Overexpression of transposable elements is associated with immune evasion and poor outcome in colorectal cancer.

[1]  A. Hutchins,et al.  Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE , 2021, Nature Communications.

[2]  K. Nephew Turning Up the Heat on the Pancreatic Tumor Microenvironment by Epigenetic Priming , 2020, Cancer Research.

[3]  B. Tycko,et al.  A DNA Hypomethylating Drug Alters the Tumor Microenvironment and Improves the Effectiveness of Immune Checkpoint Inhibitors in a Mouse Model of Pancreatic Cancer , 2020, Cancer Research.

[4]  G. Cristofari,et al.  Measuring and interpreting transposable element expression , 2020, Nature Reviews Genetics.

[5]  D. Lambrechts,et al.  A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling , 2020, Cell Research.

[6]  Y. Cho,et al.  Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer , 2020, Nature Genetics.

[7]  P. Gendron,et al.  Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues , 2020, Genome Medicine.

[8]  K. Burns Our Conflict with Transposable Elements and Its Implications for Human Disease. , 2020, Annual review of pathology.

[9]  P. Hegde,et al.  Top 10 Challenges in Cancer Immunotherapy. , 2020, Immunity.

[10]  R. Herbst,et al.  Immune Cell PD-L1 Colocalizes with Macrophages and Is Associated with Outcome in PD-1 Pathway Blockade Therapy , 2019, Clinical Cancer Research.

[11]  M. Fakih,et al.  Immune overdrive signature in colorectal tumor subset predicts poor clinical outcome. , 2019, The Journal of clinical investigation.

[12]  Jinchuan Xing,et al.  SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina , 2019, Nucleic acids research.

[13]  Subha Madhavan,et al.  Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities , 2019, Cell.

[14]  Nakul M. Shah,et al.  Transposable elements drive widespread expression of oncogenes in human cancers , 2019, Nature Genetics.

[15]  Peter A. Jones,et al.  Epigenetic therapy in immune-oncology , 2019, Nature Reviews Cancer.

[16]  K. Burns,et al.  SQuIRE reveals locus-specific regulation of interspersed repeat expression , 2019, Nucleic acids research.

[17]  R. Bourgon,et al.  Transposable Element Exprssion in Tumors is Associated with Immune Infiltration and Increased Antigenicity , 2018, bioRxiv.

[18]  G. Bourque,et al.  Ten things you should know about transposable elements , 2018, Genome Biology.

[19]  P. Bose,et al.  TGF-β-associated extracellular matrix genes link cancer-associated fibroblasts to immune evasion and immunotherapy failure , 2018, Nature Communications.

[20]  J. Lunceford,et al.  Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy , 2018, Science.

[21]  Keith A. Crandall,et al.  Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression , 2018, bioRxiv.

[22]  F. Marincola,et al.  International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study , 2018, The Lancet.

[23]  Adrian V. Lee,et al.  An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics , 2018, Cell.

[24]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[25]  Steven J. M. Jones,et al.  The Immune Landscape of Cancer , 2018, Immunity.

[26]  Barry Smith,et al.  ImmPort, toward repurposing of open access immunological assay data for translational and clinical research , 2018, Scientific Data.

[27]  Camille Stephan-Otto Attolini,et al.  TGFβ drives immune evasion in genetically reconstituted colon cancer metastasis , 2018, Nature.

[28]  R. Bourgon,et al.  TGF-β attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells , 2018, Nature.

[29]  J. Whang‐Peng,et al.  PD‐L1 Expression of Tumor Cells, Macrophages, and Immune Cells in Non–Small Cell Lung Cancer Patients with Malignant Pleural Effusion , 2017, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[30]  Zhandong Liu,et al.  An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data , 2018, PSB.

[31]  Yingyan Yu Molecular classification and precision therapy of cancer: immune checkpoint inhibitors , 2018, Frontiers of Medicine.

[32]  Jeong Eon Lee,et al.  Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer , 2017, Nature Communications.

[33]  U. Lehmann,et al.  Transposable Elements in Human Cancer: Causes and Consequences of Deregulation , 2017, International journal of molecular sciences.

[34]  Eilon Barnea,et al.  Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy * , 2016, Molecular & Cellular Proteomics.

[35]  M. Beckmann,et al.  Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses , 2016, Cell.

[36]  Jeffrey S. Morris,et al.  The Consensus Molecular Subtypes of Colorectal Cancer , 2015, Nature Medicine.

[37]  Trevor J Pugh,et al.  DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts , 2015, Cell.

[38]  David C. Smith,et al.  Overall Survival and Long-Term Safety of Nivolumab (Anti-Programmed Death 1 Antibody, BMS-936558, ONO-4538) in Patients With Previously Treated Advanced Non-Small-Cell Lung Cancer. , 2015, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[39]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[40]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[41]  N. Hacohen,et al.  Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity , 2015, Cell.

[42]  H. Kohrt,et al.  Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients , 2014, Nature.

[43]  N. Neretti,et al.  Transcriptional landscape of repetitive elements in normal and cancer human cells , 2014, BMC Genomics.

[44]  F. Marincola,et al.  Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours , 2013, The Journal of pathology.

[45]  G. Getz,et al.  Inferring tumour purity and stromal and immune cell admixture from expression data , 2013, Nature Communications.

[46]  Terumasa Ikeda,et al.  Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases , 2013, Front. Microbio..

[47]  Justin Guinney,et al.  GSVA: gene set variation analysis for microarray and RNA-Seq data , 2013, BMC Bioinformatics.

[48]  Drew M. Pardoll,et al.  The blockade of immune checkpoints in cancer immunotherapy , 2012, Nature Reviews Cancer.

[49]  Benjamin Haibe-Kains,et al.  DNA methylation profiling reveals a predominant immune component in breast cancers , 2011, EMBO molecular medicine.

[50]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[51]  B. Peterlin,et al.  APOBEC3 Proteins Inhibit LINE‐1 Retrotransposition in the Absence of ORF1p Binding , 2009, Annals of the New York Academy of Sciences.

[52]  Ryan E. Mills,et al.  Which transposable elements are active in the human genome? , 2007, Trends in genetics : TIG.

[53]  R. Martienssen,et al.  Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.

[54]  W. Gerald,et al.  A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies , 2006, PLoS medicine.

[55]  Peter D Stenson,et al.  Meta‐Analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage , 2005, Human mutation.

[56]  Daniel J Sargent,et al.  Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. , 2003, The New England journal of medicine.

[57]  S. Bull,et al.  Tumor microsatellite instability and clinical outcome in young patients with colorectal cancer. , 2000, The New England journal of medicine.