A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival

[1]  F. Tang,et al.  A map of tumor–host interactions in glioma at single-cell resolution , 2020, GigaScience.

[2]  C. Brennan,et al.  Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells , 2020, Cell.

[3]  L. D. Miller,et al.  Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response , 2020, Journal for ImmunoTherapy of Cancer.

[4]  Insuk Lee,et al.  Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer , 2020, Genome Medicine.

[5]  E. Giovannetti,et al.  PTEN Alterations as a Potential Mechanism for Tumor Cell Escape from PD-1/PD-L1 Inhibition , 2019, Cancers.

[6]  N. Schultz,et al.  EGFR mutation subtypes and response to immune checkpoint blockade treatment in non-small-cell lung cancer , 2019, Annals of oncology : official journal of the European Society for Medical Oncology.

[7]  M. Ceccarelli,et al.  The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival , 2019, Communications Biology.

[8]  Ryan D. Chow,et al.  Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo. , 2019, Cell systems.

[9]  R. Rabadán,et al.  Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma , 2019, Nature Medicine.

[10]  J. Madore,et al.  Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy. , 2019, Cancer cell.

[11]  F. Marincola,et al.  The immunologic constant of rejection classification refines the prognostic value of conventional prognostic signatures in breast cancer , 2018, British Journal of Cancer.

[12]  S. Ganesh,et al.  RNAi-Mediated β-Catenin Inhibition Promotes T Cell Infiltration and Antitumor Activity in Combination with Immune Checkpoint Blockade , 2018, Molecular therapy : the journal of the American Society of Gene Therapy.

[13]  Eytan Ruppin,et al.  Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma , 2018, Nature Medicine.

[14]  G. Freeman,et al.  Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response , 2018, Nature Medicine.

[15]  F. Marincola,et al.  Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA) , 2018, Journal of Immunotherapy for Cancer.

[16]  T. Hudson,et al.  Immune oncology, immune responsiveness and the theory of everything , 2018, Journal of Immunotherapy for Cancer.

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

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

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

[20]  Tala,et al.  A metabolic function of FGFR3-TACC3 gene fusions in cancer , 2017, Nature.

[21]  T. Chan,et al.  Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab , 2017, Cell.

[22]  S. Loi,et al.  Agonist immunotherapy restores T cell function following MEK inhibition improving efficacy in breast cancer , 2017, Nature Communications.

[23]  J. Lunceford,et al.  IFN-&ggr;–related mRNA profile predicts clinical response to PD-1 blockade , 2017, The Journal of clinical investigation.

[24]  A. Moustakas,et al.  Epithelial–mesenchymal transition in cancer , 2017, Molecular oncology.

[25]  A. Tackett,et al.  Indicators of responsiveness to immune checkpoint inhibitors , 2017, Scientific Reports.

[26]  Hans Clevers,et al.  Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer , 2017, The Journal of experimental medicine.

[27]  F. Marincola,et al.  Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis , 2017, Oncoimmunology.

[28]  R. Weinberg,et al.  Emerging Biological Principles of Metastasis , 2017, Cell.

[29]  J. Sosman,et al.  Erratum: Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma (Cell (2016) 165(1) (35–44)(S009286741630215X)(10.1016/j.cell.2016.02.065)) , 2017 .

[30]  J. Lunceford,et al.  IFN- γ –related mRNA profile predicts clinical response to PD-1 blockade , 2017 .

[31]  M. Hallett,et al.  Identification of Interacting Stromal Axes in Triple-Negative Breast Cancer. , 2017, Cancer research.

[32]  H. Ishwaran,et al.  Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade , 2016, Cell.

[33]  J. Kutok,et al.  Overcoming resistance to checkpoint blockade therapy by targeting PI3Kγ in myeloid cells , 2016, Nature.

[34]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[35]  Y. Shentu,et al.  Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial , 2016, The Lancet.

[36]  M. Ceccarelli,et al.  Disentangling the relationship between tumor genetic programs and immune responsiveness. , 2016, Current opinion in immunology.

[37]  B. Saad,et al.  Analysis of PI3K pathway components in human cancers. , 2016, Oncology letters.

[38]  J. Sosman,et al.  Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma , 2016, Cell.

[39]  Shohei Koyama,et al.  Adaptive resistance to therapeutic PD-1 blockade is associated with upregulation of alternative immune checkpoints , 2016, Nature Communications.

[40]  B. Ammori,et al.  Combining FoxP3 and Helios with GARP/LAP markers can identify expanded Treg subsets in cancer patients , 2016, Oncotarget.

[41]  J. McQuade,et al.  Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. , 2016, Cancer discovery.

[42]  Steven J. M. Jones,et al.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma , 2016, Cell.

[43]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[44]  C. Rudin,et al.  Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer. , 2015, The New England journal of medicine.

[45]  S. Gabriel,et al.  Genomic correlates of response to CTLA-4 blockade in metastatic melanoma , 2015, Science.

[46]  O. Stål,et al.  Loss of protein tyrosine phosphatase, non-receptor type 2 is associated with activation of AKT and tamoxifen resistance in breast cancer , 2015, Breast Cancer Research and Treatment.

[47]  Ash A. Alizadeh,et al.  Abstract PR09: The prognostic landscape of genes and infiltrating immune cells across human cancers , 2015 .

[48]  Bert Vogelstein,et al.  PD-1 Blockade in Tumors with Mismatch-Repair Deficiency. , 2015, The New England journal of medicine.

[49]  T. Aparicio,et al.  PD-1 blockade in tumors with mismatch-repair deficiency , 2015 .

[50]  T. Gajewski,et al.  Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity , 2015, Nature.

[51]  J. Wolchok,et al.  Genetic basis for clinical response to CTLA-4 blockade. , 2015, The New England journal of medicine.

[52]  I. Melero,et al.  Genetic basis for clinical response to CTLA-4 blockade. , 2015, The New England journal of medicine.

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

[54]  J. Wolchok,et al.  Genetic basis for clinical response to CTLA-4 blockade in melanoma. , 2014, The New England journal of medicine.

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

[56]  Steven J. M. Jones,et al.  Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.

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

[58]  Jason B. Williams,et al.  Up-Regulation of PD-L1, IDO, and Tregs in the Melanoma Tumor Microenvironment Is Driven by CD8+ T Cells , 2013, Science Translational Medicine.

[59]  Jérôme Galon,et al.  The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. , 2013, Immunity.

[60]  Bart Spiessens,et al.  Predictive gene signature in MAGE-A3 antigen-specific cancer immunotherapy. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[61]  S. Enkemann,et al.  Lung tumor NF-κB signaling promotes T cell-mediated immune surveillance. , 2013, The Journal of clinical investigation.

[62]  J. Bergh,et al.  Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis , 2013, Genome Biology.

[63]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[64]  C. Sautès-Fridman,et al.  The immune contexture in human tumours: impact on clinical outcome , 2012, Nature Reviews Cancer.

[65]  D. Kranz.  Faculty Opinions recommendation of Suppression of antitumor immunity by stromal cells expressing fibroblast activation protein-alpha. , 2010 .

[66]  James O. Jones,et al.  Suppression of Antitumor Immunity by Stromal Cells Expressing , 2022 .

[67]  J. Geddes,et al.  What is a randomised controlled trial? , 2009, Epidemiologia e Psichiatria Sociale.

[68]  A. Nobel,et al.  Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[69]  Y. Wan,et al.  Transforming Growth Factor-β and the Immune Response: Implications for Anticancer Therapy , 2007, Clinical Cancer Research.

[70]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .