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At least 19 recordsLinked to original sources
PubMed1997

A novel, highly efficient peptide-HLA class I binding assay using unfolded heavy chain molecules: identification of HIV-1 derived peptides that bind to HLA-A*0201 and HLA-A*0301.

A novel cell-free, highly automated peptide-HLA binding assay has been designed during which a mixture of unfolded recombinant HLA heavy chain molecules, beta 2-microglobulin and a fluorescent labeled standard peptide is allowed to form peptide-HLA complexes. The binding of a peptide of interest is monitored as the ability to inhibit the formation of fluorescent peptide-HLA complexes. The assay was validated using published, known HLA-A* 0201 and HLA-A* 0301 binding peptides. In addition a selected set of HIV-1LAI reverse transcriptase derived 10-mer peptides, that had been selected on the basis of HLA-A* 0201 or HLA-A* 0301 binding motifs, were tested for HLA-A* 0201/A* 0301 binding. In that set we identified 8 peptides which bound with high affinity to HLA-A* 0201 and 5 peptides which bound with high affinity to HLA-A* 0301. The major advantage of the use of denatured heavy chain is the improved economy and efficiency, as unfolded protein material is in principle easily accessible by recombinant technology.

HIV Reverse Transcriptase↗
PubMed1997

Evaluation of peptide-HLA binding by an enzyme-linked assay and its application to the detailed peptide motifs for HLA-DR9 (DRB1*0901).

In our recent studies, we identified HLA-DRB1*0901-binding peptides by affinity-based selection of a phage random peptide library and showed that two major anchors (WxxS, where x is any amino acid) play an essential role in binding to DR9, determined using a radioactive peptide in combination with column chromatography. In the current study, we established an ELISA-based peptide-HLA binding assay system, with a new index (relative binding affinity: r.b.a.) for quantitation of peptide-HLA binding, using standard curves of competitive inhibition, an approach which enabled handling of a larger number of samples simultaneously. Quantitation of binding between HLA-DR9 molecules and 39 synthetic peptides showed that: (a) this system yields results which correlate with those obtained using the previous assay system (Spearman's rank correlation coefficient; the p value of the putative first anchor < 0.001, and the putative second anchor < 0.001); and (b) substituting the putative first (the most N-terminal) anchor Trp to Y, M, F, I, L, V, or C, and the putative second anchor Ser to T, G, A, V, F, or H, allow high-affinity binding to DR9.

Amino Acid Sequence↗
PubMed1997

Is celiac disease due to molecular mimicry between gliadin peptide-HLA class II molecule-T cell interactions and those of some unidentified superantigen?

This paper presents a new hypothesis for the etiology and pathogenesis of celiac disease (CD). It is our contention that CD is triggered by the binding of one or more gliadin peptides to CD-associated HLA class II molecules. Furthermore, we propose that these putative CD peptides bind to oligosaccharide residues on HLA class II molecules distal to the peptide-binding groove invoking recognition and binding by specialized subsets of gamma delta T cell receptor-bearing lymphocytes. The binding of these gamma delta T cells serves as a signal for abrogation of oral tolerance to ingested proteins setting in motion a series of immune responses directed against the small intestinal epithelium of CD patients. CD patients are victimized by this self-distructed immune response because of inheritance of certain combinations of HLA-DQ and DR haplotypes. Dimers encoded by HLA-DR haplotypes may be the primary restriction elements for lectin-like, gliadin peptides while the degree of immune suppression (or lack thereof) to ingested gliadins is governed by inherited HLA-DQ haplotypes. Finally, we speculate that molecular mimicry between one or more gliadin peptides and some, as yet unidentified, bacterial or viral superantigen plays a role in disease pathogenesis.

Adenovirus E1B Proteins↗
PubMed2026

Comprehensive Evaluation and Explainable Interpretation of Peptide-HLA Binding Prediction Tools.

