What do cancer-specific CD8+ T cells see? The contribution of immunopeptidomics

Neoantigen vaccine-induced CD4 T cells confer protective immunity in a mouse model of multiple myeloma through activation of CD8 T cells against non-vaccine, tumor-associated antigens

(2022) Selma Bekri et al.   Journal for ImmunoTherapy of Cancer

Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues

(2022) Peter Kubiniok et al.   iScience

Chasing neoantigens; invite naïve T cells to the party

(2022) Ravi Chand Bollineni et al.   CURRENT OPINION IN IMMUNOLOGY

Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability

(2022) Jenna Cleyle et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens

(2022) David Weber et al.   NATURE BIOTECHNOLOGY

Unmasking the suppressed immunopeptidome of EZH2 mutated diffuse large B-cell lymphomas with combination drug treatment

(2022) Christopher M Bourne et al.   Blood Advances

Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors

(2022) Assaf Kacen et al.   NATURE BIOTECHNOLOGY

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

(2022) Wen-Feng Zeng et al.   Nature Communications

Cellular senescence enhances adaptive anticancer immunosurveillance

(2022) Ines Marin et al.   OncoImmunology

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

(2021) Maria Virginia Ruiz Cuevas et al.   Cell Reports

Exhausted CD8+T Cells in the Tumor Immune Microenvironment: New Pathways to Therapy

(2021) Weiqin Jiang et al.   Frontiers in Immunology

Are there indeed spliced peptides in the immunopeptidome?

(2021) Arie Admon   MOLECULAR & CELLULAR PROTEOMICS

Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy

(2021) Timothy Kottke et al.   Nature Communications

IFNγ Modulates the Immunopeptidome of Triple Negative Breast Cancer Cells by Enhancing and Diversifying Antigen Processing and Presentation

(2021) Gabriel Goncalves et al.   Frontiers in Immunology

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

(2021) Ana Marcu et al.   Journal for ImmunoTherapy of Cancer

Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

(2021) Sydney X. Lu et al.   CELL

Immunopeptidogenomics: harnessing RNA-seq to illuminate the dark immunopeptidome

(2021) K.E. Scull et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

(2021) Mathias Wilhelm et al.   Nature Communications

Immunopeptidomics-Guided Warehouse Design for Peptide-Based Immunotherapy in Chronic Lymphocytic Leukemia

(2021) Annika Nelde et al.   Frontiers in Immunology

Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy

(2021) Karita Peltonen et al.   Cancers

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

The Tumor Microenvironment: A Milieu Hindering and Obstructing Antitumor Immune Responses

(2020) Alireza Labani-Motlagh et al.   Frontiers in Immunology

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

(2020) Sibylle Pfammatter et al.   ANALYTICAL CHEMISTRY

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

MHC Class I Downregulation in Cancer: Underlying Mechanisms and Potential Targets for Cancer Immunotherapy

(2020) Annelisa M. Cornel et al.   Cancers

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Measles virus-based treatments trigger a pro-inflammatory cascade and a treatment-specific immunopeptidome in glioblastoma

(2019) Srinath Rajaraman et al.   Molecular Therapy-Oncolytics

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

(2019) Markus W. Löffler et al.   Genome Medicine

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly

(2019) Jan Attig et al.   GENOME RESEARCH

Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

(2019) Alice Newey et al.   Journal for ImmunoTherapy of Cancer

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

Recent Advances in Targeting CD8 T-Cell Immunity for More Effective Cancer Immunotherapy

(2018) Aurélie Durgeau et al.   Frontiers in Immunology

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

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

CD4 + T Cell Help Confers a Cytotoxic T Cell Effector Program Including Coinhibitory Receptor Downregulation and Increased Tissue Invasiveness

(2017) Tomasz Ahrends 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

Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry?

(2017) Valentina D'Atri et al.   JOURNAL OF SEPARATION SCIENCE

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS