1
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Gerovska D, Noer JB, Qin Y, Ain Q, Januzi D, Schwab M, Witte OW, Araúzo-Bravo MJ, Kretz A. A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1 G93A model of ALS. Cell Biosci 2023; 13:170. [PMID: 37705092 PMCID: PMC10498603 DOI: 10.1186/s13578-023-01116-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Numerous genes, including SOD1, mutated in familial and sporadic amyotrophic lateral sclerosis (f/sALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. One possible outcome of chromosomal instability and repair processes is extrachromosomal circular DNA (eccDNA) formation. Therefore, eccDNA might accumulate in f/sALS with yet unknown function. METHODS We combined rolling circle amplification with linear DNA digestion to purify eccDNA from the cervical spinal cord of 9 co-isogenic symptomatic hSOD1G93A mutants and 10 controls, followed by deep short-read sequencing. We mapped the eccDNAs and performed differential analysis based on the split read signal of the eccDNAs, referred as DifCir, between the ALS and control specimens, to find differentially produced per gene circles (DPpGC) in the two groups. Compared were eccDNA abundances, length distributions and genic profiles. We further assessed proteome alterations in ALS by mass spectrometry, and matched the DPpGCs with differentially expressed proteins (DEPs) in ALS. Additionally, we aligned the ALS-specific DPpGCs to ALS risk gene databases. RESULTS We found a six-fold enrichment in the number of unique eccDNAs in the genotoxic ALS-model relative to controls. We uncovered a distinct genic circulome profile characterized by 225 up-DPpGCs, i.e., genes that produced more eccDNAs from distinct gene sequences in ALS than under control conditions. The inter-sample recurrence rate was at least 89% for the top 6 up-DPpGCs. ALS proteome analyses revealed 42 corresponding DEPs, of which 19 underlying genes were itemized for an ALS risk in GWAS databases. The up-DPpGCs and their DEP tandems mainly impart neuron-specific functions, and gene set enrichment analyses indicated an overrepresentation of the adenylate cyclase modulating G protein pathway. CONCLUSIONS We prove, for the first time, a significant enrichment of eccDNA in the ALS-affected spinal cord. Our triple circulome, proteome and genome approach provide indication for a potential importance of certain eccDNAs in ALS neurodegeneration and a yet unconsidered role as ALS biomarkers. The related functional pathways might open up new targets for therapeutic intervention.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
| | - Julie B Noer
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Yating Qin
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Quratul Ain
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
- Department of Internal Medicine IV, Hepatology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Donjetë Januzi
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Matthias Schwab
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
- Jena Center for Healthy Ageing, Jena University Hospital, Jena, Thuringia, Germany
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastian, Spain.
- Basque Foundation for Science, IKERBASQUE, 48013, Bilbao, Spain.
- Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics Group, 48149, Münster, North Rhine-Westphalia, Germany.
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940, Leioa, Spain.
| | - Alexandra Kretz
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany.
- Jena Center for Healthy Ageing, Jena University Hospital, Jena, Thuringia, Germany.
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2
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Lees WD, Christley S, Peres A, Kos JT, Corrie B, Ralph D, Breden F, Cowell LG, Yaari G, Corcoran M, Karlsson Hedestam GB, Ohlin M, Collins AM, Watson CT, Busse CE. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics (Amst) 2023; 10:100025. [PMID: 37388275 PMCID: PMC10310305 DOI: 10.1016/j.immuno.2023.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.
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Affiliation(s)
- William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, England
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering Technology and Science, Porto, Portugal
| | - Scott Christley
- Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Brian Corrie
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lindsay G. Cowell
- Peter O’Donnell Jr. School of Public Health, Department of Immunology, School of Biomedical Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Swede
| | | | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab, Lund University, Lund, Sweden
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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3
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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4
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Babrak L, Marquez S, Busse CE, Lees WD, Miho E, Ohlin M, Rosenfeld AM, Stervbo U, Watson CT, Schramm CA; AIRR Community. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol 2022; 2453:279-96. [PMID: 35622332 DOI: 10.1007/978-1-0716-2115-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
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5
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Kenter AL, Watson CT, Spille JH. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front Immunol 2021; 12:682589. [PMID: 34084176 PMCID: PMC8167033 DOI: 10.3389/fimmu.2021.682589] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023] Open
Abstract
Vast repertoires of unique antigen receptors are created in developing B and T 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 of expressed immunoglobulins and T cell receptors. This process creates the potential for an organism to respond to large numbers of different pathogens. Here, we consider the possibility that genetic polymorphisms with alterations in a vast array of regulatory elements in the immunoglobulin heavy chain (IgH) locus lead to changes in locus topology and impact immune-repertoire formation.
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Affiliation(s)
- Amy L. Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL, United States
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6
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Fukuyama J, Olson BJ, Matsen FA. Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification. J Immunol 2020; 205:936-944. [PMID: 32669310 PMCID: PMC7593666 DOI: 10.4049/jimmunol.2000092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
BCR sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation and therefore Ig diversification in mice and humans. In this proposed process, mutations in the Ig locus are introduced by copying short segments from other Ig genes. If true, this would overturn decades of research on B cell diversification and would require a complete rewrite of computational methods to analyze B cell data for these species. In this paper, we re-evaluate the templated mutagenesis hypothesis. By applying the original inferential method using potential donor templates absent from B cell genomes, we obtain estimates of the methods' false positive rates. We find false positive rates of templated mutagenesis in murine and human Ig loci that are similar to or even higher than the original rate inferences, and by considering the bases used in substitution, we find evidence that if templated mutagenesis occurs, it is at a low rate. We also show that the statistically significant results in the original paper can easily result from a slight misspecification of the null model.
