1
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Fedl AS, Tagoh H, Gruenbacher S, Sun Q, Schenk RL, Froussios K, Jaritz M, Busslinger M, Schwickert TA. Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development. Nat Immunol 2024; 25:1663-1677. [PMID: 39179932 DOI: 10.1038/s41590-024-01933-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
Early B cell lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. In the present study, we used acute protein degradation in mice to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and are essential for early B cell maintenance. Ikaros and Aiolos act as dedicated repressors to cooperatively control early B cell development. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Similar to Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B cell lymphopoiesis by five transcription factors.
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Affiliation(s)
- Anna S Fedl
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Sarah Gruenbacher
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Qiong Sun
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Robyn L Schenk
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Kimon Froussios
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| | - Tanja A Schwickert
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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2
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Yang M, Tang Y, Zhu P, Lu H, Wan X, Guo Q, Xiao L, Liu C, Guo L, Liu W, Yang Y. The advances of E2A-PBX1 fusion in B-cell acute lymphoblastic Leukaemia. Ann Hematol 2024; 103:3385-3398. [PMID: 38148344 DOI: 10.1007/s00277-023-05595-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
The E2A-PBX1 gene fusion is a common translocation in B-cell acute lymphoblastic leukaemia. Patients harbouring the E2A-PBX1 fusion gene typically exhibit an intermediate prognosis. Furthermore, minimal residual disease has unsatisfactory prognostic value in E2A-PBX1 B-cell acute lymphoblastic leukaemia. However, the mechanism of E2A-PBX1 in the occurrence and progression of B-cell acute lymphoblastic leukaemia is not well understood. Here, we mainly review the roles of E2A and PBX1 in the differentiation and development of B lymphocytes, the mechanism of E2A-PBX1 gene fusion in B-cell acute lymphoblastic leukaemia, and the potential therapeutic approaches.
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Affiliation(s)
- Mengting Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Yanhui Tang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Peng Zhu
- School of Pharmacy, Wannan Medical College, Wuhu, 241000, People's Republic of China
| | - Haiquan Lu
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaohong Wan
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Lan Xiao
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Chunyan Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
| | - You Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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3
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Priam P, Krasteva V, Rousseau P, Polsinelli A, Côté L, Desanlis I, Farah A, Lavallée VP, Kmita M, Lessard JA. Smarcd1 subunit of SWI/SNF chromatin-remodeling complexes collaborates with E2a to promote murine lymphoid specification. Dev Cell 2024:S1534-5807(24)00490-8. [PMID: 39232562 DOI: 10.1016/j.devcel.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 05/02/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Lymphocyte development from murine hematopoietic stem cells (HSCs) entails a loss of self-renewal capacity and a progressive restriction of developmental potential. Previous research from our laboratory suggests that specialized assemblies of ATP-dependent SWI/SNF chromatin-remodeling complexes play lineage-specific roles during murine hematopoiesis. Here, we demonstrate that the Smarcd1 subunit is essential for specification of lymphoid cell fate from multipotent progenitors. Acute deletion of Smarcd1 in murine adult hematopoiesis leads to lymphopenia, characterized by a near-complete absence of early lymphoid progenitors and mature B and T cells, while the myeloid and erythroid lineages remain unaffected. Mechanistically, we demonstrate that Smarcd1 is essential for the coordinated activation of a lymphoid gene signature in murine multipotent progenitors. This is achieved by interacting with the E2a transcription factor at proximal promoters and by regulating the activity of distal enhancers. Globally, these findings identify Smarcd1 as an essential chromatin remodeler that governs lymphoid cell fate.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Alexandre Polsinelli
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Laurence Côté
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ines Desanlis
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Azer Farah
- Centre de Recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | | | - Marie Kmita
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
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4
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Miyazaki M, Miyazaki K. The Function of E2A in B-Cell Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:97-113. [PMID: 39017841 DOI: 10.1007/978-3-031-62731-6_5] [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
Helix-loop-helix (HLH) transcription factors (TFs) play a key role in various cellular differentiation and function through the regulation of enhancer activity. E2A, a member of the mammalian E-protein family (class I HLH protein), is well known to play an important role in hematopoiesis, especially in adaptive lymphocyte development. E2A instructs B- and T-cell lineage development through the regulation of enhancer activity for B- or T-cell signature gene expression, including Rag1 and Rag2 (Rag1/2) genes. In this chapter, we mainly focus on the function of E2A in B-cell development and on the roles of E2A in establishing the enhancer landscape through the recruitment of EP300/KAT3B, chromatin remodeling complex, mediator, cohesion, and TET proteins. Finally, we demonstrate how E2A orchestrates the assembly of the Rag1/2 gene super-enhancer (SE) formation by changing the chromatin conformation across the Rag gene locus.
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Affiliation(s)
- Masaki Miyazaki
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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5
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Korzhenevich J, Janowska I, van der Burg M, Rizzi M. Human and mouse early B cell development: So similar but so different. Immunol Lett 2023; 261:1-12. [PMID: 37442242 DOI: 10.1016/j.imlet.2023.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Early B cell development in the bone marrow ensures the replenishment of the peripheral B cell pool. Immature B cells continuously develop from hematopoietic stem cells, in a process guided by an intricate network of transcription factors as well as chemokine and cytokine signals. Humans and mice possess somewhat similar regulatory mechanisms of B lymphopoiesis. The continuous discovery of monogenetic defects that impact early B cell development in humans substantiates the similarities and differences with B cell development in mice. These differences become relevant when targeted therapeutic approaches are used in patients; therefore, predicting potential immunological adverse events is crucial. In this review, we have provided a phenotypical classification of human and murine early progenitors and B cell stages, based on surface and intracellular protein expression. Further, we have critically compared the role of key transcription factors (Ikaros, E2A, EBF1, PAX5, and Aiolos) and chemo- or cytokine signals (FLT3, c-kit, IL-7R, and CXCR4) during homeostatic and aberrant B lymphopoiesis in both humans and mice.
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Affiliation(s)
- Jakov Korzhenevich
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, 2333, ZA Leiden, The Netherlands
| | - Marta Rizzi
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria; Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany; Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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6
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Boast B, Goel S, González-Granado LI, Niemela J, Stoddard J, Edwards ESJ, Seneviratne S, Spensberger D, Quesada-Espinosa JF, Allende LM, McDonnell J, Haseley A, Lesmana H, Walkiewicz MA, Muhammad E, Bosco JJ, Fleisher TA, Cohen S, Holland SM, van Zelm MC, Enders A, Kuehn HS, Rosenzweig SD. TCF3 haploinsufficiency defined by immune, clinical, gene-dosage, and murine studies. J Allergy Clin Immunol 2023; 152:736-747. [PMID: 37277074 PMCID: PMC10527523 DOI: 10.1016/j.jaci.2023.05.017] [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: 03/22/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND TCF3 is a transcription factor contributing to early lymphocyte differentiation. Germline monoallelic dominant negative and biallelic loss-of-function (LOF) null TCF3 mutations cause a fully penetrant severe immunodeficiency. We identified 8 individuals from 7 unrelated families with monoallelic LOF TCF3 variants presenting with immunodeficiency with incomplete clinical penetrance. OBJECTIVE We sought to define TCF3 haploinsufficiency (HI) biology and its association with immunodeficiency. METHODS Patient clinical data and blood samples were analyzed. Flow cytometry, Western blot analysis, plasmablast differentiation, immunoglobulin secretion, and transcriptional activity studies were conducted on individuals carrying TCF3 variants. Mice with a heterozygous Tcf3 deletion were analyzed for lymphocyte development and phenotyping. RESULTS Individuals carrying monoallelic LOF TCF3 variants showed B-cell defects (eg, reduced total, class-switched memory, and/or plasmablasts) and reduced serum immunoglobulin levels; most but not all presented with recurrent but nonsevere infections. These TCF3 LOF variants were either not transcribed or translated, resulting in reduced wild-type TCF3 protein expression, strongly suggesting HI pathophysiology for the disease. Targeted RNA sequencing analysis of T-cell blasts from TCF3-null, dominant negative, or HI individuals clustered away from healthy donors, implying that 2 WT copies of TCF3 are needed to sustain a tightly regulated TCF3 gene-dosage effect. Murine TCF3 HI resulted in a reduction of circulating B cells but overall normal humoral immune responses. CONCLUSION Monoallelic LOF TCF3 mutations cause a gene-dosage-dependent reduction in wild-type protein expression, B-cell defects, and a dysregulated transcriptome, resulting in immunodeficiency. Tcf3+/- mice partially recapitulate the human phenotype, underscoring the differences between TCF3 in humans and mice.
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Affiliation(s)
- Brigette Boast
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Shubham Goel
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Luis I González-Granado
- Department of Pediatrics, Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), School of Medicine, Complutense University, Madrid, Spain
| | - Julie Niemela
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Emily S J Edwards
- Department of Immunology, Monash University, and The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia
| | - Sandali Seneviratne
- Centre for Personalised Immunology and Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Dominik Spensberger
- ANU Gene Targeting Facility, Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | | - Luis M Allende
- Department of Immunology, Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - John McDonnell
- Department of Pediatric Allergy and Immunology, Cleveland Clinic, Cleveland, Ohio
| | - Alexandria Haseley
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Harry Lesmana
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio; Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Cleveland Clinic, Cleveland, Ohio
| | - Magdalena A Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Emad Muhammad
- Hematology Laboratory, Carmel Medical Center, Haifa, Spain
| | - Julian J Bosco
- Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, Australia
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Shai Cohen
- Allergy and Clinical Immunology Service, Department of Internal Medicine B, Lin and Carmel Medical Center, The Technion, Israel Institute of Technology, Haifa, Israel
| | - Steven M Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Menno C van Zelm
- Department of Immunology, Monash University, and The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia; Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, Australia
| | - Anselm Enders
- Centre for Personalised Immunology and Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md.
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7
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Goodlad JR, Xiao W, Amador C, Cook JR, Happ L, Thakkar D, Dave S, Dogan A, Duffield A, Nejati R, Ott G, Wasik M, Czader M. Phenotypic and genotypic infidelity in B-lineage neoplasms, including transdifferentiation following targeted therapy: Report from the 2021 SH/EAHP Workshop. Am J Clin Pathol 2023:7135991. [PMID: 37085149 DOI: 10.1093/ajcp/aqad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES Session 2 of the 2021 Society for Hematopathology and European Association for Haematopathology Workshop collected examples of lineage infidelity and transdifferentiation in B-lineage neoplasms, including after targeted therapy. METHODS Twenty cases were submitted. Whole-exome sequencing and genome-wide RNA expression analysis were available on a limited subsample. RESULTS A diagnosis of B-cell acute lymphoblastic leukemia (B-ALL) was rendered on at least 1 biopsy from 13 patients. There was 1 case of acute myeloid leukemia (AML); the remaining 6 cases were mature B-cell neoplasms. Targeted therapy was administered in 7 cases of B-ALL and 4 cases of mature B-cell neoplasms. Six cases of B-ALL underwent lineage switch to AML or mixed-phenotype acute leukemia at relapse, 5 of which had rearranged KMT2A. Changes in maturational state without lineage switch were observed in 2 cases. Examples of de novo aberrant T-cell antigen expression (n = 2) were seen among the mature B-cell lymphoma cohort, and their presence correlated with alterations in tumor cell gene expression patterns. CONCLUSIONS This cohort of cases enabled us to illustrate, discuss, and review current concepts of lineage switch and aberrant antigen expression in a variety of B-cell neoplasms and draw attention to the role targeted therapies may have in predisposing neoplasms to transdifferentiation as well as other, less expected changes in maturational status.
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Affiliation(s)
- John R Goodlad
- Department of Pathology, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Catalina Amador
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, US
| | - James R Cook
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, US
| | | | | | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University School of Medicine, Durham, NC, US
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Amy Duffield
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, US
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8
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Wang S, Li H, Lian Z, Deng S. The Role of m 6A Modifications in B-Cell Development and B-Cell-Related Diseases. Int J Mol Sci 2023; 24:4721. [PMID: 36902149 PMCID: PMC10003095 DOI: 10.3390/ijms24054721] [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: 12/10/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
B cells are a class of professional antigen-presenting cells that produce antibodies to mediate humoral immune response and participate in immune regulation. m6A modification is the most common RNA modification in mRNA; it involves almost all aspects of RNA metabolism and can affect RNA splicing, translation, stability, etc. This review focuses on the B-cell maturation process as well as the role of three m6A modification-related regulators-writer, eraser, and reader-in B-cell development and B-cell-related diseases. The identification of genes and modifiers that contribute to immune deficiency may shed light on regulatory requirements for normal B-cell development and the underlying mechanism of some common diseases.
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Affiliation(s)
- Shuqi Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huanxiang Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
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9
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Ding Y, Harly C, Das A, Bhandoola A. Early Development of Innate Lymphoid Cells. Methods Mol Biol 2023; 2580:51-69. [PMID: 36374450 DOI: 10.1007/978-1-0716-2740-2_3] [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] [Indexed: 06/16/2023]
Abstract
Innate lymphoid cells (ILCs) are transcriptionally and functionally similar to T cells but lack adaptive antigen receptors. They play critical roles in early defense against pathogens. In this review, we summarize recent discoveries of ILC progenitors and discuss possible mechanisms that separate ILCs from T cells. We consider mechanisms of lineage specification in early ILC development and also examine whether differences exist between adult and fetal ILC development.
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Affiliation(s)
- Yi Ding
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
| | | | - Arundhoti Das
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
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10
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Montoliu L. Transgenesis and Genome Engineering: A Historical Review. Methods Mol Biol 2023; 2631:1-32. [PMID: 36995662 DOI: 10.1007/978-1-0716-2990-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Our ability to modify DNA molecules and to introduce them into mammalian cells or embryos almost appears in parallel, starting from the 1970s of the last century. Genetic engineering techniques rapidly developed between 1970 and 1980. In contrast, robust procedures to microinject or introduce DNA constructs into individuals did not take off until 1980 and evolved during the following two decades. For some years, it was only possible to add transgenes, de novo, of different formats, including artificial chromosomes, in a variety of vertebrate species or to introduce specific mutations essentially in mice, thanks to the gene-targeting methods by homologous recombination approaches using mouse embryonic stem (ES) cells. Eventually, genome-editing tools brought the possibility to add or inactivate DNA sequences, at specific sites, at will, irrespective of the animal species involved. Together with a variety of additional techniques, this chapter will summarize the milestones in the transgenesis and genome engineering fields from the 1970s to date.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.
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11
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Sigvardsson M, Kee BL, Zúñiga-Pflücker JC, Anderson MK. Editorial: Molecular switches of the immune system: The E-protein/Id axis in hematopoietic development and function. Front Immunol 2022; 13:1062734. [DOI: 10.3389/fimmu.2022.1062734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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12
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Miyazaki M, Miyazaki K. The E-Id Axis Specifies Adaptive and Innate Lymphoid Lineage Cell Fates. J Biochem 2022; 172:259-264. [PMID: 36000775 DOI: 10.1093/jb/mvac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Our bodies are constantly threatened with the invasion of pathogens, such as bacteria and virus. Immune responses against pathogens are evoked in collaboration with adaptive and innate immune systems. Adaptive immune cells including T and B cells recognize various antigens from pathogens through the antigen recognition receptors such as Immunoglobulin (Ig) and T cell receptor (TCR), and they evoke antigen-specific immune responses to eliminate the pathogens. This specific recognition of a variety of antigens relies on the V(D)J DNA recombination of Ig and TCR genes, which is generated by the Rag (recombination activation gene) 1/Rag2 protein complex. The expression of Rag1/2 genes are stringently controlled during the T and B cell development; Rag1/2 gene expression indicates the commitment towards adaptive lymphocyte lineages. In this review article, we will discuss the developmental bifurcation between adaptive and innate lymphoid cells, and the role of transcription factors, especially the E and Id proteins, upon the lineage commitment, and the regulation of Rag gene locus.
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Affiliation(s)
- Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
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13
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Parriott G, Kee BL. E Protein Transcription Factors as Suppressors of T Lymphocyte Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:885144. [PMID: 35514954 PMCID: PMC9065262 DOI: 10.3389/fimmu.2022.885144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
T Lymphocyte Acute Lymphoblastic Leukemia (ALL) is an aggressive disease arising from transformation of T lymphocytes during their development. The mutation spectrum of T-ALL has revealed critical regulators of the growth and differentiation of normal and leukemic T lymphocytes. Approximately, 60% of T-ALLs show aberrant expression of the hematopoietic stem cell-associated helix-loop-helix transcription factors TAL1 and LYL1. TAL1 and LYL1 function in multiprotein complexes that regulate gene expression in T-ALL but they also antagonize the function of the E protein homodimers that are critical regulators of T cell development. Mice lacking E2A, or ectopically expressing TAL1, LYL1, or other inhibitors of E protein function in T cell progenitors, also succumb to an aggressive T-ALL-like disease highlighting that E proteins promote T cell development and suppress leukemogenesis. In this review, we discuss the role of E2A in T cell development and how alterations in E protein function underlie leukemogenesis. We focus on the role of TAL1 and LYL1 and the genes that are dysregulated in E2a-/- T cell progenitors that contribute to human T-ALL. These studies reveal novel mechanisms of transformation and provide insights into potential therapeutic targets for intervention in this disease.
