1
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Worth AN, Palmer VL, Schabla NM, Perry GA, Fraser-Philbin AN, Swanson PC. Receptor editing constrains development of phosphatidyl choline-specific B cells in V H12-transgenic mice. Cell Rep 2022; 39:110899. [PMID: 35705027 DOI: 10.1016/j.celrep.2022.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 11/03/2022] Open
Abstract
B1 B cells reactive to phosphatidyl choline (PtC) exhibit restricted immunoglobulin heavy chain (HC) and light chain (LC) combinations, exemplified by VH12/Vκ4/5H. Two checkpoints are thought to focus PtC+ B cell maturation in VH12-transgenic mice (VH12 mice): V-J rearrangements encoding a "permissive" LC capable of VH12 HC pairing are selected first, followed by positive selection based on PtC binding, often requiring LC receptor editing to salvage PtC- B cells and acquire PtC reactivity. However, evidence obtained from breeding VH12 mice to editing-defective dnRAG1 mice and analyzing LC sequences from PtC+ and PtC- B cell subsets instead suggests that receptor editing functions after initial positive selection to remove PtC+ B cells in VH12 mice. This offers a mechanism to constrain natural, polyreactive B cells to limit their frequency. Sequencing also reveals occasional in-frame hybrid LC genes, reminiscent of type 2 gene replacement, that, testing suggests, arise via a recombination-activating gene (RAG)-independent mechanism.
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Affiliation(s)
- Alexandra N Worth
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Victoria L Palmer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; Shoreline Biosciences, San Diego, CA 92121, USA
| | - Greg A Perry
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Anna N Fraser-Philbin
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
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2
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Li Z, Jiang N, Lim EH, Chin WHN, Lu Y, Chiew KH, Kham SKY, Yang W, Quah TC, Lin HP, Tan AM, Ariffin H, Yang JJ, Yeoh AEJ. Identifying IGH disease clones for MRD monitoring in childhood B-cell acute lymphoblastic leukemia using RNA-Seq. Leukemia 2020; 34:2418-2429. [PMID: 32099036 DOI: 10.1038/s41375-020-0774-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022]
Abstract
Identifying patient-specific clonal IGH/TCR junctional sequences is critical for minimal residual disease (MRD) monitoring. Conventionally these junctional sequences are identified using laborious Sanger sequencing of excised heteroduplex bands. We found that the IGH is highly expressed in our diagnostic B-cell acute lymphoblastic leukemia (B-ALL) samples using RNA-Seq. Therefore, we used RNA-Seq to identify IGH disease clone sequences in 258 childhood B-ALL samples for MRD monitoring. The amount of background IGH rearrangements uncovered by RNA-Seq followed the Zipf's law with IGH disease clones easily identified as outliers. Four hundred and ninety-seven IGH disease clones (median 2, range 0-7 clones/patient) are identified in 90.3% of patients. High hyperdiploid patients have the most IGH disease clones (median 3) while DUX4 subtype has the least (median 1) due to the rearrangements involving the IGH locus. In all, 90.8% of IGH disease clones found by Sanger sequencing are also identified by RNA-Seq. In addition, RNA-Seq identified 43% more IGH disease clones. In 69 patients lacking sensitive IGH targets, targeted NGS IGH MRD showed high correlation (R = 0.93; P = 1.3 × 10-14), better relapse prediction than conventional RQ-PCR MRD using non-IGH targets. In conclusion, RNA-Seq can identify patient-specific clonal IGH junctional sequences for MRD monitoring, adding to its usefulness for molecular diagnosis in childhood B-ALL.
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Affiliation(s)
- Zhenhua Li
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nan Jiang
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Evelyn Huizi Lim
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Winnie Hui Ni Chin
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yi Lu
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kean Hui Chiew
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shirley Kow Yin Kham
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Thuan Chong Quah
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Viva-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Hai Peng Lin
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Ah Moy Tan
- Department of Paediatrics, KK Women's & Children's Hospital, Singapore, Singapore
| | - Hany Ariffin
- University of Malaya Cancer Research Institute, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Allen Eng-Juh Yeoh
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Viva-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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3
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Wu J, Jia S, Wang C, Zhang W, Liu S, Zeng X, Mai H, Yuan X, Du Y, Wang X, Hong X, Li X, Wen F, Xu X, Pan J, Li C, Liu X. Minimal Residual Disease Detection and Evolved IGH Clones Analysis in Acute B Lymphoblastic Leukemia Using IGH Deep Sequencing. Front Immunol 2016; 7:403. [PMID: 27757113 PMCID: PMC5048610 DOI: 10.3389/fimmu.2016.00403] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Acute B lymphoblastic leukemia (B-ALL) is one of the most common types of childhood cancer worldwide and chemotherapy is the main treatment approach. Despite good response rates to chemotherapy regiments, many patients eventually relapse and minimal residual disease (MRD) is the leading risk factor for relapse. The evolution of leukemic clones during disease development and treatment may have clinical significance. In this study, we performed immunoglobulin heavy chain (IGH) repertoire high throughput sequencing (HTS) on the diagnostic and post-treatment samples of 51 pediatric B-ALL patients. We identified leukemic IGH clones in 92.2% of the diagnostic samples and nearly half of the patients were polyclonal. About one-third of the leukemic clones have correct open reading frame in the complementarity determining region 3 (CDR3) of IGH, which demonstrates that the leukemic B cells were in the early developmental stage. We also demonstrated the higher sensitivity of HTS in MRD detection and investigated the clinical value of using peripheral blood in MRD detection and monitoring the clonal IGH evolution. In addition, we found leukemic clones were extensively undergoing continuous clonal IGH evolution by variable gene replacement. Dynamic frequency change and newly emerged evolved IGH clones were identified upon the pressure of chemotherapy. In summary, we confirmed the high sensitivity and universal applicability of HTS in MRD detection. We also reported the ubiquitous evolved IGH clones in B-ALL samples and their response to chemotherapy during treatment.
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Affiliation(s)
- Jinghua Wu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Shan Jia
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Changxi Wang
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Sixi Liu
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiaojing Zeng
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huirong Mai
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiuli Yuan
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Yuanping Du
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xiaodong Wang
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xueyu Hong
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xuemei Li
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Feiqiu Wen
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Changgang Li
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark
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4
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Buerstedde JM, Lowndes N, Schatz DG. Induction of homologous recombination between sequence repeats by the activation induced cytidine deaminase (AID) protein. eLife 2014; 3:e03110. [PMID: 25006166 PMCID: PMC4080448 DOI: 10.7554/elife.03110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/02/2014] [Indexed: 02/06/2023] Open
Abstract
The activation induced cytidine deaminase (AID) protein is known to initiate somatic hypermutation, gene conversion or switch recombination by cytidine deamination within the immunoglobulin loci. Using chromosomally integrated fluorescence reporter transgenes, we demonstrate a new recombinogenic activity of AID leading to intra- and intergenic deletions via homologous recombination of sequence repeats. Repeat recombination occurs at high frequencies even when the homologous sequences are hundreds of bases away from the positions of AID-mediated cytidine deamination, suggesting DNA end resection before strand invasion. Analysis of recombinants between homeologous repeats yielded evidence for heteroduplex formation and preferential migration of the Holliday junctions to the boundaries of sequence homology. These findings broaden the target and off-target mutagenic potential of AID and establish a novel system to study induced homologous recombination in vertebrate cells.DOI: http://dx.doi.org/10.7554/eLife.03110.001.
