expressed in neuronal cells, adipocytes, and BM stroma cells, only B-lymphoid cells express EBF1. In the absence of EBF1, hematopoietic progenitor cells (HPCs) fail to activate the B-lineage program. This has been attributed to the ability of EBF1 to act as a pioneering factor with the ability to remodel chromatin, thereby creating a B-lymphoid-specific epigenetic landscape. Conditional inactivation of the Ebf1 gene in B-lineage cells has revealed additional functions of this protein in relation to the control of proliferation and apoptosis. This may explain why EBF1 is frequently targeted by mutations in human leukemia cases. This chapter provides an overview of the biochemical and functional properties of the EBF family proteins, with a focus on the roles of EBF1 in normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
- Division of Molecular Hematology, Lund University, Lund, Sweden.
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2
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Wray JP, Deltcheva EM, Boiers C, Richardson SЕ, Chhetri JB, Brown J, Gagrica S, Guo Y, Illendula A, Martens JHA, Stunnenberg HG, Bushweller JH, Nimmo R, Enver T. Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability. Nat Commun 2022; 13:7124. [PMID: 36411286 PMCID: PMC9678885 DOI: 10.1038/s41467-022-34653-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 11/01/2022] [Indexed: 11/22/2022] Open
Abstract
The ETV6-RUNX1 onco-fusion arises in utero, initiating a clinically silent pre-leukemic state associated with the development of pediatric B-acute lymphoblastic leukemia (B-ALL). We characterize the ETV6-RUNX1 regulome by integrating chromatin immunoprecipitation- and RNA-sequencing and show that ETV6-RUNX1 functions primarily through competition for RUNX1 binding sites and transcriptional repression. In pre-leukemia, this results in ETV6-RUNX1 antagonization of cell cycle regulation by RUNX1 as evidenced by mass cytometry analysis of B-lineage cells derived from ETV6-RUNX1 knock-in human pluripotent stem cells. In frank leukemia, knockdown of RUNX1 or its co-factor CBFβ results in cell death suggesting sustained requirement for RUNX1 activity which is recapitulated by chemical perturbation using an allosteric CBFβ-inhibitor. Strikingly, we show that RUNX1 addiction extends to other genetic subtypes of pediatric B-ALL and also adult disease. Importantly, inhibition of RUNX1 activity spares normal hematopoiesis. Our results suggest that chemical intervention in the RUNX1 program may provide a therapeutic opportunity in ALL.
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Affiliation(s)
- Jason P Wray
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Elitza M Deltcheva
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Charlotta Boiers
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Simon Е Richardson
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, CB2 0AW, UK
| | | | - John Brown
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Sladjana Gagrica
- IMED Oncology, AstraZeneca, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Yanping Guo
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Anuradha Illendula
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525, GA, Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525, GA, Nijmegen, The Netherlands
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Rachael Nimmo
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Oxford Biomedica (UK) Ltd, Windrush Court, Transport Way, Oxford, OX4 6LT, UK
| | - Tariq Enver
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK.
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden.
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden.
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3
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Lenaerts A, Kucinski I, Deboutte W, Derecka M, Cauchy P, Manke T, Göttgens B, Grosschedl R. EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors. J Exp Med 2022; 219:e20212437. [PMID: 36048017 PMCID: PMC9437269 DOI: 10.1084/jem.20212437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 08/03/2022] [Indexed: 11/04/2022] Open
Abstract
Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) generate all cells of the blood system. Despite their multipotency, MPPs display poorly understood lineage bias. Here, we examine whether lineage-specifying transcription factors, such as the B-lineage determinant EBF1, regulate lineage preference in early progenitors. We detect low-level EBF1 expression in myeloid-biased MPP3 and lymphoid-biased MPP4 cells, coinciding with expression of the myeloid determinant C/EBPα. Hematopoietic deletion of Ebf1 results in enhanced myelopoiesis and reduced HSC repopulation capacity. Ebf1-deficient MPP3 and MPP4 cells exhibit an augmented myeloid differentiation potential and a transcriptome with an enriched C/EBPα signature. Correspondingly, EBF1 binds the Cebpa enhancer, and the deficiency and overexpression of Ebf1 in MPP3 and MPP4 cells lead to an up- and downregulation of Cebpa expression, respectively. In addition, EBF1 primes the chromatin of B-lymphoid enhancers specifically in MPP3 cells. Thus, our study implicates EBF1 in regulating myeloid/lymphoid fate bias in MPPs by constraining C/EBPα-driven myelopoiesis and priming the B-lymphoid fate.
