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Zhao B, Xia Z, Yang B, Guo Y, Zhou R, Gu M, Liu M, Li Q, Bai W, Huang J, Zhang X, Zhu C, Leung KT, Chen C, Dong J. USP7 promotes IgA class switching through stabilizing RUNX3 for germline transcription activation. Cell Rep 2024; 43:114194. [PMID: 38735043 DOI: 10.1016/j.celrep.2024.114194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/04/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024] Open
Abstract
Class switch recombination (CSR) diversifies the effector functions of antibodies and involves complex regulation of transcription and DNA damage repair. Here, we show that the deubiquitinase USP7 promotes CSR to immunoglobulin A (IgA) and suppresses unscheduled IgG switching in mature B cells independent of its role in DNA damage repair, but through modulating switch region germline transcription. USP7 depletion impairs Sα transcription, leading to abnormal activation of Sγ germline transcription and increased interaction with the CSR center via loop extrusion for unscheduled IgG switching. Rescue of Sα transcription by transforming growth factor β (TGF-β) in USP7-deleted cells suppresses Sγ germline transcription and prevents loop extrusion toward IgG CSR. Mechanistically, USP7 protects transcription factor RUNX3 from ubiquitination-mediated degradation to promote Sα germline transcription. Our study provides evidence for active transcription serving as an anchor to impede loop extrusion and reveals a functional interplay between USP7 and TGF-β signaling in promoting RUNX3 expression for efficient IgA CSR.
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Affiliation(s)
- Bo Zhao
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhigang Xia
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Beibei Yang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yao Guo
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ruizhi Zhou
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mingyu Gu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Meiling Liu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qingcheng Li
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wanyu Bai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junbin Huang
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuefei Zhang
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Chengming Zhu
- Center for Scientific Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Kam Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Chen
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.
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Gothwal SK, Refaat AM, Nakata M, Stanlie A, Honjo T, Begum N. BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL. Nucleic Acids Res 2024; 52:4422-4439. [PMID: 38567724 PMCID: PMC11077081 DOI: 10.1093/nar/gkae204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 05/09/2024] Open
Abstract
Efficient repair of DNA double-strand breaks in the Ig heavy chain gene locus is crucial for B-cell antibody class switch recombination (CSR). The regulatory dynamics of the repair pathway direct CSR preferentially through nonhomologous end joining (NHEJ) over alternative end joining (AEJ). Here, we demonstrate that the histone acetyl reader BRD2 suppresses AEJ and aberrant recombination as well as random genomic sequence capture at the CSR junctions. BRD2 deficiency impairs switch (S) region synapse, optimal DNA damage response (DDR), and increases DNA break end resection. Unlike BRD4, a similar bromodomain protein involved in NHEJ and CSR, BRD2 loss does not elevate RPA phosphorylation and R-loop formation in the S region. As BRD2 stabilizes the cohesion loader protein NIPBL in the S regions, the loss of BRD2 or NIPBL shows comparable deregulation of S-S synapsis, DDR, and DNA repair pathway choice during CSR. This finding extends beyond CSR, as NIPBL and BRD4 have been linked to Cornelia de Lange syndrome, a developmental disorder exhibiting defective NHEJ and Ig isotype switching. The interplay between these proteins sheds light on the intricate mechanisms governing DNA repair and immune system functionality.
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Affiliation(s)
- Santosh K Gothwal
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Andre Stanlie
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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3
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Wright NE, Kennedy DE, Ai J, Veselits ML, Attaway M, Yoon YM, Durkee MS, Veselits J, Maienschein-Cline M, Mandal M, Clark MR. BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591154. [PMID: 38712068 PMCID: PMC11071454 DOI: 10.1101/2024.04.25.591154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Germinal center (GC) B cells segregate into three subsets that compartmentalize the antagonistic molecular programs of selection, proliferation, and somatic hypermutation. In bone marrow, the epigenetic reader BRWD1 orchestrates and insulates the sequential stages of cell proliferation and Igk recombination. We hypothesized BRWD1 might play similar insulative roles in the periphery. In Brwd1 -/- follicular B cells, GC initiation and class switch recombination following immunization were inhibited. In contrast, in Brwd1 -/- GC B cells there was admixing of chromatin accessibility across GC subsets and transcriptional dysregulation including induction of inflammatory pathways. This global molecular GC dysregulation was associated with specific defects in proliferation, affinity maturation, and tolerance. These data suggest that GC subset identity is required for some but not all GC-attributed functions. Furthermore, these data demonstrate a central role for BRWD1 in orchestrating epigenetic transitions at multiple steps along B cell developmental and activation pathways.