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Affiliation(s)
- Jean-Marie Buerstedde
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - Noel Lowndes
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, United States Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
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5
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Yu L, Guan Y. Immunologic Basis for Long HCDR3s in Broadly Neutralizing Antibodies Against HIV-1. Front Immunol 2014; 5:250. [PMID: 24917864 PMCID: PMC4040451 DOI: 10.3389/fimmu.2014.00250] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/12/2014] [Indexed: 01/18/2023] Open
Abstract
A large number of potent broadly neutralizing antibodies (bnAbs) against HIV-1 have been reported in recent years, raising hope for the possibility of an effective vaccine based on epitopes recognized by these protective antibodies. However, many of these bnAbs contain the long heavy chain complementarity-determining region 3 (HCDR3), which is viewed as an obstacle to the development of an HIV-1 vaccine targeting the bnAb responses. This mini-review summarizes the current literature and discusses the different potential immunologic mechanisms for generating long HCDR3, including D–D fusion, VH replacement, long N region addition, and skewed D–J gene usage, among which potential VH replacement products appear to be significant contributors. VH replacement occurs through recombinase activated gene-mediated secondary recombination and contributes to the diversified naïve B cell repertoire. During VH replacement, a short stretch of nucleotides from previously rearranged VH genes remains within the newly formed HCDR3, thus elongating its length. Accumulating evidence suggests that long HCDR3s are present in significant numbers in the human mature naïve B cell repertoire and are primarily generated by recombination during B cell development. These new observations indicate that long HCDR3s, though low in frequency, are a normal feature of the human antibody naïve repertoire and they appear to be selected to target conserved epitopes located in deep, partially obscured regions of the HIV-1 envelope trimer. Therefore, the presence of long HCDR3 sequences should not necessarily be viewed as an obstacle to the development of an HIV-1 vaccine based upon bnAb responses.
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Affiliation(s)
- Lei Yu
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA
| | - Yongjun Guan
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine , Baltimore, MD , USA
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6
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Ouled-Haddou H, Ghamlouch H, Regnier A, Trudel S, Herent D, Lefranc MP, Marolleau JP, Gubler B. Characterization of a new V gene replacement in the absence of activation-induced cytidine deaminase and its contribution to human B-cell receptor diversity. Immunology 2014; 141:268-75. [PMID: 24134819 DOI: 10.1111/imm.12192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 11/29/2022] Open
Abstract
In B cells, B-cell receptor (BCR) immunoglobulin revision is a common route for modifying unwanted antibody specificities via a mechanism called VH replacement. This in vivo process, mostly affecting heavy-chain rearrangement, involves the replacement of all or part of a previously rearranged IGHV gene with another germline IGHV gene located upstream. Two different mechanisms of IGHV replacement have been reported: type 1, involving the recombination activating genes complex and requiring a framework region 3 internal recombination signal; and type 2, involving an unidentified mechanism different from that of type 1. In the case of light-chain loci, BCR immunoglobulin editing ensures that a second V-J rearrangement occurs. This helps to maintain tolerance, by generating a novel BCR with a new antigenic specificity. We report that human B cells can, surprisingly, undergo type 2 replacement associated with κ light-chain rearrangements. The de novo IGKV-IGKJ products result from the partial replacement of a previously rearranged IGKV gene by a new germline IGKV gene, in-frame and without deletion or addition of nucleotides. There are wrcy/rgyw motifs at the 'IGKV donor-IGKV recipient chimera junction' as described for type 2 IGHV replacement, but activation-induced cytidine deaminase (AID) expression was not detected. This unusual mechanism of homologous recombination seems to be a variant of gene conversion-like recombination, which does not require AID. The recombination phenomenon described here provides new insight into immunoglobulin locus recombination and BCR immunoglobulin repertoire diversity.
