1
|
de Groen PC. Muons, mutations, and planetary shielding. FRONTIERS IN ASTRONOMY AND SPACE SCIENCES 2022; 9:1067491. [PMID: 36688079 PMCID: PMC9854335 DOI: 10.3389/fspas.2022.1067491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Life on earth is protected from astrophysical cosmic rays by the heliospheric magnetic and slowly varying geomagnetic fields, and by collisions with oxygen and nitrogen molecules in the atmosphere. The collisions generate showers of particles of lesser energy; only muons, a charged particle with a mass between that of an electron and a proton, can reach earth's surface in substantial quantities. Muons are easily detected, used to image interior spaces of pyramids, and known to limit the stability of qubits in quantum computing; yet, despite their charge, average energy of 4 GeV and ionizing properties, muons are not considered to affect chemical reactions or biology. In this Perspective the potential damaging effects of muons on DNA, and hence the repercussions for evolution and disease, are examined. It is argued here that the effect of muons on life through DNA mutations should be considered when investigating the protection provided by the magnetic environment and atmosphere from cosmic rays on earth and exoplanets.
Collapse
|
2
|
Mompó SM, González-Fernández Á. Antigen-Specific Human Monoclonal Antibodies from Transgenic Mice. Methods Mol Biol 2018; 1904:253-291. [PMID: 30539474 DOI: 10.1007/978-1-4939-8958-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to the difficulties found when generating fully human monoclonal antibodies (mAbs) by the traditional method, several efforts have attempted to overcome these problems, with varying levels of success. One approach has been the development of transgenic mice carrying immunoglobulin (Ig) genes in germline configuration. The engineered mouse genome can undergo productive rearrangement in the B-cell population, with the generation of mouse B lymphocytes expressing human Ig (hIg) chains. To avoid the expression of mouse heavy or light chains, the endogenous mouse Ig (mIg) loci must be silenced by gene-targeting techniques. Subsequently, to obtain antigen-specific mAbs, conventional immunization protocols can be followed and the mAb technique used (fusion of activated B cells with mouse myeloma cells, screening, cloning, freezing, and testing) with these animThis chapter summarizes the most common chromatographic mAb andals expressing human Ig genes. This chapter describes the type of transgenic-knockout mice generated for various research groups, provides examples of human mAbs developed by research groups and companies, and includes protocols of immunization, generation, production, and purification of human mAbs from such mice. In addition, it also addresses the problems detected, and includes some of the methods that can be used to analyze functional activities with human mAbs.
Collapse
Affiliation(s)
- Susana Magadán Mompó
- Immunology, Centro de Investigaciones Biomédicas (CINBIO), Centro de Investigación Singular de Galicia, Instituto de Investigación Sanitaria Galicia Sur, Universidad de Vigo, Vigo, Spain
| | - África González-Fernández
- Immunology, Centro de Investigaciones Biomédicas (CINBIO), Centro de Investigación Singular de Galicia, Instituto de Investigación Sanitaria Galicia Sur, Universidad de Vigo, Vigo, Spain.
| |
Collapse
|
3
|
Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
|
4
|
Yeap LS, Hwang JK, Du Z, Meyers RM, Meng FL, Jakubauskaitė A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW. Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes. Cell 2015; 163:1124-1137. [PMID: 26582132 DOI: 10.1016/j.cell.2015.10.042] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
In activated B lymphocytes, AID initiates antibody variable (V) exon somatic hypermutation (SHM) for affinity maturation in germinal centers (GCs) and IgH switch (S) region DNA breaks (DSBs) for class-switch recombination (CSR). To resolve long-standing questions, we have developed an in vivo assay to study AID targeting of passenger sequences replacing a V exon. First, we find AID targets SHM hotspots within V exon and S region passengers at similar frequencies and that the normal SHM process frequently generates deletions, indicating that SHM and CSR employ the same mechanism. Second, AID mutates targets in diverse non-Ig passengers in GC B cells at levels similar to those of V exons, definitively establishing the V exon location as "privileged" for SHM. Finally, Peyer's patch GC B cells generate a reservoir of V exons that are highly mutated before selection for affinity maturation. We discuss the implications of these findings for harnessing antibody diversification mechanisms.
Collapse
Affiliation(s)
- Leng-Siew Yeap
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Agnė Jakubauskaitė
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mengyuan Liu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Vinidhra Mani
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02215, USA
| | - Jing H Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
5
|
Mompó SM, González-Fernández A. Antigen-specific human monoclonal antibodies from transgenic mice. Methods Mol Biol 2014; 1060:245-276. [PMID: 24037845 DOI: 10.1007/978-1-62703-586-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Due to the difficulties found when generating fully human monoclonal antibodies (mAbs) by the traditional method, several efforts have attempted to overcome these problems, with varying levels of success. One approach has been the development of transgenic mice carrying immunoglobulin (Ig) genes in germ line configuration. The engineered mouse genome can undergo productive rearrangement in the B cell population, with the generation of mouse B lymphocytes expressing human Ig (hIg) chains. To avoid the expression of mouse heavy or light chains, the endogenous mouse Ig (mIg) loci must be silenced by gene-targeting techniques. Subsequently, to obtain antigen-specific mAbs, conventional immunization protocols can be followed and the mAb technique used (fusion of activated B cells with mouse myeloma cells, screening, cloning, freezing, and testing) with these animals expressing human Ig genes. This chapter describes the type of transgenic knockout mice generated for various research groups, provides examples of human mAbs developed by research groups and companies, and includes protocols of immunization, generation, production, and purification of human mAbs from such mice. In addition, it also addresses the problems detected, and includes some of the methods that can be used to analyze functional activities with human mAbs.
Collapse
|
6
|
Gibbons DL, Spencer J. Mouse and human intestinal immunity: same ballpark, different players; different rules, same score. Mucosal Immunol 2011; 4:148-57. [PMID: 21228770 DOI: 10.1038/mi.2010.85] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The study of animal immune physiology and animal models of human disease have accelerated many aspects of translational research by allowing direct, definitive investigations. In particular, the use of mice has allowed genetic manipulation, adoptive transfer, immunization, and focused cell and tissue sampling, which would obviously be unthinkable for studies in humans. However, the disease relevance of some animal models may be uncertain and difficulties in interpretation may occur as a consequence of immunological differences between the two species. In this review, we will consider general differences in the structure and development of human and mouse mucosal lymphoid microenvironments and then discuss species differences in mucosal B- and T-cell biology that relate to the current concepts of intestinal immune function.
Collapse
Affiliation(s)
- D L Gibbons
- Peter Gorer Department of Immunobiology, Kings College London, London, UK.
| | | |
Collapse
|
7
|
Shansab M, Selsing E. p21 is dispensable for AID-mediated class switch recombination and mutagenesis of immunoglobulin genes during somatic hypermutation. Mol Immunol 2011; 48:973-8. [PMID: 21288574 DOI: 10.1016/j.molimm.2011.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/06/2011] [Accepted: 01/07/2011] [Indexed: 01/07/2023]
Abstract
In B cells, activation-induced cytidine deaminase (AID) induces somatic hypermutation (SHM) at rearranged immunoglobulin (Ig) variable (V) regions. Previous studies have shown that both monoubiquitination of proliferating cell nuclear antigen (PCNA) and translesional DNA polymerase activity are important for inducing mutagenesis during SHM. Regulation of PCNA ubiquitination by p21, also known as Cdkn1a and p21(Cip1/Waf1), is an important mechanism that controls mutation loads in mammalian cells. In this study, we have assessed whether p21 has an in vivo function in regulating mutagenesis in B cells by analyzing SHM frequency in p21-deficient mice. Our results show that p21 is dispensable for SHM. This suggests that, during SHM of Ig genes, p21 does not act to regulate mutagenesis load. We also show that p21 transcript levels are the same in both wildtype and AID-deficient B cells during B cell activation, and that AID-mediated class switch recombination (CSR) is not affected by p21 deficiency; thereby indicating that p21 regulation in B cells is not altered by AID-induced DNA damage and that p21 has no affect on AID-dependent Ig gene diversification. Our results suggest that regulation of p21 in activated B cells is probably more important for maintaining proper cell cycle progression as opposed to promoting SHM of Ig genes.