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Affiliation(s)
- Geoffrey Parriott
- Committee on Immunology, University of Chicago, Chicago, IL, United States
| | - Barbara L Kee
- Committee on Immunology, University of Chicago, Chicago, IL, United States.,Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.,Department of Pathology, University of Chicago, Chicago, IL, United States
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14
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ILC Differentiation in the Thymus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1365:25-39. [DOI: 10.1007/978-981-16-8387-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Häfliger IM, Seefried FR, Spengeler M, Drögemüller C. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 2021; 53:95. [PMID: 34915862 PMCID: PMC8675516 DOI: 10.1186/s12711-021-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00686-3.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | | | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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16
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Zhou Y, Murre C. Bursty gene expression and mRNA decay pathways orchestrate B cell activation. SCIENCE ADVANCES 2021; 7:eabm0819. [PMID: 34860551 PMCID: PMC8641932 DOI: 10.1126/sciadv.abm0819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
It is well established that the helix-loop-helix proteins, E2A and E2-2, promote B cell activation. Here, we examined how during the course of B cell activation E2A and E2-2 gene expression is regulated. We found that E2A and E2-2 mRNA abundance concomitantly increased in activated B cells. The increase in E2A and E2-2 mRNA abundance correlated with increased cell growth. Elevated E2A and E2-2 mRNA abundance was instructed by increased transcriptional bursting frequencies and elevated E2A and E2-2 mRNA half-lives. The increase in E2A and E2-2 bursting frequencies often occurred at shared interchromosomal transcriptional hubs. We suggest that in naïve B cells low E2A and E2-2 bursting frequencies and high E2A and E2-2 mRNA decay rates instruct noisy gene expression that allows a clonal and swift response to invading pathogens whereas in activated B cells increased transcriptional bursting and low mRNA decay rates dictate an activated B lineage gene program.
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Affiliation(s)
- Yi Zhou
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92039, USA
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17
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Park S, Zhu X, Kim M, Zhao L, Cheng SY. Thyroid Hormone Receptor α1 Mutants Impair B Lymphocyte Development in a Mouse Model. Thyroid 2021; 31:994-1002. [PMID: 33267733 PMCID: PMC8349714 DOI: 10.1089/thy.2019.0782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Mutations of the thyroid hormone receptor α (THRA) gene cause resistance to thyroid hormone (RTHα). RTHα patients exhibit very mild abnormal thyroid function test results (serum triiodothyronine can be high-normal to high; thyroxine normal to low; thyrotropin is normal or mildly raised) but manifest hypothyroid symptoms with growth retardation, delayed bone development, and anemia. Much has been learned about the in vivo molecular actions in TRα1 mutants affecting abnormal growth, bone development, and anemia by using a mouse model of RTHα (Thra1PV/+ mice). However, it is not clear whether TRα1 mutants affect lymphopoiesis in RTHα patients. The present study addressed the question of whether TRα1 mutants could cause defective lymphopoiesis. Methods: We assessed lymphocyte abundance in the peripheral circulation and in the lymphoid organs of Thra1PV/+ mice. We evaluated the effect of thyroid hormone on B cell development in the bone and spleen of these mice. We identified key transcription factors that are directly regulated by TRα1 in the regulation of B cell development. Results: Compared with wild-type mice, a significant reduction in B cells, but not in T cells, was detected in the peripheral circulation, bone marrow, and spleen of Thra1PV/+ mice. The expression of key transcription regulators of B cell development, such as Ebf1, Tcf3, and Pax5, was significantly decreased in the bone marrow and spleen of Thra1PV/+ mice. We further elucidated that the Ebf1 gene, essential for lineage specification in the early B cell development, was directly regulated by TRα1. Thus, mutations of TRα1 could impair B cell development in the bone marrow via suppression of key regulators of B lymphopoiesis. Conclusions: Analysis of lymphopoiesis in a mouse model of RTHα showed that B cell lymphopoiesis was suppressed by TRα1 mutations. The suppressed development of B cells was, at least in part, via inhibition of the expression of key regulators, Ebf1, Tcf3, and Pax5, by TRα1 mutations. These findings suggest that the mutations of the THRA gene in patients could lead to B cell deficiency.
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Affiliation(s)
- Sunmi Park
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xuguang Zhu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Minjun Kim
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Li Zhao
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sheue-Yann Cheng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Address correspondence to: Sheue-Yann Cheng, PhD, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room: 5128A2, 37 Convent Drive MSC 4264, Bethesda, MD 20892-4264, USA
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18
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Sun L, Zhao X, Liu X, Zhong B, Tang H, Jin W, Clevers H, Wang H, Wang X, Dong C. Transcription factor Ascl2 promotes germinal center B cell responses by directly regulating AID transcription. Cell Rep 2021; 35:109188. [PMID: 34077723 DOI: 10.1016/j.celrep.2021.109188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/14/2020] [Accepted: 05/07/2021] [Indexed: 11/24/2022] Open
Abstract
During germinal center (GC) reactions, activated B cells undergo clonal expansion and functional maturation to produce high-affinity antibodies and differentiate into plasma and memory cells, accompanied with class-switching recombination (CSR) and somatic hypermutation (SHM). Activation-induced cytidine deaminase (AID) is responsible for both CSR and SHM in GC B cells. Transcriptional mechanisms underlying AID regulation and GC B cell reactions are still not well understood. Here, we show that expression of Ascl2 transcription factor is upregulated in GC B cells. Ectopic expression of Ascl2 promotes GC B cell development and enhances antibody production and affinity maturation. Conversely, deletion of Ascl2 in B cells impairs the GC response. Genome-wide analysis reveals that Ascl2 directly regulates GC B cell-related genes, including AID; ectopic expression of AID in Ascl2-deficient B cells rescues their antibody defects. Thus, Ascl2 regulates AID transcription and promotes GC B cell responses.
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Affiliation(s)
- Lin Sun
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Science, Beijing 100084, China
| | - Xiaohong Zhao
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xindong Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Bo Zhong
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hong Tang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Beijing, China
| | - Wei Jin
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hui Wang
- Department of Immunology and Center for Inflammation and Cancer, MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Beijing Key Lab for Immunological Research on Chronic Diseases, Beijing 100084, China.
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19
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Yoshikawa G, Miyazaki K, Ogata H, Miyazaki M. The Evolution of Rag Gene Enhancers and Transcription Factor E and Id Proteins in the Adaptive Immune System. Int J Mol Sci 2021; 22:ijms22115888. [PMID: 34072618 PMCID: PMC8199221 DOI: 10.3390/ijms22115888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive immunity relies on the V(D)J DNA recombination of immunoglobulin (Ig) and T cell receptor (TCR) genes, which enables the recognition of highly diverse antigens and the elicitation of antigen-specific immune responses. This process is mediated by recombination-activating gene (Rag) 1 and Rag2 (Rag1/2), whose expression is strictly controlled in a cell type-specific manner; the expression of Rag1/2 genes represents a hallmark of lymphoid lineage commitment. Although Rag genes are known to be evolutionally conserved among jawed vertebrates, how Rag genes are regulated by lineage-specific transcription factors (TFs) and how their regulatory system evolved among vertebrates have not been fully elucidated. Here, we reviewed the current body of knowledge concerning the cis-regulatory elements (CREs) of Rag genes and the evolution of the basic helix-loop-helix TF E protein regulating Rag gene CREs, as well as the evolution of the antagonist of this protein, the Id protein. This may help to understand how the adaptive immune system develops along with the evolution of responsible TFs and enhancers.
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Affiliation(s)
- Genki Yoshikawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan;
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan;
- Correspondence: (H.O.); (M.M.)
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
- Correspondence: (H.O.); (M.M.)
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20
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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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21
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Yi S, Huang X, Zhou S, Zhou Y, Anderson MK, Zúñiga-Pflücker JC, Luan Q, Li Y. E2A regulates neural ectoderm fate specification in human embryonic stem cells. Development 2020; 147:dev.190298. [PMID: 33144398 DOI: 10.1242/dev.190298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
E protein transcription factors are crucial for many cell fate decisions. However, the roles of E proteins in the germ-layer specification of human embryonic stem cells (hESCs) are poorly understood. We disrupted the TCF3 gene locus to delete the E protein E2A in hESCs. E2A knockout (KO) hESCs retained key features of pluripotency, but displayed decreased neural ectoderm coupled with enhanced mesoendoderm outcomes. Genome-wide analyses showed that E2A directly regulates neural ectoderm and Nodal pathway genes. Accordingly, inhibition of Nodal or E2A overexpression partially rescued the neural ectoderm defect in E2A KO hESCs. Loss of E2A had little impact on the epigenetic landscape of hESCs, whereas E2A KO neural precursors displayed increased accessibility of the gene locus encoding the Nodal agonist CRIPTO. Double-deletion of both E2A and HEB (TCF12) resulted in a more severe neural ectoderm defect. Therefore, this study reveals critical context-dependent functions for E2A in human neural ectoderm fate specification.
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Affiliation(s)
- Siqi Yi
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China.,Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Xiaotian Huang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Shixin Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | | | - Qingxian Luan
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
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22
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Ha TC, Stahlhut M, Rothe M, Paul G, Dziadek V, Morgan M, Brugman M, Fehse B, Kustikova O, Schambach A, Baum C. Multiple Genes Surrounding Bcl-xL, a Common Retroviral Insertion Site, Can Influence Hematopoiesis Individually or in Concert. Hum Gene Ther 2020; 32:458-472. [PMID: 33012194 DOI: 10.1089/hum.2019.344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Retroviral insertional mutagenesis (RIM) is both a relevant risk in gene therapy and a powerful tool for identifying genes that enhance the competitiveness of repopulating hematopoietic stem and progenitor cells (HSPCs). However, focusing only on the gene closest to the retroviral vector insertion site (RVIS) may underestimate the effects of RIM, as dysregulation of distal and/or multiple genes by a single insertion event was reported in several studies. As a proof of concept, we examined the common insertion site (CIS) Bcl-xL, which revealed seven genes located within ±150 kb from the RVIS for our study. We confirmed that Bcl-xL enhanced the competitiveness of HSPCs, whereas the Bcl-xL neighbor Id1 hindered HSPC long-term repopulation. This negative influence of Id1 could be counteracted by co-expressing Bcl-xL. Interestingly, >90% of early reconstituted myeloid cells were found to originate from transduced HSPCs upon simultaneous overexpression of Bcl-xL and Id1, which implies that Bcl-xL and Id1 can collaborate to rapidly replenish the myeloid compartment under stress conditions. To directly compare the competitiveness of HSPCs conveyed by multiple transgenes, we developed a multiple competitor competitive repopulation (MCCR) assay to simultaneously screen effects on HSPC repopulating capacity in a single mouse. The MCCR assay revealed that multiple genes within a CIS can have positive or negative impact on hematopoiesis. Furthermore, these data highlight the importance of studying multiple genes located within the proximity of an insertion site to understand complex biological effects, especially as the number of gene therapy patients increases.
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Affiliation(s)
- Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany.,Hannover Biomedical Research School, Hannover, Germany
| | - Maike Stahlhut
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Gabi Paul
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Violetta Dziadek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Martijn Brugman
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center (UKE) Hamburg-Eppendorf, Hamburg, Germany
| | - Olga Kustikova
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Baum
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
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23
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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24
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Miyazaki K, Watanabe H, Yoshikawa G, Chen K, Hidaka R, Aitani Y, Osawa K, Takeda R, Ochi Y, Tani-Ichi S, Uehata T, Takeuchi O, Ikuta K, Ogawa S, Kondoh G, Lin YC, Ogata H, Miyazaki M. The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells. Sci Immunol 2020; 5:5/51/eabb1455. [PMID: 32887843 DOI: 10.1126/sciimmunol.abb1455] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/21/2020] [Indexed: 01/09/2023]
Abstract
Cell type-specific gene expression is driven by the interplay between lineage-specific transcription factors and cis-regulatory elements to which they bind. Adaptive immunity relies on RAG-mediated assembly of T cell receptor (TCR) and immunoglobulin (Ig) genes. Although Rag1 and Rag2 expression is largely restricted to adaptive lymphoid lineage cells, it remains unclear how Rag gene expression is regulated in a cell lineage-specific manner. Here, we identified three distinct cis-regulatory elements, a T cell lineage-specific enhancer (R-TEn) and the two B cell-specific elements, R1B and R2B By generating mice lacking either R-TEn or R1B and R2B, we demonstrate that these distinct sets of regulatory elements drive the expression of Rag genes in developing T and B cells. What these elements have in common is their ability to bind the transcription factor E2A. By generating a mouse strain that carries a mutation within the E2A binding site of R-TEn, we demonstrate that recruitment of E2A to this site is essential for orchestrating changes in chromatin conformation that drive expression of Rag genes in T cells. By mapping cis-regulatory elements and generating multiple mouse strains lacking distinct enhancer elements, we demonstrate expression of Rag genes in developing T and B cells to be driven by distinct sets of E2A-dependent cis-regulatory modules.
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Affiliation(s)
- Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Genki Yoshikawa
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Kenian Chen
- Baylor Institute for Immunology Research, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Reiko Hidaka
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yuki Aitani
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Kai Osawa
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Rie Takeda
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shizue Tani-Ichi
- Laboratory of Immune Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Institute for the Advanced Study of Human Biology (WPI ASHBi), Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Gen Kondoh
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yin C Lin
- Baylor Institute for Immunology Research, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.
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25
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Pi WC, Wang J, Shimada M, Lin JW, Geng H, Lee YL, Lu R, Li D, Wang GG, Roeder RG, Chen WY. E2A-PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia. Blood 2020; 136:11-23. [PMID: 32276273 PMCID: PMC7332894 DOI: 10.1182/blood.2019003312] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/05/2020] [Indexed: 12/13/2022] Open
Abstract
E2A, a basic helix-loop-helix transcription factor, plays a crucial role in determining tissue-specific cell fate, including differentiation of B-cell lineages. In 5% of childhood acute lymphoblastic leukemia (ALL), the t(1,19) chromosomal translocation specifically targets the E2A gene and produces an oncogenic E2A-PBX1 fusion protein. Although previous studies have shown the oncogenic functions of E2A-PBX1 in cell and animal models, the E2A-PBX1-enforced cistrome, the E2A-PBX1 interactome, and related mechanisms underlying leukemogenesis remain unclear. Here, by unbiased genomic profiling approaches, we identify the direct target sites of E2A-PBX1 in t(1,19)-positive pre-B ALL cells and show that, compared with normal E2A, E2A-PBX1 preferentially binds to a subset of gene loci cobound by RUNX1 and gene-activating machineries (p300, MED1, and H3K27 acetylation). Using biochemical analyses, we further document a direct interaction of E2A-PBX1, through a region spanning the PBX1 homeodomain, with RUNX1. Our results also show that E2A-PBX1 binding to gene enhancers is dependent on the RUNX1 interaction but not the DNA-binding activity harbored within the PBX1 homeodomain of E2A-PBX1. Transcriptome analyses and cell transformation assays further establish a significant RUNX1 requirement for E2A-PBX1-mediated target gene activation and leukemogenesis. Notably, the RUNX1 locus itself is also directly activated by E2A-PBX1, indicating a multilayered interplay between E2A-PBX1 and RUNX1. Collectively, our study provides the first unbiased profiling of the E2A-PBX1 cistrome in pre-B ALL cells and reveals a previously unappreciated pathway in which E2A-PBX1 acts in concert with RUNX1 to enforce transcriptome alterations for the development of pre-B ALL.
