T cells of colorectal cancer patients’ stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells

Tumor mutational burden predicts the efficacy of pembrolizumab monotherapy: a pan-tumor retrospective analysis of participants with advanced solid tumors

(2022) Razvan Cristescu et al.   Journal for ImmunoTherapy of Cancer

Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability

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

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

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes

(2021) Jonas P. Becker et al.   iScience

CD8+ T-cell immune surveillance against a tumor antigen encoded by the oncogenic long non-coding RNA, PVT1

(2021) Yasuhiro Kikuchi et al.   Cancer Immunology Research

Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair–deficient colorectal cancer tissue

(2021) Tomomi Hirama et al.   JCI Insight

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

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors

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

Cancer statistics, 2020

(2020) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

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

(2020) Chloe Chong et al.   Nature Communications

Memory T cells: strategies for optimizing tumor immunotherapy

(2020) Qingjun Liu et al.   Protein & Cell

Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire

(2020) Sebastian P. Haen et al.   Nature Reviews Clinical Oncology

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

(2020) Laura C. Demmers et al.   Nature Communications

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

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

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

Integrated Biobanking and Tumor Model Establishment of Human Colorectal Carcinoma Provides Excellent Tools for Preclinical Research

(2019) Christina S. Mullins et al.   Cancers

Tumor organoid–T-cell coculture systems

(2019) Chiara M. Cattaneo et al.   Nature Protocols

Abstract 4627: Integrated multi-layer analysis reveals novel insights into the molecular landscape of colorectal cancer (CRC)

(2018) Manuela Salvucci et al.   CANCER RESEARCH

Identification of non-mutated neoantigens presented by TAP-deficient tumors

(2018) Koen A. Marijt et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Colorectal cancer vaccines: Tumor-associated antigens vs neoantigens

(2018) Sandra Wagner et al.   WORLD JOURNAL OF GASTROENTEROLOGY

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

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

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

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

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

CD4+ /CD8+ double-positive T cells: more than just a developmental stage?

(2014) Nana H. Overgaard et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Diversity and clonal selection in the human T-cell repertoire

(2014) Q. Qi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

(2012) Massimo Andreatta et al.   BIOINFORMATICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides

(2009) Oleg V. Krokhin et al.   ANALYTICAL CHEMISTRY