Tumor microenvironment-based signatures distinguish intratumoral heterogeneity, prognosis, and immunogenomic features of clear cell renal cell carcinoma

[1]  D. Ye,et al.  Large-Scale Proteomics Data Reveal Integrated Prognosis-Related Protein Signatures and Role of SMAD4 and RAD50 in Prognosis and Immune Infiltrations of Prostate Cancer Microenvironment , 2022, Phenomics.

[2]  A. Jemal,et al.  Cancer statistics, 2022 , 2022, CA: a cancer journal for clinicians.

[3]  D. Ye,et al.  Prognostic Immunophenotyping Clusters of Clear Cell Renal Cell Carcinoma Defined by the Unique Tumor Immune Microenvironment , 2021, Frontiers in Cell and Developmental Biology.

[4]  W. Fan,et al.  Correlating Immune Cell Infiltration Patterns with Recurrent Somatic Mutations in Advanced Clear Cell Renal Cell Carcinoma. , 2021, European urology focus.

[5]  Steven L. Chang,et al.  Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma , 2021, Cancer cell.

[6]  Steven L. Chang,et al.  Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. , 2021, Cancer cell.

[7]  Yuling Chen,et al.  High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells , 2021, Genom. Proteom. Bioinform..

[8]  Ashton C. Berger,et al.  Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma , 2020, Nature Medicine.

[9]  Xifeng Wu,et al.  Soluble immune checkpoint-related proteins as predictors of tumor recurrence, survival, and T cell phenotypes in clear cell renal cell carcinoma patients , 2019, Journal of Immunotherapy for Cancer.

[10]  Guo Ci Teo,et al.  Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma , 2019, Cell.

[11]  Ahmedin Jemal,et al.  Cancer treatment and survivorship statistics, 2019 , 2019, CA: a cancer journal for clinicians.

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

[13]  B. Rini,et al.  Treatment of renal cell carcinoma: Current status and future directions , 2017, CA: a cancer journal for clinicians.

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

[15]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[16]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

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

[18]  W. Rathmell,et al.  Renal cell carcinoma , 2014, BMJ : British Medical Journal.

[19]  R. Emerson,et al.  PD-1 blockade induces responses by inhibiting adaptive immune resistance , 2014, Nature.

[20]  R. S. Huang,et al.  Abstract 5561: Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines , 2014 .

[21]  P. A. Futreal,et al.  Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing , 2014, Nature Genetics.

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

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

[24]  The Cancer Genome Atlas Research Network.  COMPREHENSIVE MOLECULAR CHARACTERIZATION OF CLEAR CELL RENAL CELL CARCINOMA , 2013, Nature.

[25]  N. Grishin,et al.  BAP1 loss defines a new class of renal cell carcinoma , 2012, Nature Genetics.

[26]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[27]  E. Wallen,et al.  Meta-analysis of clear cell renal cell carcinoma gene expression defines a variant subgroup and identifies gender influences on tumor biology. , 2012, European urology.

[28]  P. A. Futreal,et al.  Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma , 2010, Nature.

[29]  Gurpreet W. Tang,et al.  Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes , 2009, Nature.

[30]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[31]  N. Restifo,et al.  Natural selection of tumor variants in the generation of “tumor escape” phenotypes , 2002, Nature Immunology.

[32]  Jiejie Xu,et al.  HLA class I expression predicts prognosis and therapeutic benefits from tyrosine kinase inhibitors in metastatic renal-cell carcinoma patients , 2017, Cancer Immunology, Immunotherapy.