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Affiliation(s)
- Julia Fukuyama
- Department of Statistics, Indiana University Bloomington, Bloomington, IN 47408
| | - Branden J Olson
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
- Department of Statistics, University of Washington, Seattle, WA 98195
| | - Frederick A Matsen
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
- Department of Statistics, University of Washington, Seattle, WA 98195
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7
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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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8
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Oudinet C, Braikia FZ, Dauba A, Khamlichi AA. Recombination may occur in the absence of transcription in the immunoglobulin heavy chain recombination centre. Nucleic Acids Res 2020; 48:3553-3566. [PMID: 32086526 PMCID: PMC7144927 DOI: 10.1093/nar/gkaa108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/06/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Developing B cells undergo V(D)J recombination to generate a vast repertoire of Ig molecules. V(D)J recombination is initiated by the RAG1/RAG2 complex in recombination centres (RCs), where gene segments become accessible to the complex. Whether transcription is the causal factor of accessibility or whether it is a side product of other processes that generate accessibility remains a controversial issue. At the IgH locus, V(D)J recombination is controlled by Eμ enhancer, which directs the transcriptional, epigenetic and recombinational events in the IgH RC. Deletion of Eμ enhancer affects both transcription and recombination, making it difficult to conclude if Eμ controls the two processes through the same or different mechanisms. By using a mouse line carrying a CpG-rich sequence upstream of Eμ enhancer and analyzing transcription and recombination at the single-cell level, we found that recombination could occur in the RC in the absence of detectable transcription, suggesting that Eμ controls transcription and recombination through distinct mechanisms. Moreover, while the normally Eμ-dependent transcription and demethylating activities were impaired, recruitment of chromatin remodeling complexes was unaffected. RAG1 was efficiently recruited, thus compensating for the defective transcription-associated recruitment of RAG2, and providing a mechanistic basis for RAG1/RAG2 assembly to initiate V(D)J recombination.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
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9
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Busse CE, Jackson KJL, Watson CT, Collins AM. A Proposed New Nomenclature for the Immunoglobulin Genes of Mus musculus. Front Immunol 2019; 10:2961. [PMID: 31921202 PMCID: PMC6930147 DOI: 10.3389/fimmu.2019.02961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/03/2019] [Indexed: 01/26/2023] Open
Abstract
Mammalian immunoglobulin (IG) genes are found in complex loci that contain hundreds of highly similar pseudogenes, functional genes and repetitive elements, which has made their investigation particularly challenging. High-throughput sequencing has provided new avenues for the investigation of these loci, and has recently been applied to study the IG genes of important inbred mouse strains, revealing unexpected differences between their IG loci. This demonstrated that the structural differences are of such magnitude that they call into question the merits of the current mouse IG gene nomenclatures. Three nomenclatures for the mouse IG heavy chain locus (Igh) are presently in use, and they are all positional nomenclatures using the C57BL/6 genome reference sequence as their template. The continued use of these nomenclatures requires that genes of other inbred strains be confidently identified as allelic variants of C57BL/6 genes, but this is clearly impossible. The unusual breeding histories of inbred mouse strains mean that, regardless of the genetics of wild mice, no single ancestral origin for the IG loci exists for laboratory mice. Here we present a general discussion of the challenges this presents for any IG nomenclature. Furthermore, we describe principles that could be followed in the formulation of a solution to these challenges. Finally, we propose a non-positional nomenclature that accords with the guidelines of the International Mouse Nomenclature Committee, and outline strategies that can be adopted to meet the nomenclature challenges if three systems are to give way to a new one.
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Affiliation(s)
- Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Katherine J L Jackson
- Immunology Division, The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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10
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Watson CT, Kos JT, Gibson WS, Newman L, Deikus G, Busse CE, Smith ML, Jackson KJ, Collins AM. A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunol Cell Biol 2019; 97:888-901. [PMID: 31441114 DOI: 10.1111/imcb.12288] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/05/2019] [Accepted: 08/20/2019] [Indexed: 01/20/2023]
Abstract
The genomes of classical inbred mouse strains include genes derived from all three major subspecies of the house mouse, Mus musculus. We recently posited that genetic diversity in the immunoglobulin heavy chain (IGH) gene loci of C57BL/6 and BALB/c mice reflects differences in subspecies origin. To investigate this hypothesis, we conducted high-throughput sequencing of IGH gene rearrangements to document IGH variable (IGHV), joining (IGHJ) and diversity (IGHD) genes in four inbred wild-derived mouse strains (CAST/EiJ, LEWES/EiJ, MSM/MsJ and PWD/PhJ) and a single disease model strain (NOD/ShiLtJ), collectively representing genetic backgrounds of several major mouse subspecies. A total of 341 germline IGHV sequences were inferred in the wild-derived strains, including 247 not curated in the international ImMunoGeneTics information system. By contrast, 83/84 inferred NOD IGHV genes had previously been observed in C57BL/6 mice. Variability among the strains examined was observed for only a single IGHJ gene, involving a description of a novel allele. By contrast, unexpected variation was found in the IGHD gene loci, with four previously unreported IGHD gene sequences being documented. Very few IGHV sequences of C57BL/6 and BALB/c mice were shared with strains representing major subspecies, suggesting that their IGH loci may be complex mosaics of genes of disparate origins. This suggests a similar level of diversity is likely present in the IGH loci of other classical inbred strains. This must now be documented if we are to properly understand interstrain variation in models of antibody-mediated disease.
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Affiliation(s)
- Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Leah Newman
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Melissa L Smith
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Katherine Jl Jackson
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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11
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Alberca Custodio RW, Mirotti L, Gomes E, Nunes FP, S. Vieira R, Graça L, R. Almeida R, S. Câmara NO, Russo M. Dendritic Cells Expressing MyD88 Molecule Are Necessary and Sufficient for CpG-Mediated Inhibition of IgE Production In Vivo. Cells 2019; 8:cells8101165. [PMID: 31569343 PMCID: PMC6829343 DOI: 10.3390/cells8101165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022] Open
Abstract
Elevated levels of immunoglobulin E (IgE) are associated with allergies and other immunological disorders. Sensitization with alum adjuvant favours IgE production while CpG-ODN adjuvant, a synthetic toll-like receptor 9 (TLR9) agonist, inhibits it. The cellular mechanisms underlying in vivo TLR regulation of immunoglobulin production, specially IgE, are still controversial. Specifically, TLR-mediated IgE regulation in vivo is not yet known. In this study we showed that augmented levels of IgE induced by sensitizations to OVA with or without alum adjuvant or with OVA-pulsed dendritic cells (DCs) were inhibited by co-administration of CpG. Notably, CpG-mediated suppression of IgE production required MyD88-expression on DCs but not on B-cells. This finding contrasts with previous in vitro studies reporting regulation of IgE by a direct action of CpG on B cells via MyD88 pathway. In addition, we showed that CpG also inhibited IgE production in a MyD88-dependent manner when sensitization was performed with OVA-pulsed DCs. Finally, CpG signalling through MyD88 pathway was also necessary and sufficient to prevent anaphylactic antibody production involved in active cutaneous anaphylaxis.
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Affiliation(s)
- Ricardo W. Alberca Custodio
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Luciana Mirotti
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Eliane Gomes
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Fernanda P.B. Nunes
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Raquel S. Vieira
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Luís Graça
- Institute of Molecular Medicine, University of Lisbon, 1649-028 Lisbon, Portugal;
| | - Rafael R. Almeida
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Niels O. S. Câmara
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
| | - Momtchilo Russo
- Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, Sao Paulo 05508-000, Brazil; (R.W.A.C.); (L.M.); (E.G.); (R.S.V.); (R.R.A.); (N.O.S.C.)
- Correspondence: ; Tel.: +55-1130-917-377
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12
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Dale GA, Wilkins DJ, Bohannon CD, Dilernia D, Hunter E, Bedford T, Antia R, Sanz I, Jacob J. Clustered Mutations at the Murine and Human IgH Locus Exhibit Significant Linkage Consistent with Templated Mutagenesis. J Immunol 2019; 203:1252-1264. [PMID: 31375545 PMCID: PMC6702052 DOI: 10.4049/jimmunol.1801615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/18/2019] [Indexed: 01/21/2023]
Abstract
Somatic hypermutation generates a myriad of Ab mutants in Ag-specific B cells, from which high-affinity mutants are selected. Chickens, sheep, and rabbits use nontemplated point mutations and templated mutations via gene conversion to diversify their expressed Ig loci, whereas mice and humans rely solely on untemplated somatic point mutations. In this study, we demonstrate that, in addition to untemplated point mutations, templated mutagenesis readily occurs at the murine and human Ig loci. We provide two distinct lines of evidence that are not explained by the Neuberger model of somatic hypermutation: 1) across multiple data sets there is significant linkage disequilibrium between individual mutations, especially among close mutations, and 2) among those mutations, those <8 bp apart are significantly more likely to match microhomologous regions in the IgHV repertoire than predicted by the mutation profiles of somatic hypermutation. Together, this supports the role of templated mutagenesis during somatic diversification of Ag-activated B cells.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Caitlin D Bohannon
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Trevor Bedford
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322; and
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA 30322
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329;
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13
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Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH. Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data. Front Immunol 2019; 10:129. [PMID: 30814994 PMCID: PMC6381938 DOI: 10.3389/fimmu.2019.00129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/16/2019] [Indexed: 01/10/2023] Open
Abstract
The adaptive immune receptor repertoire (AIRR) contains information on an individuals' immune past, present and potential in the form of the evolving sequences that encode the B cell receptor (BCR) repertoire. AIRR sequencing (AIRR-seq) studies rely on databases of known BCR germline variable (V), diversity (D), and joining (J) genes to detect somatic mutations in AIRR-seq data via comparison to the best-aligning database alleles. However, it has been shown that these databases are far from complete, leading to systematic misidentification of mutated positions in subsets of sample sequences. We previously presented TIgGER, a computational method to identify subject-specific V gene genotypes, including the presence of novel V gene alleles, directly from AIRR-seq data. However, the original algorithm was unable to detect alleles that differed by more than 5 single nucleotide polymorphisms (SNPs) from a database allele. Here we present and apply an improved version of the TIgGER algorithm which can detect alleles that differ by any number of SNPs from the nearest database allele, and can construct subject-specific genotypes with minimal prior information. TIgGER predictions are validated both computationally (using a leave-one-out strategy) and experimentally (using genomic sequencing), resulting in the addition of three new immunoglobulin heavy chain V (IGHV) gene alleles to the IMGT repertoire. Finally, we develop a Bayesian strategy to provide a confidence estimate associated with genotype calls. All together, these methods allow for much higher accuracy in germline allele assignment, an essential step in AIRR-seq studies.
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Affiliation(s)
- Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Moriah Gidoni
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jason A. Vander Heiden
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Kevin C. O'Connor
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Steven H. Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United States
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
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14
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Qiu X, Kumari G, Gerasimova T, Du H, Labaran L, Singh A, De S, Wood WH, Becker KG, Zhou W, Ji H, Sen R. Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus. Mol Cell 2018; 70:21-33.e6. [PMID: 29576529 DOI: 10.1016/j.molcel.2018.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/19/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022]
Abstract
Immunoglobulin heavy-chain (IgH) genes are assembled by DNA rearrangements that juxtapose a variable (VH), a diversity (DH), and a joining (JH) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (Eμ) associates with the next available CTCF binding site located close to VH81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eμ/VH81X loop leads to formation of a distorted recombination center and altered DH rearrangements and disrupts chromosome conformation that favors distal VH recombination. Cumulatively, these features drive highly skewed, Eμ-dependent recombination of VH81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal VH gene segments. Our observations demonstrate that Eμ interacts differently with IGCR1- or VH-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity.
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Affiliation(s)
- Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Gita Kumari
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Tatiana Gerasimova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Lawal Labaran
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - William H Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA.
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15
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Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Structural Variation Shapes the Landscape of Recombination in Mouse. Genetics 2017; 206:603-19. [PMID: 28592499 DOI: 10.1534/genetics.116.197988] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/13/2017] [Indexed: 01/02/2023] Open
Abstract
Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape.
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16
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Lin SG, Ba Z, Du Z, Zhang Y, Hu J, Alt FW. Highly sensitive and unbiased approach for elucidating antibody repertoires. Proc Natl Acad Sci U S A 2016; 113:7846-51. [PMID: 27354528 DOI: 10.1073/pnas.1608649113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes.