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MESH Headings
- Amino Acid Motifs
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Core Binding Factor Alpha 2 Subunit/chemistry
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/physiology
- DNA/metabolism
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic/genetics
- Histone Code
- Homeodomain Proteins/chemistry
- Homeodomain Proteins/physiology
- Humans
- Mediator Complex/metabolism
- Neoplasm Proteins/metabolism
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/physiology
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Domains
- Protein Interaction Mapping
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Structure-Activity Relationship
- Transcriptome
- p300-CBP Transcription Factors/metabolism
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Affiliation(s)
- Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology and
- Biomedical Industry PhD Program, National Yang-Ming University, Taipei, Taiwan
| | - Jun Wang
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY
| | - Jia-Wei Lin
- Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Huimin Geng
- Laboratory Medicine, UCSF School of Medicine, San Francisco, CA; and
| | - Yu-Ling Lee
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY
| | - Rui Lu
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology and
- Biomedical Industry PhD Program, National Yang-Ming University, Taipei, Taiwan
- Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan
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26
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Rao C, Malaguti M, Mason JO, Lowell S. The transcription factor E2A drives neural differentiation in pluripotent cells. Development 2020; 147:dev184093. [PMID: 32487737 PMCID: PMC7328008 DOI: 10.1242/dev.184093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of inhibitor of differentiation (Id) factors. We have previously identified the major binding partner of Id proteins in pluripotent cells as the basic helix-loop-helix (bHLH) transcription factor (TF) E2A. Id1 can prevent E2A from forming heterodimers with bHLH TFs or from forming homodimers. Here, we show that overexpression of a forced E2A homodimer is sufficient to drive robust neural commitment in pluripotent cells, even under non-permissive conditions. Conversely, we find that E2A null cells display a defect in their neural differentiation capacity. E2A acts as an upstream activator of neural lineage genes, including Sox1 and Foxd4, and as a repressor of Nodal signalling. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.
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Affiliation(s)
- Chandrika Rao
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Mattias Malaguti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - John O Mason
- Centre for Discovery Brain Sciences, University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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27
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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28
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Oudinet C, Braikia FZ, Dauba A, Khamlichi AA. Recombination may occur in the absence of transcription in the immunoglobulin heavy chain recombination centre. Nucleic Acids Res 2020; 48:3553-3566. [PMID: 32086526 PMCID: PMC7144927 DOI: 10.1093/nar/gkaa108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/06/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Developing B cells undergo V(D)J recombination to generate a vast repertoire of Ig molecules. V(D)J recombination is initiated by the RAG1/RAG2 complex in recombination centres (RCs), where gene segments become accessible to the complex. Whether transcription is the causal factor of accessibility or whether it is a side product of other processes that generate accessibility remains a controversial issue. At the IgH locus, V(D)J recombination is controlled by Eμ enhancer, which directs the transcriptional, epigenetic and recombinational events in the IgH RC. Deletion of Eμ enhancer affects both transcription and recombination, making it difficult to conclude if Eμ controls the two processes through the same or different mechanisms. By using a mouse line carrying a CpG-rich sequence upstream of Eμ enhancer and analyzing transcription and recombination at the single-cell level, we found that recombination could occur in the RC in the absence of detectable transcription, suggesting that Eμ controls transcription and recombination through distinct mechanisms. Moreover, while the normally Eμ-dependent transcription and demethylating activities were impaired, recruitment of chromatin remodeling complexes was unaffected. RAG1 was efficiently recruited, thus compensating for the defective transcription-associated recruitment of RAG2, and providing a mechanistic basis for RAG1/RAG2 assembly to initiate V(D)J recombination.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
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29
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Lejman M, Włodarczyk M, Zawitkowska J, Kowalczyk JR. Comprehensive chromosomal aberrations in a case of a patient with TCF3-HLF-positive BCP-ALL. BMC Med Genomics 2020; 13:58. [PMID: 32245383 PMCID: PMC7118981 DOI: 10.1186/s12920-020-0709-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/24/2020] [Indexed: 12/16/2022] Open
Abstract
Background The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. The TCF3-HLF fusion gene product acts as a transcriptional factor leading to the dedifferentiation of mature B lymphocytes into an immature state (lymphoid stem cells). This process initiates the formation of pre-leukaemic cells. Due to the rarity of this chromosomal aberration, only a few cases have been described in the literature. The advantage of this work is the presentation of an interesting case of clonal evolution of cancer cells and the cumulative implications (diagnostic and prognostic) of the patient’s genetic alterations. Case presentation This work presents a patient with diagnosed with TCF3-HLF-positive ALL. Moreover, the additional genetic alterations, which play a key role in the pathogenesis of ALL, were detected in this patient: deletion of a fragment from the long arm of chromosome 13 (13q12.2-q21.1) containing the RB1 gene, intragenic deletions within the PAX5 gene and NOTCH1 intragenic duplication. Conclusions A patient with coexistence of chromosomal alterations and the TCF3-HLF fusion has not yet been described. Identifying all these chromosomal aberrations at the time of diagnosis could be sufficient to determine the cumulative effects of the described deletions on the activity of other oncogenes or tumour suppressors, as well as on the clinical course of the disease. On the other hand, complex changes in the patient’s karyotype and clonal evolution of cancer cells call into question the effectiveness of experimental therapy.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, ul. Antoniego Gębali 6, Lublin, Poland.
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
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30
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Elsaid R, Yang J, Cumano A. The influence of space and time on the establishment of B cell identity. Biomed J 2019; 42:209-217. [PMID: 31627863 PMCID: PMC6818146 DOI: 10.1016/j.bj.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/21/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023] Open
Abstract
During embryonic development multiple waves of hematopoietic progenitors with distinct lineage potential are differentially regulated in time and space. Consistent with this view, some specialized lymphocytes emerge during a limited time-window in embryogenesis and migrate to the tissues where they contribute to organogenesis and to tissue homeostasis. These cells are not constantly produced by bone marrow derived hematopoietic stem cells but are maintained in tissues and self-renew throughout life. These particular cell subsets are produced from lymphoid restricted progenitors only found in the first days of fetal liver hematopoietic activity. Growing evidence of the heterogeneity and layered organization of the hematopoietic system is leading to a common view that some lymphocyte subsets are functionally different because they follow distinct developmental programs and emerge from distinct waves of lymphoid progenitors. However, understanding the influence of developmental origin and the relative contribution of local microenvironment on the development of these specialized lymphocyte subsets needs further analysis. In this review, we discuss how different pathways followed by developing B cells during ontogeny may contribute to the diverse functions.
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Affiliation(s)
- Ramy Elsaid
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Junjie Yang
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; CNBG Company, China
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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31
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Qian L, Bajana S, Georgescu C, Peng V, Wang HC, Adrianto I, Colonna M, Alberola-Ila J, Wren JD, Sun XH. Suppression of ILC2 differentiation from committed T cell precursors by E protein transcription factors. J Exp Med 2019; 216:884-899. [PMID: 30898894 PMCID: PMC6446881 DOI: 10.1084/jem.20182100] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/24/2019] [Accepted: 02/15/2019] [Indexed: 01/21/2023] Open
Abstract
Qian et al. shows that ILC2s can be generated from not only thymic multipotent progenitors but also committed T cell precursors. These processes are greatly suppressed by E protein transcription factors. Thymic ILC2s show functional differences from those made elsewhere. Current models propose that group 2 innate lymphoid cells (ILC2s) are generated in the bone marrow. Here, we demonstrate that subsets of these cells can differentiate from multipotent progenitors and committed T cell precursors in the thymus, both in vivo and in vitro. These thymic ILC2s exit the thymus, circulate in the blood, and home to peripheral tissues. Ablation of E protein transcription factors greatly promotes the ILC fate while impairing B and T cell development. Consistently, a transcriptional network centered on the ZBTB16 transcription factor and IL-4 signaling pathway is highly up-regulated due to E protein deficiency. Our results show that ILC2 can still arise from what are normally considered to be committed T cell precursors, and that this alternative cell fate is restrained by high levels of E protein activity in these cells. Thymus-derived lung ILC2s of E protein–deficient mice show different transcriptomes, proliferative properties, and cytokine responses from wild-type counterparts, suggesting potentially distinct functions.
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Affiliation(s)
- Liangyue Qian
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK
| | - Sandra Bajana
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK
| | - Constantin Georgescu
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Hong-Cheng Wang
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK
| | - Indra Adrianto
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK.,Department of Public Health Sciences, Henry Ford Health System, Detroit, MI
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Jose Alberola-Ila
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jonathan D Wren
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK
| | - Xiao-Hong Sun
- Oklahoma Medical Research Foundation, Program in Arthritis and Clinical Immunology, Oklahoma City, OK .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK.,Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
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32
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Abstract
Hematopoiesis is the process by which mature blood and immune cells are produced from hematopoietic stem and progenitor cells (HSCs and HSPCs). The last several decades of research have shed light on the origin of HSCs, as well as the heterogeneous pools of fetal progenitors that contribute to lifelong hematopoiesis. The overarching concept that hematopoiesis occurs in dynamic, overlapping waves throughout development, with each wave contributing to both continuous and developmentally limited cell types, has been solidified over the years. However, recent advances in our ability to track the production of hematopoietic cells in vivo have challenged several long-held dogmas on the origin and persistence of distinct hematopoietic cell types. In this review, we highlight emerging concepts in hematopoietic development and identify unanswered questions.
