Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements

Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer

(2023) Antonela Merlotti et al.   Science Immunology

High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

(2021) D.J. McGrail et al.   ANNALS OF ONCOLOGY

AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data

(2021) Naima Ahmed Fahmi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity

(2021) Gabriel K. Griffin et al.   NATURE

SETDB1-Mediated Silencing of Retroelements

(2020) Kei Fukuda et al.   Viruses-Basel

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

(2020) Chloe Chong et al.   Nature Communications

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

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

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

(2020) Franziska K. Geis et al.   Viruses-Basel

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade

(2018) Wanqiang Sheng et al.   CELL

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

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

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

­­­Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia­­

(2017) Trinna L. Cuellar et al.   JOURNAL OF CELL BIOLOGY

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

Tumour and host cell PD-L1 is required to mediate suppression of anti-tumour immunity in mice

(2017) Janet Lau et al.   Nature Communications

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

(2015) Michael S. Rooney et al.   CELL

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2015) Katherine B. Chiappinelli et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Neoantigens in cancer immunotherapy

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

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Immunogenicity of Murine Solid Tumor Models as a Defining Feature of In Vivo Behavior and Response to Immunotherapy

(2013) Melissa G. Lechner et al.   JOURNAL OF IMMUNOTHERAPY

Transcriptome sequencing of neonatal thymic epithelial cells

(2013) Charles St-Pierre et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Exploiting the Mutanome for Tumor Vaccination

(2012) J. C. Castle et al.   CANCER RESEARCH

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

All y’all need to know ‘bout retroelements in cancer

(2010) Victoria P. Belancio et al.   SEMINARS IN CANCER BIOLOGY

Epigenetic Dysregulation in Cancer

(2009) Andrew G. Muntean et al.   AMERICAN JOURNAL OF PATHOLOGY

Targeting Tumor Antigens to Secreted Membrane Vesicles In vivo Induces Efficient Antitumor Immune Responses

(2008) I. S. Zeelenberg et al.   CANCER RESEARCH