IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties

IMGT, the international ImMunoGeneTics information system(R) (http://imgt.cines.fr) is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates. IMGT comprises IMGT/LIGM-DB, the comprehensive database of IG and TR sequences from human and other vertebrates (76 846 sequences in September 2003). In order to define the IMGT criteria necessary for standardized statistical analyses, the sequences of the IG variable regions (V-REGIONs) from productively rearranged human IG heavy (IGH) and IG light kappa (IGK) and lambda (IGL) chains were extracted from IMGT/LIGM-DB. The framework amino acid positions of 2474 V-REGIONs (1360 IGHV, 585 IGKV, 529 IGLV) were numbered according to the IMGT unique numbering. Two statistical methods (correspondence analysis and hierarchic classification) were used to analyze the 237 framework positions (80 for IGHV, 79 for IGKV, 78 for IGLV), for three properties (hydropathy, volume and chemical characteristics) of the 20 common amino acids. Results of the analyses are shown as standardized two-dimensional representations, designated as IMGT Colliers de Perles statistical profiles. They provide a characterization of the amino acid properties at each framework position of the expressed IG V-REGIONs, and a visualization of the resemblances and differences between heavy and light, and between kappa and lambda sequences. The standardized criteria defined in this paper, amino acid positions and property classes, will be useful to study the mutations and allele polymorphisms, to establish correlations between amino acids in the IG and TR protein three-dimensional structures and to extract new knowledge from V-like domains of chains, other than IG and TR, belonging to the immunoglobulin superfamily.     

IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex

The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The initial release of the database contained a limited number of tools. As a result of feedback from our users and developments in HLA we have been able to provide new tools and facilities. The HLA sequences have also been extended to include intron sequences and the 3' and 5' untranslated regions in the alignments and also the inclusion of new genes such as MICA. The IMGT/MHC database (http://www.ebi.ac.uk/imgt/mhc) was released in March 2002 to provide a similar resource for other species. The first release of IMGT/MHC contains the sequences of non-human primates (apes, new and old world monkeys), canines and feline sequences. Further species will be added shortly and the database aims to become the primary source of MHC data for non-human sequences.     

Mechanisms for T cell receptor triggering

There is considerable controversy about the mechanism of T cell receptor (TCR) triggering, the process by which the TCR tranduces signals across the plasma membrane after binding to its ligand (an agonist peptide complexed with an MHC molecule). Three main types of mechanism have been proposed, which involve aggregation, conformational change and segregation. Here, we review recently published evidence for each type of mechanism and conclude that all three may be involved. This complexity may reflect the uniquely demanding nature of TCR-mediated antigen recognition, which requires the detection of a very weak 'signal' (very rare foreign peptide-MHC ligands) in the presence of considerable 'noise' (abundant self peptide-MHC molecules).     

A statistical framework for modeling HLA-dependent T cell response data

The identification of T cell epitopes and their HLA (human leukocyte antigen) restrictions is important for applications such as the design of cellular vaccines for HIV. Traditional methods for such identification are costly and time-consuming. Recently, a more expeditious laboratory technique using ELISpot assays has been developed that allows for rapid screening of specific responses. However, this assay does not directly provide information concerning the HLA restriction of a response, a critical piece of information for vaccine design. Thus, we introduce, apply, and validate a statistical model for identifying HLA-restricted epitopes from ELISpot data. By looking at patterns across a broad range of donors, in conjunction with our statistical model, we can determine (probabilistically) which of the HLA alleles are likely to be responsible for the observed reactivities. Additionally, we can provide a good estimate of the number of false positives generated by our analysis (i.e., the false discovery rate). This model allows us to learn about new HLA-restricted epitopes from ELISpot data in an efficient, cost-effective, and high-throughput manner. We applied our approach to data from donors infected with HIV and identified many potential new HLA restrictions. Among 134 such predictions, six were confirmed in the lab and the remainder could not be ruled as invalid. These results shed light on the extent of HLA class I promiscuity, which has significant implications for the understanding of HLA class I antigen presentation and vaccine development.     

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations

Background  

Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract.     

Specificity on a knife-edge: the alphabeta T cell receptor

The interaction between the alphabeta T cell receptor (TCR) and the peptide bound to the major histocompatibility complex class I molecule (pMHC-I) constitutes a central interaction in adaptive immunity. How these receptors interact with such low affinity while maintaining exquisite specificity for peptide antigen and host MHC (MHC-I restriction) remains a challenge to be explained by structural immunologists. Moreover, how this extracellular interaction is transmitted as an intracellular signal via the CD3 complex remains unresolved. Nevertheless, several structures of TCRs, non-liganded and ligated to a defined pMHC-I, combined with detailed biophysical analyses, have provided insight of the structural basis of MHC-I restriction. In addition, structures of isolated CD3 components have enabled T cell signalling mechanisms to be postulated. Recent findings in this area, which include seven distinct TCR/pMHC-I complexes, have fundamental implications in adaptive immunity as well as therapeutic applications to modulate the adaptive immune response.     

T cell receptor genes and T cell development in virus-transformed early T cell lines

We have derived T cell lines from mice inoculated with Gross leukemia virus, which appear to represent early T cell developmental stages and to reflect normal T cell development. These cell lines may provide a breakthrough in the study of T cell development as Abelson transformants have done for the study of B cell development. Analysis of the TCR gene expression in these cell lines reveals that the sequence of rearrangement and expression of each TCR gene is not strictly ordered. Expression of RNA for the TCR alpha and -beta genes appears to be coordinated with rearrangement at the alpha and beta loci. This is not the case for gamma gene expression. Availability of the homogeneous populations of cells represented in these cells lines allows for a more detailed molecular analysis of T cell development than was previously possible.     

