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Dauba A, Näser E, Andrieux D, Cogné M, Denizot Y, Khamlichi AA. The immunoglobulin heavy chain super enhancer controls class switch recombination in developing B cells. Sci Rep 2024; 14:7370. [PMID: 38548819 PMCID: PMC10979011 DOI: 10.1038/s41598-024-57576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to replace the initial IgM by another antibody class (IgG, IgE or IgA). CSR is preceded by transcription of the IgH constant genes and is controlled by the super-enhancer 3' regulatory region (3'RR) in an activation-specific manner. The 3'RR is composed of four enhancers (hs3a, hs1-2, hs3b and hs4). In mature B cells, 3'RR activity correlates with transcription of its enhancers. CSR can also occur in primary developing B cells though at low frequency, but in contrast to mature B cells, the transcriptional elements that regulate the process in developing B cells are ill-known. In particular, the role of the 3'RR in the control of constant genes' transcription and CSR has not been addressed. Here, by using a mouse line devoid of the 3'RR and a culture system that highly enriches in pro-B cells, we show that the 3'RR activity is indeed required for switch transcription and CSR, though its effect varies in an isotype-specific manner and correlates with transcription of hs4 enhancer only.
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Affiliation(s)
- Audrey Dauba
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Emmanuelle Näser
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Dylan Andrieux
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Michel Cogné
- MOBIDIC, INSERM U1236, Université de Rennes 1, Rennes, France
| | - Yves Denizot
- UMR CNRS 7276, INSERM U1262, Université de Limoges, CBRS, Limoges, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France.
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2
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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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3
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Denis-Lagache N, Oblet C, Marchiol T, Baylet A, Têteau O, Dalloul I, Dalloul Z, Zawil L, Dézé O, Cook-Moreau J, Saintamand A, Boutouil H, Khamlichi AA, Carrion C, Péron S, Le Noir S, Laffleur B, Cogné M. Attempts to evaluate locus suicide recombination and its potential role in B cell negative selection in the mouse. Front Immunol 2023; 14:1155906. [PMID: 37359540 PMCID: PMC10288998 DOI: 10.3389/fimmu.2023.1155906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction In mature B cells, activation-induced deaminase reshapes Ig genes through somatic hypermutation and class switch recombination of the Ig heavy chain (IgH) locus under control of its 3' cis-regulatory region (3'RR). The 3'RR is itself transcribed and can undergo "locus suicide recombination" (LSR), then deleting the constant gene cluster and terminating IgH expression. The relative contribution of LSR to B cell negative selection remains to be determined. Methods Here, we set up a knock-in mouse reporter model for LSR events with the aim to get clearer insights into the circumstances triggering LSR. In order to explore the consequences of LSR defects, we reciprocally explored the presence of autoantibodies in various mutant mouse lines in which LSR was perturbed by the lack of Sµ or of the 3'RR. Results Evaluation of LSR events in a dedicated reporter mouse model showed their occurrence in various conditions of B cell activation, notably in antigen-experienced B cells Studies of mice with LSR defects evidenced increased amounts of self-reactive antibodies. Discussion While the activation pathways associated with LSR are diverse, in vivo as well as in vitro, this study suggests that LSR may contribute to the elimination of self-reactive B cells.
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Affiliation(s)
- Nicolas Denis-Lagache
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Christelle Oblet
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Tiffany Marchiol
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Audrey Baylet
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Ophélie Têteau
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Iman Dalloul
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Zeinab Dalloul
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Lina Zawil
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | | | - Jeanne Cook-Moreau
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Alexis Saintamand
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Hend Boutouil
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS), Toulouse University, Toulouse, France
| | - Claire Carrion
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Sophie Péron
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Sandrine Le Noir
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | | | - Michel Cogné
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
- Rennes University, Inserm, Rennes, France
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4
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D'Addabbo P, Frezza D, Sulentic CE. Evolutive emergence and divergence of an Ig regulatory node: An environmental sensor getting cues from the aryl hydrocarbon receptor? Front Immunol 2023; 14:996119. [PMID: 36817426 PMCID: PMC9936319 DOI: 10.3389/fimmu.2023.996119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
One gene, the immunoglobulin heavy chain (IgH) gene, is responsible for the expression of all the different antibody isotypes. Transcriptional regulation of the IgH gene is complex and involves several regulatory elements including a large element at the 3' end of the IgH gene locus (3'RR). Animal models have demonstrated an essential role of the 3'RR in the ability of B cells to express high affinity antibodies and to express different antibody classes. Additionally, environmental chemicals such as aryl hydrocarbon receptor (AhR) ligands modulate mouse 3'RR activity that mirrors the effects of these chemicals on antibody production and immunocompetence in mouse models. Although first discovered as a mediator of the toxicity induced by the high affinity ligand 2,3,7,8-tetracholordibenzo-p-dioxin (dioxin), understanding of the AhR has expanded to a physiological role in preserving homeostasis and maintaining immunocompetence. We posit that the AhR also plays a role in human antibody production and that the 3'RR is not only an IgH regulatory node but also an environmental sensor receiving signals through intrinsic and extrinsic pathways, including the AhR. This review will 1) highlight the emerging role of the AhR as a key transducer between environmental signals and altered immune function; 2) examine the current state of knowledge regarding IgH gene regulation and the role of the AhR in modulation of Ig production; 3) describe the evolution of the IgH gene that resulted in species and population differences; and 4) explore the evidence supporting the environmental sensing capacity of the 3'RR and the AhR as a transducer of these cues. This review will also underscore the need for studies focused on human models due to the premise that understanding genetic differences in the human population and the signaling pathways that converge at the 3'RR will provide valuable insight into individual sensitivities to environmental factors and antibody-mediated disease conditions, including emerging infections such as SARS-CoV-2.
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Affiliation(s)
- Pietro D'Addabbo
- Department of Biology, University of Bari “Aldo Moro”, Bari, Italy
| | - Domenico Frezza
- Department of Biology E. Calef, University of Rome Tor Vergata, Rome, Italy
| | - Courtney E.W. Sulentic
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
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5
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Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes. Molecules 2023; 28:molecules28031159. [PMID: 36770824 PMCID: PMC9921937 DOI: 10.3390/molecules28031159] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.
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Haque F, Honjo T, Begum NA. XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation. SCIENCE ADVANCES 2022; 8:eadd1466. [PMID: 36427307 PMCID: PMC9699684 DOI: 10.1126/sciadv.add1466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The transcriptional coactivator Med12 regulates gene expression through its kinase module. Here, we show a kinase module-independent function of Med12 in CSR. Med12 is essential for super-enhancer activation by collaborating with p300-Jmjd6/Carm1 coactivator complexes. Med12 loss decreases H3K27 acetylation and eRNA transcription with concomitant impairment of AID-induced DNA breaks, S-S synapse formation, and 3'RR-Eμ interaction. CRISPR-dCas9-mediated enhancer activation reestablishes the epigenomic and transcriptional hallmarks of the super-enhancer and fully restores the Med12 depletion defects. Moreover, 3'RR-derived eRNAs are critical for promoting S region epigenetic regulation, synapse formation, and recruitment of Med12 and AID to the IgH locus. We find that XLID syndrome-associated Med12 mutations are defective in both 3'RR eRNA transcription and CSR, suggesting that B and neuronal cells may have cell-specific super-enhancer dysfunctions. We conclude that Med12 is essential for IgH 3'RR activation/eRNA transcription and plays a central role in AID-induced antibody gene diversification and genomic instability in B cells.
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Affiliation(s)
- Farazul Haque
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
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7
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The role of chromatin loop extrusion in antibody diversification. Nat Rev Immunol 2022; 22:550-566. [PMID: 35169260 PMCID: PMC9376198 DOI: 10.1038/s41577-022-00679-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Cohesin mediates chromatin loop formation across the genome by extruding chromatin between convergently oriented CTCF-binding elements. Recent studies indicate that cohesin-mediated loop extrusion in developing B cells presents immunoglobulin heavy chain (Igh) variable (V), diversity (D) and joining (J) gene segments to RAG endonuclease through a process referred to as RAG chromatin scanning. RAG initiates V(D)J recombinational joining of these gene segments to generate the large number of different Igh variable region exons that are required for immune responses to diverse pathogens. Antigen-activated mature B cells also use chromatin loop extrusion to mediate the synapsis, breakage and end joining of switch regions flanking Igh constant region exons during class-switch recombination, which allows for the expression of different antibody constant region isotypes that optimize the functions of antigen-specific antibodies to eliminate pathogens. Here, we review recent advances in our understanding of chromatin loop extrusion during V(D)J recombination and class-switch recombination at the Igh locus.
