Reliability of Computer Algorithm-Based Binding Predictions for the Identification of Leukemia Antigens.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4483-4483
Author(s):  
Marta Gomez-Nunez ◽  
Javier Pinilla-Ibarz ◽  
Tao Dao ◽  
Tatyana Korontsvit ◽  
Victoriya Zakhaleva ◽  
...  
Keyword(s):  
T Cell ◽  
Predictive Value ◽  
Peptide Binding ◽  
Class I ◽  
Cytotoxic T Cell ◽  
Antigenic Peptides ◽  
Computer Algorithms ◽  
Class I Mhc ◽  
Predictive Algorithms

Abstract Major Histocompatibility Complex class I (MHC-I) molecules present antigenic peptides to T cells on the cell surface as a prerequisite for stimulating cytotoxic T cell response. Thus, the ability to reliably identify the peptides that can bind to MHC molecules is of practical importance for rapid vaccine development. Several computer-based prediction methods have been applied to study the interaction of MHC class I/peptide binding. Here we have compared three of the most commonly used predictive algorithms BIMAS, SYFPEITHI and Rankpep with actual binding of HLA-A*0201 peptides in vitro. Forty six HLA-A*0201 peptides were selected from several target oncoproteins: Wilms’ tumor (WT1), native and imatinib- mutated bcr-abl p210 and JAK2 protein. Experimental peptide binding to HLA-A*0201 was assessed using a MHC stabilization assay on T2, TAP deficient cells. Peptides were considered to show positive in vitro binding if the mean fluorescence was at least 50 % of the binding of a high affinity reference peptide. Peptides qualified as positive in vitro if the BIMAS score was ≥ 100, the SYFPEITHI score ranked ≥ 24 or the Rankpep was ≥ 50. Results are summarized below: BIMAS SYFPEITHI RANKPEP Sensitivity 84 % 72 % 60 % Specificity 76 % 71 % 81 % Positive Predictive Value 84 % 72 % 60 % Negative Predictive Value 80 % 68 % 63 % Combining two or more computer methods did not appear to improve the predictive value. In conclusion, of the three predictive algorithms, the best correspondence with the actual MHC binding was demonstrated with the BIMAS algorithm. Predictive computer algorithms are important for preselection of potential T-cell epitope candidates for the application in vaccine design.

scholarly journals Induction of cytotoxic T lymphocytes by primary in vitro stimulation with peptides.

1988 ◽  
Vol 167 (6) ◽  
pp. 1767-1779 ◽  
Author(s):  
F R Carbone ◽  
M W Moore ◽  
J M Sheil ◽  
M J Bevan
Keyword(s):  
Influenza Virus ◽  
T Cell ◽  
Synthetic Peptide ◽  
T Cell Response ◽  
Class I ◽  
Cytotoxic T Cell ◽  
Target Cells ◽  
Spleen Cells ◽  
Class I Mhc

Antigen-specific cytotoxic T cells can be generated by primary in vitro stimulation of spleen cells from C57BL/6 mice with appropriate peptide fragments. This response can be elicited without prior in vivo immunization. Chicken OVA fragmented with either cyanogen bromide (CN OVA) or trypsin (T OVA) was used as a source of mixed peptides. A synthetic peptide, NP365-380, representing the sequence 365-380 from influenza virus A/PR/8 nucleoprotein, was also used, since this contains the main determinants recognized by CTL generated from H-2b mice infected with A/PR/8 virus. The primary in vitro cytotoxic T cell response was peptide specific, since targets were lysed only in the presence of appropriate peptide antigens. Native OVA could not elicit primary effectors in vitro nor could it sensitize targets for lysis by OVA digest-specific CTL. A synthetic peptide corresponding to residues 111-122 within the OVA sequence could sensitize targets for lysis by effectors induced against T OVA. Effectors generated by in vitro stimulation were CD8+, CD4-, and H-2Db-restricted for NP365-380 and T OVA recognition. CN OVA-specific effectors were also CD8+, CD4-, but surprisingly, were able to lyse a range of H-2-different targets in an antigen-specific manner. These effectors failed to lyse a tumor line that does not express class I MHC molecules. This broad MHC restriction pattern was also apparent at the clonal level. In all cases, the antipeptide CTL generated by primary in vitro stimulation were inefficient in lysing target cells expressing endogenous forms of antigens, such as influenza virus-infected cells or cells transfected with the OVA cDNA. However, cytotoxic T cell lines generated in vitro against the NP365-380 peptide did contain a minor population of virus-reactive cells that could be selectively expanded by stimulation with A/PR/8-infected spleen cells. These results are discussed in terms of class I-restricted T cell stimulation in the absence of antigen processing by high surface densities of peptide/MHC complexes.

scholarly journals H-2-restricted cytolytic T lymphocytes specific for HLA display T cell receptors of limited diversity.

1992 ◽  
Vol 176 (2) ◽  
pp. 439-447 ◽  
Author(s):  
J L Casanova ◽  
J C Cerottini ◽  
M Matthes ◽  
A Necker ◽  
H Gournier ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Receptors ◽  
Class I ◽  
Antigenic Peptides ◽  
Class I Mhc ◽  
Cell Receptors ◽  
Mhc Molecules ◽  
Tcr Repertoire

We previously showed that H-2Kd-restricted cytotoxic T lymphocyte (CTL) clones specific for a single nonapeptide derived from the Plasmodium berghei circumsporozoite (PbCS) protein displayed T cell receptors (TCRs) of highly diverse primary structure. We have now analyzed the TCR repertoire of CTLs that recognize a peptide derived from the human class I major histocompatibility complex (MHC) molecule HLA-Cw3 in association with the same murine class I MHC molecule H-2Kd. We first sequenced the TCR alpha and beta genes of the CTL clone Cw3/1.1 and, based on this genomic analysis, the TCR alpha and beta cDNA junctional regions of 23 independent H-2Kd-restricted CTL clones specific for HLA-Cw3. The results show that the TCR chains display very limited heterogeneity, both in terms of V alpha, J alpha, V beta, and J beta segments, and in terms of length and sequence of the CDR3 alpha and beta loops. The TCR repertoire used in vivo was then analyzed by harvesting CTL populations from the peritoneal cavity of immune mice. The peritoneal exudate lymphocytes (PELs) displayed HLA-Cw3-specific cytolytic activity in the absence of any stimulation in vitro. Remarkably, most of these freshly isolated PELs expressed TCRs that shared the same structural features as those from HLA-Cw3-reactive CTL clones. Thus, our results show that a peptide from HLA-Cw3 presented by H-2Kd selects CTLs that bear TCRs of very limited diversity in vivo. When taken together with the high diversity of the TCRs specific for the PbCS peptide, these findings suggest that natural tolerance to self peptides presented by class I MHC molecules may substantially reduce the size of the TCR repertoire of CTLs specific for antigenic peptides homologous to self.

scholarly journals T Cell Activity Correlates with Oligomeric Peptide-Major Histocompatibility Complex Binding on T Cell Surface

2001 ◽  
Vol 276 (50) ◽  
pp. 47320-47328 ◽  
Author(s):  
Jennifer Buslepp ◽  
Rui Zhao ◽  
Debora Donnini ◽  
Douglas Loftus ◽  
Mohamed Saad ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Surface ◽  
Cell Clone ◽  
Cell Activity ◽  
Class I ◽  
Antigenic Peptides ◽  
Major Histocompatibility ◽  
Class I Mhc ◽  
T Cell Clone

Recognition of virally infected cells by CD8+T cells requires differentiation between self and nonself peptide-class I major histocompatibility complexes (pMHC). Recognition of foreign pMHC by host T cells is a major factor in the rejection of transplanted organs from the same species (allotransplant) or different species (xenotransplant). AHIII12.2 is a murine T cell clone that recognizes the xenogeneic (human) class I MHC HLA-A2.1 molecule (A2) and the syngeneic murine class I MHC H-2 Dbmolecule (Db). Recognition of both A2 and Dbare peptide-dependent, and the sequences of the peptides recognized have been determined. Alterations in the antigenic peptides bound to A2 cause large changes in AHIII12.2 T cell responsiveness. Crystal structures of three representative peptides (agonist, null, and antagonist) bound to A2 partially explain the changes in AHIII12.2 responsiveness. Using class I pMHC octamers, a strong correlation is seen between T cell activity and the affinity of pMHC complexes for the T cell receptor. However, contrary to previous studies, we see similar half-lives for the pMHC multimers bound to the AHIII12.2 cell surface.

scholarly journals Antiviral cytotoxic T cell response induced by in vivo priming with a free synthetic peptide.

1990 ◽  
Vol 171 (5) ◽  
pp. 1815-1820 ◽  
Author(s):  
P Aichele ◽  
H Hengartner ◽  
R M Zinkernagel ◽  
M Schulz
Keyword(s):  
T Cell ◽  
Cell Response ◽  
Lymphocytic Choriomeningitis ◽  
Effector T Cells ◽  
T Cell Response ◽  
Class I ◽  
Cytotoxic T Cell ◽  
Effector T Cell

Induction in vivo of antiviral cytotoxic T cell response was achieved in a MHC class I-dependent fashion by immunizing mice three times with a free unmodified 15-mer peptide derived from the nucleoprotein of lymphocytic choriomeningitis virus in IFA. The effector T cells are CD8+, restricted to the class I Ld allele of the analyzed mouse strain, and are specific both at the level of secondary restimulation in vitro and at the effector T cell level. These results suggest that cocktails of viral peptides may be used as antiviral T cell vaccines.

scholarly journals CD8+ T-Cell Repertoire in Human Leukocyte Antigen Class I-Mismatched Alloreactive Immune Response

2021 ◽  
Vol 11 ◽  
Author(s):  
Florence Bettens ◽  
Zuleika Calderin Sollet ◽  
Stéphane Buhler ◽  
Jean Villard
Keyword(s):  
T Cell ◽  
Human Leukocyte ◽  
Class I ◽  
Cell Surface Expression ◽  
Cytotoxic T Cell ◽  
Cell Repertoire ◽  
Hematopoietic Stem ◽  
Inflammatory Status

In transplantation, direct allorecognition is a complex interplay between T-cell receptors (TCR) and HLA molecules and their bound peptides expressed on antigen-presenting cells. In analogy to HLA mismatched hematopoietic stem cell transplantation (HSCT), the TCR CDR3β repertoires of alloreactive cytotoxic CD8+ responder T cells, defined by the cell surface expression of CD137 and triggered in vitro by HLA mismatched stimulating cells, were analyzed in different HLA class I mismatched combinations. The same HLA mismatched stimulatory cells induced very different repertoires in distinct but HLA identical responders. Likewise, stimulator cells derived from HLA identical donors activated CD8+ cells expressing very different repertoires in the same mismatched responder. To mimic in vivo inflammation, expression of HLA class l antigens was upregulated in vitro on stimulating cells by the inflammatory cytokines TNFα and IFNβ. The repertoires differed whether the same responder cells were stimulated with cells treated or not with both cytokines. In conclusion, the selection and expansion of alloreactive cytotoxic T-cell clonotypes expressing a very diverse repertoire is observed repeatedly despite controlling for HLA disparities and is significantly influenced by the inflammatory status. This makes prediction of alloreactive T-cell repertoires a major challenge in HLA mismatched HSCT.

scholarly journals Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaohui Wei ◽  
Song Wang ◽  
Zhuolin Li ◽  
Zibin Li ◽  
Zehui Qu ◽  
...  
Keyword(s):  
De Novo ◽  
Peptide Binding ◽  
Class I ◽  
Class I Mhc ◽  
Mhc I ◽  
Anchor Residue ◽  
Binding Characteristics ◽  
Peptide Presentation ◽  
The Impact

The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD–MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.

scholarly journals CD8+ T cell recognition of an endogenously processed epitope is regulated primarily by residues within the epitope.

1992 ◽  
Vol 176 (5) ◽  
pp. 1335-1341 ◽  
Author(s):  
Y S Hahn ◽  
C S Hahn ◽  
V L Braciale ◽  
T J Braciale ◽  
C M Rice
Keyword(s):  
T Cell ◽  
Target Cell ◽  
Influenza A ◽  
Expression System ◽  
Cell Receptor ◽  
Class I ◽  
Antigenic Peptides ◽  
Peptide Fragments ◽  
Class I Mhc ◽  
Mhc Molecules

Cytotoxic T lymphocytes (CTL) recognize short antigenic peptides associated with cell surface class I major histocompatibility complex (MHC) molecules. This association presumably occurs between newly synthesized class I MHC molecules and peptide fragments in a pre-Golgi compartment. Little is known about the factors that regulate the formation of these antigenic peptide fragments within the cell. To examine the role of residues within a core epitope and in the flanking sequences for the generation and presentation of the newly synthesized peptide fragment recognized by CD8+ CTL, we have mutagenized the coding sequence for the CTL epitope spanning residues 202-221 in the influenza A/Japan/57 hemagglutinin (HA). In this study over 60 substitution mutations in the epitope were tested for their effects on target cell sensitization using a cytoplasmic viral expression system. The HA202-221 site contains two overlapping subsites defined by CTL clones 11-1 and 40-2. Mutations in HA residues 204-213 or residues 210-219 often abolished target cell lysis by CTL clones 11-1 and 40-2, respectively. Although residues outside the core epitope did not usually affect the ability to be lysed by CTL clones, substitution of a Gly residue for Val-214 abolished lysis by clone 11-1. These data suggest that residues within a site that affect MHC binding and T cell receptor recognition appear to play the predominant role in dictating the formation of the antigenic complex recognized by CD8+ CTL, and therefore the antigenicity of the protein antigen presented to CD8+ T cells. Most alterations in residues flanking the endogenously expressed epitope do not appreciably affect the generation and recognition of the site.