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17
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Collins AM, Wang Y, Roskin KM, Marquis CP, Jackson KJL. The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0236. [PMID: 26194750 DOI: 10.1098/rstb.2014.0236] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The human and mouse antibody repertoires are formed by identical processes, but like all small animals, mice only have sufficient lymphocytes to express a small part of the potential antibody repertoire. In this study, we determined how the heavy chain repertoires of two mouse strains are generated. Analysis of IgM- and IgG-associated VDJ rearrangements generated by high-throughput sequencing confirmed the presence of 99 functional immunoglobulin heavy chain variable (IGHV) genes in the C57BL/6 genome, and inferred the presence of 164 IGHV genes in the BALB/c genome. Remarkably, only five IGHV sequences were common to both strains. Compared with humans, little N nucleotide addition was seen in the junctions of mouse VDJ genes. Germline human IgG-associated IGHV genes are rare, but many murine IgG-associated IGHV genes were unmutated. Together these results suggest that the expressed mouse repertoire is more germline-focused than the human repertoire. The apparently divergent germline repertoires of the mouse strains are discussed with reference to reports that inbred mouse strains carry blocks of genes derived from each of the three subspecies of the house mouse. We hypothesize that the germline genes of BALB/c and C57BL/6 mice may originally have evolved to generate distinct germline-focused antibody repertoires in the different mouse subspecies.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 NSW, Australia
| | - Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 NSW, Australia
| | - Krishna M Roskin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 NSW, Australia
| | - Katherine J L Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 NSW, Australia Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA
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18
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Bialon M, Schellenberg L, Herzog N, Kraus S, Jörißen H, Fischer R, Stein C, Nähring J, Barth S, Püttmann C. Cloning murine antibody V-genes with non-degenerate primers and conversion to a recombinant antibody format. Monoclon Antib Immunodiagn Immunother 2016; 33:369-77. [PMID: 25545205 DOI: 10.1089/mab.2014.0044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Monoclonal antibodies are produced in cultured hybridoma cell lines, but these cells tend to be unstable; it is therefore necessary to rescue the corresponding genetic information. Here we describe an improved method for the amplification of antibody variable gene (V-gene) information from murine hybridoma cells using a panel of specific, non-degenerate primers. This primer set allows sequences to be rescued from all murine V-genes, except the lambda light chain genes, which rarely contribute to murine immune diversity. We tested the primers against a range of antibodies and recovered specific amplification products in all cases. The heavy and light chain variable regions were subsequently joined by a two-step cloning strategy or by splice overlap extension PCR.
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Affiliation(s)
- Magdalena Bialon
- 1 Department of Experimental Medicine and Immunotherapy, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University , Aachen, Germany
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19
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Braikia FZ, Conte C, Moutahir M, Denizot Y, Cogné M, Khamlichi AA. Developmental Switch in the Transcriptional Activity of a Long-Range Regulatory Element. Mol Cell Biol 2015; 35:3370-80. [PMID: 26195822 DOI: 10.1128/MCB.00509-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic gene expression is often controlled by distant regulatory elements. In developing B lymphocytes, transcription is associated with V(D)J recombination at immunoglobulin loci. This process is regulated by remote cis-acting elements. At the immunoglobulin heavy chain (IgH) locus, the 3' regulatory region (3'RR) promotes transcription in mature B cells. This led to the notion that the 3'RR orchestrates the IgH locus activity at late stages of B cell maturation only. However, long-range interactions involving the 3'RR were detected in early B cells, but the functional consequences of these interactions were unknown. Here we show that not only does the 3'RR affect transcription at distant sites within the IgH variable region but also it conveys a transcriptional silencing activity on both sense and antisense transcription. The 3'RR-mediated silencing activity is switched off upon completion of VH-DJH recombination. Our findings reveal a developmentally controlled, stage-dependent shift in the transcriptional activity of a master regulatory element.
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20
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Puget N, Leduc C, Oruc Z, Moutahir M, Le Bert M, Khamlichi AA. Complete cis Exclusion upon Duplication of the Eμ Enhancer at the Immunoglobulin Heavy Chain Locus. Mol Cell Biol 2015; 35:2231-41. [PMID: 25896912 DOI: 10.1128/MCB.00294-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Developing lymphocytes somatically diversify their antigen-receptor loci through V(D)J recombination. The process is associated with allelic exclusion, which results in monoallelic expression of an antigen receptor locus. Various cis-regulatory elements control V(D)J recombination in a developmentally regulated manner, but their role in allelic exclusion is still unclear. At the immunoglobulin heavy chain locus (IgH), the Eμ enhancer plays a critical role in V(D)J recombination. We generated a mouse line with a replacement mutation in the constant region of the locus that duplicates the Eμ enhancer and allows premature expression of the γ3 heavy chain. Strikingly, IgM expression was completely and specifically excluded in cis from the mutant allele. This cis exclusion recapitulated the main features of allelic exclusion, including differential exclusion of variable genes. Notably, sense and antisense transcription within the distal variable domain and distal V(H)-DJ(H) recombination were inhibited. cis exclusion was established and stably maintained despite an active endogenous Eμ enhancer. The data reveal the importance of the dynamic, developmental stage-dependent interplay between IgH locus enhancers and signaling in the induction and maintenance of allelic exclusion.
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21
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Puget N, Hirasawa R, Hu NS, Laviolette-Malirat N, Feil R, Khamlichi AA. Insertion of an imprinted insulator into the IgH locus reveals developmentally regulated, transcription-dependent control of V(D)J recombination. Mol Cell Biol 2015; 35:529-43. [PMID: 25403489 DOI: 10.1128/MCB.00235-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The assembly of antigen receptor loci requires a developmentally regulated and lineage-specific recombination between variable (V), diversity (D), and joining (J) segments through V(D)J recombination. The process is regulated by accessibility control elements, including promoters, insulators, and enhancers. The IgH locus undergoes two recombination steps, D-J(H) and then V(H)-DJ(H), but it is unclear how the availability of the DJ(H) substrate could influence the subsequent V(H)-DJ(H) recombination step. The Eμ enhancer plays a critical role in V(D)J recombination and controls a set of sense and antisense transcripts. We epigenetically perturbed the early events at the IgH locus by inserting the imprinting control region (ICR) of the Igf2/H19 locus or a transcriptional insulator devoid of the imprinting function upstream of the Eμ enhancer. The insertions recapitulated the main epigenetic features of their endogenous counterparts, including differential DNA methylation and binding of CTCF/cohesins. Whereas the D-J(H) recombination step was unaffected, both the insulator insertions led to a severe impairment of V(H)-DJ(H) recombination. Strikingly, the inhibition of V(H)-DJ(H) recombination correlated consistently with a strong reduction of DJ(H) transcription and incomplete demethylation. Thus, developmentally regulated transcription following D-J(H) recombination emerges as an important mechanism through which the Eμ enhancer controls V(H)-DJ(H) recombination.
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22
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Fitzsimmons SP, Aydanian AG, Clark KJ, Shapiro MA. Multiple factors influence the contribution of individual immunoglobulin light chain genes to the naïve antibody repertoire. BMC Immunol 2014; 15:51. [PMID: 25359572 PMCID: PMC4216371 DOI: 10.1186/s12865-014-0051-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 10/17/2014] [Indexed: 01/27/2023] Open
Abstract
Background The naïve antibody repertoire is initially dependent upon the number of germline V(D)J genes and the ability of recombined heavy and light chains to pair. Individual VH and VL genes are not equally represented in naïve mature B cells, suggesting that positive and negative selection also shape the antibody repertoire. Among the three member murine Vκ10 L chain family, the Vκ10C gene is under-represented in the antibody repertoire. Although it is structurally functional and accessible to both transcriptional and recombination machinery, the Vκ10C promoter is inefficient in pre-B cell lines and productive Vκ10C rearrangements are lost as development progresses from pre-B cells through mature B cells. This study examined VH/Vκ10 pairing, promoter mutations, Vκ10 transcript levels and receptor editing as possible factors that are responsible for loss of productive Vκ10C rearrangements in developing B cells. Results We demonstrate that the loss of Vκ10C expression is not due to an inability to pair with H chains, but is likely due to a combination of other factors. Levels of mRNA are low in sorted pre-B cells and undetectable in B cells. Mutation of a single base in the three prime region of the Vκ10C promoter increases Vκ10C promoter function in pre-B cell lines. Pre-B and B cells harbor disproportionate levels of receptor-edited productive Vκ10C rearrangements. Conclusions Our findings suggest that the weak Vκ10C promoter initially limits the amount of available Vκ10C L chain for pairing with H chains, resulting in sub-threshold levels of cell surface B cell receptors, insufficient tonic signaling and subsequent receptor editing to limit the numbers of Vκ10C-expressing B cells emigrating from the bone marrow to the periphery.
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Affiliation(s)
| | | | | | - Marjorie A Shapiro
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, OBP, CDER, FDA, 10903 New Hampshire Avenue, Silver Spring 20993, MD, USA.
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23
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Braikia FZ, Chemin G, Moutahir M, Khamlichi AA. Quantification of V(D)J recombination by real-time quantitative PCR. Immunol Lett 2014; 162:119-23. [PMID: 25128366 DOI: 10.1016/j.imlet.2014.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/30/2014] [Accepted: 08/03/2014] [Indexed: 11/26/2022]
Abstract
B and T lymphocytes have the unique capacity to somatically rearrange their antigen receptor loci through V(D)J recombination. D-JH and VH-DJH recombination events are usually visualized by semi-quantitative PCR followed by detection of end products, which is time consuming and requires the use of hazardous elements. Additionally, it necessitates relatively large amounts of genomic DNA which could be limiting when the cell populations of interest are rare. Here, we describe a real-time quantitative PCR assay for a fast quantification of V(D)J recombination events at the IgH locus.
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Affiliation(s)
- Fatima-Zohra Braikia
- CNRS UMR 5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); FRBT, 205 route de Narbonne, BP 64182, F-31077 Toulouse, France; Université de Toulouse; UPS; IPBS F-31077 Toulouse, France
| | - Guillaume Chemin
- CNRS UMR 5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); FRBT, 205 route de Narbonne, BP 64182, F-31077 Toulouse, France; Université de Toulouse; UPS; IPBS F-31077 Toulouse, France
| | - Mohammed Moutahir
- CNRS UMR 5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); FRBT, 205 route de Narbonne, BP 64182, F-31077 Toulouse, France; Université de Toulouse; UPS; IPBS F-31077 Toulouse, France
| | - Ahmed Amine Khamlichi
- CNRS UMR 5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); FRBT, 205 route de Narbonne, BP 64182, F-31077 Toulouse, France; Université de Toulouse; UPS; IPBS F-31077 Toulouse, France.
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24
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Lucas JS, Zhang Y, Dudko OK, Murre C. 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell 2014; 158:339-352. [PMID: 24998931 DOI: 10.1016/j.cell.2014.05.036] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/19/2014] [Accepted: 05/01/2014] [Indexed: 12/01/2022]
Abstract
During B lymphocyte development, immunoglobulin heavy-chain variable (VH), diversity (DH), and joining (JH) segments assemble to generate a diverse antigen receptor repertoire. Here, we have marked the distal VH and DH-JH-Eμ regions with Tet-operator binding sites and traced their 3D trajectories in pro-B cells transduced with a retrovirus encoding Tet-repressor-EGFP. We found that these elements displayed fractional Langevin motion (fLm) due to the viscoelastic hindrance from the surrounding network of proteins and chromatin fibers. Using fractional Langevin dynamics modeling, we found that, with high probability, DHJH elements reach a VH element within minutes. Spatial confinement emerged as the dominant parameter that determined the frequency of such encounters. We propose that the viscoelastic nature of the nuclear environment causes coding elements and regulatory elements to bounce back and forth in a spring-like fashion until specific genomic interactions are established and that spatial confinement of topological domains largely controls first-passage times for genomic interactions.