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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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5
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Al Jamal I, Parquet M, Guiyedi K, Aoufouchi S, Le Guillou M, Rizzo D, Pollet J, Dupont M, Boulin M, Faumont N, Boutouil H, Jardin F, Ruminy P, El Hamel C, Lerat J, Al Hamaoui S, Makdissy N, Feuillard J, Gachard N, Peron S. IGH 3'RR recombination uncovers a non-germinal center imprint and c-MYC-dependent IGH rearrangement in unmutated chronic lymphocytic leukemia. Haematologica 2024; 109:466-478. [PMID: 37496419 PMCID: PMC10828775 DOI: 10.3324/haematol.2023.282897] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable indolent non-Hodgkin lymphoma characterized by tumor B cells that weakly express a B-cell receptor. The mutational status of the variable region (IGHV) within the immunoglobulin heavy chain (IGH) locus is an important prognosis indicator and raises the question of the CLL cell of origin. Mutated IGHV gene CLL are genetically imprinted by activation-induced cytidine deaminase (AID). AID is also required for IGH rearrangements: class switch recombination and recombination between switch Mu (Sμ) and the 3' regulatory region (3'RR) (Sμ-3'RRrec). The great majority of CLL B cells being unswitched led us to examine IGH rearrangement blockade in CLL. Our results separated CLL into two groups on the basis of Sμ-3'RRrec counts per sample: Sμ-3'RRrecHigh cases (mostly unmutated CLL) and Sμ-3'RRrecLow cases (mostly mutated CLL), but not based on the class switch recombination junction counts. Sμ-3'RRrec appeared to be ongoing in Sμ-3'RRrecHigh CLL cells and comparison of Sμ-3'RRrec junction structural features pointed to different B-cell origins for both groups. In accordance with IGHV mutational status and PIM1 mutation rate, Sμ-3'RRrecHigh CLL harbor a non-germinal center experienced B-cell imprint while Sμ-3'RRrecLow CLL are from AID-experienced B cells from a secondary lymphoid organ. In addition to the proposals already made concerning the CLL cell of origin, our study highlights that analysis of IGH recombinatory activity can identify CLL cases from different origins. Finally, on-going Sμ-3'RRrec in Sμ-3'RRrecHigh cells appeared to presumably be the consequence of high c-MYC expression, as c-MYC overexpression potentiated IGH rearrangements and Sμ-3'RRrec, even in the absence of AID for the latter.
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Affiliation(s)
- Israa Al Jamal
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Milene Parquet
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Kenza Guiyedi
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Said Aoufouchi
- CNRS UMR9019, Gustave Roussy, B-cell and Genome Plasticity Team, Villejuif, France and Universite Paris-Saclay, Orsay
| | - Morwenna Le Guillou
- CNRS UMR9019, Gustave Roussy, B-cell and Genome Plasticity Team, Villejuif, France and Universite Paris-Saclay, Orsay
| | - David Rizzo
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Justine Pollet
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Marine Dupont
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Melanie Boulin
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Nathalie Faumont
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Hend Boutouil
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Fabrice Jardin
- Inserm U1245 and Department of Henri-Becquerel Hematology Center and Normandie Univ UNIROUEN, Rouen
| | - Philippe Ruminy
- Inserm U1245 and Department of Henri-Becquerel Hematology Center and Normandie Univ UNIROUEN, Rouen
| | - Chahrazed El Hamel
- Collection Biologique Hopital de la Mere et de l'Enfant (CB-HME), Department of Pediatrics, Limoges University Hospital, Limoges
| | - Justine Lerat
- Department of Otorinolaryngology, Limoges University Hospital, Limoges
| | - Samar Al Hamaoui
- Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Nehman Makdissy
- Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Jean Feuillard
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Nathalie Gachard
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Sophie Peron
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges.
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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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Kabrani E, Saha T, Di Virgilio M. DNA repair and antibody diversification: the 53BP1 paradigm. Trends Immunol 2023; 44:782-791. [PMID: 37640588 DOI: 10.1016/j.it.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
The DNA double-strand break (DSB) repair factor 53BP1 has long been implicated in V(D)J and class switch recombination (CSR) of mammalian lymphocyte receptors. However, the dissection of the underlying molecular activities is hampered by a paucity of studies [V(D)J] and plurality of phenotypes (CSR) associated with 53BP1 deficiency. Here, we revisit the currently accepted roles of 53BP1 in antibody diversification in view of the recent identification of its downstream effectors in DSB protection and latest advances in genome architecture. We propose that, in addition to end protection, 53BP1-mediated end-tethering stabilization is essential for CSR. Furthermore, we support a pre-DSB role during V(D)J recombination. Our perspective underscores the importance of evaluating repair of DSBs in relation to their dynamic architectural contexts.
