1
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Ralph DK, Matsen FA. Inference of B cell clonal families using heavy/light chain pairing information. PLoS Comput Biol 2022; 18:e1010723. [PMID: 36441808 PMCID: PMC9731466 DOI: 10.1371/journal.pcbi.1010723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 12/08/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.
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Affiliation(s)
- Duncan K. Ralph
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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2
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Contribution of rare mutational outcomes to broadly neutralizing antibodies. Acta Biochim Biophys Sin (Shanghai) 2022; 54:820-827. [PMID: 35713319 PMCID: PMC9828561 DOI: 10.3724/abbs.2022065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antibodies are important immune molecules that are elicited by B cells to protect our bodies during viral infections or vaccinations. In humans, the antibody repertoire is diversified by programmed DNA lesion processes to ensure specific and high affinity binding to various antigens. Broadly neutralizing antibodies (bnAbs) are antibodies that have strong neutralizing activities against different variants of a virus. bnAbs such as anti-HIV bnAbs often have special characteristics including insertions and deletions, long complementarity determining region 3 (CDR3), and high frequencies of mutations, often at improbable sites of the variable regions. These unique features are rare mutational outcomes that are acquired during antibody diversification processes. In this review, we will discuss possible mechanisms that generate these rare antibody mutational outcomes. The understanding of the mechanisms that generate these rare mutational outcomes during antibody diversification will have implications in vaccine design strategies to elicit bnAbs.
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3
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Safonova Y, Pevzner PA. V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res 2020; 30:1547-1558. [PMID: 32948615 PMCID: PMC7605257 DOI: 10.1101/gr.259598.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that these nonamers explain the vast majority of tandem fusions in human repertoires. We further reveal large clonal lineages formed by tandem fusions in antigen-stimulated immunosequencing data sets, suggesting that such data sets contain many more tandem fusions than previously thought and that about a quarter of large clonal lineages with unusually long CDR3s are generated through tandem fusions. Finally, we developed the SEARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently completed Vertebrate Genomes Project assemblies, nearly doubling the number of mammalian species with known D genes. Our analysis revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J recombination is not a "bug" but an important feature preserved throughout mammalian evolution.
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Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
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4
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Safonova Y, Pevzner PA. De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Front Immunol 2019; 10:987. [PMID: 31134072 PMCID: PMC6516046 DOI: 10.3389/fimmu.2019.00987] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/16/2019] [Indexed: 12/03/2022] Open
Abstract
The V(D)J recombination forms the immunoglobulin genes by joining the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics aims at finding alleles of germline genes across various patients. Although recent studies described algorithms for de novo inference of V and J genes from immunosequencing data, they stopped short of solving a more difficult problem of reconstructing D genes that form the highly divergent CDR3 regions and provide the most important contribution to the antigen binding. We present the IgScout algorithm for de novo D gene reconstruction and apply it to reveal new alleles of human D genes and previously unknown D genes in camel, an important model organism in immunology. We further analyze non-canonical V(DD)J recombination that results in unusually long CDR3s with tandem fused IGHD genes and thus expands the diversity of the antibody repertoires. We demonstrate that tandem CDR3s represent a consistent and functional feature of all analyzed immunosequencing datasets, reveal ultra-long CDR3s, and shed light on the mechanism responsible for their formation.
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Affiliation(s)
- Yana Safonova
- Center for Information Theory and Applications, University of California, San Diego, San Diego, CA, United States
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
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5
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Lange MD, Huang L, Yu Y, Li S, Liao H, Zemlin M, Su K, Zhang Z. Accumulation of VH Replacement Products in IgH Genes Derived from Autoimmune Diseases and Anti-Viral Responses in Human. Front Immunol 2014; 5:345. [PMID: 25101087 PMCID: PMC4105631 DOI: 10.3389/fimmu.2014.00345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/06/2014] [Indexed: 11/24/2022] Open
Abstract
VH replacement refers to RAG-mediated secondary recombination of the IgH genes, which renews almost the entire VH gene coding region but retains a short stretch of nucleotides as a VH replacement footprint at the newly generated VH–DH junction. To explore the biological significance of VH replacement to the antibody repertoire, we developed a Java-based VH replacement footprint analyzer program and analyzed the distribution of VH replacement products in 61,851 human IgH gene sequences downloaded from the NCBI database. The initial assignment of the VH, DH, and JH gene segments provided a comprehensive view of the human IgH repertoire. To our interest, the overall frequency of VH replacement products is 12.1%; the frequencies of VH replacement products in IgH genes using different VH germline genes vary significantly. Importantly, the frequencies of VH replacement products are significantly elevated in IgH genes derived from different autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and allergic rhinitis, and in IgH genes encoding various autoantibodies or anti-viral antibodies. The identified VH replacement footprints preferentially encoded charged amino acids to elongate IgH CDR3 regions, which may contribute to their autoreactivities or anti-viral functions. Analyses of the mutation status of the identified VH replacement products suggested that they had been actively involved in immune responses. These results provide a global view of the distribution of VH replacement products in human IgH genes, especially in IgH genes derived from autoimmune diseases and anti-viral immune responses.