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Affiliation(s)
- Hakim Ouled-Haddou
- Unité EA4666, SFR CAP Santé, Université Picardie Jules Verne, Amiens, France; Unité Inserm U925, Université Picardie Jules Verne, Amiens, France
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7
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Meng W, Jayaraman S, Zhang B, Schwartz GW, Daber RD, Hershberg U, Garfall AL, Carlson CS, Luning Prak ET. Trials and Tribulations with VH Replacement. Front Immunol 2014; 5:10. [PMID: 24523721 PMCID: PMC3906580 DOI: 10.3389/fimmu.2014.00010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/07/2014] [Indexed: 11/13/2022] Open
Abstract
VH replacement (VHR) is a type of antibody gene rearrangement in which an upstream heavy chain variable gene segment (VH) invades a pre-existing rearrangement (VDJ). In this Hypothesis and Theory article, we begin by reviewing the mechanism of VHR, its developmental timing and its potential biological consequences. Then we explore the hypothesis that specific sequence motifs called footprints reflect VHR versus other processes. We provide a compilation of footprint sequences from different regions of the antibody heavy chain, and include data from the literature and from a high throughput sequencing experiment to evaluate the significance of footprint sequences. We conclude by discussing the difficulties of attributing footprints to VHR.
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Affiliation(s)
- Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Sahana Jayaraman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Bochao Zhang
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA
| | - Gregory W Schwartz
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA
| | - Robert D Daber
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA ; Center for Personalized Diagnostics, University of Pennsylvania Health System , Philadelphia, PA , USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, PA , USA ; Department of Microbiology and Immunology, College of Medicine, Drexel University , Philadelphia, PA , USA
| | - Alfred L Garfall
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center , Seattle, WA , USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
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8
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Plevova K, Francova HS, Burckova K, Brychtova Y, Doubek M, Pavlova S, Malcikova J, Mayer J, Tichy B, Pospisilova S. Multiple productive immunoglobulin heavy chain gene rearrangements in chronic lymphocytic leukemia are mostly derived from independent clones. Haematologica 2013; 99:329-38. [PMID: 24038023 DOI: 10.3324/haematol.2013.087593] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In chronic lymphocytic leukemia, usually a monoclonal disease, multiple productive immunoglobulin heavy chain gene rearrangements are identified sporadically. Prognostication of such cases based on immunoglobulin heavy variable gene mutational status can be problematic, especially if the different rearrangements have discordant mutational status. To gain insight into the possible biological mechanisms underlying the origin of the multiple rearrangements, we performed a comprehensive immunogenetic and immunophenotypic characterization of 31 cases with the multiple rearrangements identified in a cohort of 1147 patients with chronic lymphocytic leukemia. For the majority of cases (25/31), we provide evidence of the co-existence of at least two B lymphocyte clones with a chronic lymphocytic leukemia phenotype. We also identified clonal drifts in serial samples, likely driven by selection forces. More specifically, higher immunoglobulin variable gene identity to germline and longer complementarity determining region 3 were preferred in persistent or newly appearing clones, a phenomenon more pronounced in patients with stereotyped B-cell receptors. Finally, we report that other factors, such as TP53 gene defects and therapy administration, influence clonal selection. Our findings are relevant to clonal evolution in the context of antigen stimulation and transition of monoclonal B-cell lymphocytosis to chronic lymphocytic leukemia.
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9
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Burmeister T, Molkentin M, Schwartz S, Gökbuget N, Hoelzer D, Thiel E, Reinhardt R. Erroneous class switching and false VDJ recombination: molecular dissection of t(8;14)/MYC-IGH translocations in Burkitt-type lymphoblastic leukemia/B-cell lymphoma. Mol Oncol 2013; 7:850-8. [PMID: 23673335 DOI: 10.1016/j.molonc.2013.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/04/2013] [Accepted: 04/16/2013] [Indexed: 12/30/2022] Open
Abstract
The chromosomal translocation t(8;14)(q24;q32) with juxtaposition of MYC to enhancer elements in the immunoglobulin heavy chain (IGH) gene locus is the genetic hallmark of the majority of Burkitt lymphoma and a subset of Diffuse large B-cell lymphoma patients. Around 3% of adult B-lineage acute lymphoblastic leukemia (ALL) patients show this aberration. Flow cytometry mostly reveals a "mature B-ALL" or "Burkitt-type" ALL immunophenotype. Using long-distance PCR for t(8;14)/MYC-IGH fusion, we investigated bone marrow, peripheral blood and a few other samples with suspected Burkitt-ALL or mature B-ALL and identified 133 MYC-IGH-positive cases. The location of the chromosomal breaks in the IGH joining and the 8 different switch regions was determined using a set of long-distance PCRs. The chromosomal breakpoints with the adjacent MYC regions on 8q24 were characterized by direct sequencing in 49 cases. The distribution of chromosomal breaks among the IGH joining and switch regions was the following: JH 23.3%, M 21.8%, G1 15.0%, G2 7.5%, G3 3.8%, G4 4.5%, A1 12.8%, A2 3.8%, E 7.5%. Two breakpoint clusters near MYC were delineated. There was no clear correlation between the degree of somatic hypermutation and the chromosomal break locations. Epstein Barr virus was detected in 5 cases (4%). This detailed and extensive molecular analysis illustrates the molecular complexity of the MYC-IGH translocations and the detected distribution of breakpoints provides additional evidence that this translocation results from failed switch and VDJ recombinations. This study may serve as a model for the analysis of other IGH translocations in B-cell lymphoma.
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Affiliation(s)
- Thomas Burmeister
- Charité, Med. Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany.
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10
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Briney BS, Jr. JEC. Secondary mechanisms of diversification in the human antibody repertoire. Front Immunol 2013; 4:42. [PMID: 23483107 PMCID: PMC3593266 DOI: 10.3389/fimmu.2013.00042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 02/05/2013] [Indexed: 12/25/2022] Open
Abstract
V(D)J recombination and somatic hypermutation (SHM) are the primary mechanisms for diversification of the human antibody repertoire. These mechanisms allow for rapid humoral immune responses to a wide range of pathogenic challenges. V(D)J recombination efficiently generate a virtually limitless diversity through random recombination of variable (V), diversity (D), and joining (J) genes with diverse non-templated junctions between the selected gene segments. Following antigen stimulation, affinity maturation by SHM produces antibodies with refined specificity mediated by mutations typically focused in complementarity determining regions (CDRs), which form the bulk of the antigen recognition site. While V(D)J recombination and SHM are responsible for much of the diversity of the antibody repertoire, there are several secondary mechanisms that, while less frequent, make substantial contributions to antibody diversity including V(DD)J recombination (or D-D fusion), SHM-associated insertions and deletions, and affinity maturation and antigen contact by non-CDR regions of the antibody. In addition to enhanced diversity, these mechanisms allow the production of antibodies that are critical to response to a variety of viral and bacterial pathogens but that would be difficult to generate using only the primary mechanisms of diversification.
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Affiliation(s)
- Bryan S. Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
| | - James E. Crowe Jr.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical CenterNashville, TN, USA
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashville, TN, USA
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11
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Hadzidimitriou A, Darzentas N, Karakoli A, Koliouskas D, Tsaftaris A, Anagnostopoulos A, Stamatopoulos K. Coexistence of different types of biallelic immunoglobulin heavy variable gene replacement events in a case of pediatric B precursor acute lymphoblastic leukemia. Leuk Lymphoma 2010; 51:1748-50. [PMID: 20578821 DOI: 10.3109/10428194.2010.496508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Lange MD, Waldbieser GC, Lobb CJ. Patterns of receptor revision in the immunoglobulin heavy chains of a teleost fish. THE JOURNAL OF IMMUNOLOGY 2009; 182:5605-22. [PMID: 19380808 DOI: 10.4049/jimmunol.0801013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
H chain cDNA libraries were constructed from the RNA derived from seven different organs and tissues from the same individual catfish. Sequence analysis of >300 randomly selected clones identified clonal set members within the same or different tissues, and some of these represented mosaic or hybrid sequences. These hybrids expressed V(H) members of the same or different V(H) families within different regions of the same clone. Within some clonal sets multiple hybrids were identified, and some of these represented the products of sequential V(H) replacement events. Different experimental methods confirmed that hybrid clones identified in the cDNA library from one tissue could be reisolated in the cDNA pool or from the total RNA derived from the same or a different tissue, indicating that these hybrids likely represented the products of in vivo receptor revision events. Murine statistical recombination models were used to evaluate cryptic recombination signal sequences (cRSS), and significant cRSS pairs in the predicted V(H) donor and recipient were identified. These models supported the hypothesis that seamless revisions may have occurred via hybrid joint formation. The heptamers of the cRSS pairs were located at different locations within the coding region, and different events resulted in the replacement of one or both CDR as well as events that replaced the upstream untranslated region and the leader region. These studies provide phylogenetic evidence that receptor revision may occur in clonally expanded B cell lineages, which supports the hypothesis that additional levels of somatic H chain diversification may exist.