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Affiliation(s)
- Eleni Kabrani
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Freie Universität Berlin, Berlin 14195, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation. Nat Commun 2023; 14:1225. [PMID: 36869028 PMCID: PMC9984487 DOI: 10.1038/s41467-023-36414-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
The mouse Igh locus is organized into a developmentally regulated topologically associated domain (TAD) that is divided into subTADs. Here we identify a series of distal VH enhancers (EVHs) that collaborate to configure the locus. EVHs engage in a network of long-range interactions that interconnect the subTADs and the recombination center at the DHJH gene cluster. Deletion of EVH1 reduces V gene rearrangement in its vicinity and alters discrete chromatin loops and higher order locus conformation. Reduction in the rearrangement of the VH11 gene used in anti-PtC responses is a likely cause of the observed reduced splenic B1 B cell compartment. EVH1 appears to block long-range loop extrusion that in turn contributes to locus contraction and determines the proximity of distant VH genes to the recombination center. EVH1 is a critical architectural and regulatory element that coordinates chromatin conformational states that favor V(D)J rearrangement.
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9
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A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Mol Cell 2023; 83:681-697.e7. [PMID: 36736317 DOI: 10.1016/j.molcel.2023.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 11/04/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023]
Abstract
Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.
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10
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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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11
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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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12
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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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13
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Lineage tracing reveals B cell antibody class switching is stochastic, cell-autonomous, and tuneable. Immunity 2022; 55:1843-1855.e6. [PMID: 36108634 DOI: 10.1016/j.immuni.2022.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
Abstract
To optimize immunity to pathogens, B lymphocytes generate plasma cells with functionally diverse antibody isotypes. By lineage tracing single cells within differentiating B cell clones, we identified the heritability of discrete fate controlling mechanisms to inform a general mathematical model of B cell fate regulation. Founder cells highly influenced clonal plasma-cell fate, whereas class switch recombination (CSR) was variegated within clones. In turn, these CSR patterns resulted from independent all-or-none expression of both activation-induced cytidine deaminase (AID) and IgH germline transcription (GLT), with the latter being randomly re-expressed after each cell division. A stochastic model premised on these molecular transition rules accurately predicted antibody switching outcomes under varied conditions in vitro and during an immune response in vivo. Thus, the generation of functionally diverse antibody types follows rules of autonomous cellular programming that can be adapted and modeled for the rational control of antibody classes for potential therapeutic benefit.
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14
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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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15
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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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16
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Oudinet C, Zhang X, Puget N, Kyritsis N, Leduc C, Braikia FZ, Dauba A, Alt FW, Khamlichi AA. Switch Tandem Repeats Influence the Choice of the Alternative End-Joining Pathway in Immunoglobulin Class Switch Recombination. Front Immunol 2022; 13:870933. [PMID: 35651614 PMCID: PMC9149575 DOI: 10.3389/fimmu.2022.870933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 11/23/2022] Open
Abstract
Immunoglobulin class switch recombination (CSR) plays an important role in humoral imm\une responses by changing the effector functions of antibodies. CSR occurs between highly repetitive switch (S) sequences located upstream of immunoglobulin constant gene exons. Switch sequences differ in size, the nature of their repeats, and the density of the motifs targeted by the activation-induced cytidine deaminase (AID), the enzyme that initiates CSR. CSR involves double-strand breaks (DSBs) at the universal Sµ donor region and one of the acceptor S regions. The DSBs ends are fused by the classical non-homologous end-joining (C-NHEJ) and the alternative-NHEJ (A-NHEJ) pathways. Of the two pathways, the A-NHEJ displays a bias towards longer junctional micro-homologies (MHs). The Sµ region displays features that distinguish it from other S regions, but the molecular basis of Sµ specificity is ill-understood. We used a mouse line in which the downstream Sγ3 region was put under the control of the Eµ enhancer, which regulates Sµ, and analyzed its recombination activity by CSR-HTGTS. Here, we show that provision of Eµ enhancer to Sγ3 is sufficient to confer the recombinational features of Sµ to Sγ3, including efficient AID recruitment, enhanced internal deletions and robust donor function in CSR. Moreover, junctions involving Sγ3 display a bias for longer MH irrespective of sequence homology with switch acceptor sites. The data suggest that the propensity for increased MH usage is an intrinsic property of Sγ3 sequence, and that the tandem repeats of the donor site influence the choice of the A-NHEJ.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Xuefei Zhang
- Program in Cellular and Molecular Medicine, Howard Hughes Medical Institute, Department of Genetics, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Nadine Puget
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Nia Kyritsis
- Program in Cellular and Molecular Medicine, Howard Hughes Medical Institute, Department of Genetics, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Claire Leduc