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Affiliation(s)
- Joseph S Lucas
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yaojun Zhang
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olga K Dudko
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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Lu J, Panavas T, Thys K, Aerssens J, Naso M, Fisher J, Rycyzyn M, Sweet RW. IgG variable region and VH CDR3 diversity in unimmunized mice analyzed by massively parallel sequencing. Mol Immunol 2014; 57:274-83. [PMID: 24211535 DOI: 10.1016/j.molimm.2013.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/11/2013] [Accepted: 09/28/2013] [Indexed: 11/24/2022]
Abstract
Most antigen-specific mouse antibodies have been derived by hybridoma technology, predominantly through use of the Balb/c strain. Much of the Balb/c germline repertoire of variable genes (V regions) is known. However, there is little information about the background expressed repertoire of IgG antibodies in mice, which reflects the baseline against which antigen-specific antibodies are generated through immunization. To assess this baseline repertoire, RNA was isolated from splenic B-cells enriched for expression of IgG from three mice. The RNA was individually amplified with three distinct PCR primer sets for comprehensive recovery of the heavy and light chain variable regions. Each PCR product was independently subjected to deep sequencing using 454 pyro-sequencing technology and analysed for redundancy, open reading frame, germline representation, and CDR3 sequence of the heavy chain variable region (VH CDR3) within and across the primer sets and mice. A highly skewed abundance of heavy and light chain variable gene usage was observed for all three primers in all three mice. While showing considerable overlap, there were differences among these profiles indicative of primer bias and animal-to-animal variation. VH CDR3 sequences were likewise highly skewed indicating that the heavy chain genes profiles substantially reflected individual antibodies. This observation was confirmed through analysis of randomly selected complete heavy chain variable sequences. However, there was very little redundancy in VH CDR3 sequences across the different mice. We conclude that the background IgG repertoire in young, unimmunized mice is highly skewed within individual mice and is diverse among them, a pattern similar to that observed in highly immunized mice.
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Khass M, Buckley K, Kapoor P, Schelonka RL, Watkins LS, Zhuang Y, Schroeder HW. Recirculating bone marrow B cells in C57BL/6 mice are more tolerant of highly hydrophobic and highly charged CDR-H3s than those in BALB/c mice. Eur J Immunol 2013; 43:629-40. [PMID: 23225217 DOI: 10.1002/eji.201242936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 11/01/2012] [Accepted: 11/30/2012] [Indexed: 11/07/2022]
Abstract
To test whether mechanisms controlling the range of diversity of the developing antibody repertoire in C57BL/6 mice (IgH(b)) operate similarly to those identified in BALB/c mice (IgH(a)), we compared the sequences of VH 7183-containing H-chain transcripts from sorted adult bone marrow C57BL/6 B-cell subsets with those previously obtained from BALB/c mice. Patterns of VDJ gene segment utilization and CDR-H3 amino acid composition, charge, and average length in C57BL/6 pro-B cells were similar, although not identical, to BALB/c pro-B cells. However, C57BL/6 mature, recirculating B cells failed to demonstrate the reduction in the use of VH81X and the narrowing in the range of variance of CDR-H3 hydrophobicity that characterizes B-cell maturation in BALB/c mice. To further test the ability of the C57BL/6 strain to discard B cells expressing highly charged CDR-H3s, we introduced a mutant IgH(a) DH allele that forces use of arginine, asparagine, and histidine. Unlike BALB/c mice, C57BL/6 mice congenic for the charged DH maintained normal numbers of mature, recirculating B cells that were enriched for charged CDR-H3s. Together these findings indicate that the mature C57BL/6 B-cell pool permits expression of immunoglobulins with antigen-binding sites that are typically discarded during late-stage bone marrow B-cell development in BALB/c mice.
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Affiliation(s)
- Mohamed Khass
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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Aoki-Ota M, Torkamani A, Ota T, Schork N, Nemazee D. Skewed primary Igκ repertoire and V-J joining in C57BL/6 mice: implications for recombination accessibility and receptor editing. J Immunol 2012; 188:2305-15. [PMID: 22287713 PMCID: PMC3288532 DOI: 10.4049/jimmunol.1103484] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Previous estimates of the diversity of the mouse Ab repertoire have been based on fragmentary data as a result of many technical limitations, in particular, the many samples necessary to provide adequate coverage. In this study, we used 5'-coding end amplification of Igκ mRNAs from bone marrow, splenic, and lymph node B cells of C57BL/6 mice combined with amplicon pyrosequencing to assess the functional and nonfunctional Vκ repertoire. To evaluate the potential effects of receptor editing, we also compared V/J associations and usage in bone marrows of mouse mutants under constitutive negative selection or an altered ability to undergo secondary recombination. To focus on preimmune B cells, our cell sorting strategy excluded memory B cells and plasma cells. Analysis of ~90 Mbp, representing >250,000 individual transcripts from 59 mice, revealed that 101 distinct functional Vκ genes are used but at frequencies ranging from ~0.001 to ~10%. Usage of seven Vκ genes made up >40% of the repertoire. A small class of transcripts from apparently nonfunctional Vκ genes was found, as were occasional transcripts from several apparently functional genes that carry aberrant recombination signals. Of 404 potential V-J combinations (101 Vκs × 4 Jκs), 398 (98.5%) were found at least once in our sample. For most Vκ transcripts, all Jκs were used, but V-J association biases were common. Usage patterns were remarkably stable in different selective conditions. Overall, the primary κ repertoire is highly skewed by preferred rearrangements, limiting Ab diversity, but potentially facilitating receptor editing.
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Affiliation(s)
- Miyo Aoki-Ota
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037
| | - Ali Torkamani
- Translational Sciences Institute, The Scripps Research Institute, La Jolla, California 92037
| | - Takayuki Ota
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037
| | - Nicholas Schork
- Translational Sciences Institute, The Scripps Research Institute, La Jolla, California 92037
| | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037
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Guo C, Gerasimova T, Hao H, Ivanova I, Chakraborty T, Selimyan R, Oltz EM, Sen R. Two forms of loops generate the chromatin conformation of the immunoglobulin heavy-chain gene locus. Cell 2011; 147:332-43. [PMID: 21982154 DOI: 10.1016/j.cell.2011.08.049] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 04/26/2011] [Accepted: 08/26/2011] [Indexed: 10/16/2022]
Abstract
The immunoglobulin heavy-chain (IgH) gene locus undergoes radial repositioning within the nucleus and locus contraction in preparation for gene recombination. We demonstrate that IgH locus conformation involves two levels of chromosomal compaction. At the first level, the locus folds into several multilooped domains. One such domain at the 3' end of the locus requires an enhancer, Eμ; two other domains at the 5' end are Eμ independent. At the second level, these domains are brought into spatial proximity by Eμ-dependent interactions with specific sites within the V(H) region. Eμ is also required for radial repositioning of IgH alleles, indicating its essential role in large-scale chromosomal movements in developing lymphocytes. Our observations provide a comprehensive view of the conformation of IgH alleles in pro-B cells and the mechanisms by which it is established.
