Thorsson, VésteinnVésteinnThorssonGibbs, David LDavid LGibbsBrown, Scott DScott DBrownWolf, DeniseDeniseWolfBortone, Dante SDante SBortoneOu Yang, Tai-HsienTai-HsienOu YangPorta-Pardo, EduardEduardPorta-PardoGao, Galen FGalen FGaoPlaisier, Christopher LChristopher LPlaisierEddy, James AJames AEddyZiv, EladEladZivCulhane, Aedin CAedin CCulhanePaull, Evan OEvan OPaullSivakumar, I K AshokI K AshokSivakumarGentles, Andrew JAndrew JGentlesMalhotra, RaunaqRaunaqMalhotraFarshidfar, FarshadFarshadFarshidfarColaprico, AntonioAntonioColapricoParker, Joel SJoel SParkerMose, Lisle ELisle EMoseVo, Nam SyNam SyVoLiu, JianfangJianfangLiuLiu, YuexinYuexinLiuRader, JanetJanetRaderDhankani, VarshaVarshaDhankaniReynolds, Sheila MSheila MReynoldsBowlby, ReanneReanneBowlbyCalifano, AndreaAndreaCalifanoCherniack, Andrew DAndrew DCherniackAnastassiou, DimitrisDimitrisAnastassiouBedognetti, DavideDavideBedognettiRao, ArvindArvindRaoChen, KenKenChenKrasnitz, AlexanderAlexanderKrasnitzHu, HaiHaiHuMalta, Tathiane MTathiane MMaltaNoushmehr, HoutanHoutanNoushmehrPedamallu, Chandra SekharChandra SekharPedamalluBullman, SusanSusanBullmanOjesina, Akinyemi IAkinyemi IOjesