scholarly journals Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors

2020 ◽  
Vol 19 (7) ◽  
pp. 1236-1247 ◽  
Author(s):  
Shutao Mei ◽  
Rochelle Ayala ◽  
Sri H. Ramarathinam ◽  
Patricia T. Illing ◽  
Pouya Faridi ◽  
...  
Keyword(s):  
T Cell ◽  
Prediction Models ◽  
Enzymatic Reaction ◽  
Retrograde Transport ◽  
T Cell Epitopes ◽  
Tissue Samples ◽  
Hla Ligand ◽  
Subsequent Degradation ◽  
Allele Specific ◽  
Asparagine Deamidation

The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Although immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens.

Human Cytotoxic T Cell Epitopes in HPV 11: Relationships between Allele-Specific Motifs, HLA Binding, and Stimulation in Vitro

1994 ◽  
pp. 227-232
Author(s):  
Huw Davies ◽  
Ian Tarpey ◽  
Simon Stacey ◽  
Julian Hickling ◽  
Jennifer Bartholomew ◽  
...  
Keyword(s):  
T Cell ◽  
Cytotoxic T Cell ◽  
T Cell Epitopes ◽  
Allele Specific ◽  
Hla Binding

scholarly journals Construction and efficacy evaluation of novel swine leukocyte antigen (SLA) class I and class II allele-specific poly-T cell epitope vaccines against porcine reproductive and respiratory syndrome virus

2020 ◽  
Vol 101 (11) ◽  
pp. 1191-1201
Author(s):  
Debin Tian ◽  
Sakthivel Subramaniam ◽  
C. Lynn Heffron ◽  
Hassan M. Mahsoub ◽  
Harini Sooryanarain ◽  
...  
Keyword(s):  
T Cell ◽  
Statistical Significance ◽  
Cell Epitope ◽  
Class Ii ◽  
Class I ◽  
Respiratory Syndrome Virus ◽  
T Cell Epitope ◽  
T Cell Epitopes ◽  
Efficacy Evaluation ◽  
Allele Specific

Porcine reproductive and respiratory syndrome virus (PRRSV) causes an economically important global swine disease. Here we report the development of subunit PRRSV-2 vaccines by expressing swine leucocyte antigen (SLA) class I and class II allele-specific epitope antigens in a robust adenovirus vector. SLA I-specific CD8 and SLA II-specific CD4 T cell epitopes of PRRSV-2 NADC20 were predicted in silico. Stable murine leukaemia cell lines (RMA-S), which are TAP-deficient and lacking endogenous class I epitope loading, were established to express different SLA I alleles. The binding stability of PRRSV T cell epitope peptides with SLA I alleles expressed on RMA-S cells was characterized. Two PRRSV poly-T cell epitope peptides were designed. NADC20-PP1 included 39 class I epitopes, consisting of 8 top-ranked epitopes specific to each of 5 SLA I alleles, and fused to 5 class II epitopes specific to SLA II alleles. NADC20-PP2, a subset of PP1, included two top-ranked class I epitopes specific to each of the five SLA I alleles. Two vaccine candidates, Ad-NADC20-PP1 and Ad-NADC20-PP2, were constructed by expressing the polytope peptides in a replication-incompetent human adenovirus 5 vector. A vaccination and challenge study in 30 piglets showed that animals vaccinated with the vaccines had numerically lower gross and histopathology lung lesions, and numerically lower PRRSV RNA loads in lung and serum after challenge compared to the controls, although there was no statistical significance. The results suggested that the Ad-NADC20-PP1 and Ad-NADC20-PP2 vaccines provided little or no protection, further highlighting the tremendous challenges faced in developing an effective subunit PRRSV-2 vaccine.

scholarly journals Molecular diagnosis angioimmunoblastic T-cell lymphoma

2019 ◽  
Vol 91 (7) ◽  
pp. 63-69
Author(s):  
N G Chernova ◽  
Y V Sidorova ◽  
S Y Smirnova ◽  
N V Ryzhikova ◽  
E E Nikulina ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Lymph Node ◽  
T Cell ◽  
Peripheral Blood ◽  
Cell Lymphoma ◽  
Cell Receptor ◽  
T Cell Lymphoma ◽  
Tissue Samples ◽  
Angioimmunoblastic T Cell Lymphoma ◽  
Allele Specific

Aim: to determine molecular diagnostics routine for different tissue samples in angioimmunoblastic T-cell lymphoma. Materials and methods. Molecular studies were performed for 84 primary AITL patients. The median age was 61 year (29-81); the male to female ratio was 48/36. T-cell and B-cell clonality was assessed by GeneScan analysis of rearranged T-cell receptor (TCRG, TCRB) and immunoglobulin heavy chain genes. For the quantitative determination of cells with RHOA G17V mutation real - time polymerase chain reaction (PCR) with allele - specific LNA modified primers was used. Results. In lymph nodes rearrangements of T-cell receptor genes were determined in 76 (90.5%) of 84 patients and were absent in 8 (9.5%) cases. Identification of the same clonal products of the TCRG and TCRB genes in the lymph node and in peripheral blood and/or bone marrow indicated the prevalence of the tumor process and was observed in 64.7% of patients. Clonal products in peripheral blood and/or bone marrow different from those in the lymph node indicated reactive cytotoxic lymphocyte population and were noted in 58.8% of AITL cases. Simultaneous detection of T- and B-cell clonality in the lymph node was observed in 20 (24.7%) of 81 patients. Cells with RHOA G17V mutation were detected in lymph node in 45 (54.9%) of 82 patients. The use of allele - specific PCR with LNA modified primers revealed presence of the tumor cells in peripheral blood in 100% and in bone marrow in 93.9% of patients with G17V RHOA mutation in the lymph nodes. Conclusion. The validity of different molecular assays performed on certain tissue samples for the diagnosis of angioimmunoblastic T-cell lymphoma has been evaluated. Quantitative allele - specific PCR assay for RHOA G17V mutation based on LNA modified primers possesses sufficient sensitivity for tumor process prevalence evaluation and minimal residual disease monitoring.

scholarly journals Machine Learning Methods for Predicting HLA-Peptide Binding Activity

2015 ◽  
Vol 9s3 ◽  
pp. BBI.S29466 ◽  
Author(s):  
Heng Luo ◽  
Hao Ye ◽  
Hui Wen Ng ◽  
Lemming Shi ◽  
Weida Tong ◽  
...  
Keyword(s):  
Machine Learning ◽  
T Cell ◽  
Prediction Models ◽  
Peptide Binding ◽  
Future Perspective ◽  
T Cell Epitopes ◽  
Binding Prediction ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Peptide Binding Prediction

As major histocompatibility complexes in humans, the human leukocyte antigens (HLAs) have important functions to present antigen peptides onto T-cell receptors for immunological recognition and responses. Interpreting and predicting HLA-peptide binding are important to study T-cell epitopes, immune reactions, and the mechanisms of adverse drug reactions. We review different types of machine learning methods and tools that have been used for HLA-peptide binding prediction. We also summarize the descriptors based on which the HLA-peptide binding prediction models have been constructed and discuss the limitation and challenges of the current methods. Lastly, we give a future perspective on the HLA-peptide binding prediction method based on network analysis.

scholarly journals The Length Distribution of Class I–Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele–Specific Binding Preference

2016 ◽  
Vol 196 (4) ◽  
pp. 1480-1487 ◽  
Author(s):  
Thomas Trolle ◽  
Curtis P. McMurtrey ◽  
John Sidney ◽  
Wilfried Bardet ◽  
Sean C. Osborn ◽  
...  
Keyword(s):  
T Cell ◽  
Specific Binding ◽  
Length Distribution ◽  
Class I ◽  
T Cell Epitopes ◽  
Binding Preference ◽  
Allele Specific

scholarly journals HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

2021 ◽  
Vol 9 (4) ◽  
pp. e002071
Author(s):  
Ana Marcu ◽  
Leon Bichmann ◽  
Leon Kuchenbecker ◽  
Daniel Johannes Kowalewski ◽  
Lena Katharina Freudenmann ◽  
...  
Keyword(s):  
T Cell ◽  
Cancer Immunotherapy ◽  
Human Tissue ◽  
Mononuclear Cells ◽  
World Population ◽  
Peripheral Blood Mononuclear ◽  
Tissue Samples ◽  
Hla Ligand ◽  
Hla Ligands ◽  
Genomic Regions

BackgroundThe human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level.MethodsHuman tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing.ResultsThe initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference.ConclusionGiven that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org.

HLA-B*27 subtype specificity determines the targeting of HLA-B*27 restricted HCV-specific CD8+ T cell epitopes

2013 ◽  
Vol 51 (01) ◽  
Author(s):  
K Nitschke ◽  
J Schmidt ◽  
HE Blum ◽  
R Thimme ◽  
C Neumann-Haefelin
Keyword(s):  
T Cell ◽  
Cd8 T Cell ◽  
T Cell Epitopes ◽  
Subtype Specificity
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