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Affiliation(s)
- Changying Guo
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
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Kolberg J, Ihle Ø, Thiede B, Aase A. Polyreactivity of monoclonal antibodies made against human erythrocyte membranes with various pathogenic bacteria. Hybridoma (Larchmt) 2011; 30:1-9. [PMID: 21466280 DOI: 10.1089/hyb.2010.0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Glycophorins comprise the major sialoglycoproteins of the human erythrocyte membrane. Several years ago we described a murine monoclonal antibody (MAb), designated 124,D-7 (IgM), developed by in vitro immunization with human erythrocyte membranes as antigen. We found the MAb reacted with a neuraminidase-dependent epitope on glycophorin A. Recent findings using ELISA with various bacteria as coating antigens have demonstrated strong cross-reactions of MAb 124,D-7 with some bacteria like Legionella and no reaction with bacteria such as Streptococcus pneumoniae. A second MAb, 130,E-4 (IgM), generated by the in vitro immunization technique, agglutinated human red cells irrespective of blood groups. This MAb showed strong cross-reactions with bacteria different from those being positive with MAb 124,D-7. The broad cross-reactivities of the two MAbs suggested that they are polyreactive antibodies. Sequencing of the V(H) and V(L) genes of MAb 124,D-7 showed germ-like sequences characteristic of polyreactive antibodies. The nucleotide sequences of the V(H) and V(L) genes of MAb 124,D-7 matched sequences coding for antibodies against CD34 and cross-reacting streptococcal antibodies. For Legionella pneumophila, the main interacting band on immunoblots was identified as the major outer membrane protein by mass spectrometry after separation by isoelectric focusing followed by SDS-PAGE. Flow cytometry showed that the epitope for MAb 124,D-7 was not displayed on live L. pneumophila but became exposed after heat treatment. Studies with one of the control MAbs, 145,F-2, directed against phosphorylcholine, which is known to be present on erythrocytes and some bacteria, showed that the epitope is deeply buried in the human erythrocyte membrane as neither neuraminidase nor papain exposed the epitope. The positive control MAb 3/1 directed against an epitope on LPS of L. pneumophila revealed weak cross-reactions with Pseudomonas aeruginosa.
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Affiliation(s)
- Jan Kolberg
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Nydalen, Oslo, Norway.
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Rapoport B, Williams RW, Chen CR, McLachlan SM. Immunoglobulin heavy chain variable region genes contribute to the induction of thyroid-stimulating antibodies in recombinant inbred mice. Genes Immun 2010; 11:254-63. [PMID: 20407472 PMCID: PMC4108286 DOI: 10.1038/gene.2010.8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Graves' hyperthyroidism is an autoimmune disease occurring spontaneously in humans and caused by autoantibodies that stimulate the thyrotropin receptor. In mice, inducing Graves'-like hyperthyroidism requires in vivo expression of the thyrotropin receptor using plasmid or adenovirus vectors. However, mice with different genetic backgrounds vary markedly in their susceptibility to induced hyperthyroidism. Further, in some strains major disparities exist between the induction of hyperthyroidism and detection of thyroid-stimulating antibodies. To break tolerance, virtually all Graves' mouse models involve immunization with human thyrotropin-receptor DNA and the standard thyroid-stimulating antibody bioassay uses cells expressing the human thyrotropin receptor. We hypothesized, and now report, that disparities between hyperthyroidism and thyroid-stimulating antibody bioactivity are explained, at least in part, by differential antibody recognition of the human vs the mouse thyrotropin receptor. The genetic basis for these species differences was explored using genotyped, recombinant-inbred mouse strains. We report that loci in the immunoglobulin heavy chain variable region as well as in the major histocompatibility complex region contribute in a strain-specific manner to the development of antibodies specific for the human or the mouse thyrotropin receptor. The novel finding of a role for immunoglobulin heavy chain variable region gene involvement in thyroid-stimulating antibody epitopic specificity provides potential insight into genetic susceptibility in human Graves' disease.
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Affiliation(s)
- B Rapoport
- Cedars-Sinai Research Institute and UCLA School of Medicine, Los Angeles, CA 90048, USA
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Winterroth L, Rivera J, Nakouzi AS, Dadachova E, Casadevall A. Neutralizing monoclonal antibody to edema toxin and its effect on murine anthrax. Infect Immun 2010; 78:2890-8. [PMID: 20385755 DOI: 10.1128/IAI.01101-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Edema factor (EF) is a component of an anthrax toxin that functions as an adenylate cyclase. Numerous monoclonal antibodies (MAbs) have been reported for the other Bacillus anthracis toxin components, but relatively few to EF have been studied. We report the generation of six murine hybridoma lines producing two IgM and four IgG1 MAbs to EF. Of the six MAbs, only one IgM neutralized EF, as assayed by an increase in cyclic AMP (cAMP) production by Chinese hamster ovary (CHO) cells. Analysis of the variable gene elements revealed that the single neutralizing MAb had a different binding site than the others. There was no competition between the neutralizing IgM and the nonneutralizing IgG MAbs indicative of different specificity. MAb-based capture enzyme-linked immunosorbent assay (ELISA) detected EF in liver lysates from mice infected with B. anthracis Sterne 34F2. Administration of the neutralizing IgM MAb to A/JCr mice lethally infected with B. anthracis strain Sterne had no significant effect on median time to death, but mice treated with the MAb were more likely to survive infection. Combining the neutralizing IgM to EF with a subprotective dose of a neutralizing MAb to protective antigen (PA) prolonged mean time to death of infected mice, suggesting that neutralization of EF and PA could produce synergistic beneficial effects. In summary, the results from our study and literature observations suggest that the majority of Abs to EF are nonneutralizing, but the toxin has some epitopes that can be targeted by the humoral response to generate useful Abs that may contribute to defense against anthrax.