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8
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Bruzeau C, Cook-Moreau J, Pinaud E, Le Noir S. Contribution of Immunoglobulin Enhancers to B Cell Nuclear Organization. Front Immunol 2022; 13:877930. [PMID: 35812441 PMCID: PMC9263370 DOI: 10.3389/fimmu.2022.877930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
B cells undergo genetic rearrangements at immunoglobulin gene (Ig) loci during B cell maturation. First V(D)J recombination occurs during early B cell stages followed by class switch recombination (CSR) and somatic hypermutation (SHM) which occur during mature B cell stages. Given that RAG1/2 induces DNA double strand breaks (DSBs) during V(D)J recombination and AID (Activation-Induced Deaminase) leads to DNA modifications (mutations during SHM or DNA DSBs during CSR), it is mandatory that IgH rearrangements be tightly regulated to avoid any mutations or translocations within oncogenes. Ig loci contain various cis-regulatory elements that are involved in germline transcription, chromatin modifications or RAG/AID recruitment. Ig cis-regulatory elements are increasingly recognized as being involved in nuclear positioning, heterochromatin addressing and chromosome loop regulation. In this review, we examined multiple data showing the critical interest of studying Ig gene regulation at the whole nucleus scale. In this context, we highlighted the essential function of Ig gene regulatory elements that now have to be considered as nuclear organizers in B lymphocytes.
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9
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Colas L, Magnan A, Brouard S. Immunoglobulin E response in health and disease beyond allergic disorders. Allergy 2022; 77:1700-1718. [PMID: 35073421 DOI: 10.1111/all.15230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/13/2021] [Accepted: 01/16/2022] [Indexed: 12/24/2022]
Abstract
Immunoglobulin E is the latest discovered of immunoglobulin family and has been long associated with anaphylaxis and worm expulsion. Immunoglobulin E, along with mast cells, basophils, and eosinophils, is also a hallmark of type 2 immunity which is dysregulated in numerous diseases such as asthma, rhinitis, atopic dermatitis, and eosinophilic esophagitis in addition to anaphylaxis as aforementioned. However, recent advances have shed light on IgE regulation and memory explaining the low level of free IgE, the scarcity of IgE plasma cells that are mainly short live and the absence of IgE memory B cells in homeostatic conditions. Furthermore, IgE was implicated in inflammatory conditions beyond allergic disorders where IgE-mediated facilitated antigen presentation can enhance cellular and humoral response against autoantigens in systemic lupus or chronic urticaria leading to more severe disease and even against neoantigen facilitating tumor cell lysis. At last, IgE was unexpectedly associated with allograft rejection or atheromatous cardiovascular diseases where precise mechanisms remain to be deciphered. The purpose of this review is to summarize these recent advances in IgE regulation, biology, and physiopathology beyond allergic diseases opening whole new fields of IgE biology to explore.
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Affiliation(s)
- Luc Colas
- Plateforme Transversale d'Allergologie et d'immunologie Clinique PFTA Clinique dermatologique CHU de Nantes Nantes France
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology Nantes France
| | - Antoine Magnan
- Hôpital Foch, Suresnes; Université de Versailles Saint‐Quentin Paris‐Saclay; INRAe Paris France
| | - Sophie Brouard
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology Nantes France
- Labex IGO Nantes France
- Centre d’Investigation Clinique en Biothérapie Centre de ressources biologiques (CRB) Nantes France
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10
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Ferrad M, Ghazzaui N, Issaoui H, Drouineau E, Oblet C, Marchiol T, Cook-Moreau J, Denizot Y. Homozygous iMycCα transgenic mice as a model of plasma B-cell lymphomas. Leuk Lymphoma 2022; 63:2114-2125. [DOI: 10.1080/10428194.2022.2064989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Melissa Ferrad
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Nour Ghazzaui
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Hussein Issaoui
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Emilie Drouineau
- I2BC, IBITEC-S, CEA, CNRS, Université Paris‐Sud, Université Paris‐Saclay, Gif-sur-Yvette, France
| | - Christelle Oblet
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Tiffany Marchiol
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Yves Denizot
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
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11
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Tarsalainen A, Maman Y, Meng FL, Kyläniemi MK, Soikkeli A, Budzynska P, McDonald JJ, Šenigl F, Alt FW, Schatz DG, Alinikula J. Ig Enhancers Increase RNA Polymerase II Stalling at Somatic Hypermutation Target Sequences. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:143-154. [PMID: 34862258 PMCID: PMC8702490 DOI: 10.4049/jimmunol.2100923] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 01/03/2023]
Abstract
Somatic hypermutation (SHM) drives the genetic diversity of Ig genes in activated B cells and supports the generation of Abs with increased affinity for Ag. SHM is targeted to Ig genes by their enhancers (diversification activators [DIVACs]), but how the enhancers mediate this activity is unknown. We show using chicken DT40 B cells that highly active DIVACs increase the phosphorylation of RNA polymerase II (Pol II) and Pol II occupancy in the mutating gene with little or no accompanying increase in elongation-competent Pol II or production of full-length transcripts, indicating accumulation of stalled Pol II. DIVAC has similar effect also in human Ramos Burkitt lymphoma cells. The DIVAC-induced stalling is weakly associated with an increase in the detection of ssDNA bubbles in the mutating target gene. We did not find evidence for antisense transcription, or that DIVAC functions by altering levels of H3K27ac or the histone variant H3.3 in the mutating gene. These findings argue for a connection between Pol II stalling and cis-acting targeting elements in the context of SHM and thus define a mechanistic basis for locus-specific targeting of SHM in the genome. Our results suggest that DIVAC elements render the target gene a suitable platform for AID-mediated mutation without a requirement for increasing transcriptional output.
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Affiliation(s)
- Alina Tarsalainen
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Yaakov Maman
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, 1311502, Israel
| | - Fei-Long Meng
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA.,Current address: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Minna K. Kyläniemi
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Current address: Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Anni Soikkeli
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Paulina Budzynska
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Jessica J. McDonald
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Current address: The Annenberg Public Policy Center, Philadelphia, PA 19104-3806, USA
| | - Filip Šenigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Praha 4, Czech Republic
| | - Frederic W. Alt
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Correspondence should be addressed to and
| | - Jukka Alinikula
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Correspondence should be addressed to and
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12
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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13
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Dauba A, Khamlichi AA. Long-Range Control of Class Switch Recombination by Transcriptional Regulatory Elements. Front Immunol 2021; 12:738216. [PMID: 34594340 PMCID: PMC8477019 DOI: 10.3389/fimmu.2021.738216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Immunoglobulin class switch recombination (CSR) plays a crucial role in adaptive immune responses through a change of the effector functions of antibodies and is triggered by T-cell-dependent as well as T-cell-independent antigens. Signals generated following encounter with each type of antigen direct CSR to different isotypes. At the genomic level, CSR occurs between highly repetitive switch sequences located upstream of the constant gene exons of the immunoglobulin heavy chain locus. Transcription of switch sequences is mandatory for CSR and is induced in a stimulation-dependent manner. Switch transcription takes place within dynamic chromatin domains and is regulated by long-range regulatory elements which promote alignment of partner switch regions in CSR centers. Here, we review recent work and models that account for the function of long-range transcriptional regulatory elements and the chromatin-based mechanisms involved in the control of CSR.
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Affiliation(s)
- Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
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14
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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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15
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Abstract
B lymphocytes change antibody heavy chain (IgH) isotypes by a recombination/deletion process called IgH class switch recombination (CSR). CSR involves introduction of DNA breaks into a donor switch (S) region and also into one of six downstream S regions, with joining of the breaks changing antibody isotype. A chromatin super-anchor, of unknown function, is located just downstream of the IgH locus. We show that complete deletion of this super-anchor variably decreases CSR to most S regions and creates an ectopic S region downstream of IgH locus that undergoes aberrant CSR-driven chromosomal rearrangements. Based on these and other findings, we conclude that the super-anchor downstream of IgH is a critical insulator for focusing potentially dangerous CSR rearrangements to the IgH locus. IgH class switch recombination (CSR) replaces Cμ constant region (CH) exons with one of six downstream CHs by joining transcription-targeted double-strand breaks (DSBs) in the Cμ switch (S) region to DSBs in a downstream S region. Chromatin loop extrusion underlies fundamental CSR mechanisms including 3′IgH regulatory region (3′IgHRR)-mediated S region transcription, CSR center formation, and deletional CSR joining. There are 10 consecutive CTCF-binding elements (CBEs) downstream of the 3′IgHRR, termed the “3′IgH CBEs.” Prior studies showed that deletion of eight 3′IgH CBEs did not detectably affect CSR. Here, we report that deletion of all 3′IgH CBEs impacts, to varying degrees, germline transcription and CSR of upstream S regions, except that of Sγ1. Moreover, deletion of all 3′IgH CBEs rendered the 6-kb region just downstream highly transcribed and caused sequences within to be aligned with Sμ, broken, and joined to form aberrant CSR rearrangements. These findings implicate the 3′IgH CBEs as critical insulators for focusing loop extrusion-mediated 3′IgHRR transcriptional and CSR activities on upstream CH locus targets.
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16
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Ouk C, Roland L, Gachard N, Poulain S, Oblet C, Rizzo D, Saintamand A, Lemasson Q, Carrion C, Thomas M, Balabanian K, Espéli M, Parrens M, Soubeyran I, Boulin M, Faumont N, Feuillard J, Vincent-Fabert C. Continuous MYD88 Activation Is Associated With Expansion and Then Transformation of IgM Differentiating Plasma Cells. Front Immunol 2021; 12:641692. [PMID: 34017329 PMCID: PMC8129569 DOI: 10.3389/fimmu.2021.641692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/14/2021] [Indexed: 11/19/2022] Open
Abstract
Activating mutations of MYD88 (MYD88L265P being the far most frequent) are found in most cases of Waldenström macroglobulinemia (WM) as well as in various aggressive B-cell lymphoma entities with features of plasma cell (PC) differentiation, such as activated B-cell type diffuse large B-cell lymphoma (DLBCL). To understand how MYD88 activation exerts its transformation potential, we developed a new mouse model in which the MYD88L252P protein, the murine ortholog of human MYD88L265P, is continuously expressed in CD19 positive B-cells together with the Yellow Fluorescent Protein (Myd88L252P mice). In bone marrow, IgM B and plasma cells were expanded with a CD138 expression continuum from IgMhigh CD138low to IgMlow CD138high cells and the progressive loss of the B220 marker. Serum protein electrophoresis (SPE) longitudinal analysis of 40 Myd88L252P mice (16 to 56 weeks old) demonstrated that ageing was first associated with serum polyclonal hyper gammaglobulinemia (hyper Ig) and followed by a monoclonal immunoglobulin (Ig) peak related to a progressive increase in IgM serum levels. All Myd88L252P mice exhibited spleen enlargement which was directly correlated with the SPE profile and was maximal for monoclonal Ig peaks. Myd88L252P mice exhibited very early increased IgM PC differentiation. Most likely due to an early increase in the Ki67 proliferation index, IgM lymphoplasmacytic (LP) and plasma cells continuously expanded with age being first associated with hyper Ig and then with monoclonal Ig peak. This peak was consistently associated with a spleen LP-like B-cell lymphoma. Clonal expression of both membrane and secreted µ chain isoforms was demonstrated at the mRNA level by high throughput sequencing. The Myd88L252P tumor transcriptomic signature identified both proliferation and canonical NF-κB p65/RelA activation. Comparison with MYD88L265P WM showed that Myd88L252P tumors also shared the typical lymphoplasmacytic transcriptomic signature of WM bone marrow purified tumor B-cells. Altogether these results demonstrate for the first time that continuous MYD88 activation is specifically associated with clonal transformation of differentiating IgM B-cells. Since MYD88L252P targets the IgM PC differentiation continuum, it provides an interesting preclinical model for development of new therapeutic approaches to both WM and aggressive MYD88 associated DLBCLs.
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Affiliation(s)
- Catherine Ouk
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Lilian Roland
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Nathalie Gachard
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Stéphanie Poulain
- UMR CANTHER « CANcer Heterogeneity, Plasticity and Resistance to THERapies » INSERM 1277-CNRS 9020 UMRS 12, University of Lille, Hematology Laboratory, Biology and Pathology Center, CHU de Lille, Lille, France
| | - Christelle Oblet
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - David Rizzo
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Alexis Saintamand
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Quentin Lemasson
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Claire Carrion
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Morgane Thomas
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Karl Balabanian
- Institut de Recherche Saint-Louis, EMiLy, INSERM U1160, University of Paris, Paris, France
| | - Marion Espéli
- Institut de Recherche Saint-Louis, EMiLy, INSERM U1160, University of Paris, Paris, France
| | - Marie Parrens
- Pathology Department, Hospital University Center of Bordeaux, Bordeaux, France
| | | | - Mélanie Boulin
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Nathalie Faumont
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Jean Feuillard
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Christelle Vincent-Fabert
- UMR CNRS 7276/INSERM U1262 CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
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17
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Bruzeau C, Moreau J, Le Noir S, Pinaud E. Panorama of stepwise involvement of the IgH 3' regulatory region in murine B cells. Adv Immunol 2021; 149:95-114. [PMID: 33993921 DOI: 10.1016/bs.ai.2021.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Among the multiple events leading to immunoglobulin (Ig) expression in B cells, stepwise activation of the Ig heavy chain locus (IgH) is of critical importance. Transcription regulation of the complex IgH locus has always been an interesting viewpoint to unravel the multiple and complex events required for IgH expression. First, regulatory germline transcripts (GLT) assist DNA remodeling events such as VDJ recombination, class switch recombination (CSR) and somatic hypermutation (SHM). Second, productive spliced transcripts restrict heavy chain protein expression associated either with the surface receptor of developing B cells or secreted in large amounts in plasma cells. One main transcriptional regulator for IgH lies at its 3' extremity and includes both a set of enhancers grouped in a large 3' regulatory region (3'RR) and a cluster of 3'CTCF-binding elements (3'CBEs). In this focused review, we will preferentially refer to evidence reported for the murine endogenous IgH locus, whether it is wt or carries deletions or insertions within the IgH 3' boundary and associated regulatory region.
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Affiliation(s)
- Charlotte Bruzeau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Jeanne Moreau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Sandrine Le Noir
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Eric Pinaud
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France.
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18
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IgH 3' regulatory region increases ectopic class switch recombination. PLoS Genet 2021; 17:e1009288. [PMID: 33556079 PMCID: PMC7869978 DOI: 10.1371/journal.pgen.1009288] [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: 05/14/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks. Class switching allows B lymphocytes to replace expression of immunoglobin M with that of immunoglobulins G, A or E. The genetic support of class switching, is a unique and large deletion uniquely occuring within the immunoglobulin heavy chain (IgH) locus. This recombination is triggered after DNA lesions inflicted by the activation-induced deaminase (AID) enzyme. In immunoglobulin light chain loci, AID only stimulates somatic hypermutation. In such a non-IgH locus, we now show that the IgH 3’ superenhancer can promote junctions between distant DNA breaks and ectopic class switch recombination. This study identifies the minimal elements necessary for class-switch recombination to occur instead of hypermutation in a locus targeted by AID, i.e. transcribed (and spliced) target sites for AID in so-called S regions, and the 3’IgH superenhancer which both helps recruit AID for DNA lesions, and helps repair these lesions through distant gene synapsis and recombination.
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19
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Laffleur B, Lim J, Zhang W, Chen Y, Pefanis E, Bizarro J, Batista CR, Wu L, Economides AN, Wang J, Basu U. Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells. Nat Genet 2021; 53:230-242. [PMID: 33526923 PMCID: PMC8011275 DOI: 10.1038/s41588-020-00772-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Noncoding RNAs are exquisitely titrated by the cellular RNA surveillance machinery for regulating diverse biological processes. The RNA exosome, the predominant 3' RNA exoribonuclease in mammalian cells, is composed of nine core and two catalytic subunits. Here, we developed a mouse model with a conditional allele to study the RNA exosome catalytic subunit DIS3. In DIS3-deficient B cells, integrity of the immunoglobulin heavy chain (Igh) locus in its topologically associating domain is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements, decreased CTCF binding to CTCF-binding elements and disorganized cohesin localization. DIS3-deficient B cells also accumulate activation-induced cytidine deaminase-mediated asymmetric nicks, altering somatic hypermutation patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased class-switch recombination but increased chromosomal translocations. Our observations of DIS3-mediated architectural regulation at the Igh locus are reflected genome wide, thus providing evidence that noncoding RNA processing is an important mechanism for controlling genome organization.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pharmacy, School of Pharmacy, Jeonbuk National University, Jeonju, South Korea
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yiyun Chen
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Evangelos Pefanis
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Jonathan Bizarro
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Carolina R Batista
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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20
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Oudinet C, Braikia FZ, Dauba A, Khamlichi AA. Mechanism and regulation of class switch recombination by IgH transcriptional control elements. Adv Immunol 2020; 147:89-137. [PMID: 32981636 DOI: 10.1016/bs.ai.2020.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Class switch recombination (CSR) plays an important role in humoral immunity by generating antibodies with different effector functions. CSR to a particular antibody isotype is induced by external stimuli, and occurs between highly repetitive switch (S) sequences. CSR requires transcription across S regions, which generates long non-coding RNAs and secondary structures that promote accessibility of S sequences to activation-induced cytidine deaminase (AID). AID initiates DNA double-strand breaks (DSBs) intermediates that are repaired by general DNA repair pathways. Switch transcription is controlled by various regulatory elements, including enhancers and insulators. The current paradigm posits that transcriptional control of CSR involves long-range chromatin interactions between regulatory elements and chromatin loops-stabilizing factors, which promote alignment of partner S regions in a CSR centre (CSRC) and initiation of CSR. In this review, we focus on the role of IgH transcriptional control elements in CSR and the chromatin-based mechanisms underlying this control.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France.
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21
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Ferrad M, Ghazzaui N, Issaoui H, Cook-Moreau J, Denizot Y. Mouse Models of c-myc Deregulation Driven by IgH Locus Enhancers as Models of B-Cell Lymphomagenesis. Front Immunol 2020; 11:1564. [PMID: 32793219 PMCID: PMC7390917 DOI: 10.3389/fimmu.2020.01564] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/15/2020] [Indexed: 01/18/2023] Open
Abstract
Chromosomal translocations linking various oncogenes to transcriptional enhancers of the immunoglobulin heavy chain (IgH) locus are often implicated as the cause of B-cell malignancies. Two major IgH transcriptional enhancers have been reported so far. The Eμ enhancer located upstream of the Cμ gene controls early events in B-cell maturation such as VDJ recombination. The 3' regulatory region (3'RR) located downstream from the Cα gene controls late events in B-cell maturation such as IgH transcription, somatic hypermutation, and class switch recombination. Convincing demonstrations of the essential contributions of both Eμ and 3'RR in B-cell lymphomagenesis have been provided by transgenic and knock-in animal models which bring the oncogene c-myc under Eμ/3'RR transcriptional control. This short review summarizes the different mouse models so far available and their interests/limitations for progress in our understanding of human c-myc-induced B-cell lymphomagenesis.
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Affiliation(s)
- Melissa Ferrad
- Inserm U1262, UMR CNRS 7276, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Nour Ghazzaui
- Inserm U1262, UMR CNRS 7276, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Hussein Issaoui
- Inserm U1262, UMR CNRS 7276, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- Inserm U1262, UMR CNRS 7276, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
| | - Yves Denizot
- Inserm U1262, UMR CNRS 7276, Equipe Labellisée LIGUE 2018, Université de Limoges, Limoges, France
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22
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Fitz J, Neumann T, Steininger M, Wiedemann EM, Garcia AC, Athanasiadis A, Schoeberl UE, Pavri R. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nat Genet 2020; 52:505-515. [PMID: 32251373 DOI: 10.1038/s41588-020-0605-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022]
Abstract
Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters.
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Affiliation(s)
- Johanna Fitz
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | | | | | | | | | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
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23
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Snyder AD, Ochs SD, Johnson BE, Sulentic CEW. Aryl hydrocarbon receptor-induced activation of the human IGH hs1.2 enhancer: Mutational analysis of putative regulatory binding motifs. Mol Immunol 2020; 120:164-178. [PMID: 32146146 DOI: 10.1016/j.molimm.2020.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/31/2019] [Accepted: 02/06/2020] [Indexed: 11/25/2022]
Abstract
The human hs1.2 enhancer within the Ig heavy chain gene (IGH) is polymorphic and associated with a number of autoimmune diseases. The polymorphic region is characterized by tandem repeats of an ∼53-bp invariant sequence containing possible binding sites for several transcription factors. Our previous studies suggest the human hs1.2 enhancer is sensitive to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and high affinity ligand of the aryl hydrocarbon receptor (AhR). TCDD induced hs1.2 enhancer activity in an AhR-dependent manner and the number of invariant sequences influenced the magnitude of activity. To better understand the regulation of human hs1.2 enhancer activity, the objective of the current study was to utilize mutational analysis and luciferase reporter constructs to evaluate the contribution of putative transcription factor binding sites to overall hs1.2 enhancer activity and modulation by TCDD. Basal and LPS-induced activity of the hs1.2 enhancer appeared to be most affected by mutation of sites outside of the invariant sequence or deletion of the entire invariant sequence; whereas sites influencing the effect of TCDD were dependent on the cellular activation state (i.e. unstimulated vs. LPS stimulation) and relatively independent of the putative AhR binding site within the invariant sequence. These results suggest that AhR activation affects human hs1.2 activity through an as yet undetermined non-canonical pathway. A better understanding regarding the role of the hs1.2 enhancer in human Ig expression and how AhR ligands modulate its activity may lead to insights into overall Ig regulation and mechanisms of dysfunction.
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Affiliation(s)
- Andrew D Snyder
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Sharon D Ochs
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Brooke E Johnson
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Courtney E W Sulentic
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States.
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24
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Chi X, Li Y, Qiu X. V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation. Immunology 2020; 160:233-247. [PMID: 32031242 DOI: 10.1111/imm.13176] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Immunoglobulins emerging from B lymphocytes and capable of recognizing almost all kinds of antigens owing to the extreme diversity of their antigen-binding portions, known as variable (V) regions, play an important role in immune responses. The exons encoding the V regions are known as V (variable), D (diversity), or J (joining) genes. V, D, J segments exist as multiple copy arrays on the chromosome. The recombination of the V(D)J gene is the key mechanism to produce antibody diversity. The recombinational process, including randomly choosing a pair of V, D, J segments, introducing double-strand breaks adjacent to each segment, deleting (or inverting in some cases) the intervening DNA and ligating the segments together, is defined as V(D)J recombination, which contributes to surprising immunoglobulin diversity in vertebrate immune systems. To enhance both the ability of immunoglobulins to recognize and bind to foreign antigens and the effector capacities of the expressed antibodies, naive B cells will undergo class switching recombination (CSR) and somatic hypermutation (SHM). However, the genetics mechanisms of V(D)J recombination, CSR and SHM are not clear. In this review, we summarize the major progress in mechanism studies of immunoglobulin V(D)J gene recombination and CSR as well as SHM, and their regulatory mechanisms.