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Affiliation(s)
- Taylor Cool
- Institute for the Biology of Stem Cells, Program in Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.
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33
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Abstract
In this review from Murre, the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed. Helix–loop–helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer–promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92903, USA
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34
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Mahdaviani SA, Rezaei N. Pulmonary Manifestations of Predominantly Antibody Deficiencies. PULMONARY MANIFESTATIONS OF PRIMARY IMMUNODEFICIENCY DISEASES 2019. [PMCID: PMC7123456 DOI: 10.1007/978-3-030-00880-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Predominantly antibody deficiencies (PADs) are the most frequent forms of primary immunodeficiency diseases (PIDs). Commonly accompanied with complications involving several body systems, immunoglobulin substitution therapy along with prophylactic antibiotics remained the cornerstone of treatment for PADs and related complications. Patients with respiratory complications should be prescribed an appropriate therapy as soon as possible and have to be adhering to more and longer medical therapies. Recent studies identified a gap for screening protocols to monitor respiratory manifestations in patients with PADs. In the present chapter, the pulmonary manifestations of different PADs for each have been discussed. The chapter is mainly focused on X-linked agammaglobulinemia, common variable immunodeficiency, activated PI3K-δ syndrome, LRBA deficiency, CD19 complex deficiencies, CD20 deficiency, other monogenic defects associated with hypogammaglobulinemia, immunoglobulin class switch recombination deficiencies affecting B-cells, transient hypogammaglobulinemia of infancy, and selective IgA deficiency.
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Affiliation(s)
- Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies Children’s Medical Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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35
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Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis. Proc Natl Acad Sci U S A 2018; 116:890-899. [PMID: 30593567 DOI: 10.1073/pnas.1809327116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The AML1-ETO fusion protein, generated by the t(8;21) chromosomal translocation, is causally involved in nearly 20% of acute myeloid leukemia (AML) cases. In leukemic cells, AML1-ETO resides in and functions through a stable protein complex, AML1-ETO-containing transcription factor complex (AETFC), that contains multiple transcription (co)factors. Among these AETFC components, HEB and E2A, two members of the ubiquitously expressed E proteins, directly interact with AML1-ETO, confer new DNA-binding capacity to AETFC, and are essential for leukemogenesis. However, the third E protein, E2-2, is specifically silenced in AML1-ETO-expressing leukemic cells, suggesting E2-2 as a negative factor of leukemogenesis. Indeed, ectopic expression of E2-2 selectively inhibits the growth of AML1-ETO-expressing leukemic cells, and this inhibition requires the bHLH DNA-binding domain. RNA-seq and ChIP-seq analyses reveal that, despite some overlap, the three E proteins differentially regulate many target genes. In particular, studies show that E2-2 both redistributes AETFC to, and activates, some genes associated with dendritic cell differentiation and represses MYC target genes. In AML patients, the expression of E2-2 is relatively lower in the t(8;21) subtype, and an E2-2 target gene, THPO, is identified as a potential predictor of relapse. In a mouse model of human t(8;21) leukemia, E2-2 suppression accelerates leukemogenesis. Taken together, these results reveal that, in contrast to HEB and E2A, which facilitate AML1-ETO-mediated leukemogenesis, E2-2 compromises the function of AETFC and negatively regulates leukemogenesis. The three E proteins thus define a heterogeneity of AETFC, which improves our understanding of the precise mechanism of leukemogenesis and assists development of diagnostic/therapeutic strategies.
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Iguchi T, Miyauchi E, Watanabe S, Masai H, Miyatake S. A BTB-ZF protein, ZNF131, is required for early B cell development. Biochem Biophys Res Commun 2018; 501:570-575. [PMID: 29750959 DOI: 10.1016/j.bbrc.2018.05.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/07/2018] [Indexed: 10/16/2022]
Abstract
Members of the BTB-ZF transcription factor family play important roles in lymphocyte development. During T cell development, ZNF131, a BTB-ZF protein, is critical for the double-negative (DN) to double-positive (DP) transition and is also involved in cell proliferation. Here, we report that knockout of Znf131 at the pre-pro-B cell stage in mb1-Cre knock-in mouse resulted in defect of pro-B to pre-B cell transition. ZNF131 was shown to be required for efficient pro-B cell proliferation as well as for immunoglobulin heavy chain gene rearrangement that occurs in the proliferating pro-B cells. We speculate that inefficient gene rearrangement may be due to loss of cell proliferation, since cell cycle progression and immunoglobulin gene rearrangement, which would occur in a mutually exclusive manner, may be interconnected or coupled to avoid occurrence of genomic instability. ZNF131 suppresses expression of Cdk inhibitor, p21cip1, and that of pro-apoptotic factors, Bax and Puma, targets of p53, to facilitate cell cycle progression and suppress unnecessary apoptosis, respectively, of pro-B cells. There results demonstrate the essential roles of ZNF131 in coordinating the B cell differentiation and proliferation.
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Affiliation(s)
- Tomohiro Iguchi
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Emako Miyauchi
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Shirokane-dai 4-6-1, Minatoku-ku, Tokyo 108-8639, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Shoichiro Miyatake
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan; Graduate School of Environmental Health Sciences, Azabu University, 1-17-71 Chuo-ku, Fuchinobe, Sagamihara, Kanagawa 252-5201, Japan.
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Bogutz AB, Oh-McGinnis R, Jacob KJ, Ho-Lau R, Gu T, Gertsenstein M, Nagy A, Lefebvre L. Transcription factor ASCL2 is required for development of the glycogen trophoblast cell lineage. PLoS Genet 2018; 14:e1007587. [PMID: 30096149 PMCID: PMC6105033 DOI: 10.1371/journal.pgen.1007587] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/22/2018] [Accepted: 07/24/2018] [Indexed: 12/22/2022] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor ASCL2 plays essential roles in diploid multipotent trophoblast progenitors, intestinal stem cells, follicular T-helper cells, as well as during epidermal development and myogenesis. During early development, Ascl2 expression is regulated by genomic imprinting and only the maternally inherited allele is transcriptionally active in trophoblast. The paternal allele-specific silencing of Ascl2 requires expression of the long non-coding RNA Kcnq1ot1 in cis and the deposition of repressive histone marks. Here we show that Del7AI, a 280-kb deletion allele neighboring Ascl2, interferes with this process in cis and leads to a partial loss of silencing at Ascl2. Genetic rescue experiments show that the low level of Ascl2 expression from the paternal Del7AI allele can rescue the embryonic lethality associated with maternally inherited Ascl2 mutations, in a level-dependent manner. Despite their ability to support development to term, the rescued placentae have a pronounced phenotype characterized by severe hypoplasia of the junctional zone, expansion of the parietal trophoblast giant cell layer, and complete absence of invasive glycogen trophoblast cells. Transcriptome analysis of ectoplacental cones at E7.5 and differentiation assays of Ascl2 mutant trophoblast stem cells show that ASCL2 is required for the emergence or early maintenance of glycogen trophoblast cells during development. Our work identifies a new cis-acting mutation interfering with Kcnq1ot1 silencing function and establishes a novel critical developmental role for the transcription factor ASCL2. By controlling precise networks of target genes, transcription factors play important roles in cell fate determination during development. The Ascl2 gene codes for a transcription factor essential for the maintenance of progenitor cell populations able to differentiate into specialized cell types in the intestine and in the extra-embryonic trophoblast lineage. The trophoblast is an essential component of the placenta, an organ required for development of the embryo in placental mammals. Ascl2 belongs to a group of unusual genes, called imprinted genes, which are expressed from only a single parental copy. Ascl2 is only expressed from the maternally inherited copy in the trophoblast, the paternal copy being kept silent. Here, we describe an engineered deletion neighboring Ascl2 that interferes with the complete silencing of the paternal copy of the gene. We show that the low amount of ASCL2 produced from this deletion can rescue the embryonic lethality associated with non-functional maternal copies of Ascl2. Although the rescued embryos can often survive to term, their placenta is highly disorganized and lacks members of a specific cell lineage, the trophoblast glycogen cells. By analyzing the transcriptional profile of mutant trophoblast progenitors in vivo and of differentiated trophoblast stem cells, we show that ASCL2 plays a very early role in the formation of this cell lineage.
