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Challenges in Antigen Identification—HLA Peptides and TCR Receptors

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Immunology".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 9245

Special Issue Editor

Agency for Science, Technology and Research (A*STAR), Institute of Molecular and Cell Biology (IMCB), Singapore 138632, Singapore
Interests: quantitative mass spectrometry; proteome wide modifications dynamics (phosphorylation, ubiqutinylation); surface cell markers; biomarkers discovery; HLA/MHC peptide identification; patient tailored therapies; dendritc cells-based vaccines; infectious diseases; neglected tropical disease; inflammation; auto-immuno diseases; T-cell-antigen presenting cells interactions

Special Issue Information

Dear Colleagues,

Significant progress in biomedical sciences and technology breakthroughs which has occurred in recent decades has enabled scientists to accelerate research and perform routine analysis using cutting-edge technologies (whole genome sequencing, transcriptome sequencing, single cell analysis (genomic techniques), proteome analysis (mass spectrometry), and phenotypic screens, i.e., immune cell typing (CyTOF/Flow cytometry) within days. The accompanying development of multidimensional (multi-omics) data integration using bioinformatics and systems biology tools enables the efficient mining of these information-rich datasets. With these tools, we can successfully expedite personalized medicine and targeted therapies based on the integration of a substantial set of patient-specific data.

This appears to be extremely relevant when we consider the varying rates of success in cancer treatment across the population. One of the challenging areas of personalized therapies is the discovery of major histocompatibility complex (MHC)/human leukocyte antigen (HLA) presented antigens and co-responding T-cell receptors (TCR). Due to the combinatorial diversity among individuals, the exact definition of the antigen in the particular HLA context has to be precisely determined so as to ensure efficient cellular immune response against particular pathogens.

This Special Issue, “Challenges in Antigen Identification—HLA Peptides and TCR Receptors”, will cover a selection of recent research topics and current review articles in the area of HLA peptide identification aproaches, peptide vaccines, and specific TCR identification. 

Dr. Radoslaw Sobota
Guest Editor

Manuscript Submission Information

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Keywords

  • Antigen presentation
  • HLA/MHC peptides
  • Precision medicine
  • Mass spectrometry
  • TCR diversity
  • Neoantigens
  • Peptide vaccines
  • Autoimmunity

Published Papers (3 papers)

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Research

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11 pages, 1960 KiB  
Article
Acid Stripping after Infection Improves the Detection of Viral HLA Class I Natural Ligands Identified by Mass Spectrometry
by Elena Lorente, Miguel Marcilla, Patricia G. de la Sota, Adriana Quijada-Freire, Carmen Mir and Daniel López
Int. J. Mol. Sci. 2021, 22(19), 10503; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910503 - 29 Sep 2021
Cited by 2 | Viewed by 1785
Abstract
Identification of a natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune response. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by antigen [...] Read more.
Identification of a natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune response. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by antigen processing in live cells. In infected cells, in addition to this complex HLA ligandome, a minority of peptides from degradation of the few proteins encoded by the viral genome are also bound to HLA class I molecules. In this study, the standard immunopeptidomics strategy was modified to include the classical acid stripping treatment after virus infection to enrich the HLA ligandome in virus ligands. Complexes of HLA-B*27:05-bound peptide pools were isolated from vaccinia virus (VACV)-infected cells treated with acid stripping after virus infection. The HLA class I ligandome was identified using high throughput mass spectrometry analyses, yielding 37 and 51 natural peptides processed and presented untreated and after acid stripping treatment VACV-infected human cells, respectively. Most of these virus ligands were identified in both conditions, but exclusive VACV ligands detected by mass spectrometry detected on acid stripping treatment doubled the number of those identified in the untreated VACV-infected condition. Theoretical binding affinity prediction of the VACV HLA-B*27:05 ligands and acute antiviral T cell response characterization in the HLA transgenic mice model showed no differences between HLA ligands identified under the two conditions: untreated and under acid stripping condition. These findings indicated that acid stripping treatment could be useful to identify HLA class I ligands from virus-infected cells. Full article
(This article belongs to the Special Issue Challenges in Antigen Identification—HLA Peptides and TCR Receptors)
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17 pages, 11425 KiB  
Article
Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus
by Mohamed A. Soltan, Muhammad Alaa Eldeen, Nada Elbassiouny, Ibrahim Mohamed, Dalia A. El-damasy, Eman Fayad, Ola A. Abu Ali, Nermin Raafat, Refaat A. Eid and Ahmed A. Al-Karmalawy
Int. J. Mol. Sci. 2021, 22(17), 9330; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179330 - 28 Aug 2021
Cited by 30 | Viewed by 3516
Abstract
Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. [...] Read more.
Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-3 and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine. Full article
(This article belongs to the Special Issue Challenges in Antigen Identification—HLA Peptides and TCR Receptors)
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Review

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15 pages, 616 KiB  
Review
The Impact of the ‘Mis-Peptidome’ on HLA Class I-Mediated Diseases: Contribution of ERAP1 and ERAP2 and Effects on the Immune Response
by Valentina Tedeschi, Giorgia Paldino, Fabiana Paladini, Benedetta Mattorre, Loretta Tuosto, Rosa Sorrentino and Maria Teresa Fiorillo
Int. J. Mol. Sci. 2020, 21(24), 9608; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21249608 - 17 Dec 2020
Cited by 19 | Viewed by 3233
Abstract
The strong association with the Major Histocompatibility Complex (MHC) class I genes represents a shared trait for a group of autoimmune/autoinflammatory disorders having in common immunopathogenetic basis as well as clinical features. Accordingly, the main risk factors for Ankylosing Spondylitis (AS), prototype of [...] Read more.
The strong association with the Major Histocompatibility Complex (MHC) class I genes represents a shared trait for a group of autoimmune/autoinflammatory disorders having in common immunopathogenetic basis as well as clinical features. Accordingly, the main risk factors for Ankylosing Spondylitis (AS), prototype of the Spondyloarthropathies (SpA), the Behçet’s disease (BD), the Psoriasis (Ps) and the Birdshot Chorioretinopathy (BSCR) are HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02, respectively. Despite the strength of the association, the HLA pathogenetic role in these diseases is far from being thoroughly understood. Furthermore, Genome-Wide Association Studies (GWAS) have highlighted other important susceptibility factors such as Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and, less frequently, ERAP2 that refine the peptidome presented by HLA class I molecules to CD8+ T cells. Mass spectrometry analysis provided considerable knowledge of HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02 immunopeptidome. However, the combined effect of several ERAP1 and ERAP2 allelic variants could generate an altered pool of peptides accounting for the “mis-immunopeptidome” that ranges from suboptimal to pathogenetic/harmful peptides able to induce non-canonical or autoreactive CD8+ T responses, activation of NK cells and/or garbling the classical functions of the HLA class I molecules. This review will focus on this class of epitopes as possible elicitors of atypical/harmful immune responses which can contribute to the pathogenesis of chronic inflammatory diseases. Full article
(This article belongs to the Special Issue Challenges in Antigen Identification—HLA Peptides and TCR Receptors)
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