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Ma F, Cao Y, Du H, Braikia FZ, Zong L, Ollikainen N, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sarantopoulou D, Ziman A, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R. Three-dimensional chromatin reorganization regulates B cell development during ageing. Nat Cell Biol 2024; 26:991-1002. [PMID: 38866970 PMCID: PMC11178499 DOI: 10.1038/s41556-024-01424-9] [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: 11/01/2022] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
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Affiliation(s)
- Fei Ma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Fatima Zohra Braikia
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Le Zong
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Noah Ollikainen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Marc Bayer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Satabdi Nandi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | | | - Aisha Haley Bianchi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA.
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2
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Lee HW, Chen SJ, Tsai KJ, Hsu KS, Chen YF, Chang CH, Lin HH, Hsueh WY, Hsieh HP, Lee YF, Chiang HC, Chang JY. Targeting cathepsin S promotes activation of OLF1-BDNF/TrkB axis to enhance cognitive function. J Biomed Sci 2024; 31:46. [PMID: 38725007 PMCID: PMC11084077 DOI: 10.1186/s12929-024-01037-2] [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: 11/27/2023] [Accepted: 04/27/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Cathepsin S (CTSS) is a cysteine protease that played diverse roles in immunity, tumor metastasis, aging and other pathological alterations. At the cellular level, increased CTSS levels have been associated with the secretion of pro-inflammatory cytokines and disrupted the homeostasis of Ca2+ flux. Once CTSS was suppressed, elevated levels of anti-inflammatory cytokines and changes of Ca2+ influx were observed. These findings have inspired us to explore the potential role of CTSS on cognitive functions. METHODS We conducted classic Y-maze and Barnes Maze tests to assess the spatial and working memory of Ctss-/- mice, Ctss+/+ mice and Ctss+/+ mice injected with the CTSS inhibitor (RJW-58). Ex vivo analyses including long-term potentiation (LTP), Golgi staining, immunofluorescence staining of sectioned whole brain tissues obtained from experimental animals were conducted. Furthermore, molecular studies were carried out using cultured HT-22 cell line and primary cortical neurons that treated with RJW-58 to comprehensively assess the gene and protein expressions. RESULTS Our findings reported that targeting cathepsin S (CTSS) yields improvements in cognitive function, enhancing both working and spatial memory in behavior models. Ex vivo studies showed elevated levels of long-term potentiation levels and increased synaptic complexity. Microarray analysis demonstrated that brain-derived neurotrophic factor (BDNF) was upregulated when CTSS was knocked down by using siRNA. Moreover, the pharmacological blockade of the CTSS enzymatic activity promoted BDNF expression in a dose- and time-dependent manner. Notably, the inhibition of CTSS was associated with increased neurogenesis in the murine dentate gyrus. These results suggested a promising role of CTSS modulation in cognitive enhancement and neurogenesis. CONCLUSION Our findings suggest a critical role of CTSS in the regulation of cognitive function by modulating the Ca2+ influx, leading to enhanced activation of the BDNF/TrkB axis. Our study may provide a novel strategy for improving cognitive function by targeting CTSS.
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Affiliation(s)
- Hao-Wei Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
- Taipei Cancer Center, TMU Research Center of Cancer Translational Medicine, Taipei Medical University Hospital, College of Medicine, Taipei Medical University, No. 252, Wuxing St., Xinyi Dist., Taipei, 110301, Taiwan (R.O.C.)
| | - Szu-Jung Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuei-Sen Hsu
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Fan Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chih-Hua Chang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Han Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Yun Hsueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yueh-Feng Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Huai-Chueh Chiang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jang-Yang Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan.
- Taipei Cancer Center, TMU Research Center of Cancer Translational Medicine, Taipei Medical University Hospital, College of Medicine, Taipei Medical University, No. 252, Wuxing St., Xinyi Dist., Taipei, 110301, Taiwan (R.O.C.).
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3
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Morgan AT, Amor DJ, St John MD, Scheffer IE, Hildebrand MS. Genetic architecture of childhood speech disorder: a review. Mol Psychiatry 2024; 29:1281-1292. [PMID: 38366112 PMCID: PMC11189821 DOI: 10.1038/s41380-024-02409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Severe speech disorders lead to poor literacy, reduced academic attainment and negative psychosocial outcomes. As early as the 1950s, the familial nature of speech disorders was recognized, implying a genetic basis; but the molecular genetic basis remained unknown. In 2001, investigation of a large three generational family with severe speech disorder, known as childhood apraxia of speech (CAS), revealed the first causative gene; FOXP2. A long hiatus then followed for CAS candidate genes, but in the past three years, genetic analysis of cohorts ascertained for CAS have revealed over 30 causative genes. A total of 36 pathogenic variants have been identified from 122 cases across 3 cohorts in this nascent field. All genes identified have been in coding regions to date, with no apparent benefit at this stage for WGS over WES in identifying monogenic conditions associated with CAS. Hence current findings suggest a remarkable one in three children have a genetic variant that explains their CAS, with significant genetic heterogeneity emerging. Around half of the candidate genes identified are currently supported by medium (6 genes) to strong (9 genes) evidence supporting the association between the gene and CAS. Despite genetic heterogeneity; many implicated proteins functionally converge on pathways involved in chromatin modification or transcriptional regulation, opening the door to precision diagnosis and therapies. Most of the new candidate genes for CAS are associated with previously described neurodevelopmental conditions that include intellectual disability, autism and epilepsy; broadening the phenotypic spectrum to a distinctly milder presentation defined by primary speech disorder in the setting of normal intellect. Insights into the genetic bases of CAS, a severe, rare speech disorder, are yet to translate to understanding the heritability of more common, typically milder forms of speech or language impairment such as stuttering or phonological disorder. These disorders likely follow complex inheritance with polygenic contributions in many cases, rather than the monogenic patterns that underly one-third of patients with CAS. Clinical genetic testing for should now be implemented for individuals with CAS, given its high diagnostic rate, which parallels many other neurodevelopmental disorders where this testing is already standard of care. The shared mechanisms implicated by gene discovery for CAS highlight potential new targets for future precision therapies.
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Affiliation(s)
- Angela T Morgan
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- Speech Pathology, University of Melbourne, Melbourne, VIC, Australia.
- Speech Pathology, Royal Children's Hospital, Melbourne, VIC, Australia.
| | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Miya D St John
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Speech Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Ingrid E Scheffer
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Epilepsy Research Centre, Austin Health, Melbourne, VIC, Australia
| | - Michael S Hildebrand
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Epilepsy Research Centre, Austin Health, Melbourne, VIC, Australia
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4
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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5
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Zolotarev N, Wang Y, Du M, Bayer M, Grosschedl A, Cisse I, Grosschedl R. Regularly spaced tyrosines in EBF1 mediate BRG1 recruitment and formation of nuclear subdiffractive clusters. Genes Dev 2024; 38:4-10. [PMID: 38233109 PMCID: PMC10903943 DOI: 10.1101/gad.350828.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
B lineage priming by pioneer transcription factor EBF1 requires the function of an intrinsically disordered region (IDR). Here, we examine the role of regularly spaced tyrosines in the IDR as potential determinants of IDR function and activity of EBF1. We found that four Y > A mutations in EBF1 reduced the formation of condensates in vitro and subdiffractive clusters in vivo. Notably, Y > A mutant EBF1 was inefficient in promoting B cell differentiation and showed impaired chromatin binding, recruitment of BRG1, and activation of specific target genes. Thus, regularly spaced tyrosines in the IDR contribute to the biophysical and functional properties of EBF1.
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Affiliation(s)
- Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Yuanting Wang
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Manyu Du
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Anna Grosschedl
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Ibrahim Cisse
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany;
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6
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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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7
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Kim EE, Shekhar A, Ramachandran J, Khodadadi-Jamayran A, Liu FY, Zhang J, Fishman GI. The transcription factor EBF1 non-cell-autonomously regulates cardiac growth and differentiation. Development 2023; 150:dev202054. [PMID: 37787076 PMCID: PMC10652039 DOI: 10.1242/dev.202054] [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: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Reciprocal interactions between non-myocytes and cardiomyocytes regulate cardiac growth and differentiation. Here, we report that the transcription factor Ebf1 is highly expressed in non-myocytes and potently regulates heart development. Ebf1-deficient hearts display myocardial hypercellularity and reduced cardiomyocyte size, ventricular conduction system hypoplasia, and conduction system disease. Growth abnormalities in Ebf1 knockout hearts are observed as early as embryonic day 13.5. Transcriptional profiling of Ebf1-deficient embryonic cardiac non-myocytes demonstrates dysregulation of Polycomb repressive complex 2 targets, and ATAC-Seq reveals altered chromatin accessibility near many of these same genes. Gene set enrichment analysis of differentially expressed genes in cardiomyocytes isolated from E13.5 hearts of wild-type and mutant mice reveals significant enrichment of MYC targets and, consistent with this finding, we observe increased abundance of MYC in mutant hearts. EBF1-deficient non-myocytes, but not wild-type non-myocytes, are sufficient to induce excessive accumulation of MYC in co-cultured wild-type cardiomyocytes. Finally, we demonstrate that BMP signaling induces Ebf1 expression in embryonic heart cultures and controls a gene program enriched in EBF1 targets. These data reveal a previously unreported non-cell-autonomous pathway controlling cardiac growth and differentiation.