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Affiliation(s)
- Aaron B. Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Rosemary Oh-McGinnis
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Karen J. Jacob
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Rita Ho-Lau
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ting Gu
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Marina Gertsenstein
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
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Qureshi S, Sheikh MDA, Qamar FN. Autosomal Recessive Agammaglobulinemia - first case with a novel TCF3 mutation from Pakistan. Clin Immunol 2018; 198:100-101. [PMID: 30063982 DOI: 10.1016/j.clim.2018.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 11/26/2022]
Abstract
Autosomal Recessive Agammaglobulinemia (ARA) is an uncommon type of primary immunodeficiency characterized by mutations in genes responsible for early B cell differentiation and function. One such gene is the TCF3 gene, which encodes a transcription factor important for immunoglobulin gene expression. We present the case of a 9 year old girl with history of diarrhea and recurrent pneumonias. Laboratory investigation showed significantly reduced levels of immunoglobulins along with a significant fall in the number of CD19+ cells. Genetic analysis identified a TCF3 gene base deletion covering exons 5-11.
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Affiliation(s)
- Sonia Qureshi
- Department of Pediatric and Child Health, Aga Khan University Hospital, Pakistan
| | | | - Farah Naz Qamar
- Department of Pediatric and Child Health, Aga Khan University Hospital, Pakistan.
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Paradoxical role of Id proteins in regulating tumorigenic potential of lymphoid cells. Front Med 2018; 12:374-386. [PMID: 30043222 DOI: 10.1007/s11684-018-0652-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
A family of transcription factors known as Id proteins, or inhibitor of DNA binding and differentiation, is capable of regulating cell proliferation, survival and differentiation, and is often upregulated in multiple types of tumors. Due to their ability to promote self-renewal, Id proteins have been considered as oncogenes, and potential therapeutic targets in cancer models. On the contrary, certain Id proteins are reported to act as tumor suppressors in the development of Burkitt's lymphoma in humans, and hepatosplenic and innate-like T cell lymphomas in mice. The contexts and mechanisms by which Id proteins can serve in such contradictory roles to determine tumor outcomes are still not well understood. In this review, we explore the roles of Id proteins in lymphocyte development and tumorigenesis, particularly with respect to inhibition of their canonical DNA binding partners known as E proteins. Transcriptional regulation by E proteins, and their antagonism by Id proteins, act as gatekeepers to ensure appropriate lymphocyte development at key checkpoints. We re-examine the derailment of these regulatory mechanisms in lymphocytes that facilitate tumor development. These mechanistic insights can allow better appreciation of the context-dependent roles of Id proteins in cancers and improve considerations for therapy.
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Jiang X, Yang Z. Multiple biological functions of transcription factor 21 in the development of various cancers. Onco Targets Ther 2018; 11:3533-3539. [PMID: 29950858 PMCID: PMC6016277 DOI: 10.2147/ott.s164033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transcription factor 21 (TCF21) is a basic helix–loop–helix transcription factor that binds to DNA and regulates cell differentiation and cell fate specification through mesenchymal–epithelial transition during development. The TCF21 gene is epigenetically inactivated in many types of human cancers and exerts a wide variety of functions, including the regulation of epithelial–mesenchymal transition, invasion, metastasis, cell cycle, and autophagy. This review focuses on research progress in relation to the roles of TCF21 in tumor development. We systematically consider multiple pathological functions of TCF21 in various cancers, revealing the molecular bases of its diverse biological roles and providing new directions for future research.
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Affiliation(s)
- Xiaodi Jiang
- Department of Infectious Disease, The Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhi Yang
- Department of Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
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Row RH, Pegg A, Kinney BA, Farr GH, Maves L, Lowell S, Wilson V, Martin BL. BMP and FGF signaling interact to pattern mesoderm by controlling basic helix-loop-helix transcription factor activity. eLife 2018; 7:31018. [PMID: 29877796 PMCID: PMC6013256 DOI: 10.7554/elife.31018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 05/26/2018] [Indexed: 02/06/2023] Open
Abstract
The mesodermal germ layer is patterned into mediolateral subtypes by signaling factors including BMP and FGF. How these pathways are integrated to induce specific mediolateral cell fates is not well understood. We used mesoderm derived from post-gastrulation neuromesodermal progenitors (NMPs), which undergo a binary mediolateral patterning decision, as a simplified model to understand how FGF acts together with BMP to impart mediolateral fate. Using zebrafish and mouse NMPs, we identify an evolutionarily conserved mechanism of BMP and FGF-mediated mediolateral mesodermal patterning that occurs through modulation of basic helix-loop-helix (bHLH) transcription factor activity. BMP imparts lateral fate through induction of Id helix loop helix (HLH) proteins, which antagonize bHLH transcription factors, induced by FGF signaling, that specify medial fate. We extend our analysis of zebrafish development to show that bHLH activity is responsible for the mediolateral patterning of the entire mesodermal germ layer.
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Affiliation(s)
- Richard H Row
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Amy Pegg
- MRC Center for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian A Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Gist H Farr
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, United States
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, United States.,Division of Cardiology, Department of Pediatrics, University of Washington, Seattle, United States
| | - Sally Lowell
- MRC Center for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Valerie Wilson
- MRC Center for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
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Up-regulation of Transcription Factor 3 Is Correlated With Poor Prognosis in Cervical Carcinoma. Int J Gynecol Cancer 2018; 27:1422-1430. [PMID: 28604457 DOI: 10.1097/igc.0000000000001032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Transcription factor 3 (TCF3, or E2A) is a multifunctional bHLH (basic helix loop helix) transcription factor. The role of TCF3 expression in cancer and the multiple cell signaling pathways that regulate or are influenced by TCF3 are unclear. Therefore, the expression level of TCF3 in patients with cervical squamous cell carcinoma (CSCC) is discussed in this study. METHODS Total RNA was extracted using real-time quantitative reverse transcription-polymerase chain reaction. Western blotting was applied to confirm the results. Immunohistochemistry was used to characterize the expression patterns of TCF3 in CSCC specimens. The close relationship between the expression levels of TCF3 and the 5-year overall survival time was described by survival curves. The association between TCF3 expression and clinicopathological characteristics of 119 CSCC patients was analyzed by Chi-square, Fisher exact test, and Cox regression analysis. TCF3 was overexpressed or inhibited by plasmid transfection, and the proliferation, invasion, and migration of cells were detected using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), wound healing, and Transwell assays. RESULTS The expression of TCF3 was higher in CSCC tissues than in nonmalignant cervical tissues. Messenger RNA (mRNA) and protein in patient tissues were increased compared with nonmalignant cervical tissues. Moreover, the level of expression in early-stage disease was higher than in the advanced stage. From FIGO (International Federation of Gynecology and Obstetrics) stages I to IV, immunohistochemistry staining intensity gradually increased. A high level of expression was closely related to clinical stages. The expression of TCF3 was negatively correlated with overall survival time. TCF3 can promote HeLa cell growth, invasion, and migration in vitro. CONCLUSIONS Based on our results, TCF3 is clearly associated with the progression of CSCC. This is the first time that it has been reported that TCF3 can act as a tumor promoter in cervical cancer and thus might be of great significance in the prognosis of CSCC.
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Malouf C, Ottersbach K. Molecular processes involved in B cell acute lymphoblastic leukaemia. Cell Mol Life Sci 2018; 75:417-446. [PMID: 28819864 PMCID: PMC5765206 DOI: 10.1007/s00018-017-2620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
Abstract
B cell leukaemia is one of the most frequent malignancies in the paediatric population, but also affects a significant proportion of adults in developed countries. The majority of infant and paediatric cases initiate the process of leukaemogenesis during foetal development (in utero) through the formation of a chromosomal translocation or the acquisition/deletion of genetic material (hyperdiploidy or hypodiploidy, respectively). This first genetic insult is the major determinant for the prognosis and therapeutic outcome of patients. B cell leukaemia in adults displays similar molecular features as its paediatric counterpart. However, since this disease is highly represented in the infant and paediatric population, this review will focus on this demographic group and summarise the biological, clinical and epidemiological knowledge on B cell acute lymphoblastic leukaemia of four well characterised subtypes: t(4;11) MLL-AF4, t(12;21) ETV6-RUNX1, t(1;19) E2A-PBX1 and t(9;22) BCR-ABL1.
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Affiliation(s)
- Camille Malouf
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Katrin Ottersbach
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK.
