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Lerner LK, Bonte D, Le Guillou M, Mohammad MM, Kasraian Z, Sarasin A, Despras E, Aoufouchi S. Expression of Constitutive Fusion of Ubiquitin to PCNA Restores the Level of Immunoglobulin A/T Mutations During Somatic Hypermutation in the Ramos Cell Line. Front Immunol 2022; 13:871766. [PMID: 35432321 PMCID: PMC9010874 DOI: 10.3389/fimmu.2022.871766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/11/2022] [Indexed: 12/05/2022] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes is a B cell specific process required for the generation of specific and high affinity antibodies during the maturation of the immune response against foreign antigens. This process depends on the activity of both activation-induced cytidine deaminase (AID) and several DNA repair factors. AID-dependent SHM creates the full spectrum of mutations in Ig variable (V) regions equally distributed at G/C and A/T bases. In most mammalian cells, deamination of deoxycytidine into uracil during S phase induces targeted G/C mutagenesis using either direct replication of uracils or TLS mediated bypass, however only the machinery of activated B lymphocytes can generate A/T mutagenesis around AID-created uracils. The molecular mechanism behind the latter remains incompletely understood to date. However, the lack of a cellular model that reproduces both G/C and A/T mutation spectra constitutes the major hurdle to elucidating it. The few available B cell lines used thus far to study Ig SHM indeed undergo mainly G/C mutations, that make them inappropriate or of limited use. In this report, we show that in the Ramos cell line that undergoes constitutive G/C-biased SHM in culture, the low rate of A/T mutations is due to an imbalance in the ubiquitination/deubiquitination reaction of PCNA, with the deubiquitination reaction being predominant. The inhibition of the deubiquitinase complex USP1-UAF1 or the expression of constitutive fusion of ubiquitin to PCNA provides the missing clue required for DNA polymerase η recruitment and thereafter the introduction of A/T base pair (bp) mutations during the process of IgV gene diversification. This study reports the establishment of the first modified human B cell line that recapitulates the mechanism of SHM of Ig genes in vitro.
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Affiliation(s)
- Leticia K. Lerner
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dorine Bonte
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Morwenna Le Guillou
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Mahwish Mian Mohammad
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Sorbonne Université, Paris, France
| | - Zeinab Kasraian
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Alain Sarasin
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Emmanuelle Despras
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Said Aoufouchi
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Sorbonne Université, Paris, France
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2
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Voss JE, Gonzalez-Martin A, Andrabi R, Fuller RP, Murrell B, McCoy LE, Porter K, Huang D, Li W, Sok D, Le K, Briney B, Chateau M, Rogers G, Hangartner L, Feeney AJ, Nemazee D, Cannon P, Burton DR. Reprogramming the antigen specificity of B cells using genome-editing technologies. eLife 2019; 8:42995. [PMID: 30648968 PMCID: PMC6355199 DOI: 10.7554/elife.42995] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022] Open
Abstract
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody (bnAb), PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination of variable (V), diversity (D) and joining (J) genes. The modified locus expresses PG9 HC which pairs with native light chains (LCs) resulting in the cell surface expression of HIV specific B cell receptors (BCRs). Endogenous activation-induced cytidine deaminase (AID) in engineered cells allowed for Ig class switching and generated BCR variants with improved HIV neutralizing activity. Thus, BCRs engineered in this way retain the genetic flexibility normally required for affinity maturation during adaptive immune responses. Peripheral blood derived primary B cells from three different donors were edited using this strategy. Engineered cells could bind the PG9 epitope and sequenced mRNA showed PG9 HC transcribed as several different isotypes after culture with CD40 ligand and IL-4.
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Affiliation(s)
- James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Alicia Gonzalez-Martin
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Roberta P Fuller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, San Diego, United States.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Wenjuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Morgan Chateau
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Geoffrey Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Paula Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, United States
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Castiblanco DP, Norton DD, Maul RW, Gearhart PJ. J H6 downstream intronic sequence is dispensable for RNA polymerase II accumulation and somatic hypermutation of the variable gene in Ramos cells. Mol Immunol 2018; 97:101-108. [PMID: 29625296 DOI: 10.1016/j.molimm.2018.03.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/09/2018] [Accepted: 03/30/2018] [Indexed: 02/03/2023]
Abstract
Activation-induced deaminase (AID) introduces nucleotide substitutions within the variable region of immunoglobulin genes to promote antibody diversity. This activity, which is limited to 1.5 kb downstream of the variable gene promoter, mutates both the coding exon and downstream intronic sequences. We recently reported that RNA polymerase II accumulates in these regions during transcription in mice. This build-up directly correlates with the area that is accessible to AID, and manipulation of RNA polymerase II levels alters the mutation frequency. To address whether the intronic DNA sequence by itself can regulate RNA polymerase II accumulation and promote mutagenesis, we deleted 613 bp of DNA downstream of the JH6 intron in the human Ramos B cell line. The loss of this sequence did not alter polymerase abundance or mutagenesis in the variable gene, suggesting that most of the intronic sequence is dispensable for somatic hypermutation.
