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Results for “Positive selection”

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PubMed2001

Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates.

The nature of selection on capsid genes of foot-and-mouth disease virus (FMDV) was characterized by examining the ratio of nonsynonymous to synonymous substitutions in 11 data sets of sequences obtained from six different serotypes of FMDV. Using a method of analysis that assigns each codon position to one of a number of estimated values of nonsynonymous to synonymous ratio, significant evidence of positive selection was identified in 5 data sets, operating at 1-7% of codon positions. Evidence of positive selection was identified in complete capsid sequences of serotypes A and C and in VP1 sequences of serotypes SAT 1 and 2. Sequences of serotype SAT-2 recovered from a persistently infected African buffalo also revealed evidence for positive selection. Locations of codons under positive selection coincide closely with those of antigenic sites previously identified with the use of monoclonal antibody escape mutants. The vast majority of codons are under mild to strong purifying selection. However, these results suggest that arising antigenic variants benefit from a selective advantage in their interaction with the immune system, either during the course of an infection or in transmission to individuals with previous exposure to antigen. Analysis of amino acid usage at sites under positive selection indicates that this selective advantage can be conferred by amino acid substitutions that share physicochemically similar properties.

Amino Acid Sequence↗

PubMed1997

Deficient positive selection of CD4 T cells in mice displaying altered repertoires of MHC class II-bound self-peptides.

The role of self-peptides in positive selection of CD4+ T cells has been controversial. We show that some self-peptides are presented by the MHC class II molecule I-A(b) in mice lacking Ii or H-2M but not in mice expressing a transgene-encoded peptide fused to I-A(b). In experiments using specific antibodies to block selection, these low-abundance self-peptides were implicated in the positive selection of some CD4+ T cells in H-2M-/- mice. However, all three mutant backgrounds failed to positively select two class II-restricted transgenic T cell receptors. Our findings suggest that minor components of the self-peptide repertoire can contribute to positive selection of a significant number of CD4+ T cells. In addition, the data suggest that T cell receptor repertoires selected in wild-type mice and in mice displaying limited spectra of self-peptides are distinct.

Animals↗

PubMed1995

Requirement for extrathymic class I histocompatibility antigens for positive selection of thymus-derived T lymphocytes.

We have examined whether the thymus can produce immature T cell precursors for subsequent positive selection in the periphery. Using the intestine as a model system, we demonstrate that extrathymic MHC class I molecules positively select thymus-derived TCR-alpha beta CD8+ intestinal intraepithelial lymphocytes. Grafting of MHC class I+ thymus onto MHC class I- hosts resulted in the generation of donor and host-derived CD4-CD8+ T cells in lymph node, but few TCR-alpha beta CD4-CD8+ intraepithelial lymphocytes. The results indicate that the intestine can act as a site of positive selection for thymus-derived T cells. Bone marrow reconstitution studies demonstrated that non-hematopoietic, radiation-resistant cells, perhaps intestinal epithelial cells, were responsible for extrathymic positive selection of thymus-derived T cells. These findings demonstrate that the thymus can support organ-specific immunity via provision of targeted precursor populations.

Animals↗

PubMed2004

The regulated expression of a diverse set of genes during thymocyte positive selection in vivo.

A signal initiated by the newly formed Ag receptor is integrated with microenvironmental cues during T cell development to ensure positive selection of CD4+CD8+ progenitors into functionally mature CD4+ or CD8+ T lymphocytes. During this transition, a survival program is initiated, TCR gene recombination ceases, cells migrate into a new thymic microenvironment, the responsiveness of the Ag receptor is tuned, and the cells commit to a specific T lineage. To determine potential regulators of these processes, we used mRNA microarray analysis to compare gene expression changes in CD4+CD8+ thymocytes from TCR transgenic mice that have received a TCR selection signal with those that had not received a signal. We found 129 genes with expression that changed significantly during positive selection, the majority of which were not previously appreciated. A large number of these changes were confirmed by real-time PCR or flow cytometry. We have combined our findings with gene changes reported in the literature to provide a comprehensive report of the genes regulated during positive selection, and we attempted to assign these genes to positive selection process categories.

Animals↗

PubMed1999

Positive selection of thymocytes: the long and winding road.

Positive selection is a crucial stage in T-cell development because it is here that CD4+CD8+ cells bearing T-cell receptors that interact with self-major histocompatibility complex molecules are rescued from cell death, resulting in the generation of mature T cells. Here, Graham Anderson and colleagues review recent studies indicating that positive selection is a multistage process involving interactions with thymic epithelium.

Animals↗

PubMed1995

The influence of invariant chain on the positive selection of single T cell receptor specificities.

The appearance of peptide-loaded major histocompatibility complex (MHC) class II molecules at the cell surface depends critically on the invariant chain (Ii). We have studied the influence of Ii on the positive selection of CD4+ T cells, mediated by class II molecules expressed on thymic stromal cells. Invariant chain-deficient mice (Iio) were crossed with different T cell receptor (TcR) transgenic strains and the emergence of mature CD4 single-positive thymocytes measured in Iio/TcR transgenic offspring. Positive selection was nearly absent in Iio/2B4 mice, which display receptors specific for a moth cytochrome c (MCC) peptide in the context of Ek. In addition, no T cell response was elicited when nontransgenic Iio animals were injected with this peptide, even though antigen-presenting cells (APC) from such mice were perfectly capable of presenting it, suggesting that selection of the entire anti-MCC 88-103 repertoire depends on Ii. Positive selection also appeared strongly reduced in another line of Iio/TcR transgenic mice (Iio/BDC2.5). However, in sharp contrast, a third line (Iio/3A9) exhibited almost normal positive selection of thymocytes displaying the transgene-encoded receptor. These thymocytes were exported to the periphery: peripheral T cells could respond normally to the appropriate peptide in vitro. The most likely interpretation of these findings is that selection of most CD4+ T cells depends on MHC class II complexes loaded with peptide in an Ii-dependent pathway, but some can be selected on class II complexes that are either loaded along an alternative, Ii-independent, route or are empty. This is consistent with the involvement of peptide in positive selection of CD4+ T cells, for which there exists little prior evidence.

Animals↗

PubMed2005

Statistical properties of the methods for detecting positively selected amino acid sites.

Parsimony and Bayesian methods have been developed for detecting positively selected amino acid sites. It has been reported that the parsimony method is generally conservative. In contrast, the Bayesian method is known to identify more positively selected sites than the parsimony method, especially when the number of sequences analyzed is small, although the interpretation of results obtained from the former method is controversial. Here I show that the likelihood-ratio test (LRT) of the Bayesian method corresponds to the parsimony method with window analysis, by analyzing the nucleotide sequences encoding the trans-activator (tax) gene of human T-cell lymphotropic virus type I (HTLV-I). It is also indicated that in the parsimony method, the test of selective neutrality using the binomial probability tends to be conservative, but the Monte Carlo simulation is useful for solving this problem. In addition, in the Bayesian method, the bootstrap method appears to produce similar results to the LRT. This information may be useful for improving the methods for detecting positively selected amino acid sites.

Amino Acid Sequence↗

PubMed2006

Modulating the proteinase inhibitory profile of a plant cystatin by single mutations at positively selected amino acid sites.

Cysteine proteinase inhibitors of the cystatin superfamily have several important functions in plants, including the inhibition of exogenous cysteine proteinases during herbivory or infection. Here we used a maximum-likelihood approach to assess whether plant cystatins, like other proteins implicated in host-pest interactions, have been subject to positive selection during the course of their evolution. Several amino acid sites were identified as being positively selected in cystatins from either Poaceae (monocots) and Solanaceae (dicots). These hypervariable sites were located at strategic positions on the protein: on each side of the conserved glycine residues in the N-terminal trunk, within the first and second inhibitory loops entering the active site of target enzymes, and surrounding the larfav motif, a sequence of unknown function conserved among plant cystatins. Supporting the assumption that positively selected, hypervariable sites are indicative of amino acid sites implicated in functional diversity, mutants of the 8th cystatin unit of tomato multicystatin including alternative residues at positively selected sites in the N-terminal trunk exhibited highly variable affinities for the cysteine proteases papain, cathepsin B and cathepsin H. Overall, these observations support the hypothesis that plant cystatins have been under selective pressure to evolve in response to predatory challenges by herbivorous enemies. They also indicate the potential of site-directed mutagenesis at positively selected sites for the generation of cystatins with improved binding properties.

Amino Acids↗

PubMed1994

Positive selection of CD4+ T cells by TCR ligation without aggregation even in the absence of MHC.

The developmental fate of immature thymocytes is determined by the specificity of their T-cell antigen receptors (TCRs). Immature CD4+8+ thymocytes are positively selected to differentiate into mature T cells by recognition of peptides associated with major histocompatibility complex (MHC) encoded molecules on thymic epithelial cells. But neither the identity of molecules transducing positive selection signals nor the nature of the signals themselves is fully known. Here we report that direct ligation of TCR molecules by monoclonal antibodies specific for either clonotypic or CD3 chains can signal immature thymocytes to differentiate into mature CD4+8- T cells, even in the absence of MHC expression and MHC-dependent CD4 co-receptor signalling. Moreover, we show that TCR engagement induces positive selection signals only in the absence of TCR aggregation and that TCR aggregation is inhibitory for positive selection. Thus, low valency of TCR crosslinking is a critical parameter, distinguishing positive selection from other TCR-mediated signalling events.

Animals↗

PubMed2001

Specialisation of thymic epithelial cells for positive selection of CD4+8+ thymocytes.

Following their migration into the thymus, hemopoeitic stem cell precursors enter a complex developmental pathway involving proliferation, differentiation and alphabetaT-cell receptor (alphabetaTCR)-mediated selection procedures, in order to generate mature T-cell populations ready for export to the periphery. Thus, a critical stage during intrathymic T-cell development involves the generation of functionally mature CD4+8- and CD4-8+ cells from immature CD4+8- precursor thymocytes, a poorly understood process referred to as positive selection. While interactions between the alphabetaTCR and MHC-peptide complexes are known to be essential for the initiation of positive selection, additional unknown signals are also required. Using an in vitro reaggregate thymic organ culture system which allows comparison of the abilities of various cell types to induce maturation of CD4+8+ precursors, we provide evidence that both MHC-peptide complexes and specialised accessory molecules must be provided by thymic epithelium for efficient mediation of positive selection. Moreover, analysis of positive selection in the presence of thymic and non-thymic stromal cells expressing MHC class II molecules with the same limited peptide array suggests that this unique ability of thymic epithelium to mediate positive selection of CD4+8- cells is not solely due to presentation of a specialised peptide repertoire, but is dependent upon provision of specialised accessory interactions.

Animals↗

PubMed1993

Fibroblasts can induce thymocyte positive selection in vivo.

During development in the thymus, thymocytes bearing alpha beta T-cell receptors are selected to mature if the receptors they bear are able to interact in some way with major histocompatibility complex (MHC) proteins expressed on thymic stromal cells. It has been shown that thymus cortical epithelial cells are usually the cells presenting the MHC molecules involved in this process of so-called positive selection. Here we tested the ability of fibroblasts to mediate positive selection in vivo. Fibroblasts transfected with the genes for the MHC I-Ab proteins were injected intrathymically into irradiated H-2k animals reconstituted with H-2bxk F1 fetal liver cells. Eight weeks later, the recipient mice were immunized and shown to contain peptide-specific I-Ab-restricted T cells. This demonstrates the ability of I-Ab-transfected fibroblasts to participate in positive selection. Thus a cell type that is not specialized to process and present antigens in the context of MHC class II molecules can mediate positive selection when transfected with an appropriate MHC molecule. The data also support the idea that the ability to mediate positive selection may not be limited to thymic cortical epithelium.

Animals↗

PubMed2005

CD19 regulates positive selection and maturation in B lymphopoiesis: lack of CD19 imposes developmental arrest of immature B cells and consequential stimulation of receptor editing.

Ligand-independent signals that are produced by the B-cell antigen receptor (BCR) confer an important positive selection checkpoint for immature B cells. Generation of inappropriate signals imposes developmental arrest of immature B cells, though the fate of these cells has not been investigated. Studies have shown that the lack of CD19 results in inappropriate signaling. In immunoglobulin transgenic mice, this inappropriate signaling impairs positive selection and stimulates receptor editing. Here, we studied the extent and significance of receptor editing in CD19-regulated positive selection of normal, nontransgenic B lymphopoiesis, using our bone marrow culture system. We found that the lack of CD19 resulted in elevated tonic signaling and impaired maturation, as revealed by surface marker expression and by functional assays. Immature CD19-/- B cells did not suppress RAG and underwent intensive receptor editing attempts in culture. Finally, in vivo analysis of light-chain isotype expression and Jkappa use in CD19-/- mice validated our in vitro observations. Our results suggest that CD19 has an important function in regulating positive selection and maturation of nontransgenic B-cell precursors and that receptor editing is an important salvage mechanism for immature B cells that fail positive selection.

Animals↗

PubMed2000

Positive selection is limited by available peptide-dependent MHC conformations.

Recent data suggest that the diversity of self peptides presented in the thymus during development contributes to positive selection of a diverse T cell repertoire. We sought to determine whether a previously defined "hole in the immunological repertoire" could be explained by the absence of an appropriate selecting self peptide. The repertoire defect in question is the inability of bm8 mice to make an H-2K-restricted response to OVA. Like other OVA-specific, H-2K-restricted receptors, OT-I-transgenic T cells are not positively selected in bm8 mice. Using criteria we had previously established for identifying positive selection ligands, we found peptides that could restore positive selection of OT-I thymocytes in bm8 mice. Thus, the T cell repertoire can be limited by a requirement for specific self peptides during development. Data with MHC-specific Abs suggested that peptides might be able to force MHC residues to adopt different conformations in Kb vs Kbm8. This shows that peptides can potentially contribute to ligand diversity both directly (via variability in the solvent-exposed side chains) and indirectly (through their effect on the MHC conformation). Our data support a model where self peptide diversity allows selection of T cells specific for a broad range of MHC conformations.

Animals↗

PubMed1990

Role of self-peptides in positively selecting the T-cell repertoire.

