DIY: Visualizing the immune landscape of tumors using transcriptome and methylome data.

[1]  S. M. Vareki.  High and low mutational burden tumors versus immunologically hot and cold tumors and response to immune checkpoint inhibitors , 2018 .

[2]  Y. Samuels,et al.  Cancer research in the era of immunogenomics , 2018, ESMO Open.

[3]  M. Dhodapkar,et al.  Checkpoint Inhibition in Myeloma: Opportunities and Challenges , 2018, Front. Immunol..

[4]  X. Liu,et al.  Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response , 2018, Nature Medicine.

[5]  E. King,et al.  Pan-cancer deconvolution of tumour composition using DNA methylation , 2018, Nature Communications.

[6]  J. Koropatnick,et al.  Treatment-naïve HPV+ head and neck cancers display a T-cell-inflamed phenotype distinct from their HPV- counterparts that has implications for immunotherapy , 2018, Oncoimmunology.

[7]  B. Fox,et al.  Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors , 2018, Nature Communications.

[8]  I. Hellstrom,et al.  Tumor Regression and Cure Depends on Sustained Th1 Responses , 2018, Journal of immunotherapy.

[9]  M. Fehlings,et al.  Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates , 2018, Nature.

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

[11]  Peter W. Laird,et al.  Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.

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

[13]  Z. Trajanoski,et al.  Quantifying tumor-infiltrating immune cells from transcriptomics data , 2018, Cancer Immunology, Immunotherapy.

[14]  Matthew Collin,et al.  Human dendritic cell subsets: an update , 2018, Immunology.

[15]  Edmond Sabo,et al.  The role of tumor-infiltrating lymphocytes (TILs) as a predictive biomarker of response to anti-PD1 therapy in patients with metastatic non-small cell lung cancer or metastatic melanoma , 2018, Medical Oncology.

[16]  G. Belz,et al.  Natural killer cells and anti-tumor immunity. , 2017, Molecular immunology.

[17]  N. Pochet,et al.  Transcriptional signature of human pro-inflammatory TH17 cells identifies reduced IL10 gene expression in multiple sclerosis , 2017, Nature Communications.

[18]  M. Zaidi,et al.  TAMeless traitors: macrophages in cancer progression and metastasis , 2017, British Journal of Cancer.

[19]  W. Guo,et al.  Elevated Th22 cells and related cytokines in patients with epithelial ovarian cancer , 2017, Medicine.

[20]  G. Freeman,et al.  Enhancing CD8+ T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy. , 2017, Cancer cell.

[21]  J. Barrett,et al.  Analysis of Class I Major Histocompatibility Complex Gene Transcription in Human Tumors Caused by Human Papillomavirus Infection , 2017, Viruses.

[22]  L. Emens.  Breast Cancer Immunotherapy: Facts and Hopes , 2017, Clinical Cancer Research.

[23]  J. Torchia,et al.  Human papillomavirus dysregulates the cellular apparatus controlling the methylation status of H3K27 in different human cancers to consistently alter gene expression regardless of tissue of origin , 2017, Oncotarget.

[24]  Tinghua Cao,et al.  RORγt and RORα signature genes in human Th17 cells , 2017, PloS one.

[25]  Laurence Zitvogel,et al.  The immune contexture in cancer prognosis and treatment , 2017, Nature Reviews Clinical Oncology.

[26]  D. Fisher,et al.  Immune and molecular correlates in melanoma treated with immune checkpoint blockade , 2017, Cancer.

[27]  I. Wistuba,et al.  VISTA is an inhibitory immune checkpoint that is increased after ipilimumab therapy in patients with prostate cancer , 2017, Nature Medicine.

[28]  D. Farber,et al.  Dendritic Cells Display Subset and Tissue‐Specific Maturation Dynamics over Human Life , 2017, Immunity.

[29]  S. Carter,et al.  Loss of PTEN Is Associated with Resistance to Anti‐PD‐1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma , 2017, Immunity.

[30]  Alberto Mantovani,et al.  Tumour-associated macrophages as treatment targets in oncology , 2017, Nature Reviews Clinical Oncology.

[31]  Pornpimol Charoentong,et al.  Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade , 2016, bioRxiv.

[32]  B. Ruffell,et al.  Dendritic Cells and Cancer Immunity. , 2016, Trends in immunology.

[33]  Patrick Danaher,et al.  Gene expression markers of Tumor Infiltrating Leukocytes , 2016, Journal of Immunotherapy for Cancer.

[34]  E. Elkord,et al.  Regulatory T Cells in the Tumor Microenvironment and Cancer Progression: Role and Therapeutic Targeting , 2016, Vaccines.

[35]  Jordan Anaya,et al.  OncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAs , 2016, PeerJ Comput. Sci..

[36]  J. Aguillón,et al.  Gene Expression Profiling of Human Monocyte-derived Dendritic Cells – Searching for Molecular Regulators of Tolerogenicity , 2015, Front. Immunol..

[37]  Jian Huang,et al.  Serum IL-10 Predicts Worse Outcome in Cancer Patients: A Meta-Analysis , 2015, PloS one.

[38]  P. Klenerman,et al.  CD39 Expression Identifies Terminally Exhausted CD8+ T Cells , 2015, PLoS pathogens.

[39]  A. Koch,et al.  MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data , 2015, BMC Genomics.

[40]  F. Gao,et al.  Th22 cell accumulation is associated with colorectal cancer development. , 2015, World journal of gastroenterology.

[41]  M. Kaplan,et al.  The development and in vivo function of T helper 9 cells , 2015, Nature Reviews Immunology.

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

[43]  M. Smyth,et al.  Balancing natural killer cell activation through paired receptors , 2015, Nature Reviews Immunology.