Collapse
Affiliation(s)
- Maryam Shansab
- Program in Immunology and Department of Pathology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | | |
Collapse
|
8
|
Sabouri Z, Okazaki IM, Shinkura R, Begum N, Nagaoka H, Tsuchimoto D, Nakabeppu Y, Honjo T. Apex2 is required for efficient somatic hypermutation but not for class switch recombination of immunoglobulin genes. Int Immunol 2009; 21:947-55. [PMID: 19556307 DOI: 10.1093/intimm/dxp061] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The DNA cleavage step in both the class switch recombination (CSR) and somatic hypermutation (SHM) of Ig genes is initiated by activation-induced cytidine deaminase (AID). However, the detailed mechanisms of the DNA strand cleavage in SHM and CSR are still largely unknown. Recently, the apurinic/apyrimidinic endonucleases, Apex1 and Apex2, were reported to be involved in the DNA cleavage step of CSR. Here, we examined the role of Apex2 in SHM using Apex2-deficient mice and found that the Apex2 deficiency caused a drastic reduction in the frequency of SHM and the number of mutations per mutated clone without affecting the pattern of base substitution. These results suggest that Apex2 may play a critical role in SHM through its 3'-5' exonuclease activity. Unexpectedly, the efficiency of CSR was not reduced in Apex2-deficient B cells. In addition, Apex1 knockdown in CH12F3-2 B lymphoma cells did not affect the CSR frequency, suggesting that neither Apex1 nor Apex2 plays a major role in CSR.
Collapse
Affiliation(s)
- Zahra Sabouri
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Kyoto, Japan
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Spencer J, Barone F, Dunn-Walters D. Generation of Immunoglobulin diversity in human gut-associated lymphoid tissue. Semin Immunol 2009; 21:139-46. [PMID: 19233686 DOI: 10.1016/j.smim.2009.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 01/20/2009] [Indexed: 02/05/2023]
Abstract
The organised gut associated lymphoid tissue (GALT) exists adjacent to an extensive and diverse luminal flora. The follicle associated epithelium and associated dendritic cells and lymphocytes form a tightly fortified gateway between the flora and the host that permits connectivity between them and chronic activation of the lymphoid compartment. As a consequence, plasma cell precursors are generated continuously, and in abundance, in GALT by clonal proliferation. Clonal proliferation alone on this scale would reduce the spectrum of B cell specificity. To compensate, GALT also houses molecular machinery that diversifies the receptor repertoire by somatic hypermutation, class switch recombination and receptor revision. These three processes of enhancing the diversity of mature B cells ensure that although clonally related plasma cells may secrete immunoglobulin side by side in the mucosa they rarely have identical antigen binding sites.
Collapse
Affiliation(s)
- Jo Spencer
- Peter Gorer Department of Immunobiology, King's College London, Guy's Hospital Campus, St Thomas' St, London SE1 9RT, United Kingdom
| | | | | |
Collapse
|
10
|
Steele EJ. Mechanism of somatic hypermutation: critical analysis of strand biased mutation signatures at A:T and G:C base pairs. Mol Immunol 2008; 46:305-20. [PMID: 19062097 DOI: 10.1016/j.molimm.2008.10.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 10/14/2008] [Indexed: 12/17/2022]
Abstract
The DNA sequence data of the somatic hypermutation (SHM) field published since 1984 has been critically reviewed. The analysis has revealed three strand biased mutation signatures. The first concerns the mutations generated at G:C base pairs in mice genetically deficient in uracil-DNA glycosylase and MSH2-MSH6-mediated mismatch repair. Such mice display the AID deaminase footprint and here C mutations exceed G mutations at least 1.5-fold. This supports earlier and more recent studies claiming that dC-to-dU deaminations occur preferentially in the single stranded DNA regions of the displaced nontranscribed strand (NTS) during transcription. The second concerns the signature generated in immunised mice where G mutations exceed C mutations by at least 1.7-fold. This is a newly identified strand bias which has previously gone undetected. It is consistent with the polynucleotide polymerisation signature of RNA polymerase II copying the template DNA strand carrying AID-mediated lesions generated at C bases, viz. uracils and abasic sites. A reverse transcription step would then need to intervene to fix the mutation pattern in DNA. The third concerns the long recognised strand biased signature generated in normal aged or actively immunised mice whereby A mutations exceed T mutations by two- to three-fold. It is argued that this pattern is best understood as a combination of adenosine-to-inosine (A-to-I) RNA editing followed by a reverse transcription step fixing the A-to-G, as well as A-to-T and A-to-C, as strand biased mutation signatures in DNA. The reasons why the AID-linked RNA polymerase II mutation signature had previously gone undetected are discussed with regard to limitations of standard PCR-based SHM assay techniques. It is concluded that the most economical SHM mechanism involves both DNA and RNA deaminations coupled to a reverse transcription process, most likely involving DNA polymerase eta acting in its reverse transcriptase mode. Experimental approaches to differentiate this RNA-based model from the standard DNA deamination model are discussed.
Collapse
Affiliation(s)
- Edward J Steele
- Genomic Interactions Group and CILR, Research School of Biological Sciences, The Institute of Advanced Studies, Australian National University, Canberra, ACT 2601, Australia.
| |
Collapse
|
11
|
Han JH, Akira S, Calame K, Beutler B, Selsing E, Imanishi-Kari T. Class switch recombination and somatic hypermutation in early mouse B cells are mediated by B cell and Toll-like receptors. Immunity 2007; 27:64-75. [PMID: 17658280 PMCID: PMC2082107 DOI: 10.1016/j.immuni.2007.05.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 04/09/2007] [Accepted: 05/25/2007] [Indexed: 11/18/2022]
Abstract
Activation-induced cytidine deaminase (AID) is required for immunoglobulin (Ig) gene class switch recombination (CSR), somatic hypermutation (SHM), and somatic hyperconversion. In general, high AID expression is found in mature B cells that are responding to antigens. However, AID expression and SHM have also been detected in developing B cells from transgenic mice that have a limited Ig repertoire. Here we demonstrate that AID expression, ongoing CSR, and active SHM occur in developing B cells from wild-type mice. Further, our results suggest that somatic variants arising from developing B cells in the bone marrow further diversify in the spleen of unimmunized mice. AID expression in developing B cells is T cell independent but involves engagement of B cell receptors and Toll-like receptors. Early AID expression can increase the preimmune repertoire of developing B cells, may provide an innate population of IgG- and IgA-expressing cells, and could be involved in receptor editing of self-reactive immature B cells.
Collapse
Affiliation(s)
- Jin-Hwan Han
- Program in Immunology and Department of Pathology, Sackler School of Graduate Biomedical Sciences and Tufts University School of Medicine, Boston, MA 02111, USA
| | | | | | | | | | | |
Collapse
|
12
|
Shinkura R, Okazaki IM, Muto T, Begum NA, Honjo T. Regulation of AID function in vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 596:71-81. [PMID: 17338177 DOI: 10.1007/0-387-46530-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Reiko Shinkura
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan 606-8501
| | | | | | | | | |
Collapse
|
13
|
Steele EJ, Lindley RA, Wen J, Weiller GF. Computational analyses show A-to-G mutations correlate with nascent mRNA hairpins at somatic hypermutation hotspots. DNA Repair (Amst) 2006; 5:1346-63. [PMID: 16884961 DOI: 10.1016/j.dnarep.2006.06.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 06/06/2006] [Indexed: 12/24/2022]
Abstract
Activation-induced cytidine deaminase (AID) initiates Phase I somatic hypermutation (SHM) of antibody genes by deaminating deoxy-cytosine to deoxy-uracil (C-to-U). These lesions trigger Phase II, a poorly understood process of error-prone repair targeting A-T pairs by DNA polymerase eta (Pol eta). Since Pol eta is also a reverse transcriptase, Phase II could involve copying off RNA as well as DNA templates. We explore this idea further since in an RNA-based pathway it is conceivable that adenosine-to-inosine (A-to-I) RNA editing causes A-to-G transitions since I like G pairs with C. Adenosine deaminases (ADARs) are known to preferentially edit A nucleotides that are preceded by an A or U (W) in double-stranded RNA substrates. On this assumption and using a theoretical bioinformatics approach we show that a significant and specific correlation (P<0.002) exists between the frequency of WA-to-WG mutations and the number of mRNA hairpins that could potentially form at the mutation site. This implies roles for both RNA editing and reverse transcription during SHM in vivo and suggests definitive genetic experiments targeting the appropriate ADAR1 isoform (gammaINF-ADAR1) and/or Ig pre-mRNA templates.