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Howard Hughes Medical Institute, Department of Genetics, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
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17
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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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18
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Sun X, Bai J, Xu J, Xi X, Gu M, Zhu C, Xue H, Chen C, Dong J. Multiple DSB Resection Activities Redundantly Promote Alternative End Joining-Mediated Class Switch Recombination. Front Cell Dev Biol 2021; 9:767624. [PMID: 34926456 PMCID: PMC8671047 DOI: 10.3389/fcell.2021.767624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023] Open
Abstract
Alternative end joining (A-EJ) catalyzes substantial level of antibody class switch recombination (CSR) in B cells deficient for classical non-homologous end joining, featuring increased switch (S) region DSB resection and junctional microhomology (MH). While resection has been suggested to initiate A-EJ in model DSB repair systems using engineered endonucleases, the contribution of resection factors to A-EJ-mediated CSR remains unclear. In this study, we systematically dissected the requirement for individual DSB resection factors in A-EJ-mediated class switching with a cell-based assay system and high-throughput sequencing. We show that while CtIP and Mre11 both are mildly required for CSR in WT cells, they play more critical roles in mediating A-EJ CSR, which depend on the exonuclease activity of Mre11. While DNA2 and the helicase/HRDC domain of BLM are required for A-EJ by mediating long S region DSB resection, in contrast, Exo1's resection-related function does not play any obvious roles for class switching in either c-NHEJ or A-EJ cells, or mediated in an AID-independent manner by joining of Cas9 breaks. Furthermore, ATM and its kinase activity functions at least in part independent of CtIP/Mre11 to mediate A-EJ switching in Lig4-deficient cells. In stark contrast to Lig4 deficiency, 53BP1-deficient cells do not depend on ATM/Mre11/CtIP for residual joining. We discuss the roles for each resection factor in A-EJ-mediated CSR and suggest that the extent of requirements for resection is context dependent.
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Affiliation(s)
- Xikui Sun
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jingning Bai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiejie Xu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xiaoli Xi
- Department of Gastroenterology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingyu Gu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Chengming Zhu
- Research Center of the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hongman Xue
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
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19
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The role of HIRA-dependent H3.3 deposition and its modifications in the somatic hypermutation of immunoglobulin variable regions. Proc Natl Acad Sci U S A 2021; 118:2114743118. [PMID: 34873043 DOI: 10.1073/pnas.2114743118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The H3.3 histone variant and its chaperone HIRA are involved in active transcription, but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells are not yet fully understood. In this study, we show that the knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of the immunoglobulin heavy chain (IgH) in the human Ramos B cell line without changing the levels of activation-induced deaminase and other major proteins known to be involved in SHM. Except for H3K79me2/3 and Spt5, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells, and this was accompanied by decreased nascent transcription in the IgH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the IgH locus was also reduced in the HIRA KO. Somewhat surprisingly, HIRA loss increased the chromatin accessibility of the IgH V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with the HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IgH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription-associated chromatin structure and accessibility contribute to SHM in human B cells.
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20
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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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21
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Shen HM, Wuerffel R, Cantillo JF, Priyadarshi S, Lei X, Liang J, Wu YL, Kenter AL. Loop extrusion promotes an alternate pathway for isotype switching. Cell Rep 2021; 37:110059. [PMID: 34818547 PMCID: PMC8979556 DOI: 10.1016/j.celrep.2021.110059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Class-switch recombination (CSR) involves replacement of the Cμ
constant region with another downstream CH region. CSR is initiated
by activation-induced cytidine deaminase (AID)-mediated DNA breaks that are
targeted to transcriptionally active switch (S) regions. S region promoters
(Prs) direct synapsis by associating with the Eμ and 3′Eα
enhancers that jointly anchor a chromatin loop. We report that asymmetric loop
extrusion allows 3′Eα to track along the locus and form Pr-Pr-E
interactions that mediate CSR between downstream S regions, followed by
switching to donor Sμ. This alternative pathway bypasses sequential
switching and creates immunoglobulin (Ig)E+ B cells in the absence of
IgG1 expression. Based on the analysis of diagnostic CSR products in B cell
subsets, we identify a BCR-negative cell intermediate that is pivotal to
efficient CSR. Shen et al. report that 3′Eα tracks along the Igh locus via
unidirectional loop extrusion to form germline transcript promoter (Pr)-Pr-E
interactions that mediate an alternative CSR pathway. B cell intermediates of
CSR are identified, which are AID-dependent, surface BCR-negative, and in the
G1 phase of the cell cycle.
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Affiliation(s)
- Hong Ming Shen
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Jose F Cantillo
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Saurabh Priyadarshi
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Xue Lei
- Department of Bioengineering, University of Illinois Colleges of Engineering and Medicine, Chicago, IL 60612-7344, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois Colleges of Engineering and Medicine, Chicago, IL 60612-7344, USA
| | - Yee Ling Wu
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA.
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22
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Rogers GL, Cannon PM. Genome edited B cells: a new frontier in immune cell therapies. Mol Ther 2021; 29:3192-3204. [PMID: 34563675 PMCID: PMC8571172 DOI: 10.1016/j.ymthe.2021.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022] Open
Abstract
Cell therapies based on reprogrammed adaptive immune cells have great potential as "living drugs." As first demonstrated clinically for engineered chimeric antigen receptor (CAR) T cells, the ability of such cells to undergo clonal expansion in response to an antigen promotes both self-renewal and self-regulation in vivo. B cells also have the potential to be developed as immune cell therapies, but engineering their specificity and functionality is more challenging than for T cells. In part, this is due to the complexity of the immunoglobulin (Ig) locus, as well as the requirement for regulated expression of both cell surface B cell receptor and secreted antibody isoforms, in order to fully recapitulate the features of natural antibody production. Recent advances in genome editing are now allowing reprogramming of B cells by site-specific engineering of the Ig locus with preformed antibodies. In this review, we discuss the potential of engineered B cells as a cell therapy, the challenges involved in editing the Ig locus and the advances that are making this possible, and envision future directions for this emerging field of immune cell engineering.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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23
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Dalloul I, Laffleur B, Dalloul Z, Wehbi B, Jouan F, Brauge B, Derouault P, Moreau J, Kracker S, Fischer A, Durandy A, Le Noir S, Cogné M. UnAIDed Class Switching in Activated B-Cells Reveals Intrinsic Features of a Self-Cleaving IgH Locus. Front Immunol 2021; 12:737427. [PMID: 34777346 PMCID: PMC8581400 DOI: 10.3389/fimmu.2021.737427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Activation-induced deaminase (AID) is the major actor of immunoglobulin (Ig) gene diversification in germinal center B-cells. From its first description, it was considered as mandatory for class switch recombination (CSR), and this discovery initiated a long quest for all of the AID-interacting factors controlling its activity. The mechanisms focusing AID-mediated DNA lesions to given target sequences remain incompletely understood with regards the detailed characterization of optimal substrates in which cytidine deamination will lead to double strand breaks (DSBs) and chromosomal cleavage. In an effort to reconsider whether such CSR breaks absolutely require AID, we herein provide evidence, based on deep-sequencing approaches, showing that this dogma is not absolute in both human and mouse B lymphocytes. In activated B-cells from either AID-deficient mice or human AID-deficient patients, we report an intrinsic ability of the IgH locus to undergo "on-target" cleavage and subsequent synapsis of broken regions in conditions able to yield low-level CSR. DNA breaks occur in such conditions within the same repetitive S regions usually targeted by AID, but their repair follows a specific pathway with increased usage of microhomology-mediated repair. These data further demonstrate the role of AID machinery as not initiating de novo chromosomal cleavage but rather catalyzing a process which spontaneously initiates at low levels in an appropriately conformed IgH locus.
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Affiliation(s)
- Iman Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Brice Laffleur
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Zeinab Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Batoul Wehbi
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Florence Jouan
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Baptiste Brauge
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Paco Derouault
- Centre Hospitalier Universitaire (CHU) Dupuytren, Limoges, France
| | - Jeanne Moreau
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Sven Kracker
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Alain Fischer
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Anne Durandy
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Sandrine Le Noir
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Michel Cogné
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
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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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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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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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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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Three-dimensional genome rewiring during the development of antibody-secreting cells. Biochem Soc Trans 2021; 48:1109-1119. [PMID: 32453419 PMCID: PMC7329350 DOI: 10.1042/bst20191104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023]
Abstract
The development of B lymphocytes into antibody-secreting plasma cells is central to the adaptive immune system in that it confers protective and specific antibody response against invading pathogen. This developmental process involves extensive morphological and functional alterations that begin early after antigenic stimulation. These include chromatin restructuring that is critical in regulating gene expression, DNA rearrangement and other cellular processes. Here we outline the recent understanding of the three-dimensional architecture of the genome, specifically focused on its contribution to the process of B cell activation and terminal differentiation into antibody-secreting cells.
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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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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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Saha T, Sundaravinayagam D, Di Virgilio M. Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination. Trends Biochem Sci 2020; 46:184-199. [PMID: 33250286 DOI: 10.1016/j.tibs.2020.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AID-induced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation.
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Affiliation(s)
- Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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32
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Wu L, Schatz DG. Making ends meet in class switch recombination. Cell Res 2020; 30:711-712. [PMID: 32451457 PMCID: PMC7609326 DOI: 10.1038/s41422-020-0342-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lizhen Wu
- Department of immunobiology, Yale School of Medicine, New Haven, CT, 06519, USA
| | - David G Schatz
- Department of immunobiology, Yale School of Medicine, New Haven, CT, 06519, USA.