[44]  P. Validire,et al.  CD8+CD103+ Tumor–Infiltrating Lymphocytes Are Tumor-Specific Tissue-Resident Memory T Cells and a Prognostic Factor for Survival in Lung Cancer Patients , 2015, The Journal of Immunology.

[45]  F. Végran,et al.  Th9 Cells: a Novel Cd4 T-cell Subset in the Immune War against Cancer the Role of Cd4 T-cell Polarization in Cancer the Biology of Th9 Cells the Mechanism of the Antitumor Effects of Th9 Future Direction and Concluding Remarks , 2022 .

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

[47]  S. Mehrotra,et al.  Th17 Cells in Cancer: The Ultimate Identity Crisis , 2014, Front. Immunol..

[48]  Chester Ni,et al.  Identification of a specific gene signature in human Th1/17 cells (BA13P.126) , 2014, Journal of Immunology.

[49]  Xin Wang,et al.  Role of high expression of IL-9 in prognosis of CLL. , 2014, International journal of clinical and experimental pathology.

[50]  Y. Natkunam,et al.  Expression of the activating receptor, NKp46 (CD335), in human natural killer and T-cell neoplasia. , 2013, American journal of clinical pathology.

[51]  M. Kaplan,et al.  Th9 cell development requires a BATF-regulated transcriptional network. , 2013, The Journal of clinical investigation.

[52]  Z. Trajanoski,et al.  Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. , 2013, Immunity.

[53]  H. Schreiber,et al.  Innate and adaptive immune cells in the tumor microenvironment , 2013, Nature Immunology.

[54]  G. Coukos,et al.  CD137 Accurately Identifies and Enriches for Naturally Occurring Tumor-Reactive T Cells in Tumor , 2013, Clinical Cancer Research.

[55]  A. Bovier,et al.  Plasticity of tumour and immune cells: a source of heterogeneity and a cause for therapy resistance? , 2013, Nature Reviews Cancer.

[56]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[57]  I. Ellis,et al.  CD8+ T lymphocytes infiltrating breast cancer , 2012, Oncoimmunology.

[58]  K. Oestreich,et al.  Transcriptional mechanisms that regulate T helper 1 cell differentiation. , 2012, Current opinion in immunology.

[59]  B. Xia,et al.  CD4+T Cells: Differentiation and Functions , 2012, Clinical & developmental immunology.

[60]  K. Gunderson,et al.  High density DNA methylation array with single CpG site resolution. , 2011, Genomics.

[61]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[62]  G. D. de Bock,et al.  The prognostic influence of tumour-infiltrating lymphocytes in cancer: a systematic review with meta-analysis , 2011, British Journal of Cancer.

[63]  G. Hill,et al.  CD4+CD25+ regulatory T cells control CD8+ T-cell effector differentiation by modulating IL-2 homeostasis , 2011, Proceedings of the National Academy of Sciences.

[64]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[65]  Zlatko Trajanoski,et al.  Histopathologic-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[66]  J. Fechner,et al.  An Interaction between Kynurenine and the Aryl Hydrocarbon Receptor Can Generate Regulatory T Cells , 2010, The Journal of Immunology.

[67]  S. Durham,et al.  Th22 cells represent a distinct human T cell subset involved in epidermal immunity and remodeling. , 2009, The Journal of clinical investigation.

[68]  L. Coussens,et al.  Polarized immune responses differentially regulate cancer development , 2008, Immunological reviews.

[69]  Edgar Erdfelder,et al.  G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences , 2007, Behavior research methods.

[70]  V. Reuter,et al.  CD8 tumor-infiltrating lymphocytes are predictive of survival in muscle-invasive urothelial carcinoma , 2007, Proceedings of the National Academy of Sciences.

[71]  Gerd Ritter,et al.  Intraepithelial CD8+ tumor-infiltrating lymphocytes and a high CD8+/regulatory T cell ratio are associated with favorable prognosis in ovarian cancer. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  P. Lipponen,et al.  Tumour-infiltrating lymphocytes: A prognostic factor of PSA-free survival in patients with local prostate carcinoma treated by radical prostatectomy. , 2005, Anticancer research.

[73]  T. Schumacher,et al.  On the Role of Melanoma-Specific CD8+ T-Cell Immunity in Disease Progression of Advanced-Stage Melanoma Patients , 2004, Clinical Cancer Research.

[74]  Akiko Kikuchi-Maki,et al.  NKp44 Triggers NK Cell Activation through DAP12 Association That Is Not Influenced by a Putative Cytoplasmic Inhibitory Sequence 1 , 2004, The Journal of Immunology.

[75]  T. Oshikiri,et al.  CD8+ Tumor-Infiltrating Lymphocytes Together with CD4+ Tumor-Infiltrating Lymphocytes and Dendritic Cells Improve the Prognosis of Patients with Pancreatic Adenocarcinoma , 2004, Pancreas.

[76]  B. Plougastel,et al.  Immune functions encoded by the natural killer gene complex , 2003, Nature Reviews Immunology.

[77]  D. Munn,et al.  Tryptophan deprivation sensitizes activated T cells to apoptosis prior to cell division , 2002, Immunology.

[78]  G. Damonte,et al.  Tryptophan-derived Catabolites Are Responsible for Inhibition of T and Natural Killer Cell Proliferation Induced by Indoleamine 2,3-Dioxygenase , 2002, The Journal of experimental medicine.

[79]  A. Borrie,et al.  T Lymphocyte-Based Cancer Immunotherapeutics. , 2018, International review of cell and molecular biology.

[80]  K. Kinzler,et al.  The vigorous immune microenvironment of microsatellite instable colon cancer is balanced by multiple counter-inhibitory checkpoints , 2015, Journal of Immunotherapy for Cancer.