Collapse
Affiliation(s)
- Edward J Steele
- Genomic Interactions Group & CILR, Research School of Biological Sciences, Australian National University, Canberra, Australia.
| | | | | | | |
Collapse
|
14
|
Mastache EF, Lindroth K, Fernández C, González-Fernández A. Somatic hypermutation of Ig genes is affected differently by failures in apoptosis caused by disruption of Fas (lpr mutation) or by overexpression of Bcl-2. Scand J Immunol 2006; 63:420-9. [PMID: 16764695 DOI: 10.1111/j.1365-3083.2006.001758.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The effects of the two main apoptotic pathways on the somatic hypermutation process were analysed. Transgenic mice carrying the V(kappa)Ox1-J(kappa)5 rat transgene were crossed with Fas-deficient lpr mice or with mice overexpressing the Bcl-2 protein. The transgenic V(kappa)Ox1 segment and the endogenous JH4-C(micro) Ig intron from Peyer's patches germinal centre B cells were sequenced to study the intrinsic somatic hypermutation process without the skewing effects of specific antigen selection. The lpr/ox mice displayed, in both regions, a high level of mutations with a normal pattern of substitutions. On the contrary, the bcl-2/ox mice displayed a lower level of mutations with an altered pattern, showing a decreased mutational rate in the intrinsic hotspots of the V(kappa)Ox1 gene. Our results suggest that the lpr mutation does not have a direct effect on the somatic hypermutation process, but rather on the negative selection of B cells in the germinal centres, leading to the accumulation of recurrent mutations. In contrast, Bcl-2 overexpression might influence the somatic hypermutational process either by altering the incorporation of mutations or by enhancing the repair mechanism(s). The present work supports the hypothesis that both apoptotic pathways, Fas and Bcl-2, play distinct roles in the germinal centre reactions.
Collapse
Affiliation(s)
- E F Mastache
- Area of Immunology, Faculty of Biology, Vigo University, Vigo, Spain
| | | | | | | |
Collapse
|
15
|
Muto T, Okazaki IM, Yamada S, Tanaka Y, Kinoshita K, Muramatsu M, Nagaoka H, Honjo T. Negative regulation of activation-induced cytidine deaminase in B cells. Proc Natl Acad Sci U S A 2006; 103:2752-7. [PMID: 16477013 PMCID: PMC1413812 DOI: 10.1073/pnas.0510970103] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Both class switch recombination (CSR) and somatic hypermutation (SHM) of the Ig genes require the activity of activation-induced cytidine deaminase (AID). Expression of AID is restricted to B cells in the germinal centers of the lymphoid organs, where activated B cells undergo CSR and SHM. We previously showed that constitutive and systemic expression of AID leads to tumorigenesis in T cells and lung epithelium, but not in B cells. This finding led us to suspect that transgenic AID may be inactivated at least in part in B cells. To address this issue, we generated conditional AID-transgenic mice that constitutively express AID only in B cells. Studies on the cross between the AID-transgenic and AID-deficient mice showed that abundant AID protein accumulated by constitutive expression is inactivated in B cells, possibly providing an explanation for the absence of deregulation of CSR and SHM in AID-transgenic B cells.
Collapse
Affiliation(s)
- Taro Muto
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
| | - Il-mi Okazaki
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
| | - Shuichi Yamada
- Animal Research Laboratory, Bioscience Research and Education Center, Akita University, Hondo 1-1-1, Akita 010-8543, Japan
| | - Yoshimasa Tanaka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Corporation, and Laboratory of Immunology and Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan; and
| | - Kazuo Kinoshita
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
| | - Masamichi Muramatsu
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
| | - Hitoshi Nagaoka
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
| | - Tasuku Honjo
- *Department of Immunology and Genomic Medicine, Graduate School of Medicine, and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
16
|
Zan H, Shima N, Xu Z, Al-Qahtani A, Evinger III AJ, Zhong Y, Schimenti JC, Casali P. The translesion DNA polymerase theta plays a dominant role in immunoglobulin gene somatic hypermutation. EMBO J 2005; 24:3757-69. [PMID: 16222339 PMCID: PMC1276717 DOI: 10.1038/sj.emboj.7600833] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 09/12/2005] [Indexed: 11/08/2022] Open
Abstract
Immunoglobulin (Ig) somatic hypermutation (SHM) critically underlies the generation of high-affinity antibodies. Mutations can be introduced by error-prone polymerases such as polymerase zeta (Rev3), a mispair extender, and polymerase eta, a mispair inserter with a preference for dA/dT, while repairing DNA lesions initiated by AID-mediated deamination of dC to yield dU:dG mismatches. The partial impairment of SHM observed in the absence of these polymerases led us to hypothesize a main role for another translesion DNA polymerase. Here, we show that deletion in C57BL/6J mice of the translesion polymerase theta, which possesses a dual nucleotide mispair inserter-extender function, results in greater than 60% decrease of mutations in antigen-selected V186.2DJ(H) transcripts and greater than 80% decrease in mutations in the Ig H chain intronic J(H)4-iEmu sequence, together with significant alterations in the spectrum of the residual mutations. Thus, polymerase theta plays a dominant role in SHM, possibly by introducing mismatches while bypassing abasic sites generated by UDG-mediated deglycosylation of AID-effected dU, by extending DNA past such abasic sites and by synthesizing DNA during dU:dG mismatch repair.
Collapse
Affiliation(s)
- Hong Zan
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| | - Naoko Shima
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Zhenming Xu
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| | - Ahmed Al-Qahtani
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| | - Albert J Evinger III
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| | - Yuan Zhong
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Paolo Casali
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA, USA
| |
Collapse
|
17
|
Mayorov VI, Rogozin IB, Adkison LR, Frahm C, Kunkel TA, Pavlov YI. Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes. BMC Immunol 2005; 6:10. [PMID: 15949042 PMCID: PMC1180437 DOI: 10.1186/1471-2172-6-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2005] [Accepted: 06/10/2005] [Indexed: 12/02/2022] Open
Abstract
Background Antibody genes are diversified by somatic hypermutation (SHM), gene conversion and class-switch recombination. All three processes are initiated by the activation-induced deaminase (AID). According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T). Results To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. Conclusion The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C base pairs during SHM.
Collapse
Affiliation(s)
| | - Igor B Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda MD 20894, USA
- Institute of Cytology and Genetics SD RAS, Novosibirsk 630090, Russia
| | | | - Christin Frahm
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Thomas A Kunkel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
18
|
Stoel M, Jiang HQ, van Diemen CC, Bun JCAM, Dammers PM, Thurnheer MC, Kroese FGM, Cebra JJ, Bos NA. Restricted IgA repertoire in both B-1 and B-2 cell-derived gut plasmablasts. THE JOURNAL OF IMMUNOLOGY 2005; 174:1046-54. [PMID: 15634929 DOI: 10.4049/jimmunol.174.2.1046] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mucosal IgA is the most abundantly produced Ig upon colonization of the intestinal tract with commensal organisms in the majority of mammals. The repertoire of these IgA molecules is still largely unknown; a large amount of the mucosal IgA cannot be shown to react with the inducing microorganisms. Analysis of the repertoire of used H chain Ig (V(H)) genes by H-CDR3 spectrotyping, cloning, and sequencing of V(H) genes from murine intestinal IgA-producing plasma cells reveals a very restricted usage of V(H) genes and multiple clonally related sequences. The restricted usage of V(H) genes is a very consistent observation, and is observed for IgA plasma cells derived from B-1 or conventional B-2 cells from different mouse strains. Clonal patterns from all analyzed V(H) gene sequences show mainly independently acquired somatic mutations in contrast to the clonal evolution patterns often observed as a consequence of affinity maturation in germinal center reactions in peripheral lymphoid organs and Peyer's patches. Our data suggest a model of clonal expansion in which many mucosal IgA-producing B cells develop in the absence of affinity maturation. The affinity of most produced IgA might not be the most critical factor for its possible function to control the commensal organisms, but simply the abundance of large amounts of IgA that can bind with relatively unselected affinity to redundant epitopes on such organisms.
Collapse
Affiliation(s)
- Maaike Stoel
- Department of Cell Biology, Section Histology and Immunology, University of Groningen, Faculty Medical Sciences, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Cole MF, Evans MK, Kirchherr JL, Sheridan MJ, Bowden GHW. Study of humoral immunity to commensal oral bacteria in human infants demonstrates the presence of secretory immunoglobulin A antibodies reactive with Actinomyces naeslundii genospecies 1 and 2 ribotypes. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2005; 11:473-82. [PMID: 15138172 PMCID: PMC404577 DOI: 10.1128/cdli.11.3.473-482.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mouths of three human infants were examined from birth to age 2 years to detect colonization of Actinomyces naeslundii genospecies 1 and 2. These bacteria did not colonize until after tooth eruption. The diversity of posteruption isolates was determined by ribotyping. Using immunoblotting and enzyme-linked immunosorbent assay, we determined the reactivity of secretory immunoglobulin A (SIgA) antibodies in saliva samples collected from each infant before and after colonization against cell wall proteins from their own A. naeslundii strains and carbohydrates from standard A. naeslundii genospecies 1 and 2 strains. A. naeslundii genospecies 1 and 2 carbohydrate-reactive SIgA antibodies were not detected in any saliva sample. However, SIgA antibodies reactive with cell wall proteins were present in saliva before these bacteria colonized the mouth. These antibodies could be almost completely removed by absorption with A. odontolyticus, a species known to colonize the human mouth shortly after birth. However, after colonization by A. naeslundii genospecies 1 and 2, specific antibodies were induced that could not be removed by absorption with A. odontolyticus. Cluster analysis of the patterns of reactivity of postcolonization salivary antibodies from each infant with antigens from their own strains showed that not only could these antibodies discriminate among strains but antibodies in saliva samples collected at different times showed different reactivity patterns. Overall, these data suggest that, although much of the salivary SIgA antibodies reactive with A. naeslundii genospecies 1 and 2 are directed against genus-specific or more broadly cross-reactive antigens, species, genospecies, and possibly strain-specific antibodies are induced in response to colonization.
Collapse
Affiliation(s)
- Michael F Cole
- Georgetown University Medical Center, Department of Microbiology and Immunology, Med-Dent Bldg., Rm. S.E. 308A, 3900 Reservoir Rd., N.W., Washington, DC 20057, USA.
| | | | | | | | | |
Collapse
|
20
|
Steele EJ, Franklin A, Blanden RV. Genesis of the strand‐biased signature in somatic hypermutation of rearranged immunoglobulin variable genes. Immunol Cell Biol 2004; 82:209-18. [PMID: 15061776 DOI: 10.1046/j.0818-9641.2004.01224.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The history and current development of the reverse transcriptase model of somatic hypermutation (RT-model) is reviewed with particular reference to the genesis of strand-biased mutation signatures in rearranged immunoglobulin variable genes (V(D)J). The recent disagreement in the field as to whether strand bias really exists or not has been critically analysed and the confusion traced to the putative presence, in some mutated V(D)J sequence collections, of polymerase chain reaction (PCR)-recombinant artefacts. Recent analysis of somatic hypermutation in xeroderma pigmentosum variant patients, by the group of PJ Gearhart and others, has established that the Y-family translesion DNA repair enzyme, DNA polymerase eta (eta), is responsible for the striking A-T targeted strand-bias mutation signature seen in all mouse and human collections of somatically mutated V(D)J sequences. This evidence, together with our own recent demonstration that human DNA polymerase eta is a reverse transcriptase, leads to the conclusion that the strand-biased A-T mutation signature is caused either by: (i) error-prone DNA-dependent DNA repair synthesis by pol-eta of single-strand nicks preferentially in the non-transcribed strand; and/or (ii) by error-prone cDNA synthesis of the transcribed strand by pol-eta using the pre-mRNA as the copying template, primed by the nicked transcribed DNA strand, followed by replacement of the original transcribed strand by cDNA. Analysis of the total mutation pattern also suggests that the major transitions observed in SHM (A-->G, C-->T and G-->A) can be explained by known RNA editing mechanisms active on pre-mRNA which are then written into cDNA during synthesis of the transcribed strand by error-prone cellular reverse transcriptases such as pol-eta.
Collapse
Affiliation(s)
- Edward J Steele
- Division of Immunology and Genetics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.
| | | | | |
Collapse
|
21
|
Mao C, Jiang L, Melo-Jorge M, Puthenveetil M, Zhang X, Carroll MC, Imanishi-Kari T. T cell-independent somatic hypermutation in murine B cells with an immature phenotype. Immunity 2004; 20:133-44. [PMID: 14975236 DOI: 10.1016/s1074-7613(04)00019-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Revised: 12/15/2003] [Accepted: 12/17/2003] [Indexed: 11/18/2022]
Abstract
Somatic hypermutation contributes to the generation of antibody diversity and is strongly associated with the maturation of antigen-specific immune responses. We asked whether somatic hypermutation also plays a role in the generation of the murine immunoglobulin repertoire during B cell development. To facilitate identification of somatic mutations, we examined mouse systems in which only antibodies expressing lambda1, lambda2, and lambdax light chains can be generated. Somatic mutations were found in cells, which, by surface markers, RAG expression, and rapid turnover, had the phenotype of immature B cells. In addition, expression of AID was detected in these cells. The mutations were limited to V regions and were localized in known hotspots. Mutation frequency was not diminished in the absence of T cells. Our results support the idea that somatic hypermutation can occur in murine immature B cells and may represent a mechanism for enlarging the V gene repertoire.
Collapse
Affiliation(s)
- Changchuin Mao
- Department of Pathology and Program in Immunology, Tufts University School of Medicine, Boston, MA 02111, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Immunoglobulin A is the most abundant immunoglobulin isotype in mucosal secretions. In this review, we summarize recent advances in our understanding of the sites, mechanisms and functions of intestinal IgA synthesis in mice. On the basis of these recent findings, we propose an updated model for the induction and regulation of IgA responses in the gut. In addition, we discuss new insights into the role of IgA in the maintenance of gut homeostasis and into the reciprocal interactions between gut B cells and the bacterial flora.
Collapse
Affiliation(s)
- Sidonia Fagarasan
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | | |
Collapse
|
23
|
Carril MS, Aragón JP, González Fernández A. Age-related accumulation of memory cells in mouse Peyer's patches. Immunol Lett 2002; 83:39-45. [PMID: 12057853 DOI: 10.1016/s0165-2478(02)00072-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of memory cells seems to take place in the germinal centres, which are chronically present in Peyer's patches (PPs). We report here age-associated changes in the lymphocyte compartment and in the number of PPs of unimmunised mice. Mice 4 weeks old do not exhibit well constituted germinal centres, but just only 1 week later, the mice develop a normal germinal centre reaction, which is maintained until late ages (mice 30 weeks old), to decrease thereafter in older mice. In addition, we also show that memory cells accumulate in PPs in old mice, being the main population CD44(+) CD62L(-) CD49d(+) CD40(+) CD25(-) B cells. These data suggest that memory B cells tend to accumulate in PPs in ageing mice, even when the GC reaction has already decreased.