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Affiliation(s)
- Xiying Chi
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yue Li
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
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25
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Heltzel JMH, Gearhart PJ. What Targets Somatic Hypermutation to the Immunoglobulin Loci? Viral Immunol 2019; 33:277-281. [PMID: 31770070 DOI: 10.1089/vim.2019.0149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the most profound enigmas in B cell biology is how activation-induced deaminase (AID) is targeted to a very small region of DNA in the immunoglobulin loci. Two specific regions are singled out: the variable region of 2 kb that contains rearranged genes on the heavy, κ light, and λ light chain loci, and the switch region of ∼4 kb that contains an extensive stretch of G:C rich DNA on the heavy chain locus. Transcription is required for AID recruitment; however, many genes are also highly transcribed and do not undergo the catastrophic mutagenesis that occurs in variable and switch regions. The DNA sequences of these regions cause RNA polymerase II to accumulate for an extended distance of 2-4 kb. The stalled polymerases then recruit the transcription cofactor Spt5, and AID, which deaminates cytosines to uracils in exposed transcription bubbles. Thus, the immunoglobulin loci are unique in that a favorable combination of DNA sequences and 3' transcription enhancers make them the perfect storm for AID-induced somatic hypermutation.
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Affiliation(s)
- Justin M H Heltzel
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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26
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Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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27
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Two modes of cis-activation of switch transcription by the IgH superenhancer. Proc Natl Acad Sci U S A 2019; 116:14708-14713. [PMID: 31266889 DOI: 10.1073/pnas.1902250116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
B cell isotype switching plays an important role in modulating adaptive immune responses. It occurs in response to specific signals that often induce different isotype (I) promoters driving transcription of switch regions, located upstream of the Ig heavy chain (IgH) constant genes. The transcribed switch regions can recombine, leading to a change of the constant gene and, consequently, of antibody isotype. Switch transcription is controlled by the superenhancer 3' regulatory region (3'RR) that establishes long-range chromatin cis-interactions with I promoters. Most stimuli induce more than one I promoter, and switch transcription can occur on both chromosomes. Therefore, it is presently unknown whether induced I promoters compete for the 3'RR on the same chromosome. Here we performed single-chromosome RT-qPCR assays to examine switch transcription monoallelically in the endogenous context. We show that there are two modes of 3'RR-mediated activation of I promoters: coactivation and competition. The nature of the inducing signal plays a pivotal role in determining the mode of activation. Furthermore, we provide evidence that, in its endogenous setting, the 3'RR has a bidirectional activity. We propose that the coactivation and competition modes mediated by the 3'RR may have evolved to cope with the different kinetics of primary immune responses.
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28
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Dalloul I, Boyer F, Dalloul Z, Pignarre A, Caron G, Fest T, Chatonnet F, Delaloy C, Durandy A, Jeannet R, Lereclus E, Boutouil H, Aldigier JC, Péron S, Le Noir S, Cook-Moreau J, Cogné M. Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues. PLoS Genet 2019; 15:e1007721. [PMID: 31199803 PMCID: PMC6594652 DOI: 10.1371/journal.pgen.1007721] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 06/26/2019] [Accepted: 05/14/2019] [Indexed: 12/24/2022] Open
Abstract
B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin (Ig) genes by activation-induced deaminase (AID). AID promotes affinity maturation of Ig variable regions and class switch recombination (CSR) in mature B lymphocytes. In the IgH locus, these processes are under control of the 3' regulatory region (3'RR) super-enhancer, a region demonstrated in the mouse to be both transcribed and itself targeted by AID-mediated recombination. Alternatively to CSR, IgH deletions joining Sμ to "like-switch" DNA repeats that flank the 3' super-enhancer can thus accomplish so-called "locus suicide recombination" (LSR) in mouse B-cells. Using an optimized LSR-seq high throughput method, we now show that AID-mediated LSR is evolutionarily conserved and also actively occurs in humans, providing an activation-induced cell death pathway in multiple conditions of B-cell activation. LSR either focuses on the functional IgH allele or is bi-allelic, and its signature is mainly detected when LSR is ongoing while it vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells. Highly diversified breakpoints are distributed either within the upstream (3'RR1) or downstream (3'RR2) copies of the IgH 3' super-enhancer and all conditions activating CSR in vitro also seem to trigger LSR although TLR ligation appeared the most efficient. Molecular analysis of breakpoints and junctions confirms that LSR is AID-dependent and reveals junctional sequences somehow similar to CSR junctions but with increased usage of microhomologies.
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Affiliation(s)
- Iman Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - François Boyer
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Zeinab Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Gersende Caron
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | - Thierry Fest
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Céline Delaloy
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Robin Jeannet
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Emilie Lereclus
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Hend Boutouil
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Sophie Péron
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Sandrine Le Noir
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
| | - Michel Cogné
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
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29
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Issaoui H, Ghazzaui N, Ferrad M, Boyer F, Denizot Y. Class switch recombination junctions are not affected by the absence of the immunoglobulin heavy chain E μ enhancer. Cell Mol Immunol 2019; 16:671-673. [PMID: 30967637 DOI: 10.1038/s41423-019-0229-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 01/18/2023] Open
Affiliation(s)
- Hussein Issaoui
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, University of Limoges, CBRS, rue Pr. Descottes, 87025, Limoges, France
| | - Nour Ghazzaui
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, University of Limoges, CBRS, rue Pr. Descottes, 87025, Limoges, France
| | - Mélissa Ferrad
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, University of Limoges, CBRS, rue Pr. Descottes, 87025, Limoges, France
| | - François Boyer
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, University of Limoges, CBRS, rue Pr. Descottes, 87025, Limoges, France
| | - Yves Denizot
- UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, University of Limoges, CBRS, rue Pr. Descottes, 87025, Limoges, France.
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30
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Oudinet C, Braikia FZ, Dauba A, Santos JM, Khamlichi AA. Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus. PLoS Genet 2019; 15:e1007930. [PMID: 30779742 PMCID: PMC6380546 DOI: 10.1371/journal.pgen.1007930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Abstract
DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease. Mammalian genomes are predominantly methylated at CpG dinucleotides. Unmethylated CpGs are often associated with active regulatory sequences while methylated CpGs are often linked to transcriptional silencing. Previous studies on CpG methylation led to the notion that transcription initiation is more sensitive to CpG methylation than transcriptional elongation. The immunoglobulin heavy chain (IgH) constant locus comprises multiple inducible constant genes and is expressed exclusively in B lymphocytes. The developmental B cell stage at which methylation patterns of the IgH constant genes are established, and the role of CpG methylation in their expression, are unknown. Here, we find that methylation patterns at most cis-acting elements of the IgH constant genes are established and maintained independently of B cell activation or promoter activity. Moreover, one of the promoters, but not the enhancers, is hypomethylated in sperm and early embryonic cells, and is targeted by different demethylation pathways, including AID, UNG, and ATM pathways. Combined, the data suggest that, rather than being prominently involved in the regulation of the IgH constant locus expression, DNA methylation may primarily contribute to its epigenetic pre-marking.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Joana M. Santos
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail:
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31
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The immunoglobulin heavy chain 3' regulatory region superenhancer controls mouse B1 B-cell fate and late VDJ repertoire diversity. Blood Adv 2019; 2:252-262. [PMID: 29437640 DOI: 10.1182/bloodadvances.2017014423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/27/2017] [Indexed: 01/18/2023] Open
Abstract
The immunoglobulin heavy chain (IgH) 3' regulatory region (3'RR) superenhancer controls B2 B-cell IgH transcription and cell fate at the mature stage but not early repertoire diversity. B1 B cells represent a small percentage of total B cells differing from B2 B cells by several points such as precursors, development, functions, and regulation. B1 B cells act at the steady state to maintain homeostasis in the organism and during the earliest phases of an immune response, setting them at the interface between innate and acquired immunity. We investigated the role of the 3'RR superenhancer on B1 B-cell fate. Similar to B2 B cells, the 3'RR controls μ transcription and cell fate in B1 B cells. In contrast to B2 B cells, 3'RR deletion affects B1 B-cell late repertoire diversity. Thus, differences exist for B1 and B2 B-cell 3'RR control during B-cell maturation. For the first time, these results highlight the contribution of the 3'RR superenhancer at this interface between innate and acquired immunity.
