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

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

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

CEA expression heterogeneity and plasticity confer resistance to the CEA-targeting bispecific immunotherapy antibody cibisatamab (CEA-TCB) in patient-derived colorectal cancer organoids

(2019) Reyes Gonzalez-Exposito et al.   Journal for ImmunoTherapy of Cancer

Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer

(2019) Andrew Woolston et al.   CANCER CELL

Atezolizumab with or without cobimetinib versus regorafenib in previously treated metastatic colorectal cancer (IMblaze370): a multicentre, open-label, phase 3, randomised, controlled trial

(2019) Cathy Eng et al.   LANCET ONCOLOGY

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

(2018) Markus W. Löffler et al.   CANCER RESEARCH

Personalized vaccines for cancer immunotherapy

(2018) Ugur Sahin et al.   SCIENCE

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

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

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

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

(2017) Diego Chowell et al.   SCIENCE

Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

(2017) Eric Letouzé et al.   Nature Communications

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization

(2017) Markus Müller et al.   Frontiers in Immunology

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg et al.   CURRENT OPINION IN IMMUNOLOGY

MAP Kinase Inhibition Promotes T Cell and Anti-tumor Activity in Combination with PD-L1 Checkpoint Blockade

(2016) Peter J.R. Ebert et al.   IMMUNITY

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

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

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

The BRAF and MEK Inhibitors Dabrafenib and Trametinib: Effects on Immune Function and in Combination with Immunomodulatory Antibodies Targeting PD-1, PD-L1, and CTLA-4

(2015) L. Liu et al.   CLINICAL CANCER RESEARCH

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

HLA Class II Antigen Expression in Colorectal Carcinoma Tumors as a Favorable Prognostic Marker

(2015) Giuseppe Sconocchia et al.   NEOPLASIA

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Clinical Effects of Adjuvant Active Specific Immunotherapy Differ between Patients with Microsatellite-Stable and Microsatellite-Instable Colon Cancer

(2011) V. A. de Weger et al.   CLINICAL CANCER RESEARCH

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis

(2009) Fabiana Bettoni et al.   GENOMICS

Systematic Characterisation of Cellular Localisation and Expression Profiles of Proteins Containing MHC Ligands

(2009) Agnieszka S. Juncker et al.   PLoS One