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Affiliation(s)
- Miles D Lange
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
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13
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Mierau M, Drexler GA, Kutzera A, Braunschmidt K, Ellwart J, Eckardt-Schupp F, Fritz E, Bachl J, Jungnickel B. Non-conservative homologous recombination in human B lymphocytes is promoted by activation-induced cytidine deaminase and transcription. Nucleic Acids Res 2008; 36:5591-601. [PMID: 18757891 PMCID: PMC2553578 DOI: 10.1093/nar/gkn542] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
During secondary immunoglobulin (Ig) diversification in vertebrates, the sequence of the variable region of Ig genes may be altered by templated or non-templated mechanisms. In both cases, cytidine deamination by activation-induced cytidine deaminase (AID) in the transcribed Ig loci leads to DNA lesions, which are repaired by conservative homologous recombination (HR) during Ig gene conversion, or by non-templated mutagenesis during somatic hypermutation. The molecular basis for the differential use of these two pathways in different species is unclear. While experimental ablation of HR in avian cells performing Ig gene conversion may promote a switch to somatic hypermutation, the activity of HR processes in intrinsically hypermutating mammalian cells has not been measured to date. Employing a functional HR assay in human germinal centre like B cell lines, we detect elevated HR activity that can be enhanced by transcription and AID. Products of such recombination events mostly arise through non-conservative HR pathways, while the activity of conservative HR is low to absent. Our results identify non-conservative HR as a novel DNA transaction pathway promoted by AID and suggest that somatic hypermutation in germinal centre B cells may be based on a physiological suppression of conservative HR.
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Affiliation(s)
- Maren Mierau
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Guido A. Drexler
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - André Kutzera
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Kerstin Braunschmidt
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Joachim Ellwart
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Friederike Eckardt-Schupp
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Eberhard Fritz
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Jürgen Bachl
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
| | - Berit Jungnickel
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Institute of Radiobiology, Helmholtz Center Munich, National Research Center for Environmental Health, D-85764 Neuherberg, Radiobiological Institute, Ludwig-Maximilians-University, D-80336 Munich, Institute of Molecular Immunology, Helmholtz Center Munich, National Research Center for Environmental Health, D-81377 Munich, Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena and 4-Antibody, WRO-1096.3, Schwarzwaldallee 215, CH-4002 Basel, Switzerland
- *To whom correspondence should be addressed. Tel: +49 89 7099 209; Fax: +49 89 7099 500;
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14
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Davila M, Liu F, Cowell LG, Lieberman AE, Heikamp E, Patel A, Kelsoe G. Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells. ACTA ACUST UNITED AC 2007; 204:3195-208. [PMID: 18056287 PMCID: PMC2150985 DOI: 10.1084/jem.20071224] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Receptor editing is believed to play the major role in purging newly formed B cell compartments of autoreactivity by the induction of secondary V(D)J rearrangements. In the process of immunoglobulin heavy (H) chain editing, these secondary rearrangements are mediated by direct VH-to-JH joining or cryptic recombination signals (cRSs) within VH gene segments. Using a statistical model of RS, we have identified potential cRSs within VH gene segments at conserved sites flanking complementarity-determining regions 1 and 2. These cRSs are active in extrachromosomal recombination assays and cleaved during normal B cell development. Cleavage of multiple VH cRSs was observed in the bone marrow of C57BL/6 and RAG2:GFP and μMT congenic animals, and we determined that cRS cleavage efficiencies are 30–50-fold lower than a physiological RS. cRS signal ends are abundant in pro–B cells, including those recovered from μMT mice, but undetectable in pre– or immature B cells. Thus, VH cRS cleavage regularly occurs before the generation of functional preBCR and BCR. Conservation of cRSs distal from the 3′ end of VH gene segments suggests a function for these cryptic signals other than VH gene replacement.
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Affiliation(s)
- Marco Davila
- Department of Immunology, Duke University, Durham, NC 27710, USA
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15
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Nikolajczyk BS, Sardi SH, Tumang JR, Ganley-Leal LM. Immunoglobulin kappa enhancers are differentially regulated at the level of chromatin structure. Mol Immunol 2007; 44:3407-15. [PMID: 17382392 PMCID: PMC2442924 DOI: 10.1016/j.molimm.2007.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 02/10/2007] [Accepted: 02/14/2007] [Indexed: 12/19/2022]
Abstract
The kappa intronic and the kappa 3' enhancers synergize to regulate recombination and transcription of the Ig kappa locus. Although these enhancers have overlapping functions, the kappa i enhancer appears to predominate during receptor editing, while the kappa 3' enhancer may be more important for initiating Ig kappa germline transcription to target locus recombination and, later in development, somatic hypermutation. Changes in chromatin structure appear to regulate both enhancers, and previous reports suggest that both enhancers are packaged into an accessible chromatin structure only in B lineage cells. Why these enhancers cannot activate the demethylated, accessible, protein-associated Ig kappa allele in pro-B cells is not known. Furthermore, how the enhancers function to reactivate the locus for receptor editing or to quantitatively promote hypermutation in B cells is vague. Quantitative analysis of Ig enhancer chromatin structure in murine pro-, pre-and splenic B cells demonstrated that the kappa i enhancer maintains a highly accessible chromatin structure under a variety of conditions. This stable chromatin structure mirrored the highly accessible structure characterizing the Ig mu intronic enhancer, despite the fact that Ig mu is activated prior to Ig kappa during B cell development. Surprisingly, parallel analysis of the kappa 3' enhancer demonstrated its accessible chromatin structure is markedly unstable, as characterized by sensitivity to changes in environmental conditions. These data unexpectedly suggest that kappa locus regulation is compartmentalized along the gene in B lineage cells. Furthermore, these findings raise the possibility that environmentally dependent regulation of kappa 3' enhancer structure underlies changes in kappa activation during B cell development.
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Affiliation(s)
- Barbara S Nikolajczyk
- Departments of Microbiology and Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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16
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Nagawa F, Kishishita N, Shimizu K, Hirose S, Miyoshi M, Nezu J, Nishimura T, Nishizumi H, Takahashi Y, Hashimoto SI, Takeuchi M, Miyajima A, Takemori T, Otsuka AJ, Sakano H. Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice. Nat Immunol 2006; 8:206-13. [PMID: 17187071 DOI: 10.1038/ni1419] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 11/06/2006] [Indexed: 12/20/2022]
Abstract
Jawless vertebrates have acquired immunity but do not have immunoglobulin-type antigen receptors. Variable lymphocyte receptors (VLRs) have been identified in lamprey that consist of multiple leucine-rich repeat (LRR) modules. An active VLR gene is generated by the assembly of a series of variable gene segments, including many that encode LRRs. Stepwise assembly of the gene segments seems to occur by replacement of the intervening DNA between the 5' and 3' constant-region genes. Here we report that lamprey (Lethenteron japonicum) assemble their VLR genes by a process involving 'copy choice'. Regions of short homology seemed to prime copying of donor LRR-encoding sequences into the recipient gene. Those LRR-encoding germline sequences were abundant and shared extensive sequence homologies. Such genomic organization permits initiation of copying anywhere in an LRR-encoding module for the generation of various hybrid LRRs. Thus, a vast repertoire of recombinant VLR genes could be generated not only by copying of various LRR segments in diverse combinations but also by the use of multiple sites in an LRR gene segment for priming.