Collapse
Affiliation(s)
- Marta Sánchez Carril
- Area of Immunology, Faculty of Sciences, University of Vigo, Lagoas Marcosende s/n, 36200 Vigo, Pontevedra, Spain
| | | | | |
Collapse
|
24
|
Pavlov YI, Rogozin IB, Galkin AP, Aksenova AY, Hanaoka F, Rada C, Kunkel TA. Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase eta during copying of a mouse immunoglobulin kappa light chain transgene. Proc Natl Acad Sci U S A 2002; 99:9954-9. [PMID: 12119399 PMCID: PMC126606 DOI: 10.1073/pnas.152126799] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To test the hypothesis that inaccurate DNA synthesis by mammalian DNA polymerase eta (pol eta) contributes to somatic hypermutation (SHM) of Ig genes, we measured the error specificity of mouse pol eta during synthesis of each strand of a mouse Ig kappa light chain transgene. We then compared the results to the base substitution specificity of SHM of this same gene in the mouse. The in vitro and in vivo base substitution spectra shared a number of common features. A highly significant correlation was observed for overall substitutions at A-T pairs but not for substitutions at G-C pairs. Sixteen mutational hotspots at A-T pairs observed in vivo were also found in spectra generated by mouse pol eta in vitro. The correlation was strongest for errors made by pol eta during synthesis of the non-transcribed strand, but it was also observed for synthesis of the transcribed strand. These facts, and the distribution of substitutions generated in vivo, support the hypothesis that pol eta contributes to SHM of Ig genes at A-T pairs via short patches of low fidelity DNA synthesis of both strands, but with a preference for the non-transcribed strand.
Collapse
Affiliation(s)
- Youri I Pavlov
- Laboratories of Molecular Genetics and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | | | | | | | | | | | | |
Collapse
|
25
|
Lee SS, Tranchina D, Ohta Y, Flajnik MF, Hsu E. Hypermutation in shark immunoglobulin light chain genes results in contiguous substitutions. Immunity 2002; 16:571-82. [PMID: 11970880 DOI: 10.1016/s1074-7613(02)00300-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Among 631 substitutions present in 90 nurse shark immunoglobulin light chain somatic mutants, 338 constitute 2-4 bp stretches of adjacent changes. An absence of mutations in perinatal sequences and the bias for one mutating V gene in adults suggest that the diversification is antigen dependent. The substitutions shared no patterns, and the absence of donor sequences, including from family members, supports the idea that most changes arose from nontemplated mutation. The tandem mutations as a group are distinguished by consistently fewer transition changes and an A bias. We suggest this is one of several pathways of hypermutation diversifying shark antigen-receptor genes--point mutations, tandem mutations, and mutations with a G-C preference--that coevolved with or preceded gene rearrangement.
Collapse
Affiliation(s)
- Susan S Lee
- Department of Physiology and Pharmacology, The State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
| | | | | | | | | |
Collapse
|
26
|
Gearhart PJ, Wood RD. Emerging links between hypermutation of antibody genes and DNA polymerases. Nat Rev Immunol 2001; 1:187-92. [PMID: 11905827 DOI: 10.1038/35105009] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Substantial antibody variability is created when nucleotide substitutions are introduced into immunoglobulin variable genes by a controlled process of hypermutation. Evidence points to a mechanism involving DNA repair events at sites of targeted breaks. In vertebrate cells, there are many recently identified DNA polymerases that inaccurately copy templates. Some of these are candidates for enzymes that introduce base changes during hypermutation. Recent research has focused on possible roles for DNA polymerases zeta (POLZ), eta (POLH), iota (POLI), and mu (POLM) in the process.
Collapse
Affiliation(s)
- P J Gearhart
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA.
| | | |
Collapse
|
27
|
Kodama M, Hayashi R, Nishizumi H, Nagawa F, Takemori T, Sakano H. The PU.1 and NF-EM5 binding motifs in the Igkappa 3' enhancer are responsible for directing somatic hypermutations to the intrinsic hotspots in the transgenic Vkappa gene. Int Immunol 2001; 13:1415-22. [PMID: 11675373 DOI: 10.1093/intimm/13.11.1415] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Somatic hypermutation is a key mechanism in generating Ig with higher affinities to antigen, a process known as affinity maturation. Using Igkappa transgenes, the 3' enhancer (kappaE3') has been shown to play an important role in introducing hypermutations. In order to identify the cis-acting elements that regulate hypermutagenesis, we have generated transgenic substrates containing mutations/deletions in the kappaE3' region. Here, we report that base substitutions in the kappaE3', either in the PU.1 or in the NF-EM5 binding motif, not only reduce the mutation rate but also disrupt the directed mutagenesis in the intrinsic hotspots of the Igkappa transgene.
Collapse
Affiliation(s)
- M Kodama
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | | | | | | | | | | |
Collapse
|
28
|
Wrammert J, Vingsbo Lundberg C, Leanderson T. A transgenic marker expressed on discrete populations during B-cell development. Scand J Immunol 2001; 54:357-65. [PMID: 11555402 DOI: 10.1046/j.1365-3083.2001.00968.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe a transgenic mouse strain that selectively express a surface marker (huCD25) on transitional B cells, pre-B cells and a lineage unidentified bone marrow (BM) population. We show that a subpopulation of B cells in Peyer's patches, spleen, blood and BM expressed the transgenic huCD25 marker on the cell surface. In the spleen, the huCD25 expression was found on transitional B cells, that had not yet been recruited into the recirculating pool. In the BM a fraction of the B220low surface immunoglobulin (Ig) negative PB493+ pre-B cells were huCD25+. HuCD25 expression was also seen on practically all immature B cells while the mature recirculating B cells did not express huCD25. A huCD25+B220- cell population was also found in the BM that had not rearranged the Ig heavy chain locus and did not express the lineage markers CD3, T-cell receptor (TCR), CD19 and Mac-1. A low expression of CD4 on these cells may indicate that they represent a noncommitted, hematopoetic progenitor cell population.
Collapse
Affiliation(s)
- J Wrammert
- Section for Immunology, Department of Cell and Molecular Biology, Lund University, Lund, Sweden.
| | | | | |
Collapse
|
29
|
Rada C, Milstein C. The intrinsic hypermutability of antibody heavy and light chain genes decays exponentially. EMBO J 2001; 20:4570-6. [PMID: 11500383 PMCID: PMC125579 DOI: 10.1093/emboj/20.16.4570] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Somatic hypermutation, essential for the affinity maturation of antibodies, is restricted to a small segment of DNA. The upstream boundary is sharp and is probably related to transcription initiation. However, for reasons unknown, the hypermutation domain does not encompass the whole transcription unit, notably the C-region exon. Since analysis of the downstream decay of hypermutation is obscured by sequence-dependent hot and cold spots, we describe a strategy to minimize these fluctuations by computing mutations of different sequences located at similar distances from the promoter. We pool large databases of mutated heavy and light chains and analyse the decay of mutation frequencies. We define an intrinsic decay of probability of mutation that is remarkably similar for heavy and light chains, faster than anticipated and consistent with an exponential fit. Indeed, quite apart from hot spots, the intrinsic probability of mutation at CDR1 can be almost twice that of CDR3. The analysis has mechanistic implications for current and future models of hypermutation.
Collapse
Affiliation(s)
- C Rada
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
| | | |
Collapse
|
30
|
Rogozin IB, Pavlov YI, Bebenek K, Matsuda T, Kunkel TA. Somatic mutation hotspots correlate with DNA polymerase eta error spectrum. Nat Immunol 2001; 2:530-6. [PMID: 11376340 DOI: 10.1038/88732] [Citation(s) in RCA: 256] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mutational spectra analysis of 15 immunoglobulin genes suggested that consensus motifs RGYW and WA were universal descriptors of somatic hypermutation. Highly mutable sites, "hotspots", that matched WA were preferentially found in one DNA strand and RGYW hotspots were found in both strands. Analysis of base-substitution hotspots in DNA polymerase error spectra showed that 33 of 36 hotspots in the human polymerase eta spectrum conformed to the WA consensus. This and four other characteristics of polymerase eta substitution specificity suggest that errors introduced by this enzyme during synthesis of the nontranscribed DNA strand in variable regions may contribute to strand-specific somatic hypermutagenesis of immunoglobulin genes at A-T base pairs.
Collapse
Affiliation(s)
- I B Rogozin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | | | | | | |
Collapse
|
31
|
Affiliation(s)
- N A Bos
- Department of Cell Biology, Immunology Section, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, the Netherlands.
| | | | | |
Collapse
|
32
|
Storb U, Peters A, Kim N, Shen HM, Bozek G, Michael N, Hackett J, Klotz E, Reynolds JD, Loeb LA, Martin TE. Molecular aspects of somatic hypermutation of immunoglobulin genes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2001; 64:227-34. [PMID: 11232290 DOI: 10.1101/sqb.1999.64.227] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- U Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Jolly CJ, Neuberger MS. Somatic hypermutation of immunoglobulin kappa transgenes: association of mutability with demethylation. Immunol Cell Biol 2001; 79:18-22. [PMID: 11168618 DOI: 10.1046/j.1440-1711.2001.00968.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Following antigen encounter, immunoglobulin genes are diversified by somatic hypermutation. The mechanism by which this mutational process preferentially targets immunoglobulin genes is not known, but is likely linked to transcription. However, transcription is not sufficient to ensure mutability. Here, by polymerase chain reaction amplification of bisulfite-modified DNA, the pattern of demethylation within the Igkappa mutation domain is analysed and transgenes are used to identify an association between demethylation and mutability. In mice carrying an Igkappa transgene that is well transcribed but only poorly targeted for hypermutation, the mutated transgene copies have been demethylated within the mutation domain, whereas the methylated copies remain unmutated. Thus, the hypermutation mechanism only acts on immunoglobulin gene targets that are demethylated as well as transcribed, although transcription and demethylation do not themselves guarantee mutability.
Collapse
Affiliation(s)
- C J Jolly
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | |
Collapse
|
34
|
Verdier M, Jayat C, Ratinaud MH, Troutaud D. Optimization of cell permeabilization for multiparametric flow cytometric analysis with lectin staining. CYTOMETRY 2000; 41:55-61. [PMID: 10942897 DOI: 10.1002/1097-0320(20000901)41:1<55::aid-cyto8>3.0.co;2-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND This study was undertaken in mice to develop a reproducible procedure of cell permeabilization, allowing intracellular protein staining by immunofluorescence (i.e., Bcl-2) without losing surface labeling especially for lectins (i.e., B220 and peanut agglutinin [PNA]). This article reports results obtained with different permeabilization protocols. METHODS Lymphoid cells were extracted and prepared from Peyer's patches and spleen. After surface labeling using anti-B220-Cy-chrome and PNA-biotin/streptavidin-phycoerythrin, we comparatively tested three permeabilization protocols: saponin 0.3%, methanol 70%, and the commercial kit Dako Intrastain. Final Bcl-2 staining was performed and cells were analyzed by flow cytometry. RESULTS With 0.3% saponin as the permeabilization reagent, a significant loss of lectin labeling was observed when comparing mono PNA and triple (i.e. , B220-PNA-Bcl-2) staining (74.8% and 22.5% positive cells, respectively). Quality of PNA staining was conserved with Intrastain when comparing multiparametric versus monoparametric stainings (82. 4% of positive cells versus 78.3%, respectively). Intrastain preserved scatter characteristics (69.9% of total cells in the lymphocyte gate with Intrastain versus 13.7% with saponin 0.3% and 20.9% with methanol 70%). This protocol has been used for a preliminary multiparametric analysis in order to quantify Bcl-2 expression in PNA/B220-positive cells. CONCLUSION This protocol may be useful to assess simultaneously lectin cell surface labeling and intracellular target staining.
Collapse
Affiliation(s)
- M Verdier
- EP CNRS 118, Faculté des Sciences, Limoges, France.
| | | | | | | |
Collapse
|
35
|
Davis DP, Khurana R, Meredith S, Stevens FJ, Argon Y. Mapping the Major Interaction Between Binding Protein and Ig Light Chains to Sites Within the Variable Domain. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.163.7.3842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Newly synthesized Ig chains are known to interact in vivo with the binding protein (BiP), a major peptide-binding chaperone in the endoplasmic reticulum. The predominant interactions between the light chain and BiP are observed early in the folding pathway, when the light chain is either completely reduced, or has only one disulfide bond. In this study, we describe the in vitro reconstitution of BiP binding to the variable domain of light chains (VL). Binding of deliberately unfolded VL was dramatically more avid than that of folded VL, mimicking the interaction in vivo. Furthermore, VL binding was inhibited by addition of ATP, was competed with excess unlabeled VL, and was demonstrated with several different VL proteins. Using this assay, peptides derived from the VL sequence were tested experimentally for their ability to bind BiP. Four peptides from both β sheets of VL were shown to bind BiP specifically, two with significantly higher affinity. As few as these two peptide sites, one from each β sheet of VL, are sufficient to explain the association of BiP with the entire light chain. These results suggest how BiP directs the folding of Ig in vivo and how it may be used in shaping the B cell repertoire.
Collapse
Affiliation(s)
- David P. Davis
- *Department of Pathology and
- 6S. Aviel et al., submitted for publication
- †Committee on Immunology, University of Chicago, Chicago, IL 60637; and
- 6S. Aviel et al., submitted for publication
| | - Ritu Khurana
- *Department of Pathology and
- 6S. Aviel et al., submitted for publication
- †Committee on Immunology, University of Chicago, Chicago, IL 60637; and
- 6S. Aviel et al., submitted for publication
| | - Stephen Meredith
- *Department of Pathology and
- 6S. Aviel et al., submitted for publication
| | - Fred J. Stevens
- ‡Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, Argonne, IL 60439
- 6S. Aviel et al., submitted for publication
| | - Yair Argon
- *Department of Pathology and
- 6S. Aviel et al., submitted for publication
- †Committee on Immunology, University of Chicago, Chicago, IL 60637; and
- 6S. Aviel et al., submitted for publication
| |
Collapse
|
36
|
Yi M, Wu P, Trevorrow KW, Claflin L, Garrard WT. Evidence That the Igκ Gene MAR Regulates the Probability of Premature V-J Joining and Somatic Hypermutation. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.10.6029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The Igκ gene contains an evolutionarily conserved nuclear matrix association region (MAR) adjacent to the intronic enhancer. To test for the function of this MAR, we created mouse lines with a targeted MAR deletion. In MAR knockout animals, the immune system was normal in nearly all respects, including the distributions of various B cell populations and Ab levels. However, in pro-B cells, enhanced rearrangement was noted on the MAR− allele in heterozygotes. In addition, the efficiencies for targeting and generating somatic mutations were reduced on MAR-deleted alleles. These results provide evidence for the MAR negatively regulating the probability of premature rearrangement and positively regulating the probability of somatic hypermutation.
Collapse
Affiliation(s)
- Ming Yi
- *Department of Molecular Biology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75235; and
| | - Peiqing Wu
- †Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kenneth W. Trevorrow
- *Department of Molecular Biology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75235; and
| | - Latham Claflin
- †Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - William T. Garrard
- *Department of Molecular Biology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75235; and
| |
Collapse
|
37
|
Abstract
Single IgA- or IgM-secreting plasma cells were isolated from histological sections of human jejunum and terminal ileum, and Ig heavy chain variable (VH) region genes were amplified and sequenced. Taken together, 62 of 63 cells analyzed harbored somatically mutated VH region genes, indicating that the vast majority of both IgA- and IgM-secreting intestinal plasma cells derive from germinal center B cells. On average, rearranged VH genes of IgA- and IgM-secreting plasma cells showed a mutation frequency of 9.0 % and 8.5 %, respectively, which exceeds the level of somatic mutation of V region genes carried by human memory B cells. Moreover, we detected deletions or insertions in the complementarity-determining regions of 5 of the 58 functional VH region genes analyzed, suggesting that these alterations may contribute to the diversification of the human antibody repertoire in the course of an immune reaction.