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DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2020; 117:22953-22961. [PMID: 32868446 DOI: 10.1073/pnas.2007455117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical nonhomologous end-joining (cNHEJ) factor. Naïve B cells undergo class switch recombination (CSR) to generate antibodies with different isotypes by joining two DNA double-strand breaks at different switching regions via the cNHEJ pathway. DNA-PK and the cNHEJ pathway play important roles in the DNA repair phase of CSR. To initiate cNHEJ, KU binds to DNA ends and recruits and activates DNA-PK. Activated DNA-PK phosphorylates DNA-PKcs at the S2056 and T2609 clusters. Loss of T2609 cluster phosphorylation increases radiation sensitivity but whether T2609 phosphorylation has a role in physiological DNA repair remains elusive. Using the DNA-PKcs 5A mouse model carrying alanine substitutions at the T2609 cluster, here we show that loss of T2609 phosphorylation of DNA-PKcs does not affect the CSR efficiency. Yet, the CSR junctions recovered from DNA-PKcs 5A/5A B cells reveal increased chromosomal translocations, extensive use of distal switch regions (consistent with end resection), and preferential usage of microhomology-all signs of the alternative end-joining pathway. Thus, these results uncover a role of DNA-PKcs T2609 phosphorylation in promoting cNHEJ repair pathway choice during CSR.
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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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Nandi S, Liang G, Sindhava V, Angireddy R, Basu A, Banerjee S, Hodawadekar S, Zhang Y, Avadhani NG, Sen R, Atchison ML. YY1 control of mitochondrial-related genes does not account for regulation of immunoglobulin class switch recombination in mice. Eur J Immunol 2020; 50:822-838. [PMID: 32092784 PMCID: PMC8287517 DOI: 10.1002/eji.201948385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/30/2019] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Immunoglobulin class switch recombination (CSR) occurs in activated B cells with increased mitochondrial mass and membrane potential. Transcription factor Yin Yang 1 (YY1) is critical for CSR and for formation of the DNA loops involved in this process. We therefore sought to determine if YY1 knockout impacts mitochondrial gene expression and mitochondrial function in murine splenic B cells, providing a potential mechanism for regulating CSR. We identified numerous genes in splenic B cells differentially regulated when cells are induced to undergo CSR. YY1 conditional knockout caused differential expression of 1129 genes, with 59 being mitochondrial-related genes. ChIP-seq analyses showed YY1 was directly bound to nearly half of these mitochondrial-related genes. Surprisingly, at the time when YY1 knockout dramatically reduces DNA loop formation and CSR, mitochondrial mass and membrane potential were not significantly impacted, nor was there a significant change in mitochondrial oxygen consumption, extracellular acidification rate, or mitochondrial complex I or IV activities. Our results indicate that YY1 regulates numerous mitochondrial-related genes in splenic B cells, but this does not account for the impact of YY1 on CSR or long-distance DNA loop formation.
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Affiliation(s)
- Satabdi Nandi
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanxiang Liang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vishal Sindhava
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajesh Angireddy
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Basu
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarmistha Banerjee
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suchita Hodawadekar
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Zhang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Narayan G. Avadhani
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Michael L. Atchison
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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36
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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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37
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Feng Y, Seija N, Di Noia JM, Martin A. AID in Antibody Diversification: There and Back Again. Trends Immunol 2020; 41:586-600. [PMID: 32434680 PMCID: PMC7183997 DOI: 10.1016/j.it.2020.04.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023]
Abstract
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic hypermutation (SHM) and class switch recombination (CSR). AID thus potentiates the humoral response to clear pathogens. Marking the 20th anniversary of the discovery of AID, we review the current understanding of AID function. We discuss AID biochemistry and how error-free forms of DNA repair are co-opted to prioritize mutagenesis over accuracy during antibody diversification. We discuss the regulation of DNA double-strand break (DSB) repair pathways during CSR. We describe genomic targeting of AID as a multilayered process involving chromatin architecture, cis- and trans-acting factors, and determining mutagenesis – distinct from AID occupancy at loci that are spared from mutation. Subverted base excision repair (BER) and mismatch repair (MMR) pathways act concertedly to generate antibody sequence diversity during SHM. In CSR, DNA DSBs are repaired by the nonhomologous end-joining pathway involving the 53BP1–Rif1–Shieldin axis, and by an alternative end-joining pathway involving HMCES (5-Hydroxymethylcytosine binding, ES-cell-specific) that binds and protects resected DSB ends. Genomic targeting of AID appears to be multilayered, with inbuilt redundancy, but robust enough to ensure that most of the genome is spared from AID activity. Cis elements and genome topology act together with trans-acting factors involved in transcription and RNA processing to determine AID activity at specific Ig regions. Other loci sharing genomic and transcriptional features with the Ig are collaterally targeted during SHM and CSR.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Noé Seija
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Javier M Di Noia