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Affiliation(s)
- Eugene E. Kim
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Akshay Shekhar
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jayalakshmi Ramachandran
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Fang-Yu Liu
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jie Zhang
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Glenn I. Fishman
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
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8
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Yin S, Ma XY, Sun YF, Yin YQ, Long Y, Zhao CL, Ma JW, Li S, Hu Y, Li MT, Hu G, Zhou JW. RGS5 augments astrocyte activation and facilitates neuroinflammation via TNF signaling. J Neuroinflammation 2023; 20:203. [PMID: 37674228 PMCID: PMC10481574 DOI: 10.1186/s12974-023-02884-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Astrocytes contribute to chronic neuroinflammation in a variety of neurodegenerative diseases, including Parkinson's disease (PD), the most common movement disorder. However, the precise role of astrocytes in neuroinflammation remains incompletely understood. Herein, we show that regulator of G-protein signaling 5 (RGS5) promotes neurodegenerative process through augmenting astrocytic tumor necrosis factor receptor (TNFR) signaling. We found that selective ablation of Rgs5 in astrocytes caused an inhibition in the production of cytokines resulting in mitigated neuroinflammatory response and neuronal survival in animal models of PD, whereas overexpression of Rgs5 had the opposite effects. Mechanistically, RGS5 switched astrocytes from neuroprotective to pro-inflammatory property via binding to the receptor TNFR2. RGS5 also augmented TNFR signaling-mediated pro-inflammatory response by interacting with the receptor TNFR1. Moreover, interrupting RGS5/TNFR interaction by either RGS5 aa 1-108 or small molecular compounds feshurin and butein, suppressed astrocytic cytokine production. We showed that the transcription of astrocytic RGS5 was controlled by transcription factor early B cell factor 1 whose expression was reciprocally influenced by RGS5-modulated TNF signaling. Thus, our study indicates that beyond its traditional role in G-protein coupled receptor signaling, astrocytic RGS5 is a key modulator of TNF signaling circuit with resultant activation of astrocytes thereby contributing to chronic neuroinflammation. Blockade of the astrocytic RGS5/TNFR interaction is a potential therapeutic strategy for neuroinflammation-associated neurodegenerative diseases.
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Affiliation(s)
- Shu Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Xin-Yue Ma
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Ying-Feng Sun
- Center for Brain Disorders Research, Center of Parkinson's Disease, Capital Medical University, Beijing Institute for Brain Disorders, Beijing, 100053, China
| | - Yan-Qing Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Ying Long
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Chun-Lai Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Jun-Wei Ma
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Sen Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Yan Hu
- Guangdong Provincial Key Laboratory of Brain Function, Disease, Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ming-Tao Li
- Guangdong Provincial Key Laboratory of Brain Function, Disease, Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Gang Hu
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
| | - Jia-Wei Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Shanghai Center for Brain Science, Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
- Co-Innovation Center of Neuroregeneration, School of Medicine, Nantong University, Nantong, 226001, Jiangsu, China.
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9
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Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
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10
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Jung MM, Shen S, Botten GA, Olender T, Katsumura KR, Johnson KD, Soukup AA, Liu P, Zhang Q, Jensvold ZD, Lewis PW, Beagrie RA, Low JK, Yang L, Mackay JP, Godley LA, Brand M, Xu J, Keles S, Bresnick EH. Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks. J Clin Invest 2023; 133:e162685. [PMID: 36809258 PMCID: PMC10065080 DOI: 10.1172/jci162685] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Although certain human genetic variants are conspicuously loss of function, decoding the impact of many variants is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) with a germline GATA2 variant that inserts 9 amino acids between the 2 zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer-mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter-zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2 deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced granulocyte-macrophage colony-stimulating factor (GM-CSF) and elevated IL-6 signaling. As insufficient GM-CSF signaling caused pulmonary alveolar proteinosis and excessive IL-6 signaling promoted bone marrow failure and GATA2 deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.
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Affiliation(s)
- Mabel Minji Jung
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Siqi Shen
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Giovanni A. Botten
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Koichi R. Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Peng Liu
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Qingzhou Zhang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Zena D. Jensvold
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Robert A. Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jason K.K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lihua Yang
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lucy A. Godley
- Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Marjorie Brand
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jian Xu
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sunduz Keles
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
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11
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Development and validation of a novel immune-related prognostic signature in lung squamous cell carcinoma patients. Sci Rep 2022; 12:20737. [PMID: 36456645 PMCID: PMC9715950 DOI: 10.1038/s41598-022-23140-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/25/2022] [Indexed: 12/05/2022] Open
Abstract
Lung Squamous Cell Carcinoma (LUSC) is an aggressive malignancy with limited therapeutic options. The response to immune therapy is a determining factor for the prognosis of LUSC patients. This study aimed to develop a reliable immune-related prognostic signature in LUSC. We extracted gene expression and clinical data of LUSC from The Cancer Genome Atlas (TCGA). A total of 502 patients enrolled and were divided into respond and non-responder groups by the TIDE algorithm. The CIBERSORT algorithm and the LM22 gene signature were used to analyze the distribution of immune cells in LUSC. Efficacy and response strength of immunotherapy are calculated by the tumor mutation burden (TMB) and ESTIMATE Score. Differentially expressed genes (DEGs) between the two groups were analyzed. The differential expression genes related to overall survival were pointed as hub DEGs, and a prognostic signature was constructed with lasso regression analysis. LUSC patients were divided into responder and non-responder groups based on the response to immunotherapy. The distribution of immune cells was significantly different between the two groups. Forty-four DGEs were considered as overall survival-related genes. A prognostic signature was constructed, consisting of 11 hub-DGEs, including MMP20, C18orf26, CASP14, FAM71E2, OPN4, CGB5, DIRC1, C9orf11, SPATA8, C9orf144B, and ZCCHC5. The signature can accurately distinguish LUSC patients into high and low-risk groups. Moreover, the high-risk group had a shorter survival time than the low-risk group. The area under the ROC curve was 0.67. The multivariate Cox regression showed that the risk score calculated by the constructed signature was an independent prognostic predictor for LUSC patients. In short, we established a novel immune-related prognostic signature in LUCS, which has significant sensitivity and accuracy in predicting the prognosis of patients. Our research can guide the evaluation of the prognosis of LUSC patients in clinical, and the discovered immune-related genes can provide a theoretical basis for the discovery of new therapeutic targets.
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12
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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; 219:213432. [PMID: 36048017 PMCID: PMC9437269 DOI: 10.1084/jem.20212437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [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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13
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Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells. Proc Natl Acad Sci U S A 2022; 119:e2208522119. [PMID: 35939714 PMCID: PMC9388157 DOI: 10.1073/pnas.2208522119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein, and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions. Proximity-dependent biotin identification (Bio-ID) mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3 and a strong pathway relationship to interleukin-2 regulated genes, which are known to govern cytotoxicity pathways. Chromatin immunoprecipitation and DNA sequencing analysis defined a canonical EBF4 binding motif, 5'-CCCNNGG/AG-3', closely related to the EBF1 binding site; using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted assay for transposase-accessible chromatin sequencing in EBF4-overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together, our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.
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14
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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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15
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Deisseroth CA, Lerma VC, Magyar CL, Pfliger JM, Nayak A, Bliss ND, LeMaire AW, Narayanan V, Balak C, Zanni G, Valente EM, Bertini E, Benke PJ, Wangler MF, Chao HT. An Integrated Phenotypic and Genotypic Approach Reveals a High-Risk Subtype Association for EBF3 Missense Variants Affecting the Zinc Finger Domain. Ann Neurol 2022; 92:138-153. [PMID: 35340043 DOI: 10.1002/ana.26359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Collier/Olf/EBF (COE) transcription factors have distinct expression patterns in the developing and mature nervous system. To date, a neurological disease association has been conclusively established for only the Early B-cell Factor-3 (EBF3) COE family member through the identification of heterozygous loss-of-function variants in individuals with autism spectrum/neurodevelopmental disorders (NDD). Here, we identify a symptom severity risk association with missense variants primarily disrupting the zinc finger domain (ZNF) in EBF3-related NDD. METHODS A phenotypic assessment of 41 individuals was combined with a literature meta-analysis for a total of 83 individuals diagnosed with EBF3-related NDD. Quantitative diagnostic phenotypic and symptom severity scales were developed to compare EBF3 variant type and location to identify genotype-phenotype correlations. To stratify the effects of EBF3 variants disrupting either the DNA-binding domain (DBD) or the ZNF, we used in vivo fruit fly UAS-GAL4 expression and in vitro luciferase assays. RESULTS We show that patient symptom severity correlates with EBF3 missense variants perturbing the ZNF, which is a key protein domain required for stabilizing the interaction between EBF3 and the target DNA sequence. We found that ZNF-associated variants failed to restore viability in the fruit fly and impaired transcriptional activation. However, the recurrent variant EBF3 p.Arg209Trp in the DBD is capable of partially rescuing viability in the fly and preserved transcriptional activation. INTERPRETATION We describe a symptom severity risk association with ZNF perturbations and EBF3 loss-of-function in the largest reported cohort to date of EBF3-related NDD patients. This analysis should have potential predictive clinical value for newly identified patients with EBF3 gene variants. ANN NEUROL 2022;92:138-153.
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Affiliation(s)
- Cole A Deisseroth
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Vanesa C Lerma
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Christina L Magyar
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Jessica Mae Pfliger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Development, Disease Models, and Therapeutics Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Aarushi Nayak
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Nathan D Bliss
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Ashley W LeMaire
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christopher Balak
- Biomedical Sciences Graduate Program, University of California at San Diego, San Diego, CA, USA
| | - Ginevra Zanni
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Michael F Wangler
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, USA
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16
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Peña-Pérez L, Kharazi S, Frengen N, Krstic A, Bouderlique T, Hauenstein J, He M, Somuncular E, Li Wang X, Dahlberg C, Gustafsson C, Johansson AS, Walfridsson J, Kadri N, Woll P, Kierczak M, Qian H, Westerberg L, Luc S, Månsson R. FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors. Front Immunol 2022; 13:880668. [PMID: 35603175 PMCID: PMC9116193 DOI: 10.3389/fimmu.2022.880668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 12/23/2022] Open
Abstract
The development of B cells relies on an intricate network of transcription factors critical for developmental progression and lineage commitment. In the B cell developmental trajectory, a temporal switch from predominant Foxo3 to Foxo1 expression occurs at the CLP stage. Utilizing VAV-iCre mediated conditional deletion, we found that the loss of FOXO3 impaired B cell development from LMPP down to B cell precursors, while the loss of FOXO1 impaired B cell commitment and resulted in a complete developmental block at the CD25 negative proB cell stage. Strikingly, the combined loss of FOXO1 and FOXO3 resulted in the failure to restrict the myeloid potential of CLPs and the complete loss of the B cell lineage. This is underpinned by the failure to enforce the early B-lineage gene regulatory circuitry upon a predominantly pre-established open chromatin landscape. Altogether, this demonstrates that FOXO3 and FOXO1 cooperatively govern early lineage restriction and initiation of B-lineage commitment in CLPs.
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Affiliation(s)
- Lucía Peña-Pérez
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shabnam Kharazi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicolai Frengen
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aleksandra Krstic
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thibault Bouderlique
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Julia Hauenstein
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Minghui He
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ece Somuncular
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoze Li Wang
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Carin Dahlberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Gustafsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Sofie Johansson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Julian Walfridsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nadir Kadri
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Petter Woll
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hong Qian
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lisa Westerberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sidinh Luc
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Hematology Center, Karolinska University Hospital, Stockholm, Sweden
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17
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Notter DR, Heidaritabar M, Burke JM, Shirali M, Murdoch BM, Morgan JLM, Morota G, Sonstegard TS, Becker GM, Spangler GL, MacNeil MD, Miller JE. Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires. Front Genet 2022; 13:866176. [PMID: 35591856 PMCID: PMC9110833 DOI: 10.3389/fgene.2022.866176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/14/2022] [Indexed: 01/31/2023] Open
Abstract
Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and 91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations between markers and FEC EBV were initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70 Mb, with LD among these SNP of r2 ≤ 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9 Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mb codes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.
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Affiliation(s)
- David R. Notter
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: David R. Notter,
| | - Marzieh Heidaritabar
- Livestock Gentec, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Joan M. Burke
- United States Department of Agriculture, Agricultural Research Service, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | | | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Gabrielle M. Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Gordon L. Spangler
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Michael D. MacNeil
- Delta G, Miles City, MT, United States
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - James E. Miller
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
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18
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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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Ren A, Sun J, Yin W, Westerberg LS, Miller H, Lee P, Candotti F, Guan F, Lei J, Gong Q, Chen Y, Liu C. Signaling networks in B cell development and related therapeutic strategies. J Leukoc Biol 2021; 111:877-891. [PMID: 34528729 DOI: 10.1002/jlb.2ru0221-088rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
B cells are essential for Ab production during humoral immune responses. From decades of B cell research, there is now a detailed understanding of B cell subsets, development, functions, and most importantly, signaling pathways. The complicated pathways in B cells and their interactions with each other are stage-dependent, varying with surface marker expression during B cell development. With the increasing understanding of B cell development and signaling pathways, the mechanisms underlying B cell related diseases are being unraveled as well, making it possible to provide more precise and effective treatments. In this review, we describe several essential and recently discovered signaling pathways in B cell development and take a look at newly developed therapeutic strategies targeted at B cell signaling.
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Affiliation(s)
- Anwen Ren
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianxuan Sun
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yin
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lisa S Westerberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Heather Miller
- The Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China.,Clinical Molecular Immunology Center, School of Medicine, Yangtze University, Jingzhou, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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20
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Mai H, Chen J, Chen H, Liu Z, Huang G, Wang J, Xiao Q, Ren W, Zhou B, Hou J, Jiang D. Fine Mapping of the MHC Region Identifies Novel Variants Associated with HBV-Related Hepatocellular Carcinoma in Han Chinese. J Hepatocell Carcinoma 2021; 8:951-961. [PMID: 34430511 PMCID: PMC8378933 DOI: 10.2147/jhc.s321919] [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: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Genome-wide association studies identified susceptibility loci in the major histocompatibility complex region for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). However, the causal variants underlying HBV-related HCC pathogenesis remain elusive. Methods With a total of 1,161 HBV-related HCC cases and 1,353 chronic HBV carriers without HCC, we imputed human leukocyte antigen (HLA) variants based on a Chinese HLA reference panel and evaluated the associations of these variants with the risk of HBV-related HCC. Conditional analyses were used to identify independent signals associated with the risk of HBV-related HCC (P false-discovery rate (FDR) <0.20). A total of 14,930 variants within the MHC region were genotyped or imputed. Results We identified two variants, rs114401688 (P = 1.05 × 10−6, PFDR = 2.43 × 10−3) and rs115126566 (P = 9.04 × 10−5, PFDR = 1.77 × 10−1), that are independently associated with the risk of HBV-related HCC. Single nucleotide polymorphism (SNP) rs114401688 is in linkage disequilibrium with a previously reported SNP rs9275319. In the current study, we found that its association with HCC could be explained by HLA-DQB1*04 and HLA-DRB1*04. SNP rs115126566 is a novel risk variant and may function by regulating transcriptions of HLA-DPA1/DPB1 through enhancer-mediated mechanisms. HLA zygosity analysis showed that homozygosity at HLA-DQB1 gene is suggestively associated with a higher risk of HCC (P = 0.10) and the risk was more pronounced in the older age group (age ≥50, P = 0.03). Discussion Our findings further the understanding of the genetic basis for HBV-related HCC predisposition in chronic HBV carriers.
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Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, People's Republic of China
| | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Guanlin Huang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jialin Wang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Qianyi Xiao
- School of Public Health, Fudan University, Shanghai, 200032, People's Republic of China
| | - Weihua Ren
- Central Laboratory, First Affiliated Hospital, Henan University of Science and Technology, Luoyang, Henan Province, 471009, People's Republic of China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
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21
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Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons. Sci Rep 2021; 11:16977. [PMID: 34417498 PMCID: PMC8379280 DOI: 10.1038/s41598-021-96263-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/04/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin architecture influences transcription by modulating the physical access of regulatory factors to DNA, playing fundamental roles in cell identity. Studies on dopaminergic differentiation have identified coding genes, but the relationship with non-coding genes or chromatin accessibility remains elusive. Using RNA-Seq and ATAC-Seq we profiled differentially expressed transcripts and open chromatin regions during early dopaminergic neuron differentiation. Hierarchical clustering of differentially expressed genes, resulted in 6 groups with unique characteristics. Surprisingly, the abundance of long non-coding RNAs (lncRNAs) was high in the most downregulated transcripts, and depicted positive correlations with target mRNAs. We observed that open chromatin regions decrease upon differentiation. Enrichment analyses of accessibility depict an association between open chromatin regions and specific functional pathways and gene-sets. A bioinformatic search for motifs allowed us to identify transcription factors and structural nuclear proteins that potentially regulate dopaminergic differentiation. Interestingly, we also found changes in protein and mRNA abundance of the CCCTC-binding factor, CTCF, which participates in genome organization and gene expression. Furthermore, assays demonstrated co-localization of CTCF with Polycomb-repressed chromatin marked by H3K27me3 in pluripotent cells, progressively decreasing in neural precursor cells and differentiated neurons. Our work provides a unique resource of transcription factors and regulatory elements, potentially involved in the acquisition of human dopaminergic neuron cell identity.
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22
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Rakhra G, Rakhra G. Zinc finger proteins: insights into the transcriptional and post transcriptional regulation of immune response. Mol Biol Rep 2021; 48:5735-5743. [PMID: 34304391 PMCID: PMC8310398 DOI: 10.1007/s11033-021-06556-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Zinc finger proteins encompass one of the unique and large families of proteins with diversified biological functions in the human body. These proteins are primarily considered to be DNA binding transcription factors; however, owing to the diverse array of zinc-finger domains, they are able to interact with molecules other than DNA like RNA, proteins, lipids and PAR (poly-ADP-ribose). Evidences from recent scientific studies have provided an insight into the potential functions of zinc finger proteins in immune system regulation both at the transcriptional and post transcriptional level. However, the mechanism and importance of zinc finger proteins in the regulation of immune response is not very well defined and understood. This review highlights in detail the importance of zinc finger proteins in the regulation of immune system at transcriptional and post transcriptional level. CONCLUSION Different types of zinc finger proteins are involved in immune system regulation and their mechanism of regulation is discussed herewith.
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Affiliation(s)
- Gurseen Rakhra
- Department of Nutrition & Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research & Studies, Faridabad, Haryana, 121004, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India.
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23
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van Schoonhoven A, Huylebroeck D, Hendriks RW, Stadhouders R. 3D genome organization during lymphocyte development and activation. Brief Funct Genomics 2021; 19:71-82. [PMID: 31819944 PMCID: PMC7115705 DOI: 10.1093/bfgp/elz030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Chromosomes have a complex three-dimensional (3D) architecture comprising A/B compartments, topologically associating domains and promoter-enhancer interactions. At all these levels, the 3D genome has functional consequences for gene transcription and therefore for cellular identity. The development and activation of lymphocytes involves strict control of gene expression by transcription factors (TFs) operating in a three-dimensionally organized chromatin landscape. As lymphocytes are indispensable for tissue homeostasis and pathogen defense, and aberrant lymphocyte activity is involved in a wide range of human morbidities, acquiring an in-depth understanding of the molecular mechanisms that control lymphocyte identity is highly relevant. Here we review current knowledge of the interplay between 3D genome organization and transcriptional control during B and T lymphocyte development and antigen-dependent activation, placing special emphasis on the role of TFs.
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Affiliation(s)
- Anne van Schoonhoven
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.,Department of Cell Biology,Erasmus MC, Rotterdam, the Netherlands
| | | | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.,Department of Cell Biology,Erasmus MC, Rotterdam, the Netherlands
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24
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Yi E, Zhang J, Zheng M, Zhang Y, Liang C, Hao B, Hong W, Lin B, Pu J, Lin Z, Huang P, Li B, Zhou Y, Ran P. Long noncoding RNA IL6-AS1 is highly expressed in chronic obstructive pulmonary disease and is associated with interleukin 6 by targeting miR-149-5p and early B-cell factor 1. Clin Transl Med 2021; 11:e479. [PMID: 34323408 PMCID: PMC8288003 DOI: 10.1002/ctm2.479] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Chronic obstructive pulmonary disease is a complex condition with multiple etiologies, including inflammation. We identified a novel long noncoding RNA (lncRNA), interleukin 6 antisense RNA 1 (IL6-AS1), which is upregulated in this disease and is associated with airway inflammation. We found that IL6-AS1 promotes the expression of inflammatory factors, especially interleukin (IL) 6. Mechanistically, cytoplasmic IL6-AS1 acts as an endogenous sponge by competitively binding to the microRNA miR-149-5p to stabilize IL-6 mRNA. Nuclear IL6-AS1 promotes IL-6 transcription by recruiting early B-cell factor 1 to the IL-6 promoter, which increases the methylation of the H3K4 histone and acetylation of the H3K27 histone. We propose a model of lncRNA expression in both the nucleus and cytoplasm that exerts similar effects through differing mechanisms, and IL6-AS1 probably increases inflammation via multiple pathways.
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Affiliation(s)
- Erkang Yi
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Jiahuan Zhang
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Mengning Zheng
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Yi Zhang
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdong510000China
| | - Chunxiao Liang
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Binwei Hao
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Wei Hong
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdong510000China
| | - Biting Lin
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdong510000China
| | - Jinding Pu
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Zhiwei Lin
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdong510000China
| | - Peiyu Huang
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Bing Li
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdong510000China
| | - Yumin Zhou
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
| | - Pixin Ran
- National Center for Respiratory MedicineState Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical University151 Yanjiang Xi RoadGuangzhouGuangdong510000China
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25
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Genome-wide interference of ZNF423 with B-lineage transcriptional circuitries in acute lymphoblastic leukemia. Blood Adv 2021; 5:1209-1223. [PMID: 33646306 DOI: 10.1182/bloodadvances.2020001844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/21/2021] [Indexed: 11/20/2022] Open
Abstract
Aberrant expression of the transcriptional modulator and early B-cell factor 1 (EBF1) antagonist ZNF423 has been implicated in B-cell leukemogenesis, but its impact on transcriptional circuitries in lymphopoiesis has not been elucidated in a comprehensive manner. Herein, in silico analyses of multiple expression data sets on 1354 acute leukemia samples revealed a widespread presence of ZNF423 in various subtypes of acute lymphoblastic leukemia (ALL). Average expression of ZNF423 was highest in ETV6-RUNX1, B-other, and TCF3-PBX1 ALL followed by BCR-ABL, hyperdiploid ALL, and KMT2A-rearranged ALL. In a KMT2A-AFF1 pro-B ALL model, a CRISPR-Cas9-mediated genetic ablation of ZNF423 decreased cell viability and significantly prolonged survival of mice upon xenotransplantation. For the first time, we characterized the genome-wide binding pattern of ZNF423, its impact on the chromatin landscape, and differential gene activities in a B-lineage context. In general, chromatin-bound ZNF423 was associated with a depletion of activating histone marks. At the transcriptional level, EBF1-dependent transactivation was disrupted by ZNF423, whereas repressive and pioneering activities of EBF1 were not discernibly impeded. Unexpectedly, we identified an enrichment of ZNF423 at canonical EBF1-binding sites also in the absence of EBF1, which was indicative of intrinsic EBF1-independent ZNF423 activities. A genome-wide motif search at EBF1 target gene loci revealed that EBF1 and ZNF423 co-regulated genes often contain SMAD1/SMAD4-binding motifs as exemplified by the TGFB1 promoter, which was repressed by ZNF423 outcompeting EBF1 by depending on its ability to bind EBF1 consensus sites and to interact with EBF1 or SMADs. Overall, these findings underscore the wide scope of ZNF423 activities that interfere with B-cell lymphopoiesis and contribute to leukemogenesis.
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26
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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: 5] [Impact Index Per Article: 1.7] [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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27
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Nieminen-Pihala V, Tarkkonen K, Laine J, Rummukainen P, Saastamoinen L, Nagano K, Baron R, Kiviranta R. Early B-cell Factor1 (Ebf1) promotes early osteoblast differentiation but suppresses osteoblast function. Bone 2021; 146:115884. [PMID: 33582307 DOI: 10.1016/j.bone.2021.115884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/22/2020] [Accepted: 02/09/2021] [Indexed: 11/17/2022]
Abstract
Early B cell factor 1 (Ebf1) is a transcription factor that regulates B cell, neuronal cell and adipocyte differentiation. We and others have shown that Ebf1 is expressed in osteoblasts and that global deletion of Ebf1 results in increased bone formation in vivo. However, as Ebf1 is expressed in multiple tissues and cell types, it has remained unclear, which of the phenotypic changes in bone are derived from bone cells. The aim of this study was to determine the cell-autonomous and differentiation stage-specific roles of Ebf1 in osteoblasts. In vitro, haploinsufficient Ebf1+/- calvarial cells showed impaired osteoblastic differentiation indicated by lower alkaline phosphatase (ALP) activity and reduced mRNA expression of osteoblastic genes, while overexpression of Ebf1 in wild type mouse calvarial cells led to enhanced osteoblast differentiation with increased expression of Osterix (Osx). We identified a putative Ebf1 binding site in the Osterix promoter by ChIP assay in MC3T3-E1 osteoblasts and showed that Ebf1 was able to activate Osx-luc reporter construct that included this Ebf1 binding site, suggesting that Ebf1 indeed regulates osteoblast differentiation by inducing Osterix expression. To reconcile our previous data and that of others with our novel findings, we hypothesized that Ebf1 could have a dual role in osteoblast differentiation promoting early but inhibiting late stages of differentiation and osteoblast function. To test this hypothesis in vivo, we generated conditional Ebf1 knockout mice, in which Ebf1 deletion was targeted to early or late osteoblasts by crossing Ebf1fl/fl mice with Osx- or Osteocalcin (hOC)-Cre mouse lines, respectively. Deletion of Ebf1 in early Ebf1Osx-/- osteoblasts resulted in significantly increased bone volume and trabecular number at 12 weeks by μCT analysis, while Ebf1hOC-/- mice did not have a bone phenotype. To conclude, our data demonstrate that Ebf1 promotes early osteoblast differentiation by regulating Osterix expression. However, Ebf1 inhibits bone accrual in the Osterix expressing osteoblasts in vivo but it is redundant in the maintenance of mature osteoblast function.
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Affiliation(s)
| | - Kati Tarkkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Julius Laine
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | - Kenichi Nagano
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA
| | - Roland Baron
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA
| | - Riku Kiviranta
- Institute of Biomedicine, University of Turku, Turku, Finland; Department of Endocrinology, Division of Medicine, University of Turku and Turku University Hospital, Turku, Finland.
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TETology: Epigenetic Mastermind in Action. Appl Biochem Biotechnol 2021; 193:1701-1726. [PMID: 33694104 DOI: 10.1007/s12010-021-03537-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Cytosine methylation is a well-explored epigenetic modification mediated by DNA methyltransferases (DNMTs) which are considered "methylation writers"; cytosine methylation is a reversible process. The process of removal of methyl groups from DNA remained unelucidated until the discovery of ten-eleven translocation (TET) proteins which are now considered "methylation editors." TET proteins are a family of Fe(II) and alpha-ketoglutarate-dependent 5-methyl cytosine dioxygenases-they convert 5-methyl cytosine to 5-hydroxymethyl cytosine, and to further oxidized derivatives. In humans, there are three TET paralogs with tissue-specific expression, namely TET1, TET2, and TET3. Among the TETs, TET2 is highly expressed in hematopoietic stem cells where it plays a pleiotropic role. The paralogs also differ in their structure and DNA binding. TET2 lacks the CXXC domain which mediates DNA binding in the other paralogs; thus, TET2 requires interactions with other proteins containing DNA-binding domains for effectively binding to DNA to bring about the catalysis. In addition to its role as methylation editor of DNA, TET2 also serves as methylation editor of RNA. Thus, TET2 is involved in epigenetics as well as epitranscriptomics. TET2 mutations have been found in various malignant hematological disorders like acute myeloid leukemia, and non-malignant hematological disorders like myelodysplastic syndromes. Increasing evidence shows that TET2 plays an important role in the non-hematopoietic system as well. Hepatocellular carcinoma, gastric cancer, prostate cancer, and melanoma are some non-hematological malignancies in which a role of TET2 has been implicated. Loss of TET2 is also associated with atherosclerotic vascular lesions and endometriosis. The current review elaborates on the role of structure, catalysis, physiological functions, pathological alterations, and methods to study TET2, with specific emphasis on epigenomics and epitranscriptomics.
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EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex. Sci Rep 2021; 11:1537. [PMID: 33452395 PMCID: PMC7810865 DOI: 10.1038/s41598-021-81000-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/28/2020] [Indexed: 12/15/2022] Open
Abstract
PAX5 and EBF1 work synergistically to regulate genes that are involved in B lymphocyte differentiation. We used the KIS-1 diffuse large B cell lymphoma cell line, which is reported to have elevated levels of PAX5 expression, to investigate the mechanism of EBF1- and PAX5-regulated gene expression. We demonstrate the lack of expression of hallmark B cell genes, including CD19, CD79b, and EBF1, in the KIS-1 cell line. Upon restoration of EBF1 expression we observed activation of CD19, CD79b and other genes with critical roles in B cell differentiation. Mass spectrometry analyses of proteins co-immunoprecipitated with PAX5 in KIS-1 identified components of the MLL H3K4 methylation complex, which drives histone modifications associated with transcription activation. Immunoblotting showed a stronger association of this complex with PAX5 in the presence of EBF1. Silencing of KMT2A, the catalytic component of MLL, repressed the ability of exogenous EBF1 to activate transcription of both CD19 and CD79b in KIS-1 cells. We also find association of PAX5 with the MLL complex and decreased CD19 expression following silencing of KMT2A in other human B cell lines. These data support an important role for the MLL complex in PAX5-mediated transcription regulation.
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Dang TN, Taylor JL, Kilroy G, Yu Y, Burk DH, Floyd ZE. SIAH2 is Expressed in Adipocyte Precursor Cells and Interacts with EBF1 and ZFP521 to Promote Adipogenesis. Obesity (Silver Spring) 2021; 29:98-107. [PMID: 33155406 PMCID: PMC7902405 DOI: 10.1002/oby.23013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Expression of zinc finger protein 423 (ZFP423), a key proadipogenic transcription factor in adipocyte precursor cells, is regulated by interaction of the proadipogenic early B-cell factor 1 (EBF1) and antiadipogenic ZFP521. The ubiquitin ligase seven-in-absentia homolog 2 (SIAH2) targets ZFP521 for degradation. This study asked whether SIAH2 is expressed in adipocyte precursor cells and whether SIAH2 interacts with ZFP521 and EBF1 to regulate ZFP521 protein levels during adipogenesis. METHODS SIAH2 expression in precursor cells was assessed in primary cells and tissues from wild-type and SIAH2 null mice fed a control or high-fat diet. Primary cells, 3T3-L1 preadipocytes, and HEK293T cells were used to analyze Siah2, Ebf1, and Zfp521 expression and SIAH2-mediated changes in ZFP521 and EBF1 protein levels. RESULTS Siah2 is expressed in platelet-derived growth factor receptor α (PDGFRα)+ and stem cell antigen-1 (SCA1)+ adipocyte precursor cells. SIAH2 depletion reduces Ebf1 gene expression and increases EBF1 protein levels in early but not late adipogenesis. In early adipogenesis, SIAH2 forms a protein complex with EBF1 and ZFP521 to enhance SIAH2-mediated ubiquitylation and degradation of ZFP521 while increasing EBF1 protein levels. CONCLUSIONS Siah2 is expressed in PDGFRα+ adipocyte precursor cells and is linked to precursor cell commitment to adipogenesis by interacting with EBF1 and ZFP521 proteins to target the antiadipogenic ZFP521 for degradation.
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Affiliation(s)
- Thanh N Dang
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Jessica L Taylor
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Gail Kilroy
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Yongmei Yu
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - David H Burk
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Z Elizabeth Floyd
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
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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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Hosein Pour Feizi A, Zeinali S, Toporski J, Sheervalilou R, Mehranfar S. Frequency and Correlation of Common Genes Copy Number Alterations in Childhood Acute Lymphoblastic Leukemia with Prognosis. Asian Pac J Cancer Prev 2020; 21:3493-3500. [PMID: 33369444 PMCID: PMC8046302 DOI: 10.31557/apjcp.2020.21.12.3493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Indexed: 11/25/2022] Open
Abstract
Objective: It was shown by genomic profiling that despite no detectable chromosomal abnormalities a proportion of children with pre-B acute lymphoblastic leukemia harbors copy number alterations (CNA) of genes playing role in B-cell development and function. The aim of the study was to determine the frequency of CNA in pediatric acute lymphoblastic leukemia and correlate these findings with clinical outcome. Methods: DNA extracted from peripheral blood or bone marrow at diagnosis/relapse of fifty newly diagnosed children with precursor B-cell acute lymphoblastic leukemia was analyzed for CNA with multiplex ligation-dependent probe amplification. Results: The analysis revealed 76 CNA in 24 patients most frequently found in PAR1 (17%), CDKN2A/B (15.7%) and PAX5 (14.4%) genes. There were significant CNA co-occurrences between PAX5, CDKN2A/B, BTG1, ETV6, PAR1 or XP22 genes, (p<0.020) and the high-risk group. There was a significant correlation between EBF1, RB1, and IKZF1 alterations and bone marrow relapse. Patients with CNA in screened genes are more likely to succumb to their disease except for those with PAR1 or XP22 genes (p<0.050). Conclusion: The multiplex ligation-dependent probe amplification could be considered as an independent diagnostic tool allowing prompt identification of patients at high risk of treatment failure and, subsequently, a more adequate treatment approach.
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Affiliation(s)
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Kawsar Human Genetics Research Center, Kawsar Genomics Center, Tehran, Iran
| | - Jacek Toporski
- Department of Clinical Sciences, Pediatric Oncology and Hematology, University of Lund, Lund, Sweden
| | | | - Sahar Mehranfar
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.,Social Determinate of Health Research Center, Clinical Research Institute Urmia University of Medical Science, Urmia, Iran
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Wang Y, Zolotarev N, Yang CY, Rambold A, Mittler G, Grosschedl R. A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin. Immunity 2020; 53:1151-1167.e6. [DOI: 10.1016/j.immuni.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023]
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Ramamoorthy S, Kometani K, Herman JS, Bayer M, Boller S, Edwards-Hicks J, Ramachandran H, Li R, Klein-Geltink R, Pearce EL, Grün D, Grosschedl R. EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression, and folate metabolism. Genes Dev 2020; 34:1503-1519. [PMID: 33004416 PMCID: PMC7608749 DOI: 10.1101/gad.340216.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
In this study, Ramamoorthy et al. investigate EBF1 and PAX5 combined haploinsufficiency in the development of a B-ALL phenotype in mice. Using transcriptional and metabolomic profiling, the authors report that EBF1 and Pax5 may safeguard early stage B cells from transformation to B-ALL by limiting IL-7 signaling, folate metabolism, and Myc expression. EBF1 and PAX5 mutations are associated with the development of B progenitor acute lymphoblastic leukemia (B-ALL) in humans. To understand the molecular networks driving leukemia in the Ebf1+/−Pax5+/− (dHet) mouse model for B-ALL, we interrogated the transcriptional profiles and chromatin status of leukemic cells, preleukemic dHet pro-B, and wild-type pro-B cells with the corresponding EBF1 and Pax5 cistromes. In dHet B-ALL cells, many EBF1 and Pax5 target genes encoding pre-BCR signaling components and transcription factors were down-regulated, whereas Myc and genes downstream from IL-7 signaling or associated with the folate pathway were up-regulated. We show that blockade of IL-7 signaling in vivo and methotrexate treatment of leukemic cells in vitro attenuate the expansion of leukemic cells. Single-cell RNA-sequencing revealed heterogeneity of leukemic cells and identified a subset of wild-type pro-B cells with reduced Ebf1 and enhanced Myc expression that show hallmarks of dHet B-ALL cells. Thus, EBF1 and Pax5 may safeguard early stage B cells from transformation to B-ALL by limiting IL-7 signaling, folate metabolism and Myc expression.
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Affiliation(s)
- Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kohei Kometani
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Josip S Herman
- Laboratory of Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,International Max Planck Research School, University of Freiburg, 79104 Freiburg, Germany
| | - Marc Bayer
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,International Max Planck Research School, University of Freiburg, 79104 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joy Edwards-Hicks
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- 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
| | - Ramon Klein-Geltink
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Dominic Grün
- Laboratory of Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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Li Y, Osuma A, Correa E, Okebalama MA, Dao P, Gaylord O, Aburas J, Islam P, Brown AE, Kratsios P. Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function. eLife 2020; 9:59464. [PMID: 33001031 PMCID: PMC7529460 DOI: 10.7554/elife.59464] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023] Open
Abstract
Terminal selectors are transcription factors (TFs) that establish during development and maintain throughout life post-mitotic neuronal identity. We previously showed that UNC-3/Ebf, the terminal selector of C. elegans cholinergic motor neurons (MNs), acts indirectly to prevent alternative neuronal identities (Feng et al., 2020). Here, we globally identify the direct targets of UNC-3. Unexpectedly, we find that the suite of UNC-3 targets in MNs is modified across different life stages, revealing ‘temporal modularity’ in terminal selector function. In all larval and adult stages examined, UNC-3 is required for continuous expression of various protein classes (e.g. receptors, transporters) critical for MN function. However, only in late larvae and adults, UNC-3 is required to maintain expression of MN-specific TFs. Minimal disruption of UNC-3’s temporal modularity via genome engineering affects locomotion. Another C. elegans terminal selector (UNC-30/Pitx) also exhibits temporal modularity, supporting the potential generality of this mechanism for the control of neuronal identity.
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Affiliation(s)
- Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Anthony Osuma
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Edgar Correa
- Department of Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States
| | | | - Pauline Dao
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Olivia Gaylord
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States
| | - Jihad Aburas
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Priota Islam
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - André Ex Brown
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States.,Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States.,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, United States
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Shen Z, Chen Y, Li L, Liu L, Peng M, Chen X, Wu X, Sferra TJ, Wu M, Lin X, Cheng Y, Chu J, Shen A, Peng J. Transcription Factor EBF1 Over-Expression Suppresses Tumor Growth in vivo and in vitro via Modulation of the PNO1/p53 Pathway in Colorectal Cancer. Front Oncol 2020; 10:1035. [PMID: 32676457 PMCID: PMC7333669 DOI: 10.3389/fonc.2020.01035] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/26/2020] [Indexed: 01/12/2023] Open
Abstract
Early B cell factor 1 (EBF1) has been identified as an upstream transcription factor of the potential oncogene PNO1 and is involved in the growth of colorectal cancer (CRC) cells. However, its expression, biological function, and underlying mechanism of action in most solid tumors remain largely unknown. We postulated that EBF1 has a role in the pathophysiology of CRC. Analysis of EBF1 mRNA expression in CRC tumor samples from several public databases and directly from banked tissues revealed that EBF1 mRNA expression is lower in CRC tissue compared to non-cancerous colorectal tissue. Survival analysis of multiple datasets revealed that low EBF1 expression was correlated with shorter overall survival, relapse-free survival, and event-free survival in CRC patients. Transduction of lentivirus encoding full length EBF1 followed by in vitro and in vivo assays demonstrated that EBF1 over-expression in CRC cell lines suppresses cell growth by inhibiting cell viability, cell survival, and induces cell cycle arrest and apoptosis. Mechanistic investigation indicated that EBF1 over-expression down-regulates PNO1 mRNA and protein expression, as well as transcriptional activity while up-regulating the expression of p53 and p21 proteins. These findings suggest that EBF1 is a novel potential tumor suppressor in CRC with prognostic value for the identification of patients at high-risk of relapse.
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Affiliation(s)
- Zhiqing Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Youqin Chen
- Department of Pediatrics, Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH, United States
| | - Li Li
- Department of Health Management, Fujian Provincial Hospital, Fuzhou, China
| | - Liya Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Meizhong Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoping Chen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiangyan Wu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Thomas J Sferra
- Department of Pediatrics, Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH, United States
| | - Meizhu Wu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoying Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Ying Cheng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jianfeng Chu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Aling Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats. Cells 2020; 9:cells9061435. [PMID: 32527043 PMCID: PMC7348746 DOI: 10.3390/cells9061435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.
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Modular Organization of Cis-regulatory Control Information of Neurotransmitter Pathway Genes in Caenorhabditis elegans. Genetics 2020; 215:665-681. [PMID: 32444379 DOI: 10.1534/genetics.120.303206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
We explore here the cis-regulatory logic that dictates gene expression in specific cell types in the nervous system. We focus on a set of eight genes involved in the synthesis, transport, and breakdown of three neurotransmitter systems: acetylcholine (unc-17 /VAChT, cha-1 /ChAT, cho-1 /ChT, and ace-2 /AChE), glutamate (eat-4 /VGluT), and γ-aminobutyric acid (unc-25 /GAD, unc-46 /LAMP, and unc-47 /VGAT). These genes are specifically expressed in defined subsets of cells in the nervous system. Through transgenic reporter gene assays, we find that the cellular specificity of expression of all of these genes is controlled in a modular manner through distinct cis-regulatory elements, corroborating the previously inferred piecemeal nature of specification of neurotransmitter identity. This modularity provides the mechanistic basis for the phenomenon of "phenotypic convergence," in which distinct regulatory pathways can generate similar phenotypic outcomes (i.e., the acquisition of a specific neurotransmitter identity) in different neuron classes. We also identify cases of enhancer pleiotropy, in which the same cis-regulatory element is utilized to control gene expression in distinct neuron types. We engineered a cis-regulatory allele of the vesicular acetylcholine transporter, unc-17 /VAChT, to assess the functional contribution of a "shadowed" enhancer. We observed a selective loss of unc-17 /VAChT expression in one cholinergic pharyngeal pacemaker motor neuron class and a behavioral phenotype that matches microsurgical removal of this neuron. Our analysis illustrates the value of understanding cis-regulatory information to manipulate gene expression and control animal behavior.
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Nelson T, Velazquez H, Troiano N, Fretz JA. Early B Cell Factor 1 (EBF1) Regulates Glomerular Development by Controlling Mesangial Maturation and Consequently COX-2 Expression. J Am Soc Nephrol 2019; 30:1559-1572. [PMID: 31405952 DOI: 10.1681/asn.2018070699] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 05/11/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND We recently showed the transcription factor Early B cell factor 1 (EBF1) is essential for the last stages of metanephric development, and that mice globally deficient in EBF1 display impaired maturation of peripheral glomeruli. EBF1 is present within multiple glomerular cell types, including the glomerular mesangium and podocytes. METHODS To identify which cell type is driving the glomerular developmental defects in the global EBF1 knockout mice, we deleted EBF1 from the mesangium/pericytes (Foxd1-cre) or podocytes (Podocin-cre) in mice. RESULTS Deletion of EBF1 from Foxd1 lineage cells resulted in hypoplastic kidneys, poorly differentiated peripheral glomeruli, and decreased proximal tubular mass in the outer cortex. Renal insufficiency was apparent at P21 when proteinuria presents, fibrosis of both the glomeruli and interstitium rapidly progresses, microthrombi appear, and hematuria develops. Approximately half of the Foxd1+, Ebf1 fl/fl mice die before they are 3 months old. Mice with podocyte-targeted deletion of EBF1 exhibited no developmental abnormalities. Mice with Ebf1 deficiency in Foxd1 lineage cells shared characteristics with Ptgs2/COX-2-insufficient models, and mechanistic investigation revealed impaired calcineurin/NFATc1 activation and decreased COX-2 expression. Deletion of COX-2 from the interstitial/mesangial lineage displayed a less severe phenotype than EBF1 deficiency in mice. Overexpressing COX-2 in the EBF1-deficient mice, however, partially restored glomerular development. CONCLUSIONS The results suggest that EBF1 regulates metanephric development at the last stages of glomerular maturation through its actions in the stromal progenitor (Foxd1+) lineage where it mediates proper regulation of calcineurin/NFAT signaling and COX-2 expression.
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Affiliation(s)
- Tracy Nelson
- Department of Orthopedics and Rehabilitation and
| | - Heino Velazquez
- Division of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
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Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun 2019; 10:3583. [PMID: 31395865 PMCID: PMC6687891 DOI: 10.1038/s41467-019-11526-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we perform saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitutions and deletions. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and comprise a rich dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.
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Yoshida T, Hu Y, Zhang Z, Emmanuel AO, Galani K, Muhire B, Snippert HJ, Williams CJ, Tolstorukov MY, Gounari F, Georgopoulos K. Chromatin restriction by the nucleosome remodeler Mi-2β and functional interplay with lineage-specific transcription regulators control B-cell differentiation. Genes Dev 2019; 33:763-781. [PMID: 31123064 PMCID: PMC6601517 DOI: 10.1101/gad.321901.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/15/2019] [Indexed: 01/08/2023]
Abstract
Here, Yoshida et al. investigate the role of Mi-2β, a SNF-2-like nucleosome remodeler and key component of the nucleosome remodeling and histone deacetylase (NuRD) complex in early B cells. They found that the nucleosome remodeler Mi-2β promotes pre-B-cell differentiation by providing repression capabilities to distinct lineage-specific transcription factor-based regulatory networks. Coordinated induction, but also repression, of genes are key to normal differentiation. Although the role of lineage-specific transcription regulators has been studied extensively, their functional integration with chromatin remodelers, one of the key enzymatic machineries that control chromatin accessibility, remains ill-defined. Here we investigate the role of Mi-2β, a SNF-2-like nucleosome remodeler and key component of the nucleosome remodeling and histone deacetylase (NuRD) complex in early B cells. Inactivation of Mi-2β arrested differentiation at the large pre-B-cell stage and caused derepression of cell adhesion and cell migration signaling factors by increasing chromatin access at poised enhancers and chromosome architectural elements. Mi-2β also supported IL-7R signaling, survival, and proliferation by repressing negative effectors of this pathway. Importantly, overexpression of Bcl2, a mitochondrial prosurvival gene and target of IL-7R signaling, partly rescued the differentiation block caused by Mi-2β loss. Mi-2β stably associated with chromatin sites that harbor binding motifs for IKAROS and EBF1 and physically associated with these transcription factors both on and off chromatin. Notably, Mi-2β shared loss-of-function cellular and molecular phenotypes with IKAROS and EBF1, albeit in a distinct fashion. Thus, the nucleosome remodeler Mi-2β promotes pre-B-cell differentiation by providing repression capabilities to distinct lineage-specific transcription factor-based regulatory networks.
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Affiliation(s)
- Toshimi Yoshida
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Yeguang Hu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Zhihong Zhang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Akinola O Emmanuel
- Knapp Center for Lupus Research, Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kiriaki Galani
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Brejnev Muhire
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02144, USA
| | - Hugo J Snippert
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Christine J Williams
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02144, USA
| | - Fotini Gounari
- Knapp Center for Lupus Research, Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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42
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Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia 2019; 33:2720-2731. [PMID: 31073152 PMCID: PMC6842075 DOI: 10.1038/s41375-019-0474-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Ikaros encodes a transcription factor that functions as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells resulted in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic, global, epigenomic and gene expression analyses to determine the mechanisms of Ikaros tumor suppressor activity. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effects of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Our results establish that Ikaros’ tumor suppressor function occurs via global regulation of the enhancer and super-enhancer landscape and through pioneering activity. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.
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Affiliation(s)
- Yali Ding
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chunhua Song
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital Southeast University, Institute of Hematology Southeast University, 210009, Nanjing, China
| | - Chandrika Gowda
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Glenn Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Mark E Reeves
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Dhimant Desai
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suming Huang
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kimberly J Payne
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Sinisa Dovat
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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Rothenberg EV. Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges. J Comput Biol 2019; 26:703-718. [PMID: 31063008 DOI: 10.1089/cmb.2019.0098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory network modeling has played a major role in advancing the understanding of developmental systems, by crystallizing structures of relevant extant information, by formally posing hypothetical functional relationships between network elements, and by offering clear predictive tests to improve understanding of the mechanisms driving developmental progression. Both ordinary differential equation (ODE)-based and Boolean models have also been highly successful in explaining dynamics within subcircuits of more complex processes. In a very small number of cases, gene regulatory network models of much more global scope have been proposed that successfully predict the dynamics of the processes establishing most of an embryonic body plan. Can such successes be expanded to very different developmental systems, including post-embryonic mammalian systems? This perspective discusses several problems that must be solved in more quantitative and predictive theoretical terms, to make this possible. These problems include: the effects of cellular history on chromatin state and how these affect gene accessibility; the dose dependence of activities of many transcription factors (a problem for Boolean models); stochasticity of some transcriptional outputs (a problem for simple ODE models); response timing delays due to epigenetic remodeling requirements; functionally different kinds of repression; and the regulatory syntax that governs responses of genes with multiple enhancers.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
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44
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Hosokawa H, Ungerbäck J, Wang X, Matsumoto M, Nakayama KI, Cohen SM, Tanaka T, Rothenberg EV. Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding. Immunity 2019; 48:1119-1134.e7. [PMID: 29924977 DOI: 10.1016/j.immuni.2018.04.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/21/2018] [Accepted: 04/19/2018] [Indexed: 01/09/2023]
Abstract
Transcription factors normally regulate gene expression through their action at sites where they bind to DNA. However, the balance of activating and repressive functions that a transcription factor can mediate is not completely understood. Here, we showed that the transcription factor PU.1 regulated gene expression in early T cell development both by recruiting partner transcription factors to its own binding sites and by depleting them from the binding sites that they preferred when PU.1 was absent. The removal of partner factors Satb1 and Runx1 occurred primarily from sites where PU.1 itself did not bind. Genes linked to sites of partner factor "theft" were enriched for genes that PU.1 represses despite lack of binding, both in a model cell line system and in normal T cell development. Thus, system-level competitive recruitment dynamics permit PU.1 to affect gene expression both through its own target sites and through action at a distance.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonas Ungerbäck
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Division of Molecular Hematology, Lund University, Sweden
| | - Xun Wang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Sarah M Cohen
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Japan; AMED-CREST, AMED, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Abstract
In this review, Boothby et al. summarize some salient advances toward elucidation of the molecular programming of the fate choices and function of B cells in the periphery. They also note unanswered questions that pertain to differences among subsets of B lymphocytes and plasma cells. Mature B lymphocytes are crucial components of adaptive immunity, a system essential for the evolutionary fitness of mammals. Adaptive lymphocyte function requires an initially naïve cell to proliferate extensively and its progeny to have the capacity to assume a variety of fates. These include either terminal differentiation (the long-lived plasma cell) or metastable transcriptional reprogramming (germinal center and memory B cells). In this review, we focus principally on the regulation of differentiation and functional diversification of the “B2” subset. An overview is combined with an account of more recent advances, including initial work on mechanisms that eliminate DNA methylation and potential links between intracellular metabolites and chromatin editing.