Collapse
Affiliation(s)
- M Fischer
- Institute for Genetics, University of Cologne, Germany
| | | |
Collapse
|
38
|
Bertocci B, Quint L, Delbos F, Garcia C, Reynaud CA, Weill JC. Probing immunoglobulin gene hypermutation with microsatellites suggests a nonreplicative short patch DNA synthesis process. Immunity 1998; 9:257-65. [PMID: 9729046 DOI: 10.1016/s1074-7613(00)80608-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
As the rate of Ig gene hypermutation approximates the level of nucleotide discrimination of DNA polymerases (10(-3) to 10(-4)), a local inhibition of proofreading and mismatch repair during semiconservative replication could generate the mutations introduced by the process. To address this question, we have constructed transgenic mice that carry a hypermutation substrate containing a "polymerase slippage trap": an Ig gene with a mono or dinucleotide tract inserted in its V region. The low amount of slippage events as compared to the number of mutations, the absence of transient misalignment mutations at the border of the repeats, and the dissociation between the amount of frameshifts and mutations when the transgene is put on mismatch repair-deficient genetic backgrounds, suggest that Ig gene hypermutation occurs by an error-prone short patch DNA synthesis taking place outside global DNA replication.
Collapse
Affiliation(s)
- B Bertocci
- INSERM U 373, Faculté de Médecine Necker-Enfants Malades, Paris, France
| | | | | | | | | | | |
Collapse
|
39
|
Milstein C, Neuberger MS, Staden R. Both DNA strands of antibody genes are hypermutation targets. Proc Natl Acad Sci U S A 1998; 95:8791-4. [PMID: 9671757 PMCID: PMC21155 DOI: 10.1073/pnas.95.15.8791] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
During the maturation of the immune response, antibody genes are subjected to localized hypermutation. Mutations are not evenly distributed along the V gene; intrinsic hot spots exist that are correlated with primary sequence motifs. Although the mechanism of hypermutation remains unknown, it has been proposed to exhibit DNA strand polarity because purine residues on the coding strand are more frequently targeted for mutation than pyrimidines. However, this polarity may not be an intrinsic property of the hypermutation mechanism but a consequence of evolutionary-selected peculiarities of V gene sequences. Furthermore, the possibility that both strands are hypermutation targets has received little attention. To discriminate between these possibilities, we have analyzed the average frequency of mutations of each of the three bases of all nucleotide triplets by using large databases taken from both V and non-V mutation targets. We also have reassessed the sequence motifs associated with hot spots. We find that even in non-Ig sequences, A mutates more than T, consistent with a strand-dependent component to targeting. However, the mutation biases of triplets and of their inverted complements are correlated, demonstrating that there is a sequence-specific but strand-independent component to mutational targeting. Thus, there are two aspects of the hypermutation process that are sensitive to local DNA sequences, one that is DNA strand-dependent and the other that is not.
Collapse
Affiliation(s)
- C Milstein
- Medical Research Council Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge CB2 2QH, United Kingdom
| | | | | |
Collapse
|
40
|
Bonfield JK, Rada C, Staden R. Automated detection of point mutations using fluorescent sequence trace subtraction. Nucleic Acids Res 1998; 26:3404-9. [PMID: 9649626 PMCID: PMC147706 DOI: 10.1093/nar/26.14.3404] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The final step in the detection of mutations is to determine the sequence of the suspected mutant and to compare it with that of the wild-type, and for this fluorescence-based sequencing instruments are widely used. We describe some simple algorithms forcomparing sequence traces which, as part of our sequence assembly and analysis package, are proving useful for the discovery of mutations and which may also help to identify misplaced readings in sequence assembly projects. The mutations can be detected automatically by a new program called TRACE_DIFF and new types of trace display in our program GAP4 greatly simplify visual checking of the assigned changes. To assess the accuracy of the automatic mutation detection algorithm we analysed 214 sequence readings from hypermutating DNA comprising a total of 108 497 bases. After the readings were assembled there were 1232 base differences, including 392 Ns and 166 alignment characters. Visual inspection of the traces established that of the 1232 differences, 353 were real mutations while the rest were due to base calling errors. The TRACE_DIFF algorithm automatically identified all but 36, with 28 false positives. Further information about the software can be obtained from http://www.mrc-lmb.cam.ac.uk/pubseq/
Collapse
Affiliation(s)
- J K Bonfield
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | | | | |
Collapse
|
41
|
Klotz EL, Hackett J, Storb U. Somatic Hypermutation of an Artificial Test Substrate Within an Igκ Transgene. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.2.782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
We have characterized a novel substrate for somatic hypermutation, confirming that non-Ig sequences can be targeted for mutation and demonstrating that this substrate allows for the rapid assay for mutations. An artificial sequence containing alternating EcoRV and PvuII sites (EPS) was inserted into the Vκ167 transgene, which is known to be a target for mutation. To assay for somatic hypermutation, the EPS is amplified using flanking transgene primers, and the PCR product is subsequently digested with either EcoRV or PvuII. A mutation is seen as the appearance of a larger fragment, indicating a base change in a restriction enzyme site. The original transgene, Vκ167/EPS, showed evidence of a low level of mutation in both splenic hybridomas and Peyer’s patch-derived or immunized splenic B220+ cells with high peanut agglutinin levels. Two derivative lines of Vκ167/EPS were made, Vκ167/POX and Vκ167/PEPS. While none of the Vκ167/POX transgenic lines demonstrated mutation, the Vκ167/PEPS transgene was highly mutated in B220+ splenic B cells with high peanut agglutinin levels at a frequency similar to that of endogenous Ig genes. An analysis of splenic RNA from the unimmunized transgenic mice indicated that the levels of stable message in splenic B cells could not be correlated with the mutation seen in GC B cells. The mutable Vκ167/PEPS transgenic line is a unique tool to study somatic hypermutation in vivo.
Collapse
Affiliation(s)
| | - John Hackett
- †Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Ursula Storb
- *Committee on Immunology and
- †Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| |
Collapse
|
42
|
Rada C, Ehrenstein MR, Neuberger MS, Milstein C. Hot spot focusing of somatic hypermutation in MSH2-deficient mice suggests two stages of mutational targeting. Immunity 1998; 9:135-41. [PMID: 9697843 DOI: 10.1016/s1074-7613(00)80595-6] [Citation(s) in RCA: 294] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Likely creation of mismatches during somatic hypermutation has stimulated interest in the effect of mismatch repair deficiency on the process. Analysis of unselected mutations in the 3' flank of VH rearrangements in germinal center B cells revealed that MSH2 deficiency caused a 5-fold reduced mutation accumulation. This might reflect ectopic effects of the Msh2 disruption; indeed, the mice exhibit other perturbations within the B cell compartment. However, that MSH2 (or factors dependent upon it) plays a role in the mechanism of mutation fixation is indicated by a strikingly increased focusing of the mutations on intrinsic hot spots. We propose two phases to hypermutation targeting. The first is hot spot focused and MSH2 independent; the second, MSH2-dependent phase yields a more even spread of mutation fixation.
Collapse
Affiliation(s)
- C Rada
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | | |
Collapse
|
43
|
Kong Q, Zhao L, Subbaiah S, Maizels N. A λ 3′ Enhancer Drives Active and Untemplated Somatic Hypermutation of a λ1 Transgene. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.1.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Somatic hypermutation is a highly regulated process that targets mutations to the rearranged Ig genes. Little is known about the cis-elements required for somatic hypermutation of the λ light chain gene. We have studied somatic hypermutation of a rearranged λ1 transgene under the control of either a λ2-4 or κ 3′ enhancer. The mutations in the transgenes were analyzed by sequencing DNA amplified from hypermutating Peyer’s patch B cells. The results indicate that the λ 3′ enhancer can drive active hypermutation of a λ1 transgene in Peyer’s patch cells. The λ1 transgene under analysis carried two marked Vλ2 genes immediately upstream that could serve as sequence donors in possible gene conversion events. There was no evidence of sequence transfer to the hypermutated λ1 gene, suggesting that gene conversion is not a major mechanism for somatic hypermutation in mice.
Collapse
Affiliation(s)
| | - Lisa Zhao
- *Molecular Biophysics and Biochemistry and
| | | | - Nancy Maizels
- *Molecular Biophysics and Biochemistry and
- †Genetics, Yale University, New Haven, CT 06520
| |
Collapse
|
44
|
Winter DB, Phung QH, Umar A, Baker SM, Tarone RE, Tanaka K, Liskay RM, Kunkel TA, Bohr VA, Gearhart PJ. Altered spectra of hypermutation in antibodies from mice deficient for the DNA mismatch repair protein PMS2. Proc Natl Acad Sci U S A 1998; 95:6953-8. [PMID: 9618520 PMCID: PMC22699 DOI: 10.1073/pnas.95.12.6953] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/1998] [Indexed: 02/07/2023] Open
Abstract
Mutations are introduced into rearranged Ig variable genes at a frequency of 10(-2) mutations per base pair by an unknown mechanism. Assuming that DNA repair pathways generate or remove mutations, the frequency and pattern of mutation will be different in variable genes from mice defective in repair. Therefore, hypermutation was studied in mice deficient for either the DNA nucleotide excision repair gene Xpa or the mismatch repair gene Pms2. High levels of mutation were found in variable genes from XPA-deficient and PMS2-deficient mice, indicating that neither nucleotide excision repair nor mismatch repair pathways generate hypermutation. However, variable genes from PMS2-deficient mice had significantly more adjacent base substitutions than genes from wild-type or XPA-deficient mice. By using a biochemical assay, we confirmed that tandem mispairs were repaired by wild-type cells but not by Pms2(-/-) human or murine cells. The data indicate that tandem substitutions are produced by the hypermutation mechanism and then processed by a PMS2-dependent pathway.
Collapse
Affiliation(s)
- D B Winter
- Laboratory of Molecular Genetics, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Blanden RV, Steele EJ. A unifying hypothesis for the molecular mechanism of somatic mutation and gene conversion in rearranged immunoglobulin variable genes. Immunol Cell Biol 1998; 76:288-93. [PMID: 9682973 DOI: 10.1046/j.1440-1711.1998.00738.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have reviewed available data concerning the mechanism of somatic hypermutation in rearranged variable genes of Ig in B lymphocytes of mice and the gene conversion process which generates diversity in these genes in the B lymphocytes of chickens. In our view, these data are consistent with a unifying hypothesis of diversity generating mechanisms involving reverse transcription to produce cDNA from RNA transcripts followed by homologous recombination into chromosomal DNA. Thus, seemingly different processes in the mouse and chicken may have a common molecular basis.
Collapse
Affiliation(s)
- R V Blanden
- Division of Immunology and Cell Biology, John Curtin School of Medical Research, Australian National University, Canberra, ACT
| | | |
Collapse
|
46
|
Neuberger MS, Ehrenstein MR, Klix N, Jolly CJ, Yélamos J, Rada C, Milstein C. Monitoring and interpreting the intrinsic features of somatic hypermutation. Immunol Rev 1998; 162:107-16. [PMID: 9602357 DOI: 10.1111/j.1600-065x.1998.tb01434.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have used both normal and transgenic mice to analyse the recruitment and targeting of somatic hypermutation to the immunoglobulin loci. We compare methods for analysing hypermutation and discuss how large databases of mutations can be assembled by PCR amplification of the rearranged V-gene flanks from the germinal centre B cells of normal mice as well as by transgene-specific amplification from transgenic B cells. Such studies confirm that hypermutation is preferentially targeted to the immunoglobulin V gene with the bcl6 gene, for example, escaping this intense mutational targeting in germinal centre B cells. We review our data concerning the nature of the hypermutation domain and the targeting of hotspots within that domain. We consider how enhancer-mediated recruitment of hypermutation to the immunoglobulin loci operates in a clonally maintained fashion and illustrate how both the degree of expression and demethylation of the transgene broadly correlate with its mutability.
Collapse
Affiliation(s)
- M S Neuberger
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | | | | | | | | | | | |
Collapse
|
47
|
Andersson K, Wrammert J, Leanderson T. Affinity selection and repertoire shift: paradoxes as a consequence of somatic mutation? Immunol Rev 1998; 162:173-82. [PMID: 9602363 DOI: 10.1111/j.1600-065x.1998.tb01440.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Affinity selection of antibodies during immune responses relies on two mechanisms, one molecular that involves the targeted introduction of somatic mutations into rearranged immunoglobulin genes and one cellular that involves the clonal expansion of B cells expressing a surface immunoglobulin with a higher affinity for antigen compared to their competitors. In this review we focus on the conditions for affinity selection during the establishment, expansion and memory phases of the immune response. We postulate that somatic mutation evolved prior to affinity selection and we present a model for selection of B cells in germinal centres. We also discuss the possibility that antibody repertoire shift occurs during the memory maintenance phase. Finally, we argue that a significant affinity selection and a selection for polyclonality of immune responses occur during this stage of the immune response.
Collapse
Affiliation(s)
- K Andersson
- Department of Cellular and Molecular Biology, Lund University, Sweden
| | | | | |
Collapse
|
48
|
Dörner T, Foster SJ, Brezinschek HP, Lipsky PE. Analysis of the targeting of the hypermutational machinery and the impact of subsequent selection on the distribution of nucleotide changes in human VHDJH rearrangements. Immunol Rev 1998; 162:161-71. [PMID: 9602362 DOI: 10.1111/j.1600-065x.1998.tb01439.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
B cells are unique in that they generate and tolerate a high rate of mutations in their antigen receptor genes and employ these mutations as a basis of avidity maturation. The precise role of the mutational machinery versus subsequent selection in determining the frequency and distribution of mutations has not been fully analyzed. To address these issues, the influence of the intrinsic mutational machinery and subsequent selection on the frequency and distribution of mutations in the expressed human immunoglobulin repertoire was analyzed. Analysis of non-productively rearranged VH genes from individual human B cells provided an opportunity to examine the immediate impact of somatic hypermutation without superimposed selective influences. Comparison with the frequency and distribution of mutations in the productively rearranged human VH genes permitted an estimate of the influences of subsequent selection.
Collapse
Affiliation(s)
- T Dörner
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas 75235-8884, USA
| | | | | | | |
Collapse
|
49
|
Affiliation(s)
- U Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA.
| |
Collapse
|
50
|
Blanden RV, Rothenfluh HS, Zylstra P, Weiller GF, Steele EJ. The signature of somatic hypermutation appears to be written into the germline IgV segment repertoire. Immunol Rev 1998; 162:117-32. [PMID: 9602358 DOI: 10.1111/j.1600-065x.1998.tb01435.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here a unifying hypothesis for the molecular mechanism of somatic hypermutation and somatic gene conversion in IgV genes involving reverse transcription using RNA templates from the V-gene loci to produce cDNA which undergoes homologous recombination with chromosomal V(D)J DNA. Experimental evidence produced over the last 20 years is essentially consistent with this hypothesis. We also review evidence suggesting that somatically generated IgV sequences from B lymphocytes have been fed back to germline DNA over evolutionary time.
Collapse
Affiliation(s)
- R V Blanden
- Division of Immunology and Cell Biology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | | | | | | | |
Collapse
|