Accurate prediction of peptide binding to human leukocyte antigen class I (HLA-I) molecules is critical for advancing immunological research, particularly in vaccine design and immunotherapy. However, limitations in model performance, interpretability, and dataset quality impede the widespread adoption of existing predictive tools. Here, we present a comprehensive evaluation of 17 HLA-I peptide binding prediction models, utilizing a meticulously curated dataset comprising over 290,000 peptides spanning 44 HLA-I alleles. We assessed model accuracy, robustness, and interpretability, employing explainability techniques such as SHAP (SHapley Additive exPlanations) and LIME (Local Interpretable Model-agnostic Explanations) to elucidate underlying prediction mechanisms. Our results reveal substantial performance disparities, with self-attention-based models, including STMHCpan and BigMHC, exhibiting superior accuracy. Notably, the capsule network model CapsNet-MHC_AN demonstrated robust performance. Models trained on eluted ligand datasets outperformed those relying on binding affinity data, underscoring the critical role of high-quality training data. Ensemble and multi-algorithm approaches further improved prediction reliability. These findings highlight the need for ongoing innovation in model architecture, integration of diverse and high-quality datasets, and incorporation of structural predictors to develop more accurate, interpretable, and clinically applicable HLA-I peptide binding prediction tools.

HLA-I binding↗
PubMed2026

Integrated Immunotherapy Target Atlas for Ewing Sarcoma.

BACKGROUND/AIM: Ewing sarcoma is a fusion-driven malignancy with low tumor mutational burden, making recurrent tumor-associated antigens with favorable tumor-to-normal contrast central to immunotherapy development. We converted the Deng et al.-defined 32-gene Ewing Sarcoma Specific Signature (ESS32) into a practical target atlas by integrating tumor RNA expression with normal-tissue context, protein evidence, subcellular localization, and therapeutic accessibility. MATERIALS AND METHODS: A 38-gene set was analyzed, including ESS32 and six comparator antigens (STEAP1, LINGO1, PRAME, CD99, CD276/B7-H3, and ENPP1). Eight Gene Expression Omnibus datasets (n=854 samples) were assigned predefined roles spanning tumor-versus-skeletal-muscle comparison, broad normal-organ context, EWSR1::FLI1 perturbation, tumor-only support cohorts, cell-line models, and cross-sarcoma comparison. Results were overlaid with Human Protein Atlas and published proteomic/surfaceome evidence. RESULTS: In GSE17674, the strongest tumor-enriched transcripts included NKX2-2, NPY1R, STEAP1, RBM11, RNF182, LIPI, CD99, STEAP2, LOXHD1, and DCDC2. Normal-tissue and compartment data substantially reordered RNA-only ranking. NKX2-2 showed the strongest Ewing-associated signal but encodes a nuclear transcription factor, favoring peptide-HLA/T-cell receptor (TCR) or vaccine development. RBM11 and LIPI emerged as high-interest intracellular/secretome-associated candidates, with an explicit epididymal/male reproductive caveat for LIPI. CD99 and NPY1R illustrated normal-cell reservoir and receptor-distribution constraints. CONCLUSION: ESS32 should be interpreted as an EWSR1::FLI1-associated RNA discovery set, not as a pre-validated target panel. Practical nomination requires integration of RNA enrichment, normal-tissue distribution, protein evidence, cellular compartment, and modality compatibility before nomination of TCR, vaccine, antibody-drug conjugate (ADC), chimeric antigen receptor (CAR), radioligand, or validation-first candidates.

Humans↗
PubMed2000

CD8+ T lymphocyte responses are induced during acute hepatitis C virus infection but are not sustained.

Cellular immune responses are likely to play a key role in determining the clinical outcome in acute infection with hepatitis C virus (HCV), but the dynamics of such responses and their relationship to viral clearance are poorly understood. In a previous study we have shown highly activated, multispecific cytotoxic T lymphocyte responses arising early and persisting in an individual who subsequently cleared the virus. In this study the HCV-specific CD8+ lymphocytes response has been similarly analyzed, using peptide-HLA class I tetramers, in a further nine individuals with documented acute HCV infection, six of whom failed to clear the virus. Significant populations of virus-specific CD8+ lymphocytes were detected at the peak of acute hepatic illness (maximally 3.5% of CD8+ lymphocytes). Frequencies were commonly lower than those seen previously and were generally not sustained. Early HCV-specific CD8+ lymphocytes showed an activated phenotype in all patients (CD38+ and HLA class II+), but this activation was short-lived. Failure to sustain sufficient numbers of activated virus-specific CD8+ lymphocytes may contribute to persistence of HCV.