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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38
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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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39
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Ghazzaui N, Issaoui H, Ferrad M, Carrion C, Cook-Moreau J, Denizot Y, Boyer F. Eμ and 3'RR transcriptional enhancers of the IgH locus cooperate to promote c-myc-induced mature B-cell lymphomas. Blood Adv 2020; 4:28-39. [PMID: 31899800 PMCID: PMC6960469 DOI: 10.1182/bloodadvances.2019000845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023] Open
Abstract
Numerous B-cell lymphomas feature translocations linking oncogenes to different locations in the immunoglobulin heavy chain (IgH) locus. During Burkitt lymphoma (BL), IgH breakpoints for c-myc translocation stand either close to JH segments or within switch regions. Transcription, accessibility, and remodeling of the IgH locus are under the control of the 2 potent cis-acting enhancer elements: Eμ and the 3' regulatory region (3'RR). To ensure their respective contributions to oncogene deregulation in the context of the endogenous IgH locus, we studied transgenic mice harboring a knock-in of c-myc in various positions of the IgH locus (3' to JH segments, 5' to Cμ with Eμ deletion and Cα). The observed spectrum of tumors, kinetics of emergence, and transcriptome analysis provide strong evidence that both Eμ and 3'RR deregulate c-myc and cooperate together to promote B-cell lymphomagenesis. Transgenics mimicking endemic BL (with c-myc placed 3' to JH segments) exhibited the highest rate of B-cell lymphoma emergence, the highest Ki67 index of proliferation, and the highest transcriptomic similarities to human BL. The 3'RR enhancer alone deregulated c-myc and initiated the development of BL-like lymphomas, suggesting that its targeting would be of therapeutic interest to reduce c-myc oncogenicity in vivo.
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Affiliation(s)
- Nour Ghazzaui
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - Hussein Issaoui
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - Mélissa Ferrad
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - Claire Carrion
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - Yves Denizot
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
| | - François Boyer
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, Institut National de la Santé et de la Recherche Médicale U1262, Equipe Labellisée Ligue 2018, Université de Limoges, Limoges, France
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40
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Abstract
DNA damage occurs on exposure to genotoxic agents and during physiological DNA transactions. DNA double-strand breaks (DSBs) are particularly dangerous lesions that activate DNA damage response (DDR) kinases, leading to initiation of a canonical DDR (cDDR). This response includes activation of cell cycle checkpoints and engagement of pathways that repair the DNA DSBs to maintain genomic integrity. In adaptive immune cells, programmed DNA DSBs are generated at precise genomic locations during the assembly and diversification of lymphocyte antigen receptor genes. In innate immune cells, the production of genotoxic agents, such as reactive nitrogen molecules, in response to pathogens can also cause genomic DNA DSBs. These DSBs in adaptive and innate immune cells activate the cDDR. However, recent studies have demonstrated that they also activate non-canonical DDRs (ncDDRs) that regulate cell type-specific processes that are important for innate and adaptive immune responses. Here, we review these ncDDRs and discuss how they integrate with other signals during immune system development and function.
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41
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Fundamental roles of chromatin loop extrusion in antibody class switching. Nature 2019; 575:385-389. [PMID: 31666703 PMCID: PMC6856444 DOI: 10.1038/s41586-019-1723-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/25/2019] [Indexed: 12/13/2022]
Abstract
Antibody class switch recombination (CSR) in B lymphocytes replaces immunoglobulin heavy chain locus (Igh) Cμ constant region exons (CHs) with one of six CHs lying 100-200 kb downstream1. Each CH is flanked upstream by an I promoter and long repetitive switch (S) region1. Cytokines and activators induce activation-induced cytidine deaminase (AID)2 and I-promoter transcription, with 3' IgH regulatory region (3' IgHRR) enhancers controlling the latter via I-promoter competition for long-range 3' IgHRR interactions3-8. Transcription through donor Sμ and an activated downstream acceptor S-region targets AID-generated deamination lesions at, potentially, any of hundreds of individual S-region deamination motifs9-11. General DNA repair pathways convert these lesions to double-stranded breaks (DSBs) and join an Sμ-upstream DSB-end to an acceptor S-region-downstream DSB-end for deletional CSR12. AID-initiated DSBs at targets spread across activated S regions routinely participate in such deletional CSR joining11. Here we report that chromatin loop extrusion underlies the mechanism11 by which IgH organization in cis promotes deletional CSR. In naive B cells, loop extrusion dynamically juxtaposes 3' IgHRR enhancers with the 200-kb upstream Sμ to generate a CSR centre (CSRC). In CSR-activated primary B cells, I-promoter transcription activates cohesin loading, leading to generation of dynamic subdomains that directionally align a downstream S region with Sμ for deletional CSR. During constitutive Sα CSR in CH12F3 B lymphoma cells, inversional CSR can be activated by insertion of a CTCF-binding element (CBE)-based impediment in the extrusion path. CBE insertion also inactivates upstream S-region CSR and converts adjacent downstream sequences into an ectopic S region by inhibiting and promoting their dynamic alignment with Sμ in the CSRC, respectively. Our findings suggest that, in a CSRC, dynamically impeded cohesin-mediated loop extrusion juxtaposes proper ends of AID-initiated donor and acceptor S-region DSBs for deletional CSR. Such a mechanism might also contribute to pathogenic DSB joining genome-wide.
