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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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Zhou X, Xian W, Zhang J, Zhu Y, Shao X, Han Y, Qi Y, Ding X, Wang X. YY1 binds to the E3' enhancer and inhibits the expression of the immunoglobulin κ gene via epigenetic modifications. Immunology 2018; 155:491-498. [PMID: 30098214 DOI: 10.1111/imm.12990] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 01/11/2023] Open
Abstract
The rearrangement and expression of immunoglobulin genes are regulated by enhancers and their binding transcriptional factors that activate or suppress the activities of the enhancers. The immunoglobulin κ (Igκ) gene locus has three important enhancers: the intrinsic enhancer (Ei), 3' enhancer (E3'), and distal enhancer (Ed). Ei and E3' are both required for Igκ gene rearrangement during early stages of B-cell development, whereas optimal expression of the rearranged Igκ gene relies on both E3' and Ed. The transcription factor YY1 affects the expression of many genes involved in B-cell development, probably by mediating interactions between their enhancers and promoters. Herein, we found that YY1 binds to the E3' enhancer and suppresses Igκ expression in B lymphoma cells by epigenetically modifying the enhancer. Knocking down YY1 enhanced Igκ expression, which was associated with increased levels of E2A (encoded by the TCF3 gene) and its binding to the E3' enhancer. Moreover, in germinal centre B cells and plasma cells, YY1 expression was reversely associated with Igκ levels, implying that YY1 might facilitate antibody affinity maturation in germinal centre B cells through the transient attenuation of Igκ expression.
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Affiliation(s)
- Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Weiwei Xian
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Jie Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yiqing Zhu
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Xiaoyi Shao
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yu Han
- Department of Occupational Medicine and Environmental Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yue Qi
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Xiaoling Ding
- Department of Gastroenterology, The Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
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Novel roles and therapeutic targets of Epstein-Barr virus-encoded latent membrane protein 1-induced oncogenesis in nasopharyngeal carcinoma. Expert Rev Mol Med 2015; 17:e15. [PMID: 26282825 DOI: 10.1017/erm.2015.13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epstein-Barr virus (EBV) was first discovered 50 years ago as an oncogenic gamma-1 herpesvirus and infects more than 90% of the worldwide adult population. Nasopharyngeal carcinoma (NPC) poses a serious health problem in southern China and is one of the most common cancers among the Chinese. There is now strong evidence supporting a role for EBV in the pathogenesis of NPC. Latent membrane protein 1 (LMP1), a primary oncoprotein encoded by EBV, alters several functional and oncogenic properties, including transformation, cell death and survival in epithelial cells in NPC. LMP1 may increase protein modification, such as phosphorylation, and initiate aberrant signalling via derailed activation of host adaptor molecules and transcription factors. Here, we summarise the novel features of different domains of LMP1 and several new LMP1-mediated signalling pathways in NPC. When then focus on the potential roles of LMP1 in cancer stem cells, metabolism reprogramming, epigenetic modifications and therapy strategies in NPC.
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Zi C, Wu Z, Wang J, Huo Y, Zhu G, Wu S, Bao W. Transcriptional activity of the FUT1 gene promoter region in pigs. Int J Mol Sci 2013; 14:24126-24134. [PMID: 24336113 PMCID: PMC3876100 DOI: 10.3390/ijms141224126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022] Open
Abstract
This study aims to provide a theoretical basis on the regulatory mechanism of the α-l,2-fucosyltransferase (FUT1) gene in pigs by analyzing the transcriptional activity of its promoter region. On the basis of the previously obtained promoter sequence, primers upstream and downstream of the gene were designed using the restriction endonucleases KpnI and HindIII respectively, and the recombinant plasmids of the pGL3-promoter were constructed by inserting promoter sequences with partially missing regions. The resultant mutants were observed by transient transfection assay into HEK293 cells, and the transcriptional activity of the promoter region was determined by luciferase activity. The 5'-flanking region of the FUT1 gene (-1150 to +50 bp) exhibited promoter activity. The -1150-bp to -849-bp region showed negative regulation of the gene. The recombinant plasmid pGL3-898 showed the strongest luciferase activity, and the activity showed a decreasing trend when the deleted region was increased. Recombinant plasmids were successfully constructed, verified, and the positive and negative regulation areas and core promoter region were detected, providing a deeper insight into the transcriptional regulatory mechanism of the FUT1 gene.