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Affiliation(s)
- Miles D Lange
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Lin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Song Li
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Hongyan Liao
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg , Marburg , Germany
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA ; The Eppley Cancer Institute, University of Nebraska Medical Center , Omaha, NE , USA ; Department of Internal Medicine, University of Nebraska Medical Center , Omaha, NE , USA
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA ; The Eppley Cancer Institute, University of Nebraska Medical Center , Omaha, NE , USA
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6
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Yu L, Guan Y. Immunologic Basis for Long HCDR3s in Broadly Neutralizing Antibodies Against HIV-1. Front Immunol 2014; 5:250. [PMID: 24917864 PMCID: PMC4040451 DOI: 10.3389/fimmu.2014.00250] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/12/2014] [Indexed: 01/18/2023] Open
Abstract
A large number of potent broadly neutralizing antibodies (bnAbs) against HIV-1 have been reported in recent years, raising hope for the possibility of an effective vaccine based on epitopes recognized by these protective antibodies. However, many of these bnAbs contain the long heavy chain complementarity-determining region 3 (HCDR3), which is viewed as an obstacle to the development of an HIV-1 vaccine targeting the bnAb responses. This mini-review summarizes the current literature and discusses the different potential immunologic mechanisms for generating long HCDR3, including D–D fusion, VH replacement, long N region addition, and skewed D–J gene usage, among which potential VH replacement products appear to be significant contributors. VH replacement occurs through recombinase activated gene-mediated secondary recombination and contributes to the diversified naïve B cell repertoire. During VH replacement, a short stretch of nucleotides from previously rearranged VH genes remains within the newly formed HCDR3, thus elongating its length. Accumulating evidence suggests that long HCDR3s are present in significant numbers in the human mature naïve B cell repertoire and are primarily generated by recombination during B cell development. These new observations indicate that long HCDR3s, though low in frequency, are a normal feature of the human antibody naïve repertoire and they appear to be selected to target conserved epitopes located in deep, partially obscured regions of the HIV-1 envelope trimer. Therefore, the presence of long HCDR3 sequences should not necessarily be viewed as an obstacle to the development of an HIV-1 vaccine based upon bnAb responses.
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Affiliation(s)
- Lei Yu
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA
| | - Yongjun Guan
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine , Baltimore, MD , USA
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7
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Huang L, Lange MD, Zhang Z. VH Replacement Footprint Analyzer-I, a Java-Based Computer Program for Analyses of Immunoglobulin Heavy Chain Genes and Potential VH Replacement Products in Human and Mouse. Front Immunol 2014; 5:40. [PMID: 24575092 PMCID: PMC3918983 DOI: 10.3389/fimmu.2014.00040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 01/22/2014] [Indexed: 11/13/2022] Open
Abstract
VH replacement occurs through RAG-mediated secondary recombination between a rearranged VH gene and an upstream unrearranged VH gene. Due to the location of the cryptic recombination signal sequence (cRSS, TACTGTG) at the 3′ end of VH gene coding region, a short stretch of nucleotides from the previous rearranged VH gene can be retained in the newly formed VH–DH junction as a “footprint” of VH replacement. Such footprints can be used as markers to identify Ig heavy chain (IgH) genes potentially generated through VH replacement. To explore the contribution of VH replacement products to the antibody repertoire, we developed a Java-based computer program, VH replacement footprint analyzer-I (VHRFA-I), to analyze published or newly obtained IgH genes from human or mouse. The VHRFA-1 program has multiple functional modules: it first uses service provided by the IMGT/V-QUEST program to assign potential VH, DH, and JH germline genes; then, it searches for VH replacement footprint motifs within the VH–DH junction (N1) regions of IgH gene sequences to identify potential VH replacement products; it can also analyze the frequencies of VH replacement products in correlation with publications, keywords, or VH, DH, and JH gene usages, and mutation status; it can further analyze the amino acid usages encoded by the identified VH replacement footprints. In summary, this program provides a useful computation tool for exploring the biological significance of VH replacement products in human and mouse.