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Affiliation(s)
- Aurelie Lenaerts
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Marta Derecka
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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4
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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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5
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Huang Y, Mei L, Wang Y, Ye H, Ma X, Zhang J, Cai M, Li P, Ge Y, Zhou Y. A Novel de novo Mutation in EBF3 Associated With Hypotonia, Ataxia, and Delayed Development Syndrome in a Chinese Boy. Front Genet 2021; 12:676832. [PMID: 34367240 PMCID: PMC8339956 DOI: 10.3389/fgene.2021.676832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Objective Global developmental delay has markedly high phenotypic and genetic heterogeneity, and is a great challenge for clinical diagnosis. Hypotonia, ataxia, and delayed development syndrome (HADDS), first reported in 2017, is one type of global development delay. The aim of the present study was to investigate the genetic etiology of a Chinese boy with global developmental delay. Methods We combined clinical and imaging phenotyping with trio whole-exome sequencing and Sanger sequencing to the patient and his clinically unaffected parents. A luciferase reporter and immunofluorescence were performed to detect the effect of mutation on transcriptional activity and subcellular localization. Results The patient presented with several previously unreported symptoms in the patients with HADDS, including hemangiomas, mild hearing abnormalities and tracheomalacia. A novel EBF3 c.589A > G missense mutation (p.Asn197Asp, p.N197D) was identified in the patient but not in his parents. By constructing the plasmid and transfecting HEK293T cells, EBF3-N197D mutant showed impaired activation of luciferase reporter expression of the p21 promoter, and the mutant affected its entry into the nucleus. Conclusion To the best of our knowledge, this is the first report of EBF3 pathogenic mutation which associated with HADDS in the Chinese population. Our results expand the phenotypes and pathogenic mutation spectrum of HADDS, thus potentially facilitating the clinical diagnosis and genetic counseling of HADDS patients.
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Affiliation(s)
- Yanru Huang
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,United Diagnostic and Research Center for Clinical Genetics, School of Public Health, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Libin Mei
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,United Diagnostic and Research Center for Clinical Genetics, School of Public Health, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Yangdan Wang
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Huiming Ye
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,United Diagnostic and Research Center for Clinical Genetics, School of Public Health, Xiamen University, Xiamen, China
| | - Xiaomin Ma
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Jian Zhang
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Meijiao Cai
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Ping Li
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Yunsheng Ge
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yulin Zhou
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,United Diagnostic and Research Center for Clinical Genetics, School of Public Health, Xiamen University, Xiamen, China
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6
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EBF1 and PAX5 control pro-B cell expansion via opposing regulation of the Myc gene. Blood 2021; 137:3037-3049. [PMID: 33619557 DOI: 10.1182/blood.2020009564] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Genes encoding B lineage-restricted transcription factors are frequently mutated in B-lymphoid leukemias, suggesting a close link between normal and malignant B-cell development. One of these transcription factors is early B-cell factor 1 (EBF1), a protein of critical importance for lineage specification and survival of B-lymphoid progenitors. Here, we report that impaired EBF1 function in mouse B-cell progenitors results in reduced expression of Myc. Ectopic expression of MYC partially rescued B-cell expansion in the absence of EBF1 both in vivo and in vitro. Using chromosome conformation analysis in combination with ATAC-sequencing, chromatin immunoprecipitation-sequencing, and reporter gene assays, six EBF1-responsive enhancer elements were identified within the Myc locus. CRISPR-Cas9-mediated targeting of EBF1-binding sites identified one element of key importance for Myc expression and pro-B cell expansion. These data provide evidence that Myc is a direct target of EBF1. Furthermore, chromatin immunoprecipitation-sequencing analysis revealed that several regulatory elements in the Myc locus are targets of PAX5. However, ectopic expression of PAX5 in EBF1-deficient cells inhibits the cell cycle and reduces Myc expression, suggesting that EBF1 and PAX5 act in an opposing manner to regulate Myc levels. This hypothesis is further substantiated by the finding that Pax5 inactivation reduces requirements for EBF1 in pro-B-cell expansion. The binding of EBF1 and PAX5 to regulatory elements in the human MYC gene in a B-cell acute lymphoblastic leukemia cell line indicates that the EBF1:PAX5:MYC regulatory loop is conserved and may control both normal and malignant B-cell development.