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Affiliation(s)
- Chen Zi
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
| | - Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
| | - Yongjiu Huo
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mail:
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China; E-Mails: (C.Z.); (Z.W.); (J.W.); (Y.H.)
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Liu H, Duan Z, Zheng H, Hu D, Li M, Tao Y, Bode AM, Dong Z, Cao Y. EBV-encoded LMP1 upregulates Igκ 3'enhancer activity and Igκ expression in nasopharyngeal cancer cells by activating the Ets-1 through ERKs signaling. PLoS One 2012; 7:e32624. [PMID: 22396784 PMCID: PMC3291551 DOI: 10.1371/journal.pone.0032624] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 02/01/2012] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence indicates that epithelial cancer cells, including nasopharyngeal carcinoma (NPC) cells, express immunoglobulins (Igs). We previously found that the expression of the kappa light chain protein in NPC cells can be upregulated by the EBV-encoded latent membrane protein 1 (LMP1). In the present study, we used NPC cell lines as models and found that LMP1-augmented kappa production corresponds with elevations in ERKs phosphorylation. PD98059 attenuates LMP1-induced ERKs phosphorylation resulting in decreased expression of the kappa light chain. ERK-specific small interfering RNA blunts LMP1-induced kappa light chain gene expression. Luciferase reporter assays demonstrate that immunoglobulin κ 3′ enhancer (3′Eκ) is active in Igκ-expressing NPC cells and LMP1 upregulates the activity of 3′Eκ in NPC cells. Moreover, mutation analysis of the PU binding site in 3′Eκ and inhibition of the MEK/ERKs pathway by PD98059 indicate that the PU site is functional and LMP1-enhanced 3′Eκ activity is partly regulated by this site. PD98059 treatment also leads to a concentration-dependent inhibition of LMP1-induced Ets-1 expression and phosphorylation, which corresponds with a dose-dependent attenuation of LMP1-induced ERK phosphorylation and kappa light chain expression. Suppression of endogenous Ets-1 by small interfering RNA is accompanied by a decrease of Ig kappa light chain expression. Gel shift assays using nuclear extracts of NPC cells indicate that the transcription factor Ets-1 is recruited by LMP1 to the PU motif within 3′Eκin vitro. ChIP assays further demonstrate Ets-1 binding to the PU motif of 3′Eκ in cells. These results suggest that LMP1 upregulates 3′Eκ activity and kappa gene expression by activating the Ets-1 transcription factor through the ERKs signaling pathway. Our studies provide evidence for a novel regulatory mechanism of kappa expression, by which virus-encoded proteins activate the kappa 3′ enhancer through activating transcription factors in non-B epithelial cancer cells.
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Affiliation(s)
- Haidan Liu
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
- State Key Laboratory of Medical Genetics, Clinical Center for Gene Diagnosis and Therapy, Central South University, The Second Xiangya Hospital, Changsha, China
- Department of Cardiothoracic Surgery, Central South University, The Second Xiangya Hospital, Changsha, China
| | - Zhi Duan
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Hui Zheng
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Duosha Hu
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Ming Li
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yongguang Tao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
- * E-mail: (ZGD); (YC)
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
- * E-mail: (ZGD); (YC)
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Das S, Nikolaidis N, Nei M. Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. Mol Immunol 2009; 46:3171-7. [PMID: 19560204 PMCID: PMC2736800 DOI: 10.1016/j.molimm.2009.05.180] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 05/30/2009] [Indexed: 11/20/2022]
Abstract
We have studied the genomic structure and evolutionary pattern of immunoglobulin kappa deleting element (KDE) and three kappa enhancers (KE5', KE3'P, and KE3'D) in eleven mammalian genomic sequences. Our results show that the relative positions and the genomic organization of the KDE and the kappa enhancers are conserved in all mammals studied and have not been affected by the local rearrangements in the immunoglobulin kappa (IGK) light chain locus over a long evolutionary time ( approximately 120 million years of mammalian evolution). Our observations suggest that the sequence motifs in these regulatory elements have been conserved by purifying selection to achieve proper regulation of the expression of the IGK light chain genes. The conservation of the three enhancers in all mammals indicates that these species may use similar mechanisms to regulate IGK gene expression. However, some activities of the IGK enhancers might have evolved in the eutherian lineage. The presence of the three IGK enhancers, KDE, and other recombining elements (REs) in all mammals (including platypus) suggest that these genomic elements were in place before the mammalian radiation.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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Abstract
The human immunoglobulins (Ig) are the products of three unlinked sets of genes: the immunoglobulin heavy (IGH), the immunoglobulin kappa (IGK), and the immunoglobulin lambda (IGL) genes, localized on chromosome 14 (14q32.33), 2 (2p12), and 22 (22q11.2), respectively. This appendix presents tabulated lists of the human immunoglobulin heavy, kappa, and lambda genes named in accordance with the International ImMunoGeneTics database (IMGT) and approved by the Human Genome Organization (HUGO) Nomenclature Committee in 1999. Three additional tables list corresponding nomenclatures for these genes.
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Affiliation(s)
- M P Lefranc
- Université Montpellier II, CNRS, Montpellier, France
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Tang WC, Yip SP, Lo KK, Ng PW, Choi PS, Lee SY, Yap MK. Linkage and association of myocilin (MYOC) polymorphisms with high myopia in a Chinese population. Mol Vis 2007; 13:534-44. [PMID: 17438518 PMCID: PMC2652017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
PURPOSE To test the association between myocilin gene (MYOC) polymorphisms and high myopia in Hong Kong Chinese by using family-based association study. METHODS A total of 162 Chinese nuclear families, consisting of 557 members, were recruited from an optometry clinic. Each family had two parents and at least one offspring with high myopia (defined as -6.00D or less for both eyes). All offspring were healthy with no clinical evidence of syndromic disease and other ocular abnormality. Genotyping was performed for two MYOC microsatellites (NGA17 and NGA19) and five tag single nucleotide polymorphisms (SNPs) spreading across the gene. The genotype data were analyzed with Family-Based Association Test (FBAT) software to check linkage and association between the genetic markers and myopia, and with GenAssoc to generate case and pseudocontrol subjects for investigating main effects of genetic markers and calculating the genotype relative risks (GRR). RESULTS FBAT analysis showed linkage and association with high myopia for two microsatellites and two SNPs under one to three genetic models after correction for multiple comparisons by false discovery rate. NGA17 at the promoter was significant under an additive model (p=0.0084), while NGA19 at the 3' flanking region showed significant results under both additive (p=0.0172) and dominant (p=0.0053) models. SNP rs2421853 (C>T) exhibited both linkage and association under additive (p=0.0009) and dominant/recessive (p=0.0041) models. SNP rs235858 (T>C) was also significant under additive (p=4.0E-6) and dominant/recessive (p=2.5E-5) models. Both SNPs were downstream of NGA19 at the 3' flanking region. Positive results for these SNPs were novel findings. A stepwise conditional logistic regression analysis of the case-pseudocontrol dataset generated by GenAssoc from the families showed that both SNPs could separately account for the association of NGA17 or NGA19, and that both SNPs contributed separate main effects to high myopia. For rs2421853 and with C/C as the reference genotype, the GRR increased from 1.678 for G/A to 2.738 for A/A (p=9.0E-4, global Wald test). For rs235858 and with G/G as the reference, the GRR increased 2.083 for G/A to 3.931 for A/A (p=2.0E-2, global Wald test). GRR estimates thus suggested an additive model for both SNPs, which was consistent with the finding that, of the three models tested, the additive model gave the lowest p values in FBAT analysis. CONCLUSIONS Linkage and association was shown between the MYOC polymorphisms and high myopia in our family-based association study. The SNP rs235858 at the 3' flanking region showed the highest degree of confidence for association.
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Affiliation(s)
- Wing Chun Tang
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ka Kin Lo
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Po Wah Ng
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Pik Shan Choi
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Sau Yin Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Maurice K.H. Yap
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
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Liu HD, Zheng H, Li M, Hu DS, Tang M, Cao Y. Upregulated expression of kappa light chain by Epstein-Barr virus encoded latent membrane protein 1 in nasopharyngeal carcinoma cells via NF-kappaB and AP-1 pathways. Cell Signal 2006; 19:419-27. [PMID: 16979873 DOI: 10.1016/j.cellsig.2006.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Accepted: 07/24/2006] [Indexed: 12/13/2022]
Abstract
B lymphocytes are generally considered to be the only source of immunoglobulins. However, increasing evidence revealed that some human epithelial cancer cell lines, including nasopharyngeal carcinoma (NPC) cell lines, expressed immunoglobulins. Moreover, we previously found that expression of kappa light chain in NPC cells could be upregulated by EBV-encoded latent membrane protein 1 (LMP1). Here, Western blot and flow cytometric analysis of intracellular kappa staining indicated that upregulation of the expression of kappa was inhibited by using LMP1-targeted DNAzyme and that Bay11-7082 and SP600125, inhibitors of JNK and NF-kappaB, respectively, inhibited LMP1-augmented kappa light chain expression in NPC cells. LMP1-positive NPC cells expressing the dominant-negative mutant of IkappaBalpha (DNMIkappaBalpha) or of c-Jun (TAM67) exhibited significantly decreasing kappa production compared with their parental cells. These results suggest that LMP1 elevated kappa light chain through activation of the NF-kappaB and AP-1 signaling pathways. The present study provided some hints of possible mechanisms by which human cancer cells of epithelial origin produced immunoglobulins.
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Affiliation(s)
- Hai-dan Liu
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Xiangya Road #110, Changsha, Hunan 410078, PR China
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Einerson RR, Law ME, Blair HE, Kurtin PJ, McClure RF, Ketterling RP, Flynn HC, Dogan A, Remstein ED. Novel FISH probes designed to detect IGK-MYC and IGL-MYC rearrangements in B-cell lineage malignancy identify a new breakpoint cluster region designated BVR2. Leukemia 2006; 20:1790-9. [PMID: 16888615 DOI: 10.1038/sj.leu.2404340] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Detection of translocations involving MYC at 8q24.1 in B-cell lineage malignancies (BCL) is important for diagnostic and prognostic purposes. However, routine detection of MYC translocations is often hampered by the wide variation in breakpoint location within the MYC region, particularly when a gene other than IGH, such as IGK or IGL, is involved. To address this issue, we developed and validated four fluorescence in situ hybridization (FISH) probes: two break apart probes to detect IGK and IGL translocations, and two dual-color, dual-fusion FISH (D-FISH) probes to detect IGK-MYC and IGL-MYC. MYC rearrangements (four IGK-MYC, 12 IGL-MYC and four unknown partner gene-MYC) were correctly identified in 20 of 20 archival BCL specimens known to have MYC rearrangements not involving IGH. Seven specimens, all of which lacked MYC rearrangements using a commercial IGH/MYC D-FISH probe, were found to have 8q24 breakpoints within a cluster region >350-645 kb 3' from MYC, provisionally designated as Burkitt variant rearrangement region 2 (BVR2). FISH is a useful ancillary tool in identifying MYC rearrangements. In light of the discovery of the distally located BVR2 breakpoint cluster region, it is important to use MYC FISH probes that cover a breakpoint region at least 1.0 Mb 3' of MYC.
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Affiliation(s)
- R R Einerson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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McDevit DC, Perkins L, Atchison ML, Nikolajczyk BS. The Ig kappa 3' enhancer is activated by gradients of chromatin accessibility and protein association. THE JOURNAL OF IMMUNOLOGY 2005; 174:2834-42. [PMID: 15728493 DOI: 10.4049/jimmunol.174.5.2834] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Igkappa locus is recombined following initiation of a signaling cascade during the early pre-B stage of B cell development. The Ig kappa3' enhancer plays an important role in normal B cell development by regulating kappa locus activation. Quantitative analyses of kappa3' enhancer chromatin structure by restriction endonuclease accessibility and protein association by chromatin immunoprecipitation in a developmental series of primary murine B cells and murine B cell lines demonstrate that the enhancer is activated progressively through multiple steps as cells mature. Moderate kappa3' chromatin accessibility and low levels of protein association in pro-B cells are increased substantially as the cells progress from pro- to pre-B, then eventually mature B cell stages. Chromatin immunoprecipitation assays suggest transcriptional regulators of the kappa3' enhancer, specifically PU.1 and IFN regulatory factor-4, exploit enhanced accessibility by increasing association as cells mature. Characterization of histone acetylation patterns at the kappa3' enhancer and experimental inhibition of histone deacetylation suggest changes therein may determine changes in enzyme and transcription factor accessibility. This analysis demonstrates kappa activation is a multistep process initiated in early B cell precursors before Igmu recombination and finalized only after the pre-B cell stage.
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Affiliation(s)
- Daniel C McDevit
- Department of Medicine, Immunobiology Unit, Evans Memorial Department of Clinical Research, Boston Medical Center, Boston, MA 02118, USA
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Wilda M, Busch K, Klose I, Keller T, Woessmann W, Kreuder J, Harbott J, Borkhardt A. Level of MYC overexpression in pediatric Burkitt's lymphoma is strongly dependent on genomic breakpoint location within the MYC locus. Genes Chromosomes Cancer 2004; 41:178-82. [PMID: 15287031 DOI: 10.1002/gcc.20063] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Increased transcriptional activity of the MYC gene is a characteristic feature of Burkitt's lymphoma. Aberrant MYC expression is caused by (1) chromosomal translocation to one of the loci carrying an immunoglobulin gene, (2) mutation within the translocated allele, (3) loss of the block to transcription elongation, or (4) promoter shift. To investigate the influence of breakpoint locations within the MYC gene on MYC transcript levels, we determined both the precise genomic MYC/IGH breakpoints and the amount of MYC mRNA in 25 samples of pediatric Burkitt's lymphoma with translocation t(8;14)(q24;q32). Patients with breakpoints that were 5' from MYC exon 1 had significantly lower expression of MYC than did patients who had a breakpoint within exon 1 or intron 1 (P < 0.05 and 0.005, respectively). The highest mRNA level of MYC (1,006 copies per 100 copies ABL1) was detected in patients with loss of the first exon and transcription initiation from a cryptic P3 promoter within the first intron of the MYC gene. In contrast, there was no obvious correlation between breakpoint locations within the IgH locus and the amount of MYC mRNA.
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Affiliation(s)
- Monika Wilda
- Department of Pediatric Hematology and Oncology, Children's University Hospital, Giessen, Germany
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Abstract
c-MYC is the prototype for oncogene activation by chromosomal translocation. In contrast to the tightly regulated expression of c-myc in normal cells, c-myc is frequently deregulated in human cancers. Herein, aspects of c-myc gene activation and the function of the c-Myc protein are reviewed. The c-myc gene produces an oncogenic transcription factor that affects diverse cellular processes involved in cell growth, cell proliferation, apoptosis and cellular metabolism. Complete removal of c-myc results in slowed cell growth and proliferation, suggesting that while c-myc is not required for cell proliferation, it acts as an integrator and accelerator of cellular metabolism and proliferation.
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Affiliation(s)
- L M Boxer
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California CA 94305, USA
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Abstract
Ets is a family of transcription factors present in species ranging from sponges to human. All family members contain an approximately 85 amino acid DNA binding domain, designated the Ets domain. Ets proteins bind to specific purine-rich DNA sequences with a core motif of GGAA/T, and transcriptionally regulate a number of viral and cellular genes. Thus, Ets proteins are an important family of transcription factors that control the expression of genes that are critical for several biological processes, including cellular proliferation, differentiation, development, transformation, and apoptosis. Here, we tabulate genes that are regulated by Ets factors and describe past, present and future strategies for the identification and validation of Ets target genes. Through definition of authentic target genes, we will begin to understand the mechanisms by which Ets factors control normal and abnormal cellular processes.
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Affiliation(s)
- V I Sementchenko
- Center for Molecular and Structural Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, SC 29403, USA
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15
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Rogers RJ, Chesrown SE, Kuo S, Monnier JM, Nick HS. Cytokine-inducible enhancer with promoter activity in both the rat and human manganese-superoxide dismutase genes. Biochem J 2000; 347 Pt 1:233-42. [PMID: 10727424 PMCID: PMC1220953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Diverse pro-inflammatory mediators regulate transcription of the gene (MnSOD) encoding the mitochondrial anti-oxidant protein manganese-superoxide dismutase. Understanding the regulation of this gene is crucial to comprehending its role in cytoprotection. In transfected lung epithelial cells, a human-growth-hormone reporter gene system was utilized to identify a potential enhancer in the MnSOD genomic fragment previously shown to contain multiple DNase-I-hypersensitive sites. Northern analysis demonstrated a 10-20-fold increase in response to pro-inflammatory mediators. Inclusion of the MnSOD genomic fragment in reporter constructs was necessary to mimic these stimulus-dependent endogenous levels. The inducible enhancer element was localized to a 260 bp fragment in intron 2, coinciding with a previously defined DNase-I-hypersensitive site. This element functions in an orientation- and position-independent manner as well as with the heterologous thymidine kinase promoter. In addition, we have demonstrated that a homologous sequence within the human MnSOD gene exhibits identical enhancer activity. A novel characteristic of the rat and human enhancer elements involves the ability to promote cytokine-inducible transcription in the absence of a classical promoter.
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Affiliation(s)
- R J Rogers
- Department of Biochemistry, University of Florida College of Medicine, Gainesville, FL, USA
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16
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Liu X, Prabhu A, Van Ness B. Developmental regulation of the kappa locus involves both positive and negative sequence elements in the 3' enhancer that affect synergy with the intron enhancer. J Biol Chem 1999; 274:3285-93. [PMID: 9920868 DOI: 10.1074/jbc.274.6.3285] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the mouse immunoglobulin kappa locus is regulated by the intron and 3' enhancers. Previously, we have reported that these enhancers can synergize at mature B cell stages. Here we present our recent studies on the identification and characterization of the 3' enhancer sequences that play important roles in this synergy. By performing mutational analyses with novel reporter constructs, we find that the 5' region of the cAMP response element (CRE), the PU. 1/PIP, and the E2A motifs of the 3' enhancer are critical for the synergy. These motifs are known to contribute to the enhancer activity. However, we also show that mutating other functionally important sequences has no significant effect on the synergy. Those sequences include the 3' region of the CRE motif, the BSAP motif, and the region 3' of the E2A motif. We have further demonstrated that either the 5'-CRE, the PU.1/PIP, or the E2A motif alone is sufficient to synergize with the intron enhancer. Moreover, the PU.1 motif appears to act as a negative element at pre-B cell stages but as a positive element at mature B cell stages. We have also identified a novel negative regulatory sequence within the 3' enhancer that contributes to the regulation of synergy, as well as developmental stage and tissue specificity of expression. While the levels of many of the 3' enhancer binding factors change very little in cell lines representing different B cell stages, the intron enhancer binding factors significantly increase at more mature B cell stages.
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Affiliation(s)
- X Liu
- Department of Biochemistry, Institute of Human Genetics and the Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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17
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Affiliation(s)
- B J Graves
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City 84132, USA
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18
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Affiliation(s)
- J R Gorman
- Howard Hughes Medical Institute, Children's Hospital, Boston, Massachusetts 02115, USA
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19
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Xu W, Murphy LJ. Isolation and characterization of the mouse beta 2/neuroD gene promoter. Biochem Biophys Res Commun 1998; 247:814-8. [PMID: 9647776 DOI: 10.1006/bbrc.1998.8897] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Beta2/neuroD is a basic helix-loop-helix protein involved in differentiation of the endocrine pancreas and the central nervous system. A 2-kb fragment containing the 5' upstream region of the mouse beta2/neuroD gene was cloned and sequenced. The cloned fragment was tested for promoter activity in six cell lines. Strong promoter activity was apparent in the three pancreatic beta cell lines, beta-HC3, beta-HC9, and NIT-1, whereas weak activity was seen in NIH 3T3, Rat-1, and MCF-7 cell lines. Analysis of promoter activity of deletion mutants in beta-HC3 cells indicated that while basal promoter activity was observed with a fragment which extended -109 bp upstream of the transcription start site, maximal activity required the fragment -2091 to -297 bp.
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Affiliation(s)
- W Xu
- Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
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20
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Wiese M, Pajeva IK. Molecular modeling study of the multidrug resistance modifiers cis- and trans-flupentixol. DIE PHARMAZIE 1997; 52:679-85. [PMID: 9347570 DOI: 10.1002/eji.1830270706] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recent drug-membrane interaction and quantitative structure-activity relationship studies of thioxanthenes and related compounds acting as multidrug resistance (MDR) modifiers pointed to the importance of the stereoisomery for their MDR reversing activity. Therefore a molecular modeling study of trans-(T) and cis-flupentixol (C) was performed in order to elucidate the observed discrepancy between equal binding potency to P-glycoprotein and different MDR reversing activity of the two stereoisomers. The results show that the 2 to 3-fold difference in MDR reversing activity of T compared to C might be related to a different orientation of the molecules in the membrane lipid environment. From the conformations generated by the SYBYL systematic search procedure those comprising local energy minima were selected and further optimized with semiempirical quantum chemistry methods. From the optimized conformations those that corresponded to 1H NMR results on drug conformations in lipid environment were selected for further molecular modeling studies. The electrostatic and lipophilic fields of T and C were compared in order to identify molecular properties related to the activity difference. The results show that the electrostatic fields of the drugs when similar in shape are dissimilar and that the lipophilic and hydrophilic regions are clearer separated in T in comparison with C. This imposes a better fitting of T compared to C to membrane lipid environment in accordance with the observed higher interaction strength of T with phospholipids.
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Affiliation(s)
- M Wiese
- Institut für Pharmazeutische Chemie, Martin-Luther-Universität Halle-Wittenberg, Germany
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21
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Mocikat R, Kardinal C, Klobeck HG. Differential interactions between the immunoglobulin heavy chain mu intron and 3' enhancer. Eur J Immunol 1995; 25:3195-8. [PMID: 7489764 DOI: 10.1002/eji.1830251132] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The immunoglobulin heavy chain 3' enhancer may be a novel type of a transcriptional regulation element in as much as its function is position dependent. We show that there are interactions between the mu intron and 3' enhancer which are differentially regulated depending on the distance between the two elements. Thus, a transcriptional repression is exerted by the 3' enhancer when juxtaposed to the intron enhancer. Whereas no or only modest synergism between the immunoglobulin mu intron and 3' enhancer has been reported to date, we show here that the stimulatory effect is substantially increased by extending the distance between the two enhancers. In our stable expression system, the mu intron enhancer insulated the test gene from neighboring chromatin.
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Affiliation(s)
- R Mocikat
- GSF-Institut für Immunologie, München, Germany
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22
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Abstract
We have introduced human germline-configuration heavy and kappa light chain minilocus transgenes into mice that have been engineered so that their endogenous heavy and kappa light chain loci are inactive. The two human transgenes are inserted by pronuclear microinjection, while the two endogenous mouse genes are disrupted by homologous recombination in embryonic stem cells. The resulting animals contain four unlinked genetic modifications and must rely on the introduced transgenes for the development of the B-cell lineage and for the generation of an antibody repertoire. The heavy chain transgene includes both the human mu and the human gamma 1 constant region gene segments, as well as upstream switch region sequences. Although mouse B cells and human B cells exhibit species-specific differences in the induction of gamma isotype expression, the transgenic mouse B cells appear to undergo regulated switching to human gamma 1 both in vivo and in vitro. This observation defines a subset of the heavy chain constant region that is sufficient for class switching, and implies that the human gamma 1 switch region includes a core of sequence that is functionally homologous to those cis-acting regulatory elements that direct mouse gamma switching.
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Affiliation(s)
- F A Harding
- GenPharm International, Mountain View, California 94043, USA
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23
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Pongubala JM, Atchison ML. Activating transcription factor 1 and cyclic AMP response element modulator can modulate the activity of the immunoglobulin kappa 3' enhancer. J Biol Chem 1995; 270:10304-13. [PMID: 7730336 DOI: 10.1074/jbc.270.17.10304] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Previously we determined that the immunoglobulin kappa 3' enhancer (kappa E3') contains at least two functional DNA sequences (PU.1/NF-EM5 and E2A) within its 132-base pair active core. We have determined that the activities of these two sequences are insufficient to account for the entire activity of the 132-base pair core. Using site-directed linker scan mutagenesis across the core fragment we identified several additional functional sequences. We used one of these functional sequences to screen a lambda gt11 cDNA expression library resulting in the isolation of cDNA clones encoding the transcription factors ATF-1 (activating transcription factor) and CREM (cyclic AMP response element modulator). Because ATF-1 and CREM are known to bind to cAMP response elements (CRE), this functional sequence was named the kappa E3'-CRE. We show that dibutyryl cAMP can increase kappa E3' enhancer activity, and in transient expression assays ATF-1 caused a 4-5-fold increase in the activity of the core enhancer while CREM-alpha expression resulted in repression of enhancer activity. RNA analyses showed increased levels of ATF-1 mRNA during B cell development and some changes in CREM transcript processing. By joining various fragments of the kappa E3' enhancer to the kappa E3'-CRE, we observed that the kappa E3'-CRE can synergistically increase transcription in association with the PU.1/NF-EM5 binding sites, suggesting a functional interaction between the proteins that bind to these DNA sequences. Consistent with this possibility, we found that ATF-1 and CREM can physically interact with PU.1. The isolation of activator and repressor proteins that bind to the kappa E3'-CRE may relate to previous conflicting results concerning the role of the cAMP signal transduction pathway in kappa gene transcription.
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Affiliation(s)
- J M Pongubala
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia 19104, USA
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24
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Hörtnagel K, Polack A, Mautner J, Feederle R, Bornkamm GW. Regulatory elements in the immunoglobulin kappa locus induce c-myc activation in Burkitt's lymphoma cells. Curr Top Microbiol Immunol 1995; 194:415-22. [PMID: 7895517 DOI: 10.1007/978-3-642-79275-5_48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
MESH Headings
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/pathology
- Chromosomes, Human, Pair 14/ultrastructure
- Chromosomes, Human, Pair 2/ultrastructure
- Chromosomes, Human, Pair 8/ultrastructure
- Enhancer Elements, Genetic
- Gene Expression Regulation, Neoplastic
- Genes, Immunoglobulin
- Genes, myc
- Genetic Vectors
- Humans
- Immunoglobulin kappa-Chains/genetics
- Plasmids
- Promoter Regions, Genetic
- Regulatory Sequences, Nucleic Acid
- Transfection
- Translocation, Genetic
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Affiliation(s)
- K Hörtnagel
- Institut für Klinische Molekularbiologie und Tumorgenetik, GSF, München
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25
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Kenter AL, Wuerffel R. S gamma 3 SNIP and SNAP binding motifs are occupied in vivo in mitogen-activated I.29 mu + cells. Curr Top Microbiol Immunol 1995; 194:431-8. [PMID: 7895519 DOI: 10.1007/978-3-642-79275-5_50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
MESH Headings
- Animals
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- Base Sequence
- Binding Sites
- DNA, Circular/genetics
- DNA, Neoplasm/metabolism
- DNA-Binding Proteins/metabolism
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Genes, Immunoglobulin
- Genes, Switch
- Immunoglobulin Heavy Chains/genetics
- Lymphocyte Activation
- Lymphoma, B-Cell/pathology
- Mice
- Mitogens/pharmacology
- Molecular Sequence Data
- NF-kappa B/metabolism
- Protein Binding
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
- Tumor Cells, Cultured
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Affiliation(s)
- A L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine at Chicago 60680
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26
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Abstract
We have used homologous recombination in ES cells to engineer B cell-deficient mice that are incapable of expressing endogenous immunoglobulin heavy and kappa light chain genes. We find that B cell development in these mutant mice can be rescued by the introduction of human germline-configuration heavy- and kappa light-chain minilocus transgenes. The transgenes rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation in response to antigen stimulation; thus recapitulating both stages of the humoral immune response using human, rather than mouse, sequences. The mice can be immunized; and human sequence, antigen specific, monoclonal antibodies can be obtained using conventional rodent hybridoma technology. These animals are also of interest for studying the normal processes of immunoglobulin gene expression. We discuss the example of heavy chain class switching, which has not been previously observed within an autonomous transgene.
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Affiliation(s)
- N Lonberg
- GenPharm International Inc., Mountain View, CA 94043, USA
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27
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Lonberg N, Taylor LD, Harding FA, Trounstine M, Higgins KM, Schramm SR, Kuo CC, Mashayekh R, Wymore K, McCabe JG. Antigen-specific human antibodies from mice comprising four distinct genetic modifications. Nature 1994; 368:856-9. [PMID: 8159246 DOI: 10.1038/368856a0] [Citation(s) in RCA: 250] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Human sequence monoclonal antibodies, which in theory combine high specificity with low immunogenicity, represent a class of potential therapeutic agents. But nearly 20 years after Köhler and Milstein first developed methods for obtaining mouse antibodies, no comparable technology exists for reliably obtaining high-affinity human antibodies directed against selected targets. Thus, rodent antibodies, and in vitro modified derivatives of rodent antibodies, are still being used and tested in the clinic. The rodent system has certain clear advantages; mice are easy to immunize, are not tolerant to most human antigens, and their B cells form stable hybridoma cell lines. To exploit these advantages, we have developed transgenic mice that express human IgM, IgG and Ig kappa in the absence of mouse IgM or Ig kappa. We report here that these mice contain human sequence transgenes that undergo V(D)J joining, heavy-chain class switching, and somatic mutation to generate a repertoire of human sequence immunoglobulins. They are also homozygous for targeted mutations that disrupt V(D)J rearrangement at the endogenous heavy- and kappa light-chain loci. We have immunized the mice with human proteins and isolated hybridomas secreting human IgG kappa antigen-specific antibodies.
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Affiliation(s)
- N Lonberg
- GenPharm International, Mountain View, California 94043
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