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Affiliation(s)
- Lin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Miles D Lange
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA ; Eppley Institute for Research in Cancer, University of Nebraska Medical Center , Omaha, NE , USA
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8
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Meng W, Jayaraman S, Zhang B, Schwartz GW, Daber RD, Hershberg U, Garfall AL, Carlson CS, Luning Prak ET. Trials and Tribulations with VH Replacement. Front Immunol 2014; 5:10. [PMID: 24523721 PMCID: PMC3906580 DOI: 10.3389/fimmu.2014.00010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/07/2014] [Indexed: 11/13/2022] Open
Abstract
VH replacement (VHR) is a type of antibody gene rearrangement in which an upstream heavy chain variable gene segment (VH) invades a pre-existing rearrangement (VDJ). In this Hypothesis and Theory article, we begin by reviewing the mechanism of VHR, its developmental timing and its potential biological consequences. Then we explore the hypothesis that specific sequence motifs called footprints reflect VHR versus other processes. We provide a compilation of footprint sequences from different regions of the antibody heavy chain, and include data from the literature and from a high throughput sequencing experiment to evaluate the significance of footprint sequences. We conclude by discussing the difficulties of attributing footprints to VHR.
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Affiliation(s)
- Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Sahana Jayaraman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Bochao Zhang
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA
| | - Gregory W Schwartz
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA
| | - Robert D Daber
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA ; Center for Personalized Diagnostics, University of Pennsylvania Health System , Philadelphia, PA , USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA ; Department of Microbiology and Immunology, College of Medicine, Drexel University , Philadelphia, PA , USA
| | - Alfred L Garfall
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center , Seattle, WA , USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
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9
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The epigenetic landscape of B lymphocyte tolerance to self. FEBS Lett 2013; 587:2067-73. [PMID: 23684644 DOI: 10.1016/j.febslet.2013.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 02/06/2023]
Abstract
Despite frequent exposures to a variety of potential triggers, including antigens produced by pathogens or commensal microbiota, B-lymphocytes are able to mount highly protective responses to a variety of threats, while remaining tolerant to self-components. A number of cytokines, signaling pathways and transcription factors have been characterized to elucidate the mechanisms underlying B cell tolerance to self. It is, however, unclear how the signals received by B-lymphocytes are converted into complex and sustained patterns of gene expression that can allow production of protective antibodies and maintain immune tolerance to self-components. Mounting evidence now suggests an important role for epigenetic mechanisms in modulating and transmitting signals for B lymphocyte tolerization to self-antigens. It is likely that a better insight into epigenetic regulation of B cell tolerance will lead to development of gene-specific therapeutic approaches that optimize host defense mechanisms to exogenous threats, while preventing development and/or progression of autoimmune inflammatory diseases.
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10
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Liu J, Lange MD, Hong SY, Xie W, Xu K, Huang L, Yu Y, Ehrhardt GRA, Zemlin M, Burrows PD, Su K, Carter RH, Zhang Z. Regulation of VH replacement by B cell receptor-mediated signaling in human immature B cells. THE JOURNAL OF IMMUNOLOGY 2013; 190:5559-66. [PMID: 23630348 DOI: 10.4049/jimmunol.1102503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
VH replacement provides a unique RAG-mediated recombination mechanism to edit nonfunctional IgH genes or IgH genes encoding self-reactive BCRs and contributes to the diversification of Ab repertoire in the mouse and human. Currently, it is not clear how VH replacement is regulated during early B lineage cell development. In this article, we show that cross-linking BCRs induces VH replacement in human EU12 μHC(+) cells and in the newly emigrated immature B cells purified from peripheral blood of healthy donors or tonsillar samples. BCR signaling-induced VH replacement is dependent on the activation of Syk and Src kinases but is inhibited by CD19 costimulation, presumably through activation of the PI3K pathway. These results show that VH replacement is regulated by BCR-mediated signaling in human immature B cells, which can be modulated by physiological and pharmacological treatments.
