Genomes and Genes
t cell receptor genes
Summary: DNA sequences, in cells of the T-lymphocyte lineage, that code for T-cell receptors. The TcR genes are formed by somatic rearrangement (see GENE REARRANGEMENT, T-LYMPHOCYTE and its children) of germline gene segments, and resemble Ig genes in their mechanisms of diversity generation and expression.
- Giudicelli V, Chaume D, Lefranc M. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2005;33:D256-61 pubmed..IMGT/GENE-DB is freely available at http://imgt.cines.fr. ..
- Lane J, Duroux P, Lefranc M. From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinformatics. 2010;11:223 pubmed publisher..In a next step, and following enrichment of its reference databases, IMGT/LIGMotif will be used to annotate IG and TR of more distantly related vertebrate species. IMGT/LIGMotif is available at http://www.imgt.org/ligmotif/. ..
- Rothenberg E. Immunology. Thymic regulation--hidden in plain sight. Science. 2005;307:858-9 pubmed
- Mühlemann O, Mock Casagrande C, Wang J, Li S, Custodio N, Carmo Fonseca M, et al. Precursor RNAs harboring nonsense codons accumulate near the site of transcription. Mol Cell. 2001;8:33-43 pubmed..Our data indicate that mRNA reading frame can influence events at or near the site of gene transcription. ..
- Parra Z, Baker M, Hathaway J, Lopez A, Trujillo J, Sharp A, et al. Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics. 2008;9:111 pubmed publisher..The availability of the first marsupial genome sequence allows investigation of these evolutionary relationships...
- Hara H, Takeda A, Takeuchi M, Wakeham A, Itie A, Sasaki M, et al. The apoptotic protease-activating factor 1-mediated pathway of apoptosis is dispensable for negative selection of thymocytes. J Immunol. 2002;168:2288-95 pubmed..We assume that mechanisms for the negative selection are composed of several cell death pathways to avoid failure of elimination of autoreactive clones. ..
- Gerstel Thompson J, Wilkey J, Baptiste J, Navas J, Pai S, Pass K, et al. High-throughput multiplexed T-cell-receptor excision circle quantitative PCR assay with internal controls for detection of severe combined immunodeficiency in population-based newborn screening. Clin Chem. 2010;56:1466-74 pubmed publisher..Population-based SCID newborn screening programs should consider multiplexing for quality assurance purposes. Potential benefits of using Multiplex Plus include the ability to perform multianalyte profiling. ..
- Hickman S, Chan J, Salgame P. Mycobacterium tuberculosis induces differential cytokine production from dendritic cells and macrophages with divergent effects on naive T cell polarization. J Immunol. 2002;168:4636-42 pubmed..We speculate that the observed difference in response of the two APC types to M. tuberculosis infection may be a reflection of their respective roles in immune initiation and granuloma regulation. ..
- Lanza A, Robustelli della Cuna F, Zibera C, Pedrazzoli P, Robustelli della Cuna G. Somatic mutations at the T-cell antigen receptor in antineoplastic drug-exposed populations: comparison with sister chromatid exchange frequency. Int Arch Occup Environ Health. 1999;72:315-22 pubmed
- Sandberg Y, Heule F, Lam K, Lugtenburg P, Wolvers Tettero I, van Dongen J, et al. Molecular immunoglobulin/T- cell receptor clonality analysis in cutaneous lymphoproliferations. Experience with the BIOMED-2 standardized polymerase chain reaction protocol. Haematologica. 2003;88:659-70 pubmed
- Kato F, Kakihara H, Kunugita N, Ootsuyama A, Norimura T. Role of p53 gene in apoptotic repair of genotoxic tissue damage in mice. J Radiat Res. 2002;43 Suppl:S209-12 pubmed..Hence, complete repair of mutagenic damage in irradiated tissues requires the integration of DNA repair and p53-dependent apoptotic tissue repair. ..
- Snyder J, Alexander Miller M, Berzofskyl J, Belyakov I. Molecular mechanisms and biological significance of CTL avidity. Curr HIV Res. 2003;1:287-94 pubmed
- Pine S, Moy F, Wiemels J, Gill R, Levendoglu Tugal O, Ozkaynak M, et al. Real-time quantitative PCR: standardized detection of minimal residual disease in pediatric acute lymphoblastic leukemia. Polymerase chain reaction. J Pediatr Hematol Oncol. 2003;25:103-8 pubmed..This standardized, real-time PCR technique should simplify monitoring MRD in clinical trials. ..
- Bettini M, Xi H, Milbrandt J, Kersh G. Thymocyte development in early growth response gene 1-deficient mice. J Immunol. 2002;169:1713-20 pubmed..Thus, Egr1 translates developmental signals into appropriate changes in gene expression at multiple stages of thymocyte development. ..
- Hughes M, Yu Y, Dudley M, Zheng Z, Robbins P, Li Y, et al. Transfer of a TCR gene derived from a patient with a marked antitumor response conveys highly active T-cell effector functions. Hum Gene Ther. 2005;16:457-72 pubmed..TCR-transduced T-cells are thus attractive candidates for evaluation in cell transfer therapies of patients with cancer. ..
- DeFina R, Liang Y, He H, Haley K, Christopher K, Finn P, et al. Analysis of immunoglobulin and T-cell receptor gene deficiency in graft rejection by gene expression profiles. Transplantation. 2004;77:580-6 pubmed..In addition, several genes are identified that are candidates as necessary for rejection. This has crucial implications for developing clinical therapies that target specific mechanisms for prolonging graft survival. ..
- Moller D. T-cell receptor genes in sarcoidosis. Sarcoidosis Vasc Diffuse Lung Dis. 1998;15:158-64 pubmed..The identification of key, clonally-expanded T-cell populations in sarcoidosis provides a potential tool for determining the specific antigens involved in the pathogenesis of sarcoidosis. ..
- Kuklina E. Revision of the antigen receptor of T-lymphocytes. Biochemistry (Mosc). 2006;71:827-37 pubmed
- Garcia K, Adams J, Feng D, Ely L. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat Immunol. 2009;10:143-7 pubmed publisher..Given these findings, a reconsideration of the TCR-peptide-MHC structural database shows that not only have the answers been there all along but also they were predictable by the first principles of physical chemistry. ..
- Gellert M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem. 2002;71:101-32 pubmed..This transposition helps to explain the mechanism of RAG action and supports earlier proposals that V(D)J recombination evolved from an ancient mobile DNA element. ..
- Annessi G, Paradisi M, Angelo C, Perez M, Puddu P, Girolomoni G. Annular lichenoid dermatitis of youth. J Am Acad Dermatol. 2003;49:1029-36 pubmed..We suggest that this is a distinctive inflammatory condition, and we propose to term it "annular lichenoid dermatitis of youth." ..
- Workman C, Vignali D. The CD4-related molecule, LAG-3 (CD223), regulates the expansion of activated T cells. Eur J Immunol. 2003;33:970-9 pubmed..We further show that LAG-3 function is mediated via its cytoplasmic domain, for which a conserved 'KIEELE' motif is essential. Our data support a role for LAG-3 in regulating the expansion of activated T cells. ..
- Maile R, Wang B, Schooler W, Meyer A, Collins E, Frelinger J. Antigen-specific modulation of an immune response by in vivo administration of soluble MHC class I tetramers. J Immunol. 2001;167:3708-14 pubmed..Our data highlight the ability of soluble MHC tetramers to identify scarce alloreactive T cell populations and the use of such tetramers to directly modulate an Ag-specific T cell response in vivo. ..
- Vanasek T, Khoruts A, Zell T, Mueller D. Antagonistic roles for CTLA-4 and the mammalian target of rapamycin in the regulation of clonal anergy: enhanced cell cycle progression promotes recall antigen responsiveness. J Immunol. 2001;167:5636-44 pubmed..CTLA-4 molecules promote clonal anergy development only indirectly by limiting cell cycle progression during the primary response. ..
- Kreuwel H, Aung S, Silao C, Sherman L. Memory CD8(+) T cells undergo peripheral tolerance. Immunity. 2002;17:73-81 pubmed..These results have a direct impact on manipulating T cell responses to self-antigens in order to improve immunotherapy of cancer and autoimmune diseases. ..
- Duszczyszyn D, Beck J, Antel J, Bar Or A, Lapierre Y, Gadag V, et al. Altered naive CD4 and CD8 T cell homeostasis in patients with relapsing-remitting multiple sclerosis: thymic versus peripheral (non-thymic) mechanisms. Clin Exp Immunol. 2006;143:305-13 pubmed..002). We conclude in RRMS that naive T subsets have homeostatic abnormalities due probably to peripheral (non-thymic) mechanisms. These abnormalities could have relevance for MS pathogenesis, as naive T cell changes may precede MS onset. ..
- Nakamura Y, Komiyama T, Furue M, Gojobori T, Akiyama Y. CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. BMC Bioinformatics. 2010;11:398 pubmed publisher..The entries in Group I are particularly crucial for cancer immunotherapy, providing supportive information for genetic engineering of novel antibody medicines, tumor-specific TR, and peptide vaccines. ..
- Pennington D, Silva Santos B, Shires J, Theodoridis E, Pollitt C, Wise E, et al. The inter-relatedness and interdependence of mouse T cell receptor gammadelta+ and alphabeta+ cells. Nat Immunol. 2003;4:991-8 pubmed..Thus, normal gammadelta cell development is dependent on the development of conventional alphabeta T cells. ..
- Vanura K, Vrsalovic M, Le T, Marculescu R, Kusec R, Jager U, et al. V(D)J targeting mistakes occur at low frequency in acute lymphoblastic leukemia. Genes Chromosomes Cancer. 2009;48:725-36 pubmed publisher..Our data suggest that, while being a potentially dangerous mechanism due to the introduction of DNA breaks, V(D)J recombination is a tightly controlled mechanism allowing for only few direct mistakes. ..
- Osella Abate S, Zaccagna A, Savoia P, Quaglino P, Salomone B, Bernengo M. Expression of apoptosis markers on peripheral blood lymphocytes from patients with cutaneous T-cell lymphoma during extracorporeal photochemotherapy. J Am Acad Dermatol. 2001;44:40-7 pubmed
- Yang S, Cohen C, Peng P, Zhao Y, Cassard L, Yu Z, et al. Development of optimal bicistronic lentiviral vectors facilitates high-level TCR gene expression and robust tumor cell recognition. Gene Ther. 2008;15:1411-23 pubmed publisher..Such optimal vectors may have immediate applications in cancer gene therapy. ..
- Cedar H, Bergman Y. Choreography of Ig allelic exclusion. Curr Opin Immunol. 2008;20:308-17 pubmed publisher..Thus, allelic exclusion appears to represent a general epigenetic phenomenon that is modeled on the same basis as X chromosome inactivation. ..
- Abbey J, O Neill H. Expression of T-cell receptor genes during early T-cell development. Immunol Cell Biol. 2008;86:166-74 pubmed..Germline transcripts could also encode a protein that plays a functional role during lymphoid cell development. In the least, germline transcripts serve as markers of early lymphoid progenitors. ..
- Hongping D, Jianlin L, Meibian Z, Wei W, Lifen J, Shijie C, et al. Detecting the cytogenetic effects in workers occupationally exposed to vincristine with four genetic tests. Mutat Res. 2006;599:152-9 pubmed..11 x 10(-4), respectively, there was a significant difference between workers and controls (P<0.01). It is found in the results of our study that the genetic damage is detectable in 15 workers occupationally exposed to vincristine. ..
- Haskins K. Pathogenic T-cell clones in autoimmune diabetes: more lessons from the NOD mouse. Adv Immunol. 2005;87:123-62 pubmed..These reagents can track T cells in vivo and thus provide new approaches for disease diagnosis and therapy as well as a versatile set of tools for basic research on how T cells contribute to autoimmune disease. ..
- MacDonald H. Development and selection of NKT cells. Curr Opin Immunol. 2002;14:250-4 pubmed..1 expression, TCR repertoire and dependence on CD1d and various glycolipids for development. Two different lineage-commitment models have been proposed, with most evidence favoring a byproduct of conventional-T-cell development. ..
- Mostoslavsky R, Alt F. Receptor revision in T cells: an open question?. Trends Immunol. 2004;25:276-9 pubmed..Although the existence of such a process in T cells remains controversial, recent studies suggest that mature T cells are able to similarly revise their receptors in the periphery. ..
- Bai L, Liu J, Kau J. T-cell clonal disorder in acquired primary pure red cell aplasia. Ann Hematol. 2004;83:544-6 pubmed
- Diab A, Deng C, Smith J, Hussain R, Phanavanh B, Lovett Racke A, et al. Peroxisome proliferator-activated receptor-gamma agonist 15-deoxy-Delta(12,14)-prostaglandin J(2) ameliorates experimental autoimmune encephalomyelitis. J Immunol. 2002;168:2508-15 pubmed..These results suggest that PPAR-gamma ligands may be a novel therapeutic agent for diseases such as multiple sclerosis. ..
- Zhang H, Zhou R. [Limitations of immunoglobulin heavy chain and T-cell receptor gene rearrangement studies by polymerase chain reaction in non-Hodgkin lymphoma]. Zhonghua Bing Li Xue Za Zhi. 2005;34:806-8 pubmed
- Zamulaeva I, Smirnova S, Orlova N, Vereshchagina O, Chekin S, Smirnova I, et al. [Somatic mutagenesis at T-cell receptor locus in inhabitants of radiation polluted regions as a result of the Chernobyl disaster]. Radiats Biol Radioecol. 2006;46:307-14 pubmed..The TCR-mutant frequency was significantly higher in persons with benign tumors of different localizations and nodules in thyroid gland than in persons without this pathology. ..
- MacPherson A, Gatto D, Sainsbury E, Harriman G, Hengartner H, Zinkernagel R. A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science. 2000;288:2222-6 pubmed
- Wu H, Said J, Ames E, Chen C, McWhorter V, Chen P, et al. First reported cases of intravascular large cell lymphoma of the NK cell type: clinical, histologic, immunophenotypic, and molecular features. Am J Clin Pathol. 2005;123:603-11 pubmed..Autopsy revealed involvement of multiple organs, including brain, kidneys, ovaries, and bone marrow. These cases represent the first documented examples of an NK cell variant of intravascular lymphoma. ..
- Dalakas M. The molecular and cellular pathology of inflammatory muscle diseases. Curr Opin Pharmacol. 2001;1:300-6 pubmed
- Ellyard J, Quah B, Simson L, Parish C. Alternatively activated macrophage possess antitumor cytotoxicity that is induced by IL-4 and mediated by arginase-1. J Immunother. 2010;33:443-52 pubmed publisher..This highlights the fine balance between stimulating the antitumorigenic and protumorigenic properties of aaMacs in tumor immunotherapy protocols. ..
- Weinberg J, Kristal L, Chooback L, Honig P, Kramer E, Lessin S. The clonal nature of pityriasis lichenoides. Arch Dermatol. 2002;138:1063-7 pubmed..The host immune response to this clone determines the clinical and histologic findings in PLEVA. ..
- Barndt R, Dai M, Zhuang Y. Functions of E2A-HEB heterodimers in T-cell development revealed by a dominant negative mutation of HEB. Mol Cell Biol. 2000;20:6677-85 pubmed..These results indicate that E2A-HEB heterodimers play obligatory roles both before and after TCRbeta gene rearrangement during the alpha/beta lineage T-cell development. ..
- Xie J, Nomura N, Lu M, Chen S, Koch G, Weng Y, et al. Antibody-mediated blockade of the CXCR3 chemokine receptor results in diminished recruitment of T helper 1 cells into sites of inflammation. J Leukoc Biol. 2003;73:771-80 pubmed..Collectively, our results suggest that CXCR3 has a critical role in T cell transmigration to sites of inflammation and thus, may serve as a molecular target for anti-inflammatory therapies. ..
- Fan L, Busser B, Lifsted T, Oukka M, Lo D, Laufer T. Antigen presentation by keratinocytes directs autoimmune skin disease. Proc Natl Acad Sci U S A. 2003;100:3386-91 pubmed..Disease can be induced by skin inflammation but not solely by activation of T cells. Thus, cutaneous immunopathology can be directed through antigen presentation by tissue-resident keratinocytes to autoreactive TCR Tg CD4(+) cells. ..
- Seewaldt S, Alferink J, Forster I. Interleukin-10 is crucial for maintenance but not for developmental induction of peripheral T cell tolerance. Eur J Immunol. 2002;32:3607-16 pubmed..Taken together, these results demonstrate that IL-10 is required to maintain T cell tolerance following exposure to enhanced antigenic stimuli but is not essential for the induction of self-tolerance. ..
- Ege M, Ma Y, Manfras B, Kalwak K, Lu H, Lieber M, et al. Omenn syndrome due to ARTEMIS mutations. Blood. 2005;105:4179-86 pubmed
- Lunde E, Western K, Rasmussen I, Sandlie I, Bogen B. Efficient delivery of T cell epitopes to APC by use of MHC class II-specific Troybodies. J Immunol. 2002;168:2154-62 pubmed..The study shows that class II-specific Troybodies can deliver a variety of T cell epitopes to professional APC for efficient presentation, in vitro as well as in vivo. Thus, Troybodies may be useful as tools in vaccine development. ..
- Haider S, Hayakawa K, Itoyama T, Sadamori N, Kurosawa N, Isobe M. TCR variable gene involvement in chromosome inversion between 14q11 and 14q24 in adult T-cell leukemia. J Hum Genet. 2006;51:326-34 pubmed..Our expression analysis, however, showed that this pseudogene was actually expressed and was capable of encoding a protein similar to ADAM21; thus we have named this gene ADAM21-like (ADAM21-L). ..