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Affiliation(s)
- Fumikiyo Nagawa
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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17
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Darlow JM, Stott DI. Gene conversion in human rearranged immunoglobulin genes. Immunogenetics 2006; 58:511-22. [PMID: 16705406 DOI: 10.1007/s00251-006-0113-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 02/23/2006] [Accepted: 03/16/2006] [Indexed: 11/26/2022]
Abstract
Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V(H) segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V(H) replacements with no addition of untemplated nucleotides at the V(H)-V(H) joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V(H) replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion.
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Affiliation(s)
- John M Darlow
- Department of Immunology, Level 4, Glasgow Biomedical Research Centre, 120 University Place, Glasgow, G12 8TA, UK.
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18
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Burmeister T, Marschalek R, Schneider B, Meyer C, Gökbuget N, Schwartz S, Hoelzer D, Thiel E. Monitoring minimal residual disease by quantification of genomic chromosomal breakpoint sequences in acute leukemias with MLL aberrations. Leukemia 2006; 20:451-7. [PMID: 16424875 DOI: 10.1038/sj.leu.2404082] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An estimated 10% of acute leukemias carry mixed-lineage leukemia (MLL) fusion genes. Approximately 50 different fusion partners of the MLL gene have already been molecularly identified. These leukemias are commonly regarded as high-risk cases and are treated accordingly with intensified therapy regimens, including hematopoietic stem cell transplantation. However, a subset of patients may achieve long-term remissions with conventional therapy. Monitoring minimal residual disease (MRD) is undoubtedly of great value in clinical decision making, also in the pre- and post-transplant setting. Here, we describe a novel method for detecting MRD in leukemias with MLL aberrations. The method is based on monitoring patient-specific chromosomal breakpoint DNA sequences. This has several advantages over other methods that are based either on detecting specific RNA molecules of MLL fusion genes or on surrogate markers. An accurate and absolute quantification of the MRD level is possible. No reference to housekeeping genes is necessary and the target structure is much more stable than any mRNA fusion transcript.
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Affiliation(s)
- T Burmeister
- Medizinische Klinik III, Campus Benjamin Franklin, Charité Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.
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19
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Rahman NS, Godderz LJ, Stray SJ, Capra JD, Rodgers KK. DNA cleavage of a cryptic recombination signal sequence by RAG1 and RAG2. Implications for partial V(H) gene replacement. J Biol Chem 2006; 281:12370-80. [PMID: 16531612 DOI: 10.1074/jbc.m507906200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody and T cell receptor genes are assembled from gene segments by V(D)J recombination to produce an almost infinitely diverse repertoire of antigen specificities. Recombination is initiated by cleavage of conserved recombination signal sequences (RSS) by RAG1 and RAG2 during lymphocyte development. Recent evidence demonstrates that recombination can occur at noncanonical RSS sites within Ig genes or at other loci, outside the context of normal lymphocyte receptor gene rearrangement. We have characterized the ability of the RAG proteins to bind and cleave a cryptic RSS (cRSS) located within an Ig V(H) gene segment. The RAG proteins bound with sequence specificity to either the consensus RSS or the cRSS. The RAG proteins nick the cRSS on both the top and bottom strands, thereby bypassing the formation of the DNA hairpin intermediate observed in RAG cleavage of canonical RSS substrates. We propose that the RAG proteins may utilize an alternative mechanism for double-stranded DNA cleavage, depending on the substrate sequence. These results have implications for further diversification of the antigen receptor repertoire as well as the role of the RAG proteins in genomic instability.
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Affiliation(s)
- Negar S Rahman
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190, USA
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