Peptide Presentation to T Cells: Solving the Immunogenic Puzzle

Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin

(2019) Ida Hafstrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse fate of ubiquitin chain moieties: The proximal is degraded with the target, and the distal protects the proximal from removal and recycles

(2019) Hao Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Most viral peptides displayed by class I MHC on infected cells are immunogenic

(2019) Nathan P. Croft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance

(2019) Jiajie Wei et al.   MOLECULAR CELL

Proteolytic dynamics of human 20S thymoproteasome

(2019) Ulrike Kuckelkorn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An introduction to chimeric antigen receptor (CAR) T-cell immunotherapy for human cancer

(2019) Steven Feins et al.   AMERICAN JOURNAL OF HEMATOLOGY

Influenza A Virus Infection Induces Viral and Cellular Defective Ribosomal Products Encoded by Alternative Reading Frames

(2019) Damien J. Zanker et al.   JOURNAL OF IMMUNOLOGY

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses

(2019) Ting Wu et al.   Nature Communications

T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes

(2019) Tomasz Kula et al.   CELL

Vaccinia Virus Strain MVA can Induce Optimal CD8+ T cell responses to Directly Primed Antigens Depending on Vaccine Design

(2019) Yik Chun Wong et al.   JOURNAL OF VIROLOGY

T-Cell Receptor Cognate Target Prediction Based on Paired α and β Chain Sequence and Structural CDR Loop Similarities

(2019) Esteban Lanzarotti et al.   Frontiers in Immunology

Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer

(2019) Alexey V. Morozov et al.   Frontiers in Oncology

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Zach Rolfs et al.   Science Immunology

Response to Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Pouya Faridi et al.   Science Immunology

An in silico—in vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients

(2019) Michele Mishto et al.   Frontiers in Immunology

Immunoribosomes: Where’s there’s fire, there’s fire

(2018) Jiajie Wei et al.   MOLECULAR IMMUNOLOGY

Production of spliced peptides by the proteasome

(2018) Nathalie Vigneron et al.   MOLECULAR IMMUNOLOGY

The C-terminal extension landscape of naturally presented HLA-I ligands

(2018) Philippe Guillaume et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics

(2018) Sri H. Ramarathinam et al.   PROTEOMICS

A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules

(2018) Denise S. M. Boulanger et al.   Frontiers in Immunology

Employing proteomics in the study of antigen presentation: an update

(2018) Sri H. Ramarathinam et al.   Expert Review of Proteomics

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

(2018) Roman Mylonas et al.   MOLECULAR & CELLULAR PROTEOMICS

Toward the development of true “off-the-shelf” synthetic T-cell immunotherapy

(2018) Shoichi Iriguchi et al.   CANCER SCIENCE

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Mapping the MHC Class I–Spliced Immunopeptidome of Cancer Cells

(2018) Juliane Liepe et al.   Cancer Immunology Research

Deciphering the MHC-associated peptidome: a review of naturally processed ligand data

(2017) Kerrie Vaughan et al.   Expert Review of Proteomics

A Case for a Human Immuno-Peptidome Project Consortium

(2017) Etienne Caron et al.   IMMUNITY

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

(2017) Zhen Shi et al.   MOLECULAR CELL

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Structure of the human MHC-I peptide-loading complex

(2017) Andreas Blees et al.   NATURE

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

(2017) Jiansheng Jiang et al.   SCIENCE

Structure of the TAPBPR–MHC I complex defines the mechanism of peptide loading and editing

(2017) Christoph Thomas et al.   SCIENCE

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Immunoproteasome functions explained by divergence in cleavage specificity and regulation

(2017) Michael B Winter et al.   eLife

Defining Viral Defective Ribosomal Products: Standard and Alternative Translation Initiation Events Generate a Common Peptide from Influenza A Virus M2 and M1 mRNAs

(2016) Ning Yang et al.   JOURNAL OF IMMUNOLOGY

Presentation of Cryptic Peptides by MHC Class I Is Enhanced by Inflammatory Stimuli

(2016) Sharanya Prasad et al.   JOURNAL OF IMMUNOLOGY

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma

(2016) Stacy A. Malaker et al.   JOURNAL OF PROTEOME RESEARCH

Specialized proteasome subunits have an essential role in the thymic selection of CD8+ T cells

(2016) Eleanor Z Kincaid et al.   NATURE IMMUNOLOGY

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

(2016) Curtis McMurtrey et al.   eLife

T Cell Antigen Receptor Recognition of Antigen-Presenting Molecules

(2015) Jamie Rossjohn et al.   Annual Review of Immunology

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Discovering protective CD8 T cell epitopes—no single immunologic property predicts it!

(2015) Pavlo Gilchuk et al.   CURRENT OPINION IN IMMUNOLOGY

The role of T cell receptor signaling thresholds in guiding T cell fate decisions

(2015) Julie Zikherman et al.   CURRENT OPINION IN IMMUNOLOGY

Definition of Proteasomal Peptide Splicing Rules for High-Efficiency Spliced Peptide Presentation by MHC Class I Molecules

(2015) Celia R. Berkers et al.   JOURNAL OF IMMUNOLOGY

Quantifying epitope presentation using mass spectrometry

(2015) Nathan P. Croft et al.   MOLECULAR IMMUNOLOGY

Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity

(2015) Derin B. Keskin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thymoproteasomes produce unique peptide motifs for positive selection of CD8+ T cells

(2015) Katsuhiro Sasaki et al.   Nature Communications

Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes

(2015) Juliane Liepe et al.   eLife

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

(2014) Michele Mishto et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

A Spliced Antigenic Peptide Comprising a Single Spliced Amino Acid Is Produced in the Proteasome by Reverse Splicing of a Longer Peptide Fragment followed by Trimming

(2014) A. Michaux et al.   JOURNAL OF IMMUNOLOGY

Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy

(2014) C Berlin et al.   LEUKEMIA

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

Insights into the initiation of TCR signaling

(2014) Arup K Chakraborty et al.   NATURE IMMUNOLOGY

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

(2014) G. P. M. Mommen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The nature and extent of contributions by defective ribosome products to the HLA peptidome

(2014) D. Bourdetsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathways of Antigen Processing

(2013) Janice S. Blum et al.   Annual Review of Immunology

MHC-NP: Predicting peptides naturally processed by the MHC

(2013) Sébastien Giguère et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Mixed Proteasomes Function To Increase Viral Peptide Diversity and Broaden Antiviral CD8+ T Cell Responses

(2013) D. Zanker et al.   JOURNAL OF IMMUNOLOGY

Antigenic peptide trimming by ER aminopeptidases—Insights from structural studies

(2013) Efstratios Stratikos et al.   MOLECULAR IMMUNOLOGY

Kinetics of Antigen Expression and Epitope Presentation during Virus Infection

(2013) Nathan P. Croft et al.   PLoS Pathogens

Constitutive and Inflammatory Immunopeptidome of Pancreatic  -Cells

(2012) N. L. Dudek et al.   DIABETES

Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

(2012) Mikkel Harndahl et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned

(2012) Stephanie Gras et al.   IMMUNOLOGICAL REVIEWS

Driving Forces of Proteasome-catalyzed Peptide Splicing in Yeast and Humans

(2012) Michele Mishto et al.   MOLECULAR & CELLULAR PROTEOMICS

Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I

(2012) S. R. Starck et al.   SCIENCE

Rapid Antigen Processing and Presentation of a Protective and Immunodominant HLA-B*27-restricted Hepatitis C Virus-specific CD8+ T-cell Epitope

(2012) Julia Schmidt et al.   PLoS Pathogens

The Human Immunopeptidome Project, a Suggestion for yet another Postgenome Next Big Thing

(2011) Arie Admon et al.   MOLECULAR & CELLULAR PROTEOMICS

Mice completely lacking immunoproteasomes show major changes in antigen presentation

(2011) Eleanor Z Kincaid et al.   NATURE IMMUNOLOGY

An antigenic peptide produced by reverse splicing and double asparagine deamidation

(2011) A. Dalet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation

(2011) S. Apcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct quantitation of MHC-bound peptide epitopes by selected reaction monitoring

(2011) Chor Teck Tan et al.   PROTEOMICS

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization

(2011) Neil Dalchau et al.   PLoS Computational Biology

Primary CTL response magnitude in mice is determined by the extent of naive T cell recruitment and subsequent clonal expansion

(2010) Nicole L. La Gruta et al.   JOURNAL OF CLINICAL INVESTIGATION

N-Glycosylation Enhances Presentation of a MHC Class I-Restricted Epitope from Tyrosinase

(2009) M. Ostankovitch et al.   JOURNAL OF IMMUNOLOGY

Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope

(2009) S. Gras et al.   JOURNAL OF IMMUNOLOGY

Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes

(2009) Jan Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self

(2008) Fiyaz Mohammed et al.   NATURE IMMUNOLOGY