Acute Disease↗
PubMed1998

Crucial role of N-terminal residue of binding peptides in recognition of the monoclonal antibody specific for the peptide-HLA-B5, -B35 complex.

The monoclonal antibody (mAb) 4D12 specific for the HLA-B5, -B35 cross-reacting group (CREG) bound to a fraction of HLA-B*3501 and HLA-B*5101 molecules carrying self-peptides. Analysis of the binding of mAb 4D12 to HLA-B*3501 and -B*5101 molecules pulsed with chemically synthesized peptides revealed that this mAb recognizes a restricted number of peptides and that P1 of the bound peptides critically influences its binding. The 4D12 mAb bound only to HLA-B*3501 molecules carrying peptides with Asn, Asp, Glu, Ser, and Val at P1. Analysis using an HLA-B*3501 crystallographic model suggested that 4D12 may recognize the side chain of the P1 residue that is pointing to the solvent. On the other hand, 4D12 bound only to HLA-B*5101 molecules carrying peptides with Asn or Asp at P1, suggesting that the 4D12 epitope formed by Glu, Ser, or Val at P1 and the A-pocket was changed by the substitution of His for Tyr at residue 171 of HLA-B*3501 molecules. This was confirmed by testing the binding of mAb 4D12 to HLA-B*3501 mutant molecules at residue 171 carrying these peptides. These results together suggest that the conformation of the A-pocket and its hydrogen bound network with the P1 residue is also critical for the binding of mAb 4D12. The present study shows the molecular basis of the specificity of 4D12 for the peptide-HLA class I complex.

Amino Acid Sequence↗
PubMed2026

Innovative CRISPR/Cas9-Based Strategy for Allele-Specific HLA Peptidome Analysis Using a Pan-HLA Antibody.

Human leukocyte antigen (HLA) immunopeptidomics is restricted by the limited availability of allele-specific antibodies and by potential artifacts introduced by HLA overexpression systems. To address these challenges, we developed a CRISPR/Cas9-based strategy that selectively deletes undesired classical class I alleles while preserving a single endogenous allele, thereby enabling allele-resolved peptidome profiling with a pan-HLA class I antibody. As a proof of concept, we edited JY cells to eliminate HLA-B&#x2217;07:02 and HLA-C&#x2217;07:02 while retaining HLA-A&#x2217;02:01 (&#x394;BC clones). Peptide-HLA complexes were immunoprecipitated from WT and &#x394;BC clones using either the pan-HLA class I antibody W6/32 or the A&#x2217;02:01-specific antibody PA2.1, followed by nanoLC-MS/MS and computational HLA assignment. Deletion of HLA-B and HLA-C alleles caused an expected &#x223c;55% reduction in total class I surface expression. Despite this, W6/32 immunoprecipitation from &#x394;BC clones recovered a comparable peptide yield to PA2.1 in WT cells. Binding predictions showed that most peptides identified in &#x394;BC clones using W6/32 were assigned to HLA-A&#x2217;02:01, with near-complete loss of HLA-B&#x2217;07:02- and HLA-C&#x2217;07:02-derived peptides. Sequence logo analysis confirmed the canonical A&#x2217;02:01 motif across conditions. The &#x394;BC W6/32 immunopeptidome exhibited a high degree of overlap (&#x223c;88%) with the WT PA2.1 repertoire, supporting the specificity and fidelity of the approach. These findings establish CRISPR-based editing of HLA alleles as a viable strategy for allele-specific immunopeptidome analysis using pan-HLA antibodies, supporting its potential application beyond this proof-of-concept system, reducing reliance on allele-specific reagents and facilitating the study of underrepresented HLA alleles.

Humans↗
PubMed2000

The human leukocyte antigen complex and chronic ocular inflammatory disorders.

PURPOSE: To review the role of gene products from the human leukocyte antigen (HLA) complex in the normal functioning of the immune system, ocular inflammation, and models of autoimmunity. METHOD: A review of recently published reports. RESULTS: Many chronic ocular inflammatory diseases are associated with specific alleles of the HLA complex. Understanding how HLA gene products function normally provides clues to the mechanism of disease associations. In the thymus, these molecules control the shape of the developing T-cell repertoire, leading to self-tolerance. In the periphery, HLA molecules bind and present peptide fragments to T cells, leading to a variety of effector functions. Although effector functions are for the most part beneficial, models are reviewed in which peptide-HLA interactions lead to T-cell responses with pathologic consequences. Herpes stromal keratitis is an informative animal model highlighting the role of self-tolerance, infection, and molecular mimicry in the development of autoimmunity. CONCLUSIONS: Human leukocyte antigen gene products may be associated with chronic inflammatory disorders through the unique presentation of "disease-inducing" peptides or the development of a T-cell repertoire prone to autoreactivity and molecular mimicry.

Animals↗
PubMed1997

Differential binding of peptides substituted at putative C-terminal anchor residue to HLA-DQ8 and DQ9 differing only at beta 57.

HLA-DQ8 (DQA1*0302-DQB1*0302: DQ beta 57 Ala) and (DQA1*0302-DQB1*0303: DQ beta 57 Asp) differ only at beta 57, at which polymorphism reportedly confers distinct susceptibility to insulin-dependent diabetes mellitus (IDDM). To identify the differential peptide binding affected by beta 57, we determined DQ9-binding peptides by affinity-based selection of a phage random peptide library using the biotinylated DQ9 complex. Nonconservative single-residue substitution of high-affinity DQ8- and DQ9-binding peptide (1KLPDYVLWSSSTVVGLGAAGA21) at the underlined residues significantly decreased the peptide binding to DQ8 and DQ9. Affinities of the wild-type 21-mer K4DYVLWSSSTV13 and K4AYAAWAAATA13 to DQ8 and DQ9 were practically the same. The K4DYVLWSSSTV13-based analogue peptides with substitutions at 12T showed that residues R, K, H, E, D, Q, N, T, S, V, L, I, F, M, W, and Y permitted binding to DQ8, whereas only R, T, V, L, I, F, M, W, and Y did so to DQ9. Thus, significant differences exist between DQ9 and DQ8, in that the majority of polar residues, regardless of their static charges at the residue 12, permitted binding to IDDM-susceptible DQ8, which is not the case for DQ9. The affinities of K4DYVLWSSSXV13 AND K4AYAAWAAAAX13 (where X is T, A, K, D, or I) were almost equal to DQ8 and DQ9, suggesting the DQ8- and DQ9-binding peptide motifs could accept both the 8-mer and 9-mer frames depending on intervening sequences between N- and C-terminal anchor residues. The biochemical basis of peptide-HLA interactions determined by DQ beta 57 is discussed.

Amino Acid Sequence↗
PubMed1994

Definition of a human suppressor T-cell epitope.

The quality of the response produced by regulatory or helper T (Th) cells presently receives much attention because of its possible implications for vaccine development and immunomodulation. Apart from cytokines and so-called costimulatory signals, antigens and the presenting major histocompatibility complex (MHC) molecules may play a role in determining the type of T-cell response generated toward antigens. To examine the role of antigen and/or HLA in control of T-cell subset activation, we have studied a special case, namely CD4+ suppressor T (Ts) cells in leprosy. Mycobacterium leprae-induced Ts cell clones have been previously isolated from peripheral blood and skin lesions of lepromatous leprosy patients and were shown to specifically down-regulate mycobacterium-specific Th cell responses. Despite considerable effort, the antigens recognized by these Ts cells have thus far not been identified. Here we report that all HLA-DR2-restricted CD4+ Ts cell clones derived from a lepromatous leprosy patient recognize an epitope that maps between the amino acid residues 439 and 448 of the mycobacterial hsp65. The peptide was presented to these Ts cells by HLA-DRB1*1503, a recently discovered HLA-DR2 variant. Non-suppressor T-cell clones derived from the same patient recognized antigens other than the hsp65 and were also stimulated by other HLA-DR2 variants. In independent cloning experiments peptide 435-449 and recombinant hsp65 induced exclusively Ts cells in this lepromatous leprosy patient. The Ts clones recognizing this particular epitope were derived from at least seven different progenitors, as they expressed different T-cell receptor alpha and beta chains. Thus, our data indicate that a specific peptide-HLA class II combination may exclusively activate Ts cells.