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Affiliation(s)
- Jing Liu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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11
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Briney BS, Jr. JEC. Secondary mechanisms of diversification in the human antibody repertoire. Front Immunol 2013; 4:42. [PMID: 23483107 PMCID: PMC3593266 DOI: 10.3389/fimmu.2013.00042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 02/05/2013] [Indexed: 12/25/2022] Open
Abstract
V(D)J recombination and somatic hypermutation (SHM) are the primary mechanisms for diversification of the human antibody repertoire. These mechanisms allow for rapid humoral immune responses to a wide range of pathogenic challenges. V(D)J recombination efficiently generate a virtually limitless diversity through random recombination of variable (V), diversity (D), and joining (J) genes with diverse non-templated junctions between the selected gene segments. Following antigen stimulation, affinity maturation by SHM produces antibodies with refined specificity mediated by mutations typically focused in complementarity determining regions (CDRs), which form the bulk of the antigen recognition site. While V(D)J recombination and SHM are responsible for much of the diversity of the antibody repertoire, there are several secondary mechanisms that, while less frequent, make substantial contributions to antibody diversity including V(DD)J recombination (or D-D fusion), SHM-associated insertions and deletions, and affinity maturation and antigen contact by non-CDR regions of the antibody. In addition to enhanced diversity, these mechanisms allow the production of antibodies that are critical to response to a variety of viral and bacterial pathogens but that would be difficult to generate using only the primary mechanisms of diversification.
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Affiliation(s)
- Bryan S. Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
| | - James E. Crowe Jr.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical CenterNashville, TN, USA
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashville, TN, USA
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12
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Huang L, Lange MD, Yu Y, Li S, Su K, Zhang Z. Contribution of V(H) replacement products in mouse antibody repertoire. PLoS One 2013; 8:e57877. [PMID: 23469094 PMCID: PMC3585286 DOI: 10.1371/journal.pone.0057877] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
VH replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS) near the 3′ end of a rearranged VH gene and the 23-bp RSS from an upstream unrearranged VH gene. Due to the location of the cRSS, VH replacement leaves a short stretch of nucleotides from the previously rearranged VH gene at the newly formed V-D junction, which can be used as a marker to identify VH replacement products. To determine the contribution of VH replacement products to mouse antibody repertoire, we developed a Java-based VH Replacement Footprint Analyzer (VHRFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify VH replacement products. The overall frequency of VH replacement products in these IgH genes is 5.29% based on the identification of pentameric VH replacement footprints at their V-D junctions. The identified VH replacement products are distributed similarly in IgH genes using most families of VH genes, although different families of VH genes are used differentially. The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.
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Affiliation(s)
- Lin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Miles D. Lange
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Song Li
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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13
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Briney BS, Willis JR, Hicar MD, Thomas JW, Crowe JE. Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire. Immunology 2012; 137:56-64. [PMID: 22612413 DOI: 10.1111/j.1365-2567.2012.03605.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Antibody heavy-chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of heavy chain complementarity determining region 3 (HCDR3) regions of extreme length and enables junctional regions that, because of the nucleotide bias of N-addition regions, are difficult to produce through normal V(D)J recombination. Although this non-classical recombination process has been observed infrequently, comprehensive analysis of the frequency and genetic characteristics of such events in the human peripheral blood antibody repertoire has not been possible because of the rarity of such recombinants and the limitations of traditional sequencing technologies. Here, through the use of high-throughput sequencing of the normal human peripheral blood antibody repertoire, we analysed the frequency and genetic characteristics of V(DD)J recombinants. We found that these recombinations were present in approximately 1 in 800 circulating B cells, and that the frequency was severely reduced in memory cell subsets. We also found that V(DD)J recombination can occur across the spectrum of diversity genes, indicating that virtually all recombination signal sequences that flank diversity genes are amenable to V(DD)J recombination. Finally, we observed a repertoire bias in the diversity gene repertoire at the upstream (5') position, and discovered that this bias was primarily attributable to the order of diversity genes in the genomic locus.