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7
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EBF1-Correlated Long Non-coding RNA Transcript Levels in 3rd Trimester Maternal Blood and Risk of Spontaneous Preterm Birth. Reprod Sci 2020; 28:541-549. [PMID: 32959224 DOI: 10.1007/s43032-020-00320-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022]
Abstract
Biomarkers associated with spontaneous preterm birth (sPTB) before labor onset could aid in prediction, triage, and stratification for testing interventions. In this study we examined maternal blood EBF1-correlated long non-coding RNAs (lncRNAs) in relation to sPTB. We retrieved all lncRNA transcripts from a public gene expression dataset (GSE59491) derived from maternal blood in trimesters 2 and 3 from a Canadian cohort with a matched set of sPTB (n = 51) and term births (n = 106). LncRNA transcripts differentially expressed (limma moderated t-tests) in sPTB vs. term were tested for correlations (Pearson) with EBF1 mRNA levels in the same blood samples. Using logistic regression, EBF1-correlated lncRNAs were divided into tertiles and assessed in relation to odds of sPTB. Two lncRNA transcripts in the 3rd trimester maternal blood were differentially expressed between sPTB and term births (all p < 0.001 and FDR < 0.250) and positively and negatively correlated with EBF1 mRNA levels. They were as follows: (1) LINC00094 r = 0.196 (95% CI: 0.039 to 0.344), p = 0.015, and BH adjusted p = 0.022 and (2) LINC00870 r = - 0.303 (95% CI: - 0.441 to - 0.152), p < 0.001, and BH adjusted p < 0.001. As compared with term births, sPTBs were more likely to be in the highest tertile of LINC00870 (odds ratio (OR) = 4.08 (95% CI 1.60, 10.40), p = 0.003) and the lowest tertile of LINC00094 (OR = 5.16 (95% CI 1.96, 13.61), p < 0.001). Two sPTB-associated EBF1-correlated lncRNAs (LINC00870 and LINC00094) had multiple potential enhancers containing EBF1 binding site(s). Our current findings, along with previous reports linking EBF1 and sPTB, motivate additional research on the EBF1 gene-related gene expression and regulation in relation to sPTB within other cohorts and within laboratory-based models.
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8
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Spontaneous loss of B lineage transcription factors leads to pre-B leukemia in Ebf1 +/-Bcl-x LTg mice. Oncogenesis 2017; 6:e355. [PMID: 28692033 PMCID: PMC5541707 DOI: 10.1038/oncsis.2017.55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 04/26/2017] [Accepted: 05/19/2017] [Indexed: 12/20/2022] Open
Abstract
Early B-cell factor 1 (EBF1) plays a central role in B-cell lineage specification and commitment. Loss of this critical transcription factor is strongly associated with high-risk, relapsed and therapy-resistant B–cell-acute lymphoblastic leukemia, especially in children. However, Ebf1 haploinsufficient mice exhibit a normal lifespan. To determine whether prolonged survival of B cells would enable tumorigenesis in Ebf1 haploinsufficient animals, we generated Ebf1+/–Bcl-xLTg mice, which express the anti-apoptotic factor Bcl-xL in B cells. Approximately half of Ebf1+/–Bcl-xLTg mice develop aggressive oligoclonal leukemia as they age, which engrafts in congenic wild-type recipients without prior conditioning. The neoplastic cells display a pre-B phenotype and express early developmental- and natural killer cell/myeloid-markers inappropriately. In addition, we found tumor cell-specific loss of several transcription factors critical for maintaining differentiation: EBF1, TCF3 and RUNX1. However, in the majority of tumors, loss of Ebf1 expression was not due to loss of heterozygosity. This is the first spontaneous mouse model of pre-B leukemia to demonstrate inappropriate expression of non-B-cell-specific genes associated with loss of Ebf1, Tcf3 and Runx1 expression.
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9
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Sleven H, Welsh SJ, Yu J, Churchill ME, Wright CF, Henderson A, Horvath R, Rankin J, Vogt J, Magee A, McConnell V, Green A, King MD, Cox H, Armstrong L, Lehman A, Nelson TN, Williams J, Clouston P, Hagman J, Németh AH, Hagman J, Németh AH. De Novo Mutations in EBF3 Cause a Neurodevelopmental Syndrome. Am J Hum Genet 2017; 100:138-150. [PMID: 28017370 DOI: 10.1016/j.ajhg.2016.11.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/22/2016] [Indexed: 11/29/2022] Open
Abstract
Early B cell factor 3 (EBF3) is an atypical transcription factor that is thought to influence the laminar formation of the cerebral cortex. Here, we report that de novo mutations in EBF3 cause a complex neurodevelopmental syndrome. The mutations were identified in two large-scale sequencing projects: the UK Deciphering Developmental Disorders (DDD) study and the Canadian Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study. The core phenotype includes moderate to severe intellectual disability, and many individuals exhibit cerebellar ataxia, subtle facial dysmorphism, strabismus, and vesicoureteric reflux, suggesting that EBF3 has a widespread developmental role. Pathogenic de novo variants identified in EBF3 include multiple loss-of-function and missense mutations. Structural modeling suggested that the missense mutations affect DNA binding. Functional analysis of mutant proteins with missense substitutions revealed reduced transcriptional activities and abilities to form heterodimers with wild-type EBF3. We conclude that EBF3, a transcription factor previously unknown to be associated with human disease, is important for brain and other organ development and warrants further investigation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - James Hagman
- Program in Molecular Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA.
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Windmill Road, Headington, Oxford OX3 7HE, UK.
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10
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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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11
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Azagra A, Román-González L, Collazo O, Rodríguez-Ubreva J, de Yébenes VG, Barneda-Zahonero B, Rodríguez J, Castro de Moura M, Grego-Bessa J, Fernández-Duran I, Islam ABMMK, Esteller M, Ramiro AR, Ballestar E, Parra M. In vivo conditional deletion of HDAC7 reveals its requirement to establish proper B lymphocyte identity and development. J Exp Med 2016; 213:2591-2601. [PMID: 27810920 PMCID: PMC5110011 DOI: 10.1084/jem.20150821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/14/2016] [Indexed: 11/05/2022] Open
Abstract
The histone deacetylase HDAC7 interacts with and represses myeloid and T cell genes in pro–B cells. HDAC7 deletion blocks early B cell development and results in severe lymphopenia. Class IIa histone deacetylase (HDAC) subfamily members are tissue-specific gene repressors with crucial roles in development and differentiation processes. A prominent example is HDAC7, a class IIa HDAC that shows a lymphoid-specific expression pattern within the hematopoietic system. In this study, we explored its potential role in B cell development by generating a conditional knockout mouse model. Our study demonstrates for the first time that HDAC7 deletion dramatically blocks early B cell development and gives rise to a severe lymphopenia in peripheral organs, while also leading to pro–B cell lineage promiscuity. We find that HDAC7 represses myeloid and T lymphocyte genes in B cell progenitors through interaction with myocyte enhancer factor 2C (MEFC2). In B cell progenitors, HDAC7 is recruited to promoters and enhancers of target genes, and its absence leads to increased enrichment of histone active marks. Our results prove that HDAC7 is a bona fide transcriptional repressor essential for B cell development.
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Affiliation(s)
- Alba Azagra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Lidia Román-González
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Olga Collazo
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Virginia G de Yébenes
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Bruna Barneda-Zahonero
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Jairo Rodríguez
- Research and Development Department, qGenomics Laboratory, 08003 Barcelona, Spain
| | - Manuel Castro de Moura
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Joaquim Grego-Bessa
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Irene Fernández-Duran
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Maribel Parra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
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12
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Tijchon E, van Emst L, Yuniati L, van Ingen Schenau D, Havinga J, Rouault JP, Hoogerbrugge PM, van Leeuwen FN, Scheijen B. Tumor suppressors BTG1 and BTG2 regulate early mouse B-cell development. Haematologica 2016; 101:e272-6. [PMID: 27036158 DOI: 10.3324/haematol.2015.139675] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Esther Tijchon
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Liesbeth van Emst
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Laurensia Yuniati
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Jørn Havinga
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jean-Pierre Rouault
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon1, France
| | | | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Laboratory of Pediatric Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
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13
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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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14
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ZNF423 and ZNF521: EBF1 Antagonists of Potential Relevance in B-Lymphoid Malignancies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:165238. [PMID: 26788497 PMCID: PMC4695665 DOI: 10.1155/2015/165238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/25/2015] [Indexed: 12/26/2022]
Abstract
The development of the B-lymphoid cell lineage is tightly controlled by the concerted action of a network of transcriptional and epigenetic regulators. EBF1, a central component of this network, is essential for B-lymphoid specification and commitment as well as for the maintenance of the B-cell identity. Genetic alterations causing loss of function of these B-lymphopoiesis regulators have been implicated in the pathogenesis of B-lymphoid malignancies, with particular regard to B-cell acute lymphoblastic leukaemias (B-ALLs), where their presence is frequently detected. The activity of the B-cell regulatory network may also be disrupted by the aberrant expression of inhibitory molecules. In particular, two multi-zinc finger transcription cofactors named ZNF423 and ZNF521 have been characterised as potent inhibitors of EBF1 and are emerging as potentially relevant contributors to the development of B-cell leukaemias. Here we will briefly review the current knowledge of these factors and discuss the importance of their functional cross talk with EBF1 in the development of B-cell malignancies.
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15
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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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16
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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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17
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Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency. Blood 2015; 125:4052-9. [PMID: 25838350 DOI: 10.1182/blood-2014-12-617282] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
Early B-cell factor 1 (Ebf1) is a transcription factor with documented dose-dependent functions in normal and malignant B-lymphocyte development. To understand more about the roles of Ebf1 in malignant transformation, we investigated the impact of reduced functional Ebf1 dosage on mouse B-cell progenitors. Gene expression analysis suggested that Ebf1 was involved in the regulation of genes important for DNA repair and cell survival. Investigation of the DNA damage in steady state, as well as after induction of DNA damage by UV light, confirmed that pro-B cells lacking 1 functional allele of Ebf1 display signs of increased DNA damage. This correlated to reduced expression of DNA repair genes including Rad51, and chromatin immunoprecipitation data suggested that Rad51 is a direct target for Ebf1. Although reduced dosage of Ebf1 did not significantly increase tumor formation in mice, a dramatic increase in the frequency of pro-B cell leukemia was observed in mice with combined heterozygous mutations in the Ebf1 and Pax5 genes, revealing a synergistic effect of combined dose reduction of these proteins. Our data suggest that Ebf1 controls DNA repair in a dose-dependent manner providing a possible explanation to the frequent involvement of EBF1 gene loss in human leukemia.
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18
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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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19
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van Galen P, Kreso A, Wienholds E, Laurenti E, Eppert K, Lechman ER, Mbong N, Hermans K, Dobson S, April C, Fan JB, Dick JE. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell 2014; 14:94-106. [PMID: 24388174 DOI: 10.1016/j.stem.2013.11.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/07/2013] [Accepted: 11/25/2013] [Indexed: 01/10/2023]
Abstract
The hematopoietic system sustains regeneration throughout life by balancing self-renewal and differentiation. To stay poised for mature blood production, hematopoietic stem cells (HSCs) maintain low-level expression of lineage-associated genes, a process termed lineage priming. Here, we modulated expression levels of Inhibitor of DNA binding (ID) proteins to ask whether lineage priming affects self-renewal of human HSCs. We found that lentiviral overexpression of ID proteins in cord blood HSCs biases myeloerythroid commitment at the expense of lymphoid differentiation. Conversely, reducing ID2 expression levels increases lymphoid potential. Mechanistically, ID2 inhibits the transcription factor E47 to attenuate B-lymphoid priming in HSCs and progenitors. Strikingly, ID2 overexpression also results in a 10-fold expansion of HSCs in serial limiting dilution assays, indicating that early lymphoid transcription factors antagonize human HSC self-renewal. The relationship between lineage priming and self-renewal can be exploited to increase expansion of transplantable human HSCs and points to broader implications for other stem cell populations.
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Affiliation(s)
- Peter van Galen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Antonija Kreso
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kolja Eppert
- Department of Pediatrics, McGill University and the Research Institute of the McGill University Health Centre, Westmount, QC H3Z 2Z3, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Karin Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stephanie Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada.
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20
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Griffin MJ, Zhou Y, Kang S, Zhang X, Mikkelsen TS, Rosen ED. Early B-cell factor-1 (EBF1) is a key regulator of metabolic and inflammatory signaling pathways in mature adipocytes. J Biol Chem 2013; 288:35925-39. [PMID: 24174531 DOI: 10.1074/jbc.m113.491936] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
EBF1 plays a crucial role in early adipogenesis; however, despite high expression in mature adipocytes, its function in these cells is currently unknown. To identify direct and indirect EBF1 targets in fat, we undertook a combination of transcriptional profiling of EBF1-deficient adipocytes and genome-wide EBF1 location analysis. Our results indicate that many components of metabolic and inflammatory pathways are positively and directly regulated by EBF1, including PI3K/AKT, MAPK, and STAT1 signaling. Accordingly, we observed significant reduction of multiple signaling events in EBF1 knockdown cells as well as a reduction in insulin-stimulated glucose uptake and lipogenesis. Inflammatory signaling, gene expression, and secretion of inflammatory cytokines were also significantly affected by loss of EBF1 in adipocytes, although ChIP-sequencing results suggest that these actions are indirect. We also found that EBF1 occupies some 35,000 sites in adipocytes, most of which occur in enhancers. Significantly, comparison with three other published EBF1 ChIP-sequencing data sets in B-cells reveals both gene- and cell type-specific patterns of EBF1 binding. These results advance our understanding of the transcriptional mechanisms regulating signaling pathways in mature fat cells and indicate that EBF1 functions as a key integrator of signal transduction, inflammation, and metabolism.
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Affiliation(s)
- Michael J Griffin
- From the Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215
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21
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Åhsberg J, Ungerbäck J, Strid T, Welinder E, Stjernberg J, Larsson M, Qian H, Sigvardsson M. Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner. J Biol Chem 2013; 288:33449-61. [PMID: 24078629 DOI: 10.1074/jbc.m113.506261] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcription factor doses are of importance for normal and malignant B-lymphocyte development; however, the understanding of underlying mechanisms and functional consequences of reduced transcription factor levels is limited. We have analyzed progenitor and B-lineage compartments in mice carrying heterozygote mutations in the E2a, Ebf1, or Pax5 gene. Although lymphoid progenitors from Ebf1 or Pax5 heterozygote mice were specified and lineage-restricted in a manner comparable with Wt progenitors, this process was severely impaired in E2a heterozygote mutant mice. This defect was not significantly enhanced upon combined deletion of E2a with Ebf1 or Pax5. Analysis of the pre-B-cell compartment in Ebf1 heterozygote mice revealed a reduction in cell numbers. These cells expressed Pax5 and other B-lineage-associated genes, and global gene expression analysis suggested that the reduction of the pre-B-cell compartment was a result of impaired pre-B-cell expansion. This idea was supported by a reduction in IL2Rα-expressing late pre-B-cells as well as by cell cycle analysis and by the finding that the complexity of the VDJ rearrangement patterns was comparable in Wt and Ebf1(+/-) pre-B-cells, although the number of progenitors was reduced. Heterozygote deletion of Ebf1 resulted in impaired response to IL7 in vitro and reduced expression levels of pre-BCR on the cell surface, providing possible explanations for the observed stage-specific reduction in cellular expansion. Thus, transcription factor doses are critical for specification as well as expansion of B-lymphoid progenitors, providing increased insight into the molecular regulation of B-cell development.
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Affiliation(s)
- Josefine Åhsberg
- From the Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty for Health Sciences, Linköping University, University Lab 1, Level 13, SE-581 85 Linköping, Sweden
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22
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Timblin GA, Schlissel MS. Ebf1 and c-Myb repress rag transcription downstream of Stat5 during early B cell development. THE JOURNAL OF IMMUNOLOGY 2013; 191:4676-87. [PMID: 24068669 DOI: 10.4049/jimmunol.1301675] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The temporal control of RAG (Rag) expression in developing lymphocytes prevents DNA breaks during periods of proliferation that could threaten genomic integrity. In developing B cells, the IL-7R and precursor B cell Ag receptor (pre-BCR) synergize to induce proliferation and the repression of Rag at the protein and mRNA levels for a brief period following successful Ig H chain gene rearrangement. Whereas the mechanism of RAG2 protein downregulation is well defined, little is known about the pathways and transcription factors that mediate transcriptional repression of Rag. Using Abelson murine leukemia virus-transformed B cells to model this stage of development, we identified early B cell factor 1 (Ebf1) as a strong repressor of Rag transcription. Short hairpin RNA-mediated knockdown of either Ebf1 or its downstream target c-Myb was sufficient to induce Rag transcription in these highly proliferative cells. Ebf1 and c-Myb antagonize Rag transcription by negatively regulating the binding of Foxo1 to the Rag locus. Ebf1 accomplishes this through both direct negative regulation of Foxo1 expression and direct positive regulation of Gfi1b expression. Ebf1 expression is driven by the IL-7R downstream effector Stat5, providing a link between the negative regulation of Rag transcription by IL-7 and a novel repressive pathway involving Ebf1 and c-Myb.
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Affiliation(s)
- Greg A Timblin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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23
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Nechanitzky R, Akbas D, Scherer S, Györy I, Hoyler T, Ramamoorthy S, Diefenbach A, Grosschedl R. Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells. Nat Immunol 2013; 14:867-75. [PMID: 23812095 DOI: 10.1038/ni.2641] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/11/2013] [Indexed: 12/13/2022]
Abstract
The transcription factors EBF1 and Pax5 have been linked to activation of the B cell lineage program and irreversible loss of alternative lineage potential (commitment), respectively. Here we conditionally deleted Ebf1 in committed pro-B cells after transfer into alymphoid mice. We found that those cells converted into innate lymphoid cells (ILCs) and T cells with variable-diversity-joining (VDJ) rearrangements of loci encoding both B cell and T cell antigen receptors. As intermediates in lineage conversion, Ebf1-deficient CD19(+) cells expressing Pax5 and transcriptional regulators of the ILC and T cell fates were detectable. In particular, genes encoding the transcription factors Id2 and TCF-1 were bound and repressed by EBF1. Thus, both EBF1 and Pax5 are required for B lineage commitment by repressing distinct and common determinants of alternative cell fates.
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Affiliation(s)
- Robert Nechanitzky
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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24
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Gene-pair expression signatures reveal lineage control. Nat Methods 2013; 10:577-83. [PMID: 23603899 PMCID: PMC4131748 DOI: 10.1038/nmeth.2445] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/11/2013] [Indexed: 11/17/2022]
Abstract
The distinct cell types of multicellular organisms arise due to constraints imposed by gene regulatory networks on the collective change of gene expression across the genome, creating self-stabilizing expression states, or attractors. We compiled a resource of curated human expression data comprising 166 cell types and 2,602 transcription regulating genes and developed a data driven method built around the concept of expression reversal defined at the level of gene pairs, such as those participating in toggle switch circuits. This approach allows us to organize the cell types into their ontogenetic lineage-relationships and to reflect regulatory relationships among genes that explain their ability to function as determinants of cell fate. We show that this method identifies genes belonging to regulatory circuits that control neuronal fate, pluripotency and blood cell differentiation, thus offering a novel large-scale perspective on lineage specification.