The fate of an immature thymocyte is determined by the specificity of its alpha beta T-cell receptor. Only cells expressing receptors that interact with sufficient affinity with major histocompatibility complex (MHC) molecules expressed on thymus epithelial cells are positively selected and go on to mature and seed the peripheral lymphoid organs. The H-2Kb class-I MHC molecule positively selects for the maturation of cytotoxic T lymphocytes that will respond in the periphery to H-2Kb cells presenting a foreign peptide. We have now analysed the ability of variant H-2Kb molecules to positively select T-cells that respond to H-2Kb with ovalbumin. Our results indicate that self-peptides, presented in the groove of the class-I molecule on thymus epithelial cells, are critically involved in positive selection of the T-cell repertoire. Furthermore, the ability of four different H-2Kb variants to select this response in the thymus correlates with their ability to present the ovalbumin peptide, indicating that a self-peptide mimic of the foreign peptide could be involved in positive selection.

Animals↗

PubMed1998

The role of peptides in thymic positive selection of class II major histocompatibility complex-restricted T cells.

A thymic epithelial cell line transfected with I-Ek was used in reaggregate cultures to study the role of peptides in positive selection of T cell receptor transgenic thymocytes. In this system, positive selection of CD4 SP cells occurred only after the addition of exogenous peptide. Analysis of antigen analogs indicated an inverse relationship between the antigenicity for peripheral T cells and the concentration of peptide required for positive selection. These data are most consistent with an avidity (rather than an affinity) model of positive selection, in which ligand density and the affinity of T cell receptor act in concert to determine the fate of developing thymocytes.

Amino Acid Sequence↗

PubMed2001

Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b.

To predict the amino acid sites important for the clearance of hepatitis C virus (HCV) subtype 1b in vivo, positively selected amino acid sites were detected by analyzing the sequence data collected from the international DNA databank. The rate of nonsynonymous substitutions per nonsynonymous site was compared with that of synonymous substitutions per synonymous site for each codon site in the entire coding region. As a result, 13 out of 3010 amino acid sites were found to be positively selected. Among the 13 positively selected amino acid sites, eight were located in the structural proteins and five were in the nonstructural proteins. Moreover, eight were located in B-cell epitopes and two were in T-cell epitopes. These observations suggest that both the antibody and the cytotoxic T lymphocyte are involved in the clearance of HCV subtype 1b in vivo. These positively selected amino acid sites represent candidate vaccination targets for HCV subtype 1b.

Amino Acids↗

PubMed2005

Bayes empirical bayes inference of amino acid sites under positive selection.

Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to model the variation in omega among sites, allowing a subset of sites to have omega > 1 while the rest of the sequence may be under purifying selection with omega < 1. An empirical Bayes (EB) approach is then used to calculate posterior probabilities that a site comes from the site class with omega > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and omega ratios for the site classes. In small data sets lacking information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated data sets. The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites.

Alleles↗

PubMed1996

A novel mouse thymocyte antigen (F3Ag): down-regulation during the CD4+CD8+ double-positive stage indicates positive selection.

We describe a novel mAb (F3) which reacts with a 65 kDa thymocyte surface protein, expressed on approximately 80% of thymocytes, referred to as F3Ag. In ontogeny, F3Ag expression begins in the CD4(-)CD8(-) double-negative (DN) CD25(+) population and is maintained through approximately 85% of the CD4(+)CD8(+) double-positive (DP) stage. DP cells with high TCR expression and CD4(+) single-positive (SP) cells are predominantly negative for F3Ag, whereas many CD8(+) SP thymocytes express F3Ag. F3Ag-DP thymocytes show a reduced expression of RAG-1 and RAG-2 compared with F3Ag+ DP cells. The shutdown of F3Ag expression during the DP stage is related to positive selection: mice deficient for MHC class I and class II molecules maintain F3Ag expression in almost all DP cells. Transgenic (tg) mice carrying TCR restricted for MHC class II show a more pronounced down-regulation of F3Ag in the DP compartment than normal mice, depending on the presence of a positively selecting MHC. The size of the F3Ag- DP subset is positively correlated with the efficacy of positive selection into the CD4(+) SP compartment. Because some CD8(+) SP cells express F3Ag, the relationship between F3Ag down-regulation and positive selection is less obvious in DP cells of mice carrying MHC class I-restricted tg TCR. However, in reaggregate thymic organ cultures, sorted F3Ag- DP cells differentiate into CD8(+) SP cells more rapidly than do F3Ag+ DP cells. Thus, after down-regulation in the DP stage, a proportion of CD8(+) SP cells appears to re-express F3Ag. In addition, the proportion of F3Ag-CD8(+) SP cells depends on the efficacy of positive selection into the CD8 lineage. Taken together, the regulation of the expression of the F3Ag appears to be associated with signals that control thymic repertoire selection.

Animals↗