Amino Acid Sequence↗
PubMed1998

Cell lines transfected with the TAP inhibitor ICP47 allow testing peptide binding to a variety of HLA class I molecules.

The immediate early protein ICP47 of the Herpes simplex virus is known to block the human transporter associated with antigen processing (TAP), thereby creating a TAP-deficient phenotype in any human cell transfected with the corresponding cDNA. Exploiting this inhibitory activity, we constructed a selection of human cell lines each co-expressing one of the cDNAs of human leukocyte antigen (HLA) class I alleles HLA-A*1101, A24, A*3101, A*6601, B8 and B*1516, and the cDNA encoding the ICP47 molecule. The cell lines generated showed diminished HLA class I surface expression and the inhibition of the TAP function was confirmed in peptide translocation assays. The addition of specific exogenous peptide ligands restored the expression of the corresponding HLA class I molecules. Thus, the ICP47 transfectants provide us with a tool to closely examine peptide-HLA class I interactions, to confirm HLA class I ligand motifs and to test peptides predicted to bind.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1998

Six unrelated HLA-DR-matched adults recognize identical CD4+ T cell epitopes from influenza A haemagglutinin that are not simply peptides with high HLA-DR binding affinities.

Influenza A/Beijing/32/92 (H3N2) haemagglutinin (HA)-specific short-term CD4+ T cell lines were generated from six unrelated HLA-DR0701, 1501 positive adults (aged 27-60 years) 3 months following administration of an influenza subunit vaccine containing HA A/Beijing/32/92. Epitope recognition was examined using 118 HA A/Beijing/32/92-specific 16mer peptides which overlapped by 11 residues and which spanned the entire molecule. Following influenza vaccination the donors recognized identical HA peptides. The selected peptides represented HA regions which have been free from extensive drift mutation since the emergence of human H3N2 influenza A strains. Using DAP DR7.0701 cells (a murine cell line expressing HLA-DR0701) as antigen-presenting cells the majority of CD4+ T cell responses were shown to be HLA-DR0701 restricted. The relationship between HA peptide recognition and relative strength of HA peptide-HLA-DR0701 binding was then explored in a competition assay with biotinylated CLIP peptide. Although peptides representing dominant HA epitopes bound to DR0701, the relationship between relative strength of binding and immunodominance was complex, and many strongly binding peptides, particularly those with glycosylation sites and showing inter-strain variation, were not recognized. These results illustrate the control HLA class II exerts over CD4+ T cell HA epitope selection in unrelated adult humans. Immunodominance appears not to be directly related to the relative strength of HA peptide-HLA class II binding, and thus reflects complex interactions between antigen processing, intracellular competition for HLA binding, TCR repertoires and repeated exposure to different strains of influenza A viruses.

Adult↗
PubMed1992

Memory T cells of a patient with follicular thyroid carcinoma recognize peptides derived from mutated p21 ras (Gln-->Leu61).

Point mutations in ras genes resulting in substitutions of amino acid Gly in positions 12 and 13, and Gln in position 61 of the ras gene product p21, are commonly found in human tumors. Peptides derived from aberrant p21 may elicit a tumor specific T cell response, provided that these peptides can bind to HLA molecules of the tumor and the patient has T cells able to recognize the corresponding peptide-HLA complex. Here we report that CD4+ T cells of memory type (CD45RO+) from a patient with a follicular thyroid carcinoma respond against a synthetic peptide derived from aberrant p21 ras having a Gln-->Leu substitution at position 61. Such responses were not observed when T cells from healthy volunteers or cancer patients where this mutation does not usually occur were stimulated with this peptide. The responding T cells did not cross-react with the corresponding peptide derived from native p21 ras nor did they recognize peptides carrying other substitutions in position 61. T cells clones were generated which recognized this Leu61 peptide when presented by HLA-DQ8 molecules. These T cell clones also recognized the corresponding intact p21 ras protein. By using several different synthetic peptides, a peptide with optimal stimulatory capacity was defined. Performing polymerase chain reaction and oligonucleotide probing we were, however, not able to detect the p21 ras gene encoding the Gln-->Leu substitution in DNA from tumor biopsies from the patient. This may indicate that tumor cells harboring the mutation leading to the Gln-->Leu substitution had been eliminated and that tumor progression was due to cells that had deleted the mutated ras gene. The finding that ras derived peptides and recombinant mutated p21 ras are immunogenic in man may form the basis for the development of cancer immunotherapy based on synthetic oncogene derived peptides.