The mouse T cell receptor: comparison of MHC-restricted receptors on two T cell hybridomas

The receptors for antigen plus a major histocompatibility complex (MHC) gene product on a T cell hybridoma specific for ovalbumin plus a Class II MHC product were compared with those on another T cell hybridoma, specific for a Class I MHC product. In each case receptor material was identified by a clone-specific monoclonal antibody. The two receptors proved to have very similar gross structures, being 70-85 kd proteins, and reducing to an acidic alpha-chain and a slightly basic beta-chain, each 40-43 kd. The charge of both the acidic and basic polypeptides varied between the two receptors studied, showing that variable amino acid sequences occur in both chains.     

T cell receptor specific apoptosis: an endogenous mechanism for T cell homeostasis and potential strategy for antigen modulation of disease

T lymphocytes can undergo an activation/proliferation response or an apoptotic response following T cell receptor engagement. The choice between these outcomes is dictated by the activation state of the T lymphocyte, the presence of interleukin-2 and the strength of the T cell receptor stimulus. Specifically, when quiescent cells encounter effectively presented antigen they are activated and begin to proliferate. In contrast, activated cells, moving through the cell cycle under the influence of IL-2, undergo apoptosis upon reencountering antigen. Both the tumour necrosis factor receptor and CD95 (FAS) are known to participate in mediating this cell death. Genetic defects in the molecules of the lymphocyte death pathway (CD95, FAS ligand, IL-2 receptor) lead to syndromes of autoimmunity and dysregulated lymphocyte homeostasis. An understanding of the principles of the autocrine feedback death model can provide the rationale basis for effective antigen specific modulation of T cell mediated disease processes.     

Chimeric immunoglobulin-T cell receptor proteins form functional receptors: implications for T cell receptor complex formation and activation

We constructed chimeric receptor chains in which an immunoglobulin heavy chain variable region (VH) from a phosphorylcholine-specific antibody is substituted for T cell receptor (Tcr) alpha and beta V regions. We demonstrate that the VH region joined to either the C alpha or the C beta region can form stable chimeric proteins in EL4 T cells. Both chimeric receptor chains associate with CD3 polypeptides in functional receptor complexes and respond to phosphorylcholine coupled to Sepharose beads. The VH-C alpha chimeric chain associates with the EL4 beta chain, while the VH-C beta chimeric protein appears to form either a homodimer or a heterodimer with the native EL4 beta chain. Thus, functional receptor complexes can be formed using two C beta regions, and the C alpha region may not be required for CD3 association and surface expression of Tcr complexes.     

The human T cell receptor genes are targets for chromosomal abnormalities in T cell tumors

T cells express either of the two forms of antigen-specific receptors, the alpha/beta and gamma/delta heterodimers. Their structure closely resembles that of immunoglobulins, and the variable part of the receptor molecule is created by somatic assembly of variable, diversity, and joining regions. The genetic structure of T cell receptor (TCR) genes and their rearrangement in T cell development have been elucidated in great detail in recent years. The human genes for the gamma and beta subunits are located on the short and long arms of chromosome 7, respectively, whereas the delta- and alpha-chain genes are located in tandem on the centromeric half of the long arm of chromosome 14. Expression of either alpha/beta or gamma/delta TCR complexes on T cells in the developing thymus is likely to proceed in an ordered fashion and results in the appearance of distinct T cell subpopulations. The process of DNA rearrangements required for the generation of functional variable region genes also predisposes lymphoid cells to aberrant DNA rearrangements, which can be detected as chromosomal abnormalities such as translocations and inversions. Molecular analysis of such aberrant rearrangements has shown that rearranging loci are fused to loci unrelated to antigen receptor genes. Furthermore, the breakpoint structures represent nonproductive intermediates in the hierarchy of physiological rearrangements. Accordingly, T cell tumors arising early in T cell development often carry chromosomal abnormalities involving the delta-chain locus, whereas tumors generated later in T cell development tend to show aberrations in the alpha-chain gene. This pattern seems to reflect the stage-specific accessibility of TCR loci for rearrangement by the recombinase machinery. This enzyme is guided by specific recombination signals that can sometimes also be found at the site of breakage on the participating locus in chromosomal abnormalities. Although some features of the mechanism of aberrant rearrangements are known, their biological consequences are less well understood. However, molecular analysis of the mechanism of chromosomal aberrations in T cell tumors suggests that their biological consequences may vary. Firm evidence for the pathogenic significance is missing for most of these lesions. This provides a challenge to molecular immunology to determine how chromosomal abnormalities are involved in tumor pathogenesis.     

T Cell Receptor Signaling Pathways： New Targets for Herpes Simplex Virus

Herpes simplex viruses (HSV-1 and HSV-2) cause global morbidity and synergistically correlate with HIV infection.HSV exists life-long in a latent form in sensory neurons with intermittent reactivation,in despite of host immune surveillance.While abundant evidence for HSV interfering with innate immune responses so as to favor the replication and propagation of the virus,several lines of evidence declare that HSV attenuates adaptive immunity by various mechanisms,including but not limited to the ablation of antigen presentation,induction of apoptosis,and interruption of cellular signaling.In this review,we will focus on the perturbative role of HSV in Tcells signaling.