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46
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Hosokawa H, Romero-Wolf M, Yui MA, Ungerbäck J, Quiloan MLG, Matsumoto M, Nakayama KI, Tanaka T, Rothenberg EV. Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16. Nat Immunol 2018; 19:1427-1440. [PMID: 30374131 PMCID: PMC6240390 DOI: 10.1038/s41590-018-0238-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Abstract
Multipotent progenitors confirm their T cell-lineage identity in the DN2 pro-T cell stages, when expression of the essential transcription factor Bcl11b begins. In vivo and in vitro stage-specific deletions globally identified Bcl11b-controlled target genes in pro-T cells. Proteomic analysis revealed that Bcl11b associates with multiple cofactors, and that its direct action was needed to recruit these cofactors to selective target sites. These sites of Bcl11b-dependent cofactor recruitment were enriched near functionally regulated target genes, and deletion of individual cofactors relieved repression of many Bcl11b-repressed genes. Runx1 collaborated with Bcl11b most frequently for both activation and repression. In parallel, Bcl11b indirectly regulated a subset of target genes by a gene network circuit via Id2 and Zbtb16 (encoding PLZF), which were directly repressed by Bcl11b and controlled distinct alternative programs. Thus, this study defines the molecular basis of direct and indirect Bcl11b actions that promote T cell identity and block alternative potentials.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonas Ungerbäck
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Maria L G Quiloan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Chiba University, Chuo-ku, Chiba, Japan.,AMED-CREST, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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47
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Ungerbäck J, Hosokawa H, Wang X, Strid T, Williams BA, Sigvardsson M, Rothenberg EV. Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1). Genome Res 2018; 28:1508-1519. [PMID: 30171019 PMCID: PMC6169891 DOI: 10.1101/gr.231423.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 08/30/2018] [Indexed: 01/09/2023]
Abstract
SPI1 (also known as PU.1) is a dominant but transient regulator in early T-cell precursors and a potent transcriptional controller of developmentally important pro-T-cell genes. Before T-lineage commitment, open chromatin is frequently occupied by PU.1, and many PU.1 sites lose accessibility when PU.1 is later down-regulated. Pioneering activity of PU.1 was tested in this developmentally dynamic context by quantitating the relationships between PU.1 occupancy and site quality and accessibility as PU.1 levels naturally declined in pro-T-cell development and by using stage-specific gain- and loss-of-function perturbations to relate binding to effects on target genes. PU.1 could bind closed genomic sites, but rapidly opened many of them, despite the absence of its frequent collaborator, CEBPA. RUNX motifs and RUNX1 binding were often linked to PU.1 at open sites, but highly expressed PU.1 could bind its sites without RUNX1. The dynamic properties of PU.1 engagements implied that PU.1 binding affinity and concentration determine its occupancy choices, but with quantitative trade-offs for occupancy between site sequence quality and stage-dependent site accessibility in chromatin. At nonpromoter sites, PU.1 binding criteria were more stringent than at promoters, and PU.1 was also much more effective as a transcriptional regulator at nonpromoter sites where local chromatin accessibility depended on the presence of PU.1. Notably, closed chromatin presented a qualitative barrier to occupancy by the PU.1 DNA-binding domain alone. Thus, effective pioneering at closed chromatin sites also depends on requirements beyond site recognition, served by non-DNA-binding domains of PU.1.
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Affiliation(s)
- Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.,Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xun Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Tobias Strid
- Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden.,Department of Clinical and Experimental Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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48
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Fan C, Tang Y, Wang J, Xiong F, Guo C, Wang Y, Xiang B, Zhou M, Li X, Wu X, Li Y, Li X, Li G, Xiong W, Zeng Z. The emerging role of Epstein-Barr virus encoded microRNAs in nasopharyngeal carcinoma. J Cancer 2018; 9:2852-2864. [PMID: 30123354 PMCID: PMC6096363 DOI: 10.7150/jca.25460] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/16/2018] [Indexed: 12/24/2022] Open
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpes virus that is closely associated with the initiation and development of nasopharyngeal carcinoma (NPC), lymphoma and other malignant tumors. EBV encodes 44 mature miRNAs that regulate viral and host cell gene expression and plays a variety of roles in biological functions and the development of cancer. In this review, we summarized the biological functions and molecular mechanisms of Epstein-Barr virus-encoded microRNAs (EBV miRNAs) in tumor immune evasion, proliferation, anti-apoptosis, invasion, metastasis and as a potential biomarker for NPC diagnosis and prognosis. The knowledge generated by EBV miRNAs can be used for EBV miRNA-based precision cancer treatments in the near future.
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Affiliation(s)
- Chunmei Fan
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Jinpeng Wang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Fang Xiong
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Guo
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xu Wu
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,Department of Chemistry, University of North Dakota, Grand Forks, North Dakota, USA
| | - Yong Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Xiaoling Li
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Science,, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
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49
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Sigvardsson M. Molecular Regulation of Differentiation in Early B-Lymphocyte Development. Int J Mol Sci 2018; 19:ijms19071928. [PMID: 29966360 PMCID: PMC6073616 DOI: 10.3390/ijms19071928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 12/15/2022] Open
Abstract
B-lymphocyte differentiation is one of the best understood developmental pathways in the hematopoietic system. Our understanding of the developmental trajectories linking the multipotent hematopoietic stem cell to the mature functional B-lymphocyte is extensive as a result of efforts to identify and prospectively isolate progenitors at defined maturation stages. The identification of defined progenitor compartments has been instrumental for the resolution of the molecular features that defines given developmental stages as well as for our understanding of the mechanisms that drive the progressive maturation process. Over the last years it has become increasingly clear that the regulatory networks that control normal B-cell differentiation are targeted by mutations in human B-lineage malignancies. This generates a most interesting link between development and disease that can be explored to improve diagnosis and treatment protocols in lymphoid malignancies. The aim of this review is to provide an overview of our current understanding of molecular regulation in normal and malignant B-cell development.
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Affiliation(s)
- Mikael Sigvardsson
- Division of Molecular Hematology, Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden.
- Department of Clinical and Experimental Medicine, Linköping University, SE-581 85 Linköping, Sweden.
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50
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EBF1 gene polymorphism and its interaction with smoking and drinking on the risk of coronary artery disease for Chinese patients. Biosci Rep 2018; 38:BSR20180324. [PMID: 29789399 PMCID: PMC6013695 DOI: 10.1042/bsr20180324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/17/2022] Open
Abstract
Objective: Early B-cell factor 1 (EBF1) is a transcription factor that is expressed in early B-cells, adipocytes, and olfactory neurons, and is essential for the maturation of early B lymphocytes. The present study analyzes the influence of EBF1 gene polymorphism and its interaction with smoking and drinking on the risk of coronary artery disease (CAD). Methods: In the present study, 243 CAD cases were enrolled as the CAD group and 215 non-CAD patients as the control group by case-control study. We analyzed their genotypes of the rs987401919, rs36071027, and rs1056065671 loci of the EBF1 gene by Sanger sequencing and detected their content of HDL-C, LDL-C, and TG. Results: The C allele at the rs987401919 and rs36071027 loci of EBF1 was found to be the risk factor for CAD (Odds ratio, OR = 1.233; 95% confidence interval, CI: 1.039-1.421; P=0.017; OR = 1.487; 95% CI: 1.015-1.823; P=0.042). The interaction between single nucleotide polymorphisms (SNP) of the rs987401919 and rs36071027 loci and smoking and drinking were distinctly associated with the incidence of CAD (P<0.05). The content of systolic blood pressure (SBP), diastolic blood pressure (DBP), HDL-C, LDL-C, and TG was distinctly changed after gene mutation at the rs987401919 and rs36071027 loci (P<0.05). Conclusion: The results of the present study show that the mutation (CT+TT) at the rs987401919 and rs36071027 loci of EBF1 and its interaction with smoking and drinking are risk factors for CAD, and that the mechanism may be related to the changes in blood pressure and blood lipid content.
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