Immune evasion proteins of human cytomegalovirus do not prevent a diverse CD8+ cytotoxic T-cell response in natural infection

Blood ◽  
2004 ◽  
Vol 104 (4) ◽  
pp. 1075-1082 ◽  
Author(s):  
Thomas J. Manley ◽  
Lisa Luy ◽  
Thomas Jones ◽  
Michael Boeckh ◽  
Helen Mutimer ◽  
...  
Keyword(s):  
T Cell ◽  
Antigen Presentation ◽  
Natural Infection ◽  
T Cell Response ◽  
Class I ◽  
Cytotoxic T Cell ◽  
Class I Mhc ◽  
Mhc Molecules ◽  
Viral Antigens ◽  
Cell Immunity

AbstractAlthough cytomegalovirus (CMV) expresses proteins that interfere with antigen presentation by class I major histocompatibility complex (MHC) molecules, CD8+ cytotoxic T cells (CTLs) are indispensable for controlling infection and maintaining latency. Here, a cytokine flow cytometry assay that employs fibroblasts infected with a mutant strain of CMV (RV798), which is deleted of the 4 viral genes that are responsible for interfering with class I MHC presentation, was used to examine the frequency and specificity of the CD8+ CTLs to CMV in immunocompetent CMV-seropositive individuals. A large fraction of the CD8+ CTL response was found to be specific for viral antigens expressed during the immediate early and early phases of virus replication and presented by fibroblasts infected with RV798 but not wild-type CMV. These results demonstrate that the inhibition of class I antigen presentation observed in CMV-infected cells in vitro is not sufficient to prevent the induction of a broad repertoire of CD8+ CTLs after natural infection in vivo. Thus, reconstitution of T-cell immunity in immunodeficient patients by cell therapy or by vaccination may need to target multiple viral antigens to completely restore immunologic control of CMV.

scholarly journals Analysis of physical interactions between peptides and HLA molecules and application to the detection of human immunodeficiency virus 1 antigenic peptides.

1990 ◽  
Vol 172 (3) ◽  
pp. 889-899 ◽  
Author(s):  
J Choppin ◽  
F Martinon ◽  
E Gomard ◽  
E Bahraoui ◽  
F Connan ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Binding Assay ◽  
Peptide Binding ◽  
Hla Class I ◽  
Class I ◽  
Antigenic Peptides ◽  
Peptide Binding Assay ◽  
Hiv 1 ◽  
Hla Molecules

The physical association of 40 antigenic peptides and purified HLA class I and class II molecules was monitored using a direct peptide binding assay (PBA) in solid phase and an inhibition peptide binding assay (IPBA) in which the competing peptide was present in a soluble phase. We also examined the ability of different peptides to inhibit the lytic activity of human antiviral cytolytic T cells towards cells incubated with the corresponding target peptide. Our results showed that: (a) Binding of a given human T cell-recognized peptide to several HLA class I and class II molecules occurred frequently. Nevertheless, preferential binding of peptides to their respective restriction molecules was also observed. (b) Binding of HLA molecules to peptides recognized by murine T cells occurred less frequently. (c) 11 of 24 (46%) randomly selected HIV-1 peptides contained agretopic residues allowing their binding to HLA molecules. (d) The kinetics of HLA/peptide association depended on the peptide tested and were faster than or similar to those reported for Ia molecules. Dissociation of these complexes was very low. (e) Peptide/HLA molecule binding was dependent on length, number of positive charges, and presence of hydrophobic residue in the peptide. (f) A correlation was demonstrated between a peptide inhibitory effect in the IPBA and its blocking effect in the cytolytic test. Our data indicated that the restriction phenomenon observed in T cell responses was not strictly related to either an elective HLA/peptide association, or a high binding capacity of a peptide to HLA molecules. These data also showed that the PBA and IPBA are appropriate for the detection of agretopic residues within HIV-1 proteins.

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