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32
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Trans-silencing effect of the 3'RR immunoglobulin heavy chain enhancer on Igκ transcription at the pro-B cell stage. Cell Mol Immunol 2018; 16:668-670. [PMID: 30523346 DOI: 10.1038/s41423-018-0189-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 01/18/2023] Open
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33
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Abstract
Immunoglobulin heavy chain (IgH) translocations are common and early oncogenic events in B cell and plasma cell malignancies including B cell non-Hodgkin's lymphoma (NHL) and multiple myeloma (MM). IgH translocations bring oncogenes into close proximity with potent enhancer elements within the IgH locus, leading to oncogene up-regulation. As IgH enhancer activity is tightly controlled by B cell lineage-specific signaling and transcriptional networks, we hypothesized that IgH enhancers are potentially druggable targets/elements. To test this, we developed a molecular imaging-based high-throughput screening platform for discovering inhibitors of IgH enhancer-driven transcriptional activity. As proof of concept, we identified a low micromolar potency molecule (compound 30666) that inhibited immunoglobulin production by MM cells and blocked expression of an array of IgH translocation-induced oncogenes (CCND1, FGFR3/MMSET, and MYC) in MM and NHL cell lines. Prolonged exposure to 30666 significantly reduced the viability of IgH translocation-positive NHL and MM cells, but was less effective against cells lacking IgH translocations. Compound 30666 exhibited suitable pharmacological properties, including metabolic stability in liver microsomes and oral bioavailability in mice, and demonstrated preclinical anti-MM activity in a plasmacytoma mouse model. Our work suggests that IgH enhancers are attractive and potentially druggable targets for IgH translocation driven malignancies.
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Affiliation(s)
- Nathan G Dolloff
- a Department of Cellular and Molecular Pharmacology & Experimental Therapeutics , Medical University of South Carolina , Charleston , SC , USA
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34
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Ghazzaui N, Issaoui H, Boyer F, Martin OA, Saintamand A, Denizot Y. 3'RR and 5'E μ immunoglobulin heavy chain enhancers are independent engines of locus remodeling. Cell Mol Immunol 2018; 16:198-200. [PMID: 30305688 DOI: 10.1038/s41423-018-0171-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Nour Ghazzaui
- CNRS UMR 7276, Inserm U1262, Université de Limoges, Limoges, France
| | - Hussein Issaoui
- CNRS UMR 7276, Inserm U1262, Université de Limoges, Limoges, France
| | - François Boyer
- CNRS UMR 7276, Inserm U1262, Université de Limoges, Limoges, France
| | | | - Alexis Saintamand
- CNRS UMR 7276, Inserm U1262, Université de Limoges, Limoges, France.,Inserm U1236, Université Rennes 1, Rennes, France
| | - Yves Denizot
- CNRS UMR 7276, Inserm U1262, Université de Limoges, Limoges, France.
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35
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Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M. The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination. Mol Cell 2018; 72:636-649.e8. [PMID: 30293785 PMCID: PMC6242708 DOI: 10.1016/j.molcel.2018.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/01/2018] [Accepted: 08/25/2018] [Indexed: 01/18/2023]
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer. ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination ZMYND8 supports efficient somatic hypermutation of the Igh variable regions ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Daniel B Rosen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Lisa Keller
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | | | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Madlen Driesner
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Roman I Subbotin
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
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36
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Kovalchuk AL, Sakai T, Qi CF, Du Bois W, Dunnick WA, Cogné M, Morse HC. 3' Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations. Oncotarget 2018; 9:34528-34542. [PMID: 30349647 PMCID: PMC6195379 DOI: 10.18632/oncotarget.26160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/06/2018] [Indexed: 01/18/2023] Open
Abstract
Myc-deregulating T(12;15) chromosomal translocations are the hallmark cytogenetic abnormalities of murine plasmacytomas (PCTs). In most PCTs, the immunoglobulin heavy chain (Igh) locus is broken between the Eμ enhancer and the 3’ regulatory region (3’RR), making the latter the major candidate for orchestrating Myc deregulation. To elucidate the role of the Igh3’RR in tumorigenesis, we induced PCTs in Bcl-xL-transgenic mice deficient for the major Igh3’RR enhancer elements, hs3b and hs4 (hs3b-4-/-). Contrary to previous observations using a mouse lymphoma model, which showed no tumors with peripheral B-cell phenotype in hs3b-4-/- mice, these animals developed T(12;15)-positive PCTs, although with a lower incidence than hs3b-4+/+ (wild-type, WT) controls. In heterozygous hs3b-4+/- mice there was no allelic bias in targeting Igh for T(12;15). Molecular analyses of Igh/Myc junctions revealed dominance of Sμ region breakpoints versus the prevalence of Sγ or Sα in WT controls. Myc expression and Ig secretion in hs3b-4-/- PCTs did not differ from WT controls. We also evaluated the effect of a complete Igh3’RR deletion on Myc expression in the context of an established Igh/Myc translocation in ARS/Igh11-transgenic PCT cell lines. Cre-mediated deletion of the Igh3’RR resulted in gradual reduction of Myc expression, loss of proliferative activity and increased cell death, confirming the necessity of the Igh3’RR for Myc deregulation by T(12;15).
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Affiliation(s)
- Alexander L Kovalchuk
- Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Tomomi Sakai
- Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Chen-Feng Qi
- Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Wendy Du Bois
- Animal Model and Genotyping Core Facility, Laboratory of Cancer Biology and Genetics, NCI, National Institute of Health, Bethesda, MD, USA
| | - Wesley A Dunnick
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Michel Cogné
- Laboratory of Immunology, CNRS UMR 7276, Université de Limoges, Limoges, France
| | - Herbert C Morse
- Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
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Cresson C, Péron S, Jamrog L, Rouquié N, Prade N, Dubois M, Hébrard S, Lagarde S, Gerby B, Mancini SJC, Cogné M, Delabesse E, Delpy L, Broccardo C. PAX5A and PAX5B isoforms are both efficient to drive B cell differentiation. Oncotarget 2018; 9:32841-32854. [PMID: 30214688 PMCID: PMC6132355 DOI: 10.18632/oncotarget.26003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 07/31/2018] [Indexed: 11/25/2022] Open
Abstract
Pax5 is the guardian of the B cell identity since it primes or enhances the expression of B cell specific genes and concomitantly represses the expression of B cell inappropriate genes. The tight regulation of Pax5 is therefore required for an efficient B cell differentiation. A defect in its dosage can translate into immunodeficiency or malignant disorders such as leukemia or lymphoma. Pax5 is expressed from two different promoters encoding two isoforms that only differ in the sequence of their first alternative exon. Very little is known regarding the role of the two isoforms during B cell differentiation and the regulation of their expression. Our work aims to characterize the mechanisms of regulation of the expression balance of these two isoforms and their implication in the B cell differentiation process using murine ex vivo analyses. We show that these two isoforms are differentially regulated but have equivalent function during early B cell differentiation and may have functional differences after B cell activation. The tight control of their expression may thus reflect a way to finely tune Pax5 dosage during B cell differentiation process.
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Affiliation(s)
- Charlotte Cresson
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Sophie Péron
- Université de Limoges-CNRS UMR 7276, F-87025 Limoges, France
| | - Laura Jamrog
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Nelly Rouquié
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Nais Prade
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse Hospital University, Oncopole, CS 53717, F-31000 Toulouse, France
| | - Marine Dubois
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Sylvie Hébrard
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Stéphanie Lagarde
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse Hospital University, Oncopole, CS 53717, F-31000 Toulouse, France
| | - Bastien Gerby
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
| | - Stéphane J C Mancini
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009 Marseille, France
| | - Michel Cogné
- Université de Limoges-CNRS UMR 7276, Institut Universitaire de France, F-87025 Limoges, France
| | - Eric Delabesse
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse Hospital University, Oncopole, CS 53717, F-31000 Toulouse, France
| | - Laurent Delpy
- Université de Limoges-CNRS UMR 7276, F-87025 Limoges, France
| | - Cyril Broccardo
- Inserm, UMR1037 CRCT, F-31000, Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Oncopole, F-31000 Toulouse, France
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38
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Deletion of the immunoglobulin heavy chain 3' regulatory region super-enhancer affects somatic hypermutation in B1 B cells. Cell Mol Immunol 2018; 16:195-197. [PMID: 30127379 DOI: 10.1038/s41423-018-0091-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 01/18/2023] Open
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39
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Duplication of a germline promoter downstream of the IgH 3' regulatory region impairs class switch recombination. Sci Rep 2018; 8:9164. [PMID: 29907762 PMCID: PMC6003904 DOI: 10.1038/s41598-018-27448-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/01/2018] [Indexed: 01/13/2023] Open
Abstract
During an adaptive immune response, B cells can change their surface immunoglobulins from IgM to IgG, IgE or IgA through a process called class switch recombination (CSR). Switching is preceded by inducible non-coding germline transcription (GLT) of the selected constant gene(s), which is largely controlled by a super-enhancer called the 3' regulatory region (3'RR). Despite intense efforts, the precise mechanisms that regulate GLT are still elusive. In order to gain additional insights into these mechanisms, we analyzed GLT and CSR in mutant B cells carrying a duplication of the promoter of the α constant gene (Iα) downstream of 3'RR. Duplication of the Iα promoter affected differently GLT and CSR. While for most isotypes a drop in GLT was accompanied by a decrease in CSR, that was not the case for switching to IgA, which diminished despite unchanged GLT. Unexpectedly, there was no obvious effect on GLT and CSR to IgG3. Remarkably, specific stimuli that normally induce switching to IgG2b had contrasting effects in mutant B cells; Iγ2b was now preferentially responsive to the stimulus that induced Iα promoter. We propose that one mechanism underlying the induced 3'RR-mediated activation of GL promoters involves, at least in part, specific transcription factories.
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40
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Issaoui H, Ghazzaui N, Saintamand A, Carrion C, Oblet C, Denizot Y. The IgH 3' regulatory region super-enhancer does not control IgA class switch recombination in the B1 lineage. Cell Mol Immunol 2018; 15:289-291. [PMID: 28990584 PMCID: PMC5843615 DOI: 10.1038/cmi.2017.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/18/2017] [Indexed: 01/18/2023] Open
Affiliation(s)
- Hussein Issaoui
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - Nour Ghazzaui
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | | | - Claire Carrion
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | | | - Yves Denizot
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
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41
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The IgH 3' regulatory region and c-myc-induced B-cell lymphomagenesis. Oncotarget 2018; 8:7059-7067. [PMID: 27729620 PMCID: PMC5351691 DOI: 10.18632/oncotarget.12535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/05/2016] [Indexed: 01/18/2023] Open
Abstract
Deregulation and mutations of c-myc have been reported in multiple mature B-cell malignancies such as Burkitt lymphoma, myeloma and plasma cell lymphoma. After translocation into the immunoglobulin heavy chain (IgH) locus, c-myc is constitutively expressed under the control of active IgH cis-regulatory enhancers. Those located in the IgH 3 regulatory region (3RR) are master control elements of transcription. Over the past decade numerous convincing demonstrations of 3RRs contribution to mature c-myc-induced lymphomagenesis have been made using transgenic models with various types of IgH-c-myc translocations and transgenes. This review highlights how IgH 3RR physiological functions play a critical role in c-myc deregulation during lymphomagenesis.
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42
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Efficient role of IgH 3' regulatory region deficient B-cells in the development of oil granulomas. Oncotarget 2018; 7:38741-38749. [PMID: 27231852 PMCID: PMC5122425 DOI: 10.18632/oncotarget.9588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 04/29/2016] [Indexed: 01/18/2023] Open
Abstract
Functional B-cells are essential for the formation of oil granulomas. The IgH 3′ regulatory region (3′RR) activates important check-points during B-cell maturation. We investigated if 3′RR-deficient B-cells remain efficient to develop oil granulomas in response to pristine. B-cells expressing an IgH 3′RR-deficient allele were similarly recruited to wild type allele expressing B-cells in the granuloma. No differences were observed between 3′RR-deficient mice and control mice for granuloma numbers, cellular composition and ability to express mRNA transcripts for several pro- and anti-inflammatory cytokines. Altogether these results suggest a normal role for 3′RR-deficient B-cells in the development of an acute B-cell-mediated inflammatory response.
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43
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Saintamand A, Ghazzaui N, Issaoui H, Denizot Y. [The IgH 3'RR: Doctor Jekyll and Mister Hyde of B-cell maturation and lymphomagenesis]. Med Sci (Paris) 2017; 33:963-970. [PMID: 29200394 DOI: 10.1051/medsci/20173311013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The four transcriptional enhancers located in the 3' regulatory region (3'RR) of the IgH locus control the late phases of B-cell maturation, namely IgH locus transcription, somatic hypermutation and class switch recombination. Doctor Jekyll by nature, the 3'RR acts as Mister Hyde in case of oncogenic translocation at the IgH locus taking under its transcriptional control the translocated oncogene. The aim of this review is to show this duality on the basis of the latest scientific advances in the structure and function of the 3'RR and to hIghlight the targeting of the 3'RR as a potential therapeutic approach in mature B-cell lymphomas.
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Affiliation(s)
- Alexis Saintamand
- UMR CNRS 7276, Université de Limoges, rue Pr Descottes, 87025 Limoges, France
| | - Nour Ghazzaui
- UMR CNRS 7276, Université de Limoges, rue Pr Descottes, 87025 Limoges, France
| | - Hussein Issaoui
- UMR CNRS 7276, Université de Limoges, rue Pr Descottes, 87025 Limoges, France
| | - Yves Denizot
- UMR CNRS 7276, Université de Limoges, rue Pr Descottes, 87025 Limoges, France
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44
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Laffleur B, Debeaupuis O, Dalloul Z, Cogné M. B Cell Intrinsic Mechanisms Constraining IgE Memory. Front Immunol 2017; 8:1277. [PMID: 29180995 PMCID: PMC5694035 DOI: 10.3389/fimmu.2017.01277] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
Memory B cells and long-lived plasma cells are key elements of adaptive humoral immunity. Regardless of the immunoglobulin class produced, these cells can ensure long-lasting protection but also long-lasting immunopathology, thus requiring tight regulation of their generation and survival. Among all antibody classes, this is especially true for IgE, which stands as the most potent, and can trigger dramatic inflammatory reactions even when present in minute amounts. IgE responses and memory crucially protect against parasites and toxic components of venoms, conferring selective advantages and explaining their conservation in all mammalian species despite a parallel broad spectrum of IgE-mediated immunopathology. Long-term memory of sensitization and anaphylactic responses to allergens constitute the dark side of IgE responses, which can trigger multiple acute or chronic pathologic manifestations, some punctuated with life-threatening events. This Janus face of the IgE response and memory, both necessary and potentially dangerous, thus obviously deserves the most elaborated self-control schemes.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | | | - Zeinab Dalloul
- UMR 7276 Centre National de la Recherche Scientifique: Contrôle de la Réponse Immune B et des Lymphoproliférations, Université de Limoges, Limoges, France
| | - Michel Cogné
- UMR 7276 Centre National de la Recherche Scientifique: Contrôle de la Réponse Immune B et des Lymphoproliférations, Université de Limoges, Limoges, France.,Institut Universitaire de France, Paris, France
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45
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Le Noir S, Laffleur B, Carrion C, Garot A, Lecardeur S, Pinaud E, Denizot Y, Skok J, Cogné M. The IgH locus 3' cis-regulatory super-enhancer co-opts AID for allelic transvection. Oncotarget 2017; 8:12929-12940. [PMID: 28088785 PMCID: PMC5355067 DOI: 10.18632/oncotarget.14585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/01/2017] [Indexed: 11/25/2022] Open
Abstract
Immunoglobulin heavy chain (IgH) alleles have ambivalent relationships: they feature both allelic exclusion, ensuring monoallelic expression of a single immunoglobulin (Ig) allele, and frequent inter-allelic class-switch recombination (CSR) reassembling genes from both alleles. The IgH locus 3' regulatory region (3'RR) includes several transcriptional cis-enhancers promoting activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) and CSR, and altogether behaves as a strong super-enhancer. It can also promote deregulated expression of translocated oncogenes during lymphomagenesis. Besides these rare, illegitimate and pathogenic interactions, we now show that under physiological conditions, the 3'RR super-enhancer supports not only legitimate cis- , but also trans-recruitment of AID, contributing to IgH inter-allelic proximity and enabling the super-enhancer on one allele to stimulate biallelic SHM and CSR. Such inter-allelic activating interactions define transvection, a phenomenon well-known in drosophila but rarely observed in mammalian cells, now appearing as a unique feature of the IgH 3'RR super-enhancer.