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42
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Amoretti-Villa R, Rogier M, Robert I, Heyer V, Reina-San-Martin B. A novel regulatory region controls IgH locus transcription and switch recombination to a subset of isotypes. Cell Mol Immunol 2019; 16:887-889. [PMID: 31384005 DOI: 10.1038/s41423-019-0267-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 01/18/2023] Open
Affiliation(s)
- Rocío Amoretti-Villa
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Mélanie Rogier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Isabelle Robert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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43
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Yu K, Lieber MR. Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 PMCID: PMC6856442 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [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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Affiliation(s)
- Kefei Yu
- Michigan State University, Department of Microbiology & Molecular Genetics, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Michael R. Lieber
- USC Norris Comprehensive Cancer Ctr., Departments of Pathology, of Molecular Microbiology & Immunology, of Biochemistry & Molecular Biology, and of the Section of Molecular & Computational Biology within the Department of Biological Sciences, 1441 Eastlake Ave., NTT5428, Los Angeles, CA 90089-9176
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44
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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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45
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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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46
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Abstract
Vast repertoires of unique antigen receptors are created in developing lymphocytes. The antigen receptor loci contain many variable (V), diversity (D), and joining (J) gene segments that are arrayed across very large genomic expanses and are joined to form variable-region exons. This process creates the potential for an organism to respond to large numbers of different pathogens. Here, we consider the underlying molecular mechanisms that favor some V genes for recombination prior to selection of the final antigen receptor repertoire. We discuss chromatin structures that form in antigen receptor loci to permit spatial proximity among the V, D, and J gene segments and how these relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, 60612-7344, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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47
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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 2019; 16:198-200. [PMID: 30305688 PMCID: PMC6355848 DOI: 10.1038/s41423-018-0171-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [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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48
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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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49
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Boutouil H, Boyer F, Cook-Moreau J, Cogné M, Péron S. IgH locus suicide recombination does not depend on NHEJ in contrast to CSR in B cells. Cell Mol Immunol 2019; 16:201-202. [PMID: 30323220 PMCID: PMC6355842 DOI: 10.1038/s41423-018-0172-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/08/2022] Open
Affiliation(s)
- Hend Boutouil
- CRIBL, UMR CNRS 7276 INSERM U1262, 87000, Limoges, France
| | - François Boyer
- CRIBL, UMR CNRS 7276 INSERM U1262, 87000, Limoges, France
| | | | - Michel Cogné
- CRIBL, UMR CNRS 7276 INSERM U1262, 87000, Limoges, France
- Institut Universitaire de France, 75000, Paris, France
| | - Sophie Péron
- CRIBL, UMR CNRS 7276 INSERM U1262, 87000, Limoges, France.
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50
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Al Ismail A, Husain A, Kobayashi M, Honjo T, Begum NA. Depletion of recombination-specific cofactors by the C-terminal mutant of the activation-induced cytidine deaminase causes the dominant negative effect on class switch recombination. Int Immunol 2019; 29:525-537. [PMID: 29136157 DOI: 10.1093/intimm/dxx061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for class-switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes. Studies on in vitro mutagenized AID as well as its mutations in human patients with hyper-IgM (HIGM)-syndrome type II revealed that C-terminal AID mutations were defective in CSR whereas their DNA cleavage and SHM activities remained intact. The C-terminal mutants of AID were speculated to exert the dominant negative effect on wild-type (WT) AID whereas its mechanism remains unknown. We generated the JP41 (R190X) mutation in one allele and a null mutation on the other allele in a mouse B cell line (CH12F3-2A) using CRISPR/Cas9 genome-editing tools and studied the effect of JP41 expression on the function of exogenously introduced WT AID fused with estrogen receptor (AIDER) in AIDJP41/∆/AIDER CH12F3-2A cells. We found that JP41 expression strongly suppressed not only CSR but also Igh/c-Myc chromosomal translocations by AIDER. We showed that the dominant negative effect is not evident at the DNA cleavage step but obvious at both deletional and inversional recombination steps. We also confirmed the dominant negative effect of other C-terminal mutants, JP8Bdel (R183X) and P20 (34-aa insertion at residue 182) in AID-deficient spleen B cells. Finally, we showed that the expression of JP41 reduced the binding of AIDER with its cofactors (hnRNP L, SERBP1 and hnRNP U). Together, these data indicate that dominant negative effect of JP41 on CSR is likely due to the depletion of the CSR-specific RNA-binding proteins from WT AID.
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Affiliation(s)
- Azza Al Ismail
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Afzal Husain
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
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