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Lin L, Flisikowski K, Schwarzenbacher H, Scharfe M, Severitt S, Blöcker H, Fries R. Characterization of the porcineAMPK alpha 2 catalytic subunitgene(PRKAA2): genomic structure, polymorphism detection and association study. Anim Genet 2010; 41:203-7. [DOI: 10.1111/j.1365-2052.2009.01971.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Immunoglobulin variable region exons are assembled from discontinuous variable (V), diversity (D), and joining (J) segments by the process of V(D)J recombination. V(D)J rearrangements of the immunoglobulin heavy chain (IgH) locus are tightly controlled in a tissue-specific, ordered and allele-specific manner by regulating accessibility of V, D, and J segments to the recombination activating gene proteins which are the specific components of the V(D)J recombinase. In this review we discuss recent advances and established models brought forward to explain the mechanisms underlying accessibility control of V(D)J recombination, including research on germline transcripts, spatial organization, and chromatin modifications of the immunoglobulin heavy chain (IgH) locus. Furthermore, we review the functions of well-described and potential new cis-regulatory elements with regard to processes such as V(D)J recombination, allelic exclusion, and IgH class switch recombination.
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Affiliation(s)
- Thomas Perlot
- The Howard Hughes Medical Institute, The Children's Hospital, Immune Disease Institute, Harvard Medical School, Boston, Massachusetts, USA
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Abstract
Because of their extreme importance to human health, we probably know more about the structure and function of antibodies than practically any other molecule. Despite all the knowledge that has been accrued in the understanding of antibodies, modern approaches, especially comparative genomics, continue to yield novel findings regarding their underlying biology and evolution. In this review, we describe recent research that led to these revelations, and discuss the broad evolutionary implications of these findings. We have restricted our discussion to three vignettes. Considerable attention has been paid to the recent discovery that the teleost IgH locus is highly similar in organization to the Tcra-Tcrd locus, implicating an evolutionary common ancestor and parallels between the functions of B and T cells during development. Second, we discuss how a new type of antibody, recently discovered in jawless vertebrates, composed not of immunoglobulins but leucine-rich repeats, sheds new light on the overall forces driving evolution of all adaptive antigen receptors. Lastly, we discuss how accumulation of genomic sequences of various human subpopulations leads to better understanding of the directionality of antibody evolution. There is always more to learn from the unfolding saga of antibodies.
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Affiliation(s)
- Nadia Danilova
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, California 90095, USA.
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Abstract
The antibody repertoire is enormous and reflects the power of combinatorial and junctional diversity to generate avast repertoire with a moderate number of V, D and J gene segments. However, although there are many VH and VK gene segments, the usage of these genes is highly unequal. In this chapter, we summarize our studies elucidating many of the factors that contribute to this unequal rearrangement frequency of individual gene segments. Firstly, there is much natural variation in the sequence of the Recombination Signal Sequences (RSS) that flank each recombining gene. This genetic variation contributes greatly to unequal recombination frequencies. However, other factors also play a major role in recombination frequencies, as evidenced by the fact that some genes with identical RSS rearrange at very different frequencies in vivo. Analysis of these gene segments by chromatin immunoprecipitation (ChIP) suggests that differences in the structure of the chromatin associated with each gene is also a major factor in differential accessibility for rearrangement. Finally, transcription factors can direct accessibility for recombination, possibly by recruiting chromatin-modifying enzymes to the vicinity of the gene segment. Together, these factors dictate the composition of the newly formed antibody repertoire.
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Affiliation(s)
- Ann J Feeney
- The Scripps Research Institute, Department of Immunology, IMM22, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.
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Bolland DJ, Wood AL, Corcoran AE. Large-Scale Chromatin Remodeling at the Immunoglobulin Heavy Chain Locus: A Paradigm for Multigene Regulation. Advances in Experimental Medicine and Biology 2009; 650:59-72. [DOI: 10.1007/978-1-4419-0296-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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McLachlan SM, Aliesky HA, Pichurin PN, Chen CR, Williams RW, Rapoport B. Shared and unique susceptibility genes in a mouse model of Graves' disease determined in BXH and CXB recombinant inbred mice. Endocrinology 2008; 149:2001-9. [PMID: 18162518 PMCID: PMC2276708 DOI: 10.1210/en.2007-1517] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Susceptibility genes for TSH receptor (TSHR) antibodies and hyperthyroidism can be probed in recombinant inbred (RI) mice immunized with adenovirus expressing the TSHR A-subunit. The RI set of CXB strains, derived from susceptible BALB/c and resistant C57BL/6 (B6) mice, were studied previously. High-resolution genetic maps are also available for RI BXH strains, derived from B6 and C3H/He parents. We found that C3H/He mice develop TSHR antibodies, and some animals become hyperthyroid after A-subunit immunization. In contrast, the responses of the F1 progeny of C3H/He x B6 mice, as well as most BXH RI strains, are dominated by the B6 resistance to hyperthyroidism. As in the CXB set, linkage analysis of BXH strains implicates different chromosomes (Chr) or loci in the susceptibility to induced TSHR antibodies vs. hyperthyroidism. Importantly, BXH and CXB mice share genetic loci controlling the generation of TSHR antibodies (Chr 17, major histocompatibility complex region, and Chr X) and development of hyperthyroidism (Chr 1 and 3). Moreover, some chromosomal linkages are unique to either BXH or CXB strains. An interesting candidate gene linked to thyroid-stimulating antibody generation in BXH mice is the Ig heavy chain locus, suggesting a role for particular germline region genes as precursors for these antibodies. In conclusion, our findings reinforce the importance of major histocompatibility complex region genes in controlling the generation of TSHR antibodies measured by TSH binding inhibition. Moreover, these data emphasize the value of RI strains to dissect the genetic basis for induced TSHR antibodies vs. their effects on thyroid function in Graves' disease.
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Affiliation(s)
- Sandra M McLachlan
- Autoimmune Disease Unit, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA.
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