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25
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Heckl D, Schwarzer A, Haemmerle R, Steinemann D, Rudolph C, Skawran B, Knoess S, Krause J, Li Z, Schlegelberger B, Baum C, Modlich U. Lentiviral vector induced insertional haploinsufficiency of Ebf1 causes murine leukemia. Mol Ther 2012; 20:1187-95. [PMID: 22472950 DOI: 10.1038/mt.2012.59] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Integrating vectors developed on the basis of various retroviruses have demonstrated therapeutic potential following genetic modification of long-lived hematopoietic stem and progenitor cells. Lentiviral vectors (LV) are assumed to circumvent genotoxic events previously observed with γ-retroviral vectors, due to their integration bias to transcription units in comparison to the γ-retroviral preference for promoter regions and CpG islands. However, recently several studies have revealed the potential for gene activation by LV insertions. Here, we report a murine acute B-lymphoblastic leukemia (B-ALL) triggered by insertional gene inactivation. LV integration occurred into the 8th intron of Ebf1, a major regulator of B-lymphopoiesis. Various aberrant splice variants could be detected that involved splice donor and acceptor sites of the lentiviral construct, inducing downregulation of Ebf1 full-length message. The transcriptome signature was compatible with loss of this major determinant of B-cell differentiation, with partial acquisition of myeloid markers, including Csf1r (macrophage colony-stimulating factor (M-CSF) receptor). This was accompanied by receptor phosphorylation and STAT5 activation, both most likely contributing to leukemic progression. Our results highlight the risk of intragenic vector integration to initiate leukemia by inducing haploinsufficiency of a tumor suppressor gene. We propose to address this risk in future vector design.
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Affiliation(s)
- Dirk Heckl
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
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26
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Györy I, Boller S, Nechanitzky R, Mandel E, Pott S, Liu E, Grosschedl R. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev 2012; 26:668-82. [PMID: 22431510 DOI: 10.1101/gad.187328.112] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into the functions of Ebf1 at distinct stages of differentiation, we conditionally inactivated Ebf1. We found that Ebf1 is required for the proliferation, survival, and signaling of pro-B cells and peripheral B-cell subsets, including B1 cells and marginal zone B cells. The proliferation defect of Ebf1-deficient pro-B cells and the impaired expression of multiple cell cycle regulators are overcome by transformation with v-Abl. The survival defect of transformed Ebf1(fl/fl) pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-x(L). In mature B cells, Ebf1 deficiency interferes with signaling via the B-cell-activating factor receptor (BAFF-R)- and B-cell receptor (BCR)-dependent Akt pathways. Moreover, Ebf1 is required for germinal center formation and class switch recombination. Genome-wide analyses of Ebf1-mediated gene expression and chromatin binding indicate that Ebf1 regulates both common and distinct sets of genes in early and late stage B cells. By regulating important components of transcription factor and signaling networks, Ebf1 appears to be involved in the coordination of cell proliferation, survival, and differentiation at multiple stages of B lymphopoiesis.
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Affiliation(s)
- Ildiko Györy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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B lymphocyte lineage specification, commitment and epigenetic control of transcription by early B cell factor 1. Curr Top Microbiol Immunol 2011; 356:17-38. [PMID: 21735360 DOI: 10.1007/82_2011_139] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Early B cell factor 1 (EBF1) is a transcription factor that is critical for both B lymphopoiesis and B cell function. EBF1 is a requisite component of the B lymphocyte transcriptional network and is essential for B lineage specification. Recent studies revealed roles for EBF1 in B cell commitment. EBF1 binds its target genes via a DNA-binding domain including a unique 'zinc knuckle', which mediates a novel mode of DNA recognition. Chromatin immunoprecipitation of EBF1 in pro-B cells defined hundreds of new, as well as previously identified, target genes. Notably, expression of the pre-B cell receptor (pre-BCR), BCR and PI3K/Akt/mTOR signaling pathways is controlled by EBF1. In this review, we highlight these current developments and explore how EBF1 functions as a tissue-specific regulator of chromatin structure at B cell-specific genes.
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