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Affiliation(s)
- Bryan S Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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14
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Murray JM, Messier T, Rivers J, O’Neill JP, Walker VE, Vacek PM, Finette BA. V(D)J Recombinase-Mediated TCR β Locus Gene Usage and Coding Joint Processing in Peripheral T Cells during Perinatal and Pediatric Development. THE JOURNAL OF IMMUNOLOGY 2012; 189:2356-64. [DOI: 10.4049/jimmunol.1200382] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Sang A, Yin Y, Zheng YY, Morel L. Animal Models of Molecular Pathology. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 105:321-70. [DOI: 10.1016/b978-0-12-394596-9.00010-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Luning Prak ET, Monestier M, Eisenberg RA. B cell receptor editing in tolerance and autoimmunity. Ann N Y Acad Sci 2011; 1217:96-121. [PMID: 21251012 DOI: 10.1111/j.1749-6632.2010.05877.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Receptor editing is the process of ongoing antibody gene rearrangement in a lymphocyte that already has a functional antigen receptor. The expression of a functional antigen receptor will normally terminate further rearrangement (allelic exclusion). However, lymphocytes with autoreactive receptors have a chance at escaping negative regulation by "editing" the specificities of their receptors with additional antibody gene rearrangements. As such, editing complicates the Clonal Selection Hypothesis because edited cells are not simply endowed for life with a single, invariant antigen receptor. Furthermore, if the initial immunoglobulin gene is not inactivated during the editing process, allelic exclusion is violated and the B cell can exhibit two specificities. Here, we describe the discovery of editing, the pathways of receptor editing at the heavy (H) and light (L) chain loci, and current evidence regarding how and where editing happens and what effects it has on the antibody repertoire.
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Affiliation(s)
- Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
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Yunk L, Meng W, Cohen PL, Eisenberg RA, Luning Prak ET. Antibodies in a heavy chain knock-in mouse exhibit characteristics of early heavy chain rearrangement. THE JOURNAL OF IMMUNOLOGY 2009; 183:452-61. [PMID: 19542457 DOI: 10.4049/jimmunol.0804060] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studies in autoantibody transgenic mice have demonstrated receptor editing rearrangements at Ab H and L chain loci. However, the physiologic role of H chain editing (V(H) replacement and rearrangement on the second allele) has been called into question. It is unclear if additional rounds of H chain rearrangement are driven by BCR specificity. In this study, we analyze the manner in which B cells undergo additional H chain rearrangements in an anti-DNA H chain knock-in mouse, B6.56R. We find that rearrangements in 56R(+) B cells tend to involve the D gene locus on both alleles and the most J(H)-proximal V(H) gene segments on the endogenous allele. As a result, some B cells exhibit V(D)J rearrangements on both H chain alleles, yet allelic exclusion is tightly maintained in mature 56R B cells. As B cells mature, a higher proportion expresses the nontransgenic H chain allele. Rearrangements on both H chain alleles exhibit junctional diversity consistent with TdT-mediated N-addition, and TdT RNA is expressed exclusively at the pro-B cell stage in B6.56R. Collectively, these findings favor a single, early window of H chain rearrangement in B6.56R that precedes the expression of a functional BCR. B cells that happen to successfully rearrange another H chain may be favored in the periphery.
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Affiliation(s)
- Lenka Yunk
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA
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18
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Nakajima PB, Kiefer K, Price A, Bosma GC, Bosma MJ. Two distinct populations of H chain-edited B cells show differential surrogate L chain dependence. THE JOURNAL OF IMMUNOLOGY 2009; 182:3583-96. [PMID: 19265137 DOI: 10.4049/jimmunol.0802533] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Developing autoreactive B cells may edit (change) their specificity by secondary H or L chain gene rearrangement. Recently, using mice hemizygous for a site-directed VDJH and VJkappa transgene (tg) encoding an autoreactive Ab, we reported ongoing L chain editing not only in bone marrow cells with a pre-B/immature B cell phenotype but also in immature/transitional splenic B cells. Using the same transgenic model, we report here that editing at the H chain locus appears to occur exclusively in bone marrow cells with a pro-B phenotype. H chain editing is shown to involve VH replacement at the tg allele or VH rearrangement at the wild-type (wt) allele when the tg is inactivated by nonproductive VH replacement. VH replacement/rearrangement at the tg/wt alleles was found to entail diverse usage of VH genes. Whereas the development of edited B cells expressing the wt allele was dependent on the lambda5 component of the surrogate L chain, the development of B cells expressing the tg allele, including those with VH replacement, appeared to be lambda5 independent. We suggest that the unique CDR3 region of the tg-encoded muH chain is responsible for the lambda5 independence of tg-expressing B cells.
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19
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Davies JM, O'Hehir RE. Immunogenetic characteristics of immunoglobulin E in allergic disease. Clin Exp Allergy 2008; 38:566-78. [DOI: 10.1111/j.1365-2222.2008.02941.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lamoureux JL, Watson LC, Cherrier M, Skog P, Nemazee D, Feeney AJ. Reduced receptor editing in lupus-prone MRL/lpr mice. ACTA ACUST UNITED AC 2007; 204:2853-64. [PMID: 17967905 PMCID: PMC2118512 DOI: 10.1084/jem.20071268] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The initial B cell repertoire contains a considerable proportion of autoreactive specificities. The first major B cell tolerance checkpoint is at the stage of the immature B cell, where receptor editing is the primary mode of eliminating self-reactivity. The cells that emigrate from the bone marrow have a second tolerance checkpoint in the transitional compartment in the spleen. Although it is known that the second checkpoint is defective in lupus, it is not clear whether there is any breakdown in central B cell tolerance in the bone marrow. We demonstrate that receptor editing is less efficient in the lupus-prone strain MRL/lpr. In an in vitro system, when receptor-editing signals are given to bone marrow immature B cells by antiidiotype antibody or after in vivo exposure to membrane-bound self-antigen, MRL/lpr 3-83 transgenic immature B cells undergo less endogenous rearrangement and up-regulate recombination activating gene messenger RNA to a lesser extent than B10 transgenic cells. CD19, along with immunoglobulin M, is down-regulated in the bone marrow upon receptor editing, but the extent of down-regulation is fivefold less in MRL/lpr mice. Less efficient receptor editing could allow some autoreactive cells to escape from the bone marrow in lupus-prone mice, thus predisposing to autoimmunity.
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Affiliation(s)
- Jennifer L Lamoureux
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
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21
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Jiang C, Foley J, Clayton N, Kissling G, Jokinen M, Herbert R, Diaz M. Abrogation of lupus nephritis in activation-induced deaminase-deficient MRL/lpr mice. THE JOURNAL OF IMMUNOLOGY 2007; 178:7422-31. [PMID: 17513793 PMCID: PMC2131724 DOI: 10.4049/jimmunol.178.11.7422] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We generated MRL/lpr mice deficient in activation-induced deaminase (AID). Because AID is required for Ig hypermutation and class switch recombination, these mice lack hypermutated IgG Abs. Unlike their AID wild-type littermates, AID-deficient MRL/lpr mice not only lacked autoreactive IgG Abs but also experienced a dramatic increase in the levels of autoreactive IgM. This phenotype in AID-deficient mice translated into a significant reduction in glomerulonephritis, minimal mononuclear cell infiltration in the kidney, and a dramatic increase in survival to levels comparable to those previously reported for MRL/lpr mice completely lacking B cells and well below those of mice lacking secreted Abs. Therefore, this study wherein littermates with either high levels of autoreactive IgM or autoreactive IgG were directly examined proves that autoreactive IgM Abs alone are not sufficient to promote kidney disease in MRL/lpr mice. In addition, the substantial decrease in mortality combined with a dramatic increase in autoreactive IgM Abs in AID-deficient MRL/lpr mice suggest that autoreactive IgM Abs might not only fail to promote nephritis but may also provide a protective role in MRL/lpr mice. This novel mouse model containing high levels of autoreactive, unmutated IgM Abs will help delineate the contribution of autoreactive IgM to autoimmunity.
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Affiliation(s)
- Chuancang Jiang
- Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Julie Foley
- Laboratory of Experimental Pathology, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Natasha Clayton
- Laboratory of Experimental Pathology, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Grace Kissling
- Biostatistics Branch, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Micheal Jokinen
- Pathology Associates, Charles River Laboratories, 11000 Weston Parkway Suite 110, Cary, NC 27513
| | - Ronald Herbert
- Laboratory of Experimental Pathology, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Marilyn Diaz
- Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
- Corresponding author information: Dr. Marilyn Diaz, Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health Sciences, National institutes of Health, 111 TW Alexander Drive, RTP, NC, 27709. Tel. 919-541-4740, E-mail:
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22
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Zhang Z. VH replacement in mice and humans. Trends Immunol 2007; 28:132-7. [PMID: 17258935 DOI: 10.1016/j.it.2007.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 01/02/2007] [Accepted: 01/18/2007] [Indexed: 02/01/2023]
Abstract
Heavy chain variable segment (V(H)) replacement refers to recombination activating gene (RAG) product-mediated secondary recombination between a previously rearranged V(H) gene and an upstream unrearranged V(H) gene. V(H) replacement was first observed in mouse pre-B cell lines and later demonstrated in knock-in mouse models carrying immunoglobulin heavy chain (IgH) genes encoding self-reactive or mono-specific antibodies or non-functional IgH rearrangements on both IgH alleles. Despite these findings, it is still difficult to find V(H) replacement intermediates during normal murine B cell development. In humans, ongoing V(H) replacement was found in a clonal B lineage EU12 cell line and in human bone marrow immature B cells. The identification of potential V(H) replacement products also suggested a potential contribution of V(H) replacement to the antibody repertoire. Here, I review the evidence for whether V(H) replacement genuinely offers an in vivo RAG-mediated recombinatorial mechanism to alter preformed IgH genes in mice and humans.
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Affiliation(s)
- Zhixin Zhang
- Division of Developmental and Clinical Immunology, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Lutz J, Müller W, Jäck HM. VH replacement rescues progenitor B cells with two nonproductive VDJ alleles. THE JOURNAL OF IMMUNOLOGY 2007; 177:7007-14. [PMID: 17082616 DOI: 10.4049/jimmunol.177.10.7007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Inaccurate VDJ rearrangements generate a large number of progenitor (pro)-B cells with two nonproductive IgH alleles. Such cells lack essential survival signals mediated by surface IgM heavy chain (muH chain) expression and are normally eliminated. However, secondary rearrangements of upstream VH gene segments into assembled VDJ exons have been described in mice transgenic for productive muH chains, a process known as VH replacement. If VH replacement was independent of muH chain signals, it could also modify nonproductive VDJ exons and thus rescue pro-B cells with unsuccessful rearrangements on both alleles. To test this hypothesis, we homologously replaced the JH cluster of a mouse with a nonproductive VDJ exon. Surprisingly, B cell development in IgHVDJ-/VDJ- mice was only slightly impaired and significant numbers of IgM-positive B cells were produced. DNA sequencing confirmed that all VDJ sequences from muH chain-positive B lymphoid cells were generated by VH replacement in a RAG-dependent manner. Another unique feature of our transgenic mice was the presence of IgH chains with unusually long CDR3-H regions. Such IgH chains were functional and only modestly counter-selected, arguing against a strict length constraint for CDR3-H regions. In conclusion, VH replacement can occur in the absence of a muH chain signal and provides a potential rescue mechanism for pro-B cells with two nonproductive IgH alleles.
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Affiliation(s)
- Johannes Lutz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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Abstract
The specificities of lymphocytes for antigen are generated by a quasi-random process of gene rearrangement that often results in non-functional or autoreactive antigen receptors. Regulation of lymphocyte specificities involves not only the elimination of cells that display 'unsuitable' receptors for antigen but also the active genetic correction of these receptors by secondary recombination of the DNA. As I discuss here, an important mechanism for the genetic correction of antigen receptors is ongoing recombination, which leads to receptor editing. Receptor editing is probably an adaptation that is necessitated by the high probability of receptor autoreactivity. In both B cells and T cells, the genes that encode the two chains of the antigen receptor seem to be specialized to promote, on the one hand, the generation of diverse specificities and, on the other hand, the regulation of these specificities through efficient editing.
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Affiliation(s)
- David Nemazee
- Department of Immunology, The Scripps Research Institute, Mail Drop IMM-29, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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