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Li R, Cauchy P, Ramamoorthy S, Boller S, Chavez L, Grosschedl R. Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming. Genes Dev 2018; 32:96-111. [PMID: 29440261 PMCID: PMC5830932 DOI: 10.1101/gad.309583.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/20/2017] [Indexed: 01/07/2023]
Abstract
B-cell fate determination requires the action of transcription factors that operate in a regulatory network to activate B-lineage genes and repress lineage-inappropriate genes. However, the dynamics and hierarchy of events in B-cell programming remain obscure. To uncouple the dynamics of transcription factor expression from functional consequences, we generated induction systems in developmentally arrested Ebf1-/- pre-pro-B cells to allow precise experimental control of EBF1 expression in the genomic context of progenitor cells. Consistent with the described role of EBF1 as a pioneer transcription factor, we show in a time-resolved analysis that EBF1 occupancy coincides with EBF1 expression and precedes the formation of chromatin accessibility. We observed dynamic patterns of EBF1 target gene expression and sequential up-regulation of transcription factors that expand the regulatory network at the pro-B-cell stage. A continuous EBF1 function was found to be required for Cd79a promoter activity and for the maintenance of an accessible chromatin domain that is permissive for binding of other transcription factors. Notably, transient EBF1 occupancy was detected at lineage-inappropriate genes prior to their silencing in pro-B cells. Thus, persistent and transient functions of EBF1 allow for an ordered sequence of epigenetic and transcriptional events in B-cell programming.
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Affiliation(s)
- Rui Li
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center, 69120 Heidelberg, Germany
- Department of Medicine, Division of Medial Genetics, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D, Pongubala JMR. Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment. Nucleic Acids Res 2017; 45:11070-11087. [PMID: 28977418 PMCID: PMC5737614 DOI: 10.1093/nar/gkx722] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination. Furthermore, although, topologically associating domains (TADs) are stable, a significant number of TADs display structural alterations that are associated with changes in cis-regulatory interaction landscape. Finally, we demonstrate the potential roles for Ebf1 and its downstream factor, Pax5, in chromatin reorganization and transcription regulation. Collectively, our studies provide a general paradigm of the dynamic relationship between chromatin reorganization and lineage-specific gene expression pattern that dictates cell-fate determination.
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Affiliation(s)
- Ravi Boya
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Anurupa Devi Yadavalli
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sameena Nikhat
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore 560065, India
| | - Jagan M R Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development. Immunity 2017; 46:818-834.e4. [PMID: 28514688 DOI: 10.1016/j.immuni.2017.04.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/26/2017] [Accepted: 04/27/2017] [Indexed: 01/24/2023]
Abstract
Innate and adaptive lymphoid development is orchestrated by the activities of E proteins and their antagonist Id proteins, but how these factors regulate early T cell progenitor (ETP) and innate lymphoid cell (ILC) development remains unclear. Using multiple genetic strategies, we demonstrated that E proteins E2A and HEB acted in synergy in the thymus to establish T cell identity and to suppress the aberrant development of ILCs, including ILC2s and lymphoid-tissue-inducer-like cells. E2A and HEB orchestrated T cell fate and suppressed the ILC transcription signature by activating the expression of genes associated with Notch receptors, T cell receptor (TCR) assembly, and TCR-mediated signaling. E2A and HEB acted in ETPs to establish and maintain a T-cell-lineage-specific enhancer repertoire, including regulatory elements associated with the Notch1, Rag1, and Rag2 loci. On the basis of these and previous observations, we propose that the E-Id protein axis specifies innate and adaptive lymphoid cell fate.
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48
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Tang J, Zha J, Guo X, Shi P, Xu B. CXCR5 +CD8 + T cells present elevated capacity in mediating cytotoxicity toward autologous tumor cells through interleukin 10 in diffuse large B-cell lymphoma. Int Immunopharmacol 2017; 50:146-151. [PMID: 28662433 DOI: 10.1016/j.intimp.2017.06.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/25/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a common and aggressive subtype of non-Hodgkin's lymphomas, with limited treatment options in refractory and relapsed patients. Growing evidence supports the notion that CD8+ T cell immunity could be utilized to eliminate B cell lymphomas. CXCR5+CD8+ T cell is a novel cell subtype and share CXCR5 expression with CD19+ tumor cells. In this study, we investigated the frequency and function of existing CXCR5+CD8+ T cells in DLBCL patients. We found that DLBCL patients as a group demonstrated significantly higher level of CXCR5+CD8+ T cells than healthy individuals, with huge variability in each patient. Using anti-CD3/CD28-stimulated CD8+ T cells as effector (E) cells and autologous CD19+ tumor cells as target (T) cells, at high E:T ratio, no difference between the intensities of CXCR5+CD8+ T cell- and CXCR5-CD8+ T cell-mediated cytotoxicity were observed. However, at intermediate and low E:T ratios, the CXCR5+CD8+ T cells presented stronger cytotoxicity than CXCR5-CD8+ T cells. The expressions of granzyme A, granzyme B, and perforin were significantly higher in CXCR5+CD8+ T cells than in CXCR5-CD8+ T cells, with no significant difference in the level of degranulation. Tumor cells in DLBCL were known to secrete high level of interleukin 10 (IL-10). We therefore blocked the IL-10/IL-10R pathway, and found that the expressions of granzyme A, granzyme B, and perforin by CXCR5+CD8+ T cells were significantly elevated. Together, these results suggest that CXCR5+CD8+ T cells are potential candidates of CD8+ T cell-based immunotherapies, could mediate elimination of autologous tumor cells in DLBCL patients, but are also susceptible to IL-10-mediated suppression.
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Affiliation(s)
- Jiahong Tang
- Department of Hematology, Nanfang Hospital, Southern medical University, Guangzhou 510515, China
| | - Jie Zha
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Xutao Guo
- Department of Hematology, Nanfang Hospital, Southern medical University, Guangzhou 510515, China
| | - Pengcheng Shi
- Department of Hematology, Nanfang Hospital, Southern medical University, Guangzhou 510515, China
| | - Bing Xu
- Department of Hematology, Nanfang Hospital, Southern medical University, Guangzhou 510515, China; Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China.
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Abstract
The success of anticancer therapy is usually limited by the development of drug resistance. Such acquired resistance is driven, in part, by intratumoural heterogeneity - that is, the phenotypic diversity of cancer cells co-inhabiting a single tumour mass. The introduction of the cancer stem cell (CSC) concept, which posits the presence of minor subpopulations of CSCs that are uniquely capable of seeding new tumours, has provided a framework for understanding one dimension of intratumoural heterogeneity. This concept, taken together with the identification of the epithelial-to-mesenchymal transition (EMT) programme as a critical regulator of the CSC phenotype, offers an opportunity to investigate the nature of intratumoural heterogeneity and a possible mechanistic basis for anticancer drug resistance. In fact, accumulating evidence indicates that conventional therapies often fail to eradicate carcinoma cells that have entered the CSC state via activation of the EMT programme, thereby permitting CSC-mediated clinical relapse. In this Review, we summarize our current understanding of the link between the EMT programme and the CSC state, and also discuss how this knowledge can contribute to improvements in clinical practice.
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50
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Saelee P, Kearly A, Nutt SL, Garrett-Sinha LA. Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1. Front Immunol 2017; 8:383. [PMID: 28439269 PMCID: PMC5383717 DOI: 10.3389/fimmu.2017.00383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/17/2017] [Indexed: 12/16/2022] Open
Abstract
Background The transcription factor Ets1 is highly expressed in B lymphocytes. Loss of Ets1 leads to premature B cell differentiation into antibody-secreting cells (ASCs), secretion of autoantibodies, and development of autoimmune disease. Despite the importance of Ets1 in B cell biology, few Ets1 target genes are known in these cells. Results To obtain a more complete picture of the function of Ets1 in regulating B cell differentiation, we performed Ets1 ChIP-seq in primary mouse B cells to identify >10,000-binding sites, many of which were localized near genes that play important roles in B cell activation and differentiation. Although Ets1 bound to many sites in the genome, it was required for regulation of less than 5% of them as evidenced by gene expression changes in B cells lacking Ets1. The cohort of genes whose expression was altered included numerous genes that have been associated with autoimmune disease susceptibility. We focused our attention on four such Ets1 target genes Ptpn22, Stat4, Egr1, and Prdm1 to assess how they might contribute to Ets1 function in limiting ASC formation. We found that dysregulation of these particular targets cannot explain altered ASC differentiation in the absence of Ets1. Conclusion We have identified genome-wide binding targets for Ets1 in B cells and determined that a relatively small number of these putative target genes require Ets1 for their normal expression. Interestingly, a cohort of genes associated with autoimmune disease susceptibility is among those that are regulated by Ets1. Identification of the target genes of Ets1 in B cells will help provide a clearer picture of how Ets1 regulates B cell responses and how its loss promotes autoantibody secretion.
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Affiliation(s)
- Prontip Saelee
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Alyssa Kearly
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
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