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The Immune Landscape of Cancer.
Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D; Wolf, Denise; Bortone, Dante S; Ou Yang, Tai-Hsien; Porta-Pardo, Eduard; Gao, Galen F; Plaisier, Christopher L; Eddy, James A; Ziv, Elad; Culhane, Aedin C; Paull, Evan O; Sivakumar, I K Ashok; Gentles, Andrew J; Malhotra, Raunaq; Farshidfar, Farshad; Colaprico, Antonio; Parker, Joel S; Mose, Lisle E; Vo, Nam Sy; Liu, Jianfang; Liu, Yuexin; Rader, Janet; Dhankani, Varsha; Reynolds, Sheila M; Bowlby, Reanne; Califano, Andrea; Cherniack, Andrew D; Anastassiou, Dimitris; Bedognetti, Davide; Mokrab, Younes; Newman, Aaron M; Rao, Arvind; Chen, Ken; Krasnitz, Alexander; Hu, Hai; Malta, Tathiane M; Noushmehr, Houtan; Pedamallu, Chandra Sekhar; Bullman, Susan; Ojesina, Akinyemi I; Lamb, Andrew; Zhou, Wanding; Shen, Hui; Choueiri, Toni K; Weinstein, John N; Guinney, Justin; Saltz, Joel; Holt, Robert A.
Afiliação
  • Thorsson V; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA. Electronic address: vesteinn.thorsson@systemsbiology.org.
  • Gibbs DL; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
  • Brown SD; Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
  • Wolf D; University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA.
  • Bortone DS; Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
  • Ou Yang TH; Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA.
  • Porta-Pardo E; Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA.
  • Gao GF; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
  • Plaisier CL; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA.
  • Eddy JA; Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA.
  • Ziv E; Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA.
  • Culhane AC; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • Paull EO; Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA.
  • Sivakumar IKA; Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA.
  • Gentles AJ; Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
  • Malhotra R; Seven Bridges Genomics, Cambridge, MA 02142, USA.
  • Farshidfar F; Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada.
  • Colaprico A; Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium.
  • Parker JS; Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
  • Mose LE; Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
  • Vo NS; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Liu J; Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA.
  • Liu Y; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Rader J; Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA.
  • Dhankani V; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
  • Reynolds SM; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
  • Bowlby R; Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
  • Califano A; Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA.
  • Cherniack AD; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
  • Anastassiou D; Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA.
  • Bedognetti D; Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar.
  • Mokrab Y; Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar.
  • Newman AM; Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
  • Rao A; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Chen K; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Krasnitz A; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
  • Hu H; Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA.
  • Malta TM; Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil.
  • Noushmehr H; Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil.
  • Pedamallu CS; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • Bullman S; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • Ojesina AI; University of Alabama at Birmingham, Birmingham, AL 35294, USA.
  • Lamb A; Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA.
  • Zhou W; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
  • Shen H; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
  • Choueiri TK; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • Weinstein JN; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Guinney J; Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA.
  • Saltz J; Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA.
  • Holt RA; Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Immunity ; 48(4): 812-830.e14, 2018 04 17.
Article em En | MEDLINE | ID: mdl-29628290
ABSTRACT
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-ß dominant-characterized by differences in macrophage or lymphocyte signatures, Th1Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genômica / Neoplasias Tipo de estudo: Prognostic_studies Limite: Adolescent / Adult / Aged / Aged80 / Child / Female / Humans / Male / Middle aged Idioma: En Revista: Immunity Assunto da revista: ALERGIA E IMUNOLOGIA Ano de publicação: 2018 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genômica / Neoplasias Tipo de estudo: Prognostic_studies Limite: Adolescent / Adult / Aged / Aged80 / Child / Female / Humans / Male / Middle aged Idioma: En Revista: Immunity Assunto da revista: ALERGIA E IMUNOLOGIA Ano de publicação: 2018 Tipo de documento: Article