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Affiliation(s)
- Diana P Castiblanco
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Darrell D Norton
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies. Proc Natl Acad Sci U S A 2017; 114:8614-8619. [PMID: 28747530 DOI: 10.1073/pnas.1709203114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Variable regions of Ig chains provide the antigen recognition portion of B-cell receptors and derivative antibodies. Ig heavy-chain variable region exons are assembled developmentally from V, D, J gene segments. Each variable region contains three antigen-contacting complementarity-determining regions (CDRs), with CDR1 and CDR2 encoded by the V segment and CDR3 encoded by the V(D)J junction region. Antigen-stimulated germinal center (GC) B cells undergo somatic hypermutation (SHM) of V(D)J exons followed by selection for SHMs that increase antigen-binding affinity. Some HIV-1-infected human subjects develop broadly neutralizing antibodies (bnAbs), such as the potent VRC01-class bnAbs, that neutralize diverse HIV-1 strains. Mature VRC01-class bnAbs, including VRC-PG04, accumulate very high SHM levels, a property that hinders development of vaccine strategies to elicit them. Because many VRC01-class bnAb SHMs are not required for broad neutralization, high overall SHM may be required to achieve certain functional SHMs. To elucidate such requirements, we used a V(D)J passenger allele system to assay, in mouse GC B cells, sequence-intrinsic SHM-targeting rates of nucleotides across substrates representing maturation stages of human VRC-PG04. We identify rate-limiting SHM positions for VRC-PG04 maturation, as well as SHM hotspots and intrinsically frequent deletions associated with SHM. We find that mature VRC-PG04 has low SHM capability due to hotspot saturation but also demonstrate that generation of new SHM hotspots and saturation of existing hotspot regions (e.g., CDR3) does not majorly influence intrinsic SHM in unmutated portions of VRC-PG04 progenitor sequences. We discuss implications of our findings for bnAb affinity maturation mechanisms.
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5
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Yuan C, Chu CC, Yan XJ, Bagnara D, Chiorazzi N, MacCarthy T. The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia. PLoS One 2017; 12:e0167602. [PMID: 28125682 PMCID: PMC5268644 DOI: 10.1371/journal.pone.0167602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023] Open
Abstract
The targeting of mutations by Activation-Induced Deaminase (AID) is a key step in generating antibody diversity at the Immunoglobulin (Ig) loci but is also implicated in B-cell malignancies such as chronic lymphocytic leukemia (CLL). AID has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) hotspots. WGCW sites, which contain an overlapping WRC hotspot on both DNA strands, mutate at much higher frequency than single hotspots. Human Ig heavy chain (IGHV) genes differ in terms of WGCW numbers, ranging from 4 for IGHV3-48*03 to as many as 12 in IGHV1-69*01. An absence of V-region mutations in CLL patients ("IGHV unmutated", or U-CLL) is associated with a poorer prognosis compared to "IGHV mutated" (M-CLL) patients. The reasons for this difference are still unclear, but it has been noted that particular IGHV genes associate with U-CLL vs M-CLL. For example, patients with IGHV1-69 clones tend to be U-CLL with a poor prognosis, whereas patients with IGHV3-30 tend to be M-CLL and have a better prognosis. Another distinctive feature of CLL is that ~30% of (mostly poor prognosis) patients can be classified into "stereotyped" subsets, each defined by HCDR3 similarity, suggesting selection, possibly for a self-antigen. We analyzed >1000 IGHV genes from CLL patients and found a highly significant statistical relationship between the number of WGCW hotspots in the germline V-region and the observed mutation frequency in patients. However, paradoxically, this correlation was inverse, with V-regions with more WGCW hotspots being less likely to be mutated, i.e., more likely to be U-CLL. The number of WGCW hotspots in particular, are more strongly correlated with mutation frequency than either non-overlapping (WRC) hotspots or more general models of mutability derived from somatic hypermutation data. Furthermore, this correlation is not observed in sequences from the B cell repertoires of normal individuals and those with autoimmune diseases.
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Affiliation(s)
- Chaohui Yuan
- Department of Applied Mathematics and Statistics, Stony Brook University, NY, United States of America
| | - Charles C Chu
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America.,Departments of Medicine and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, United States of America
| | - Xiao-Jie Yan
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America
| | - Davide Bagnara
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America
| | - Nicholas Chiorazzi
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America.,Departments of Medicine and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, NY, United States of America
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Overlapping hotspots in CDRs are critical sites for V region diversification. Proc Natl Acad Sci U S A 2015; 112:E728-37. [PMID: 25646473 DOI: 10.1073/pnas.1500788112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23*01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23*01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23*01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.
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A source of the single-stranded DNA substrate for activation-induced deaminase during somatic hypermutation. Nat Commun 2014; 5:4137. [PMID: 24923561 PMCID: PMC4154566 DOI: 10.1038/ncomms5137] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/16/2014] [Indexed: 11/08/2022] Open
Abstract
During somatic hypermutation (SHM), activation-induced deaminase (AID) mutates deoxycytidine on single-stranded DNA (ssDNA) generated by the transcription machinery, but the detailed mechanism remains unclear. Here we report a higher abundance of RNA polymerase II (Pol II) at the immunoglobulin heavy-chain variable (Igh-V) region compared with the constant region and partially transcribed Igh RNAs, suggesting a slower Pol II progression at Igh-V that could result in some early/premature transcription termination after prolonged pausing/stalling of Pol II. Knocking down RNA-exosome complexes, which could decrease premature transcription termination, leads to decreased SHM. Knocking down Spt5, which can augment premature transcription termination, leads to increase in both, SHM and the abundance of ssDNA substrates. Collectively, our data support the model that, following the reduction of Pol II progression (pausing or stalling) at the Igh-V, additional steps such as premature transcription termination are involved in providing ssDNA substrates for AID during SHM.
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