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Affiliation(s)
- Sandrine Le Noir
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Brice Laffleur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Claire Carrion
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Armand Garot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Sandrine Lecardeur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Eric Pinaud
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Yves Denizot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Jane Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michel Cogné
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
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46
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Le Noir S, Boyer F, Lecardeur S, Brousse M, Oruc Z, Cook-Moreau J, Denizot Y, Cogné M. Functional anatomy of the immunoglobulin heavy chain 3΄ super-enhancer needs not only core enhancer elements but also their unique DNA context. Nucleic Acids Res 2017; 45:5829-5837. [PMID: 28369649 PMCID: PMC5449612 DOI: 10.1093/nar/gkx203] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/22/2017] [Indexed: 01/04/2023] Open
Abstract
Cis-regulatory elements feature clustered sites for transcription factors, defining core enhancers and have inter-species homology. The mouse IgH 3΄ regulatory region (3'RR), a major B-cell super-enhancer, consists of four of such core enhancers, scattered throughout more than 25 kb of packaging 'junk DNA', the sequence of which is not conserved but follows a unique palindromic architecture which is conserved in all mammalian species. The 3'RR promotes long-range interactions and potential IgH loops with upstream promoters, controlling class switch recombination (CSR) and somatic hypermutation (SHM). It was thus of interest to determine whether this functional architecture also involves the specific functional structure of the super-enhancer itself, potentially promoted by its symmetric DNA shell. Since many transgenic 3'RR models simply linked core enhancers without this shell, it was also important to compare such a 'core 3'RR' (c3'RR) with the intact full-length super-enhancer in an actual endogenous IgH context. Packaging DNA between 3'RR core enhancers proved in fact to be necessary for optimal SHM, CSR and IgH locus expression in plasma cells. This reveals that packaging DNA can matter in the functional anatomy of a super-enhancer, and that precise evaluation of such elements requires full consideration of their global architecture.
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Affiliation(s)
- Sandrine Le Noir
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - François Boyer
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Sandrine Lecardeur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Mylène Brousse
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Zeliha Oruc
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Jeanne Cook-Moreau
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Yves Denizot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Michel Cogné
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France.,Institut Universitaire de France, Paris, France
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47
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Marina-Zárate E, Pérez-García A, Ramiro AR. CCCTC-Binding Factor Locks Premature IgH Germline Transcription and Restrains Class Switch Recombination. Front Immunol 2017; 8:1076. [PMID: 28928744 PMCID: PMC5591319 DOI: 10.3389/fimmu.2017.01076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/18/2017] [Indexed: 01/02/2023] Open
Abstract
In response to antigenic stimulation B cells undergo class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) to replace the primary IgM/IgD isotypes by IgG, IgE, or IgA. CSR is initiated by activation-induced cytidine deaminase (AID) through the deamination of cytosine residues at the switch (S) regions of IgH. B cell stimulation promotes germline transcription (GLT) of specific S regions, a necessary event prior to CSR because it facilitates AID access to S regions. Here, we show that CCCTC-binding factor (CTCF)-deficient mice are severely impaired in the generation of germinal center B cells and plasma cells after immunization in vivo, most likely due to impaired cell survival. Importantly, we find that CTCF-deficient B cells have an increased rate of CSR under various stimulation conditions in vitro. This effect is not secondary to altered cell proliferation or AID expression in CTCF-deficient cells. Instead, we find that CTCF-deficient B cells harbor an increased mutation frequency at switch regions, probably reflecting an increased accessibility of AID to IgH in the absence of CTCF. Moreover, CTCF deficiency triggers premature GLT of S regions in naïve B cells. Our results indicate that CTCF restricts CSR by enforcing GLT silencing and limiting AID access to IgH.
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Affiliation(s)
- Ester Marina-Zárate
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Arantxa Pérez-García
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Almudena R Ramiro
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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48
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IgD class switch recombination is not controlled through the immunoglobulin heavy chain 3' regulatory region super-enhancer. Cell Mol Immunol 2017; 14:871-874. [PMID: 29026218 DOI: 10.1038/cmi.2017.81] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 01/18/2023] Open
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49
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Liu J, Law RA, Koles PG, Saxe JC, Bottomley M, Sulentic CE. Allelic frequencies of the hs1.2 enhancer within the immunoglobulin heavy chain region in Dayton, Ohio patients screened for celiac disease with duodenal biopsy. Dig Liver Dis 2017; 49:887-892. [PMID: 28473300 PMCID: PMC5511760 DOI: 10.1016/j.dld.2017.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genetic and environmental factors contribute to the development of celiac disease (CD), but specific genetic predisposing factors remain poorly understood. One candidate is allele 2 of the hs1.2 enhancer within the immunoglobulin heavy chain region. In humans, there are four possible alleles and a previous study of an Italian cohort demonstrated a significantly increased frequency of allele 2 in patients with CD. AIMS The purpose of the current study was to determine if a similar association between allele 2 and CD exists in an American population from Dayton, OH. METHODS Subjects were screened for CD via esophagogastroduodenoscopy with duodenal biopsy. All biopsies were microscopically scored using a modified Marsh-Oberhuber classification. DNA was isolated from patients' buccal cells for hs1.2 genotype analysis using PCR. RESULTS Unlike the Italian cohort, allele 2 frequency was not significantly different in patients with histopathologic evidence of CD compared to patients without such evidence. However, our patient population as a whole demonstrated a significantly increased allele 2 frequency when compared to that previously reported within diverse ethnic populations. CONCLUSIONS Since our comparative control patients do not necessarily reflect a healthy control population, an overall increase in allele 2 may reflect an association between allele 2 of the hs1.2 enhancer and a spectrum of gastrointestinal disorders.
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Affiliation(s)
- Jing Liu
- Departments of Pharmacology & Toxicology, Wright State University, Dayton, OH
| | - Rebecca A. Law
- Departments of Pharmacology & Toxicology, Wright State University, Dayton, OH
| | - Paul G. Koles
- Departments of Pathology, Wright State University, Dayton, OH
| | - Jonathan C. Saxe
- Departments of Medicine, Wright State University, Dayton, OH,Departments of Dayton Gastroenterology, Dayton, OH
| | - Michael Bottomley
- Departments of Boonshoft School of Medicine and the Statistical Consulting Center, Wright State University, Dayton, OH
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50
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Inducible CTCF insulator delays the IgH 3' regulatory region-mediated activation of germline promoters and alters class switching. Proc Natl Acad Sci U S A 2017; 114:6092-6097. [PMID: 28533409 DOI: 10.1073/pnas.1701631114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to switch from IgM expression to the expression of downstream isotypes. CSR is preceded by inducible germline (GL) transcription of the constant genes and is controlled by the 3' regulatory region (3'RR) in a stimulus-dependent manner. Why the 3'RR-mediated up-regulation of GL transcription is delayed to the mature B-cell stage is presently unknown. Here we show that mice devoid of an inducible CTCF binding element, located in the α constant gene, display a marked isotype-specific increase of GL transcription in developing and resting splenic B cells and altered CSR in activated B cells. Moreover, insertion of a GL promoter downstream of the CTCF insulator led to premature activation of the ectopic promoter. This study provides functional evidence that the 3'RR has a developmentally controlled potential to constitutively activate GL promoters but that this activity is delayed, at least in part, by the CTCF insulator, which borders a transcriptionally active domain established by the 3'RR in developing B cells.
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