Adenocarcinoma↗
PubMed1994

Binding of peptides to HLA-DQ molecules: peptide binding properties of the disease-associated HLA-DQ(alpha 1*0501, beta 1*0201) molecule.

Peptide binding to DQ molecules has not previously been described. Here we report a biochemical peptide-binding assay specific for the DQ2 [i.e. DQ(alpha 1*0501, beta 1*0201)] molecule. This molecule was chosen since it shows a strong association to diseases such as celiac disease and insulin-dependent diabetes mellitus. Initially we radiolabelled some selected peptides and tested them for binding to affinity-purified DQ2 molecules. One of the peptides, a Mycobacterium bovis (MB) 65 kDa 243-255Y peptide, displayed a good signal-to-noise ratio and was thus chosen as an indicator peptide in the DQ2 binding assay. The MB 65 kDa 243-255Y peptide bound to DQ2 in a strictly pH-dependent fashion, with optimal binding around pH 5 and only weak binding at pH 7.4. The association of the MB 65 kDa 243-255Y peptide to DQ2 was slow, but once formed, the peptide-HLA complexes were very stable. The binding of peptides to DQ2 was specific, as shown in inhibition experiments with a panel of 47 peptides, differing in length, sequence, and origin. The binding of peptides to DR3 was tested in a similar assay with a Mycobacterium tuberculosis 65 kDa 3-13 peptide as the binding indicator. DQ2 and DR3 molecules bound to different sets of peptides. However, the peptide binding to DQ2 and DR3 showed, in general, similar characteristics with respect to pH dependence and kinetic parameters, indicating that the overall rules for peptide binding to DQ molecules are the same as those previously shown for human DR and murine I-A and I-E molecules.

Amino Acid Sequence↗
PubMed2000

Functional heterogeneity and high frequencies of cytomegalovirus-specific CD8(+) T lymphocytes in healthy seropositive donors.

Human cytomegalovirus (HCMV) infection is largely asymptomatic in the immunocompetent host, but remains a major cause of morbidity in immunosuppressed individuals. Using the recently described technique of staining antigen-specific CD8(+) T cells with peptide-HLA tetrameric complexes, we have demonstrated high levels of antigen-specific cells specific for HCMV peptides and show that this may exceed 4% of CD8(+) T cells in immunocompetent donors. Moreover, by staining with tetramers in combination with antibodies to cell surface markers and intracellular cytokines, we demonstrate functional heterogeneity of HCMV-specific populations. A substantial proportion of these are effector cytotoxic T lymphocytes, as demonstrated by their ability to lyse peptide-pulsed targets in "fresh" killing assays. These data suggest that the immune response to HCMV is periodically boosted by a low level of HCMV replication and that sustained immunological surveillance contributes to the maintenance of host-pathogen homeostasis. These observations should improve our understanding of the immunobiology of persistent viral infection.

CD8-Positive T-Lymphocytes↗
PubMed1997

Expansion of Immunostimulatory Dendritic Cells from Peripheral Blood of Patients with Cancer.

Clinical investigators are keenly interested in the role of antigen-presenting cells (APCs) in the initiation of immune responses because of potential use of APCs in immune cell therapy. Pioneer studies in mammals by Steinman and coworkers have demonstrated that the specialized system of APCs is constituted by bone marrow-derived dendritic cells. Dendritic cells are distinguished by their unique ability to capture, process, and present antigens into peptide-HLA complexes to naive T lymphocytes and to deliver the costimulatory signal necessary for T-lymphocyte activation. In this article, we summarize the main experimental evidence supporting the hypothesis that individuals vaccinated with manipulated dendritic cells can mount tumor-specific humoral and cellular responses. This can lead to tumor regression as well as protective immunity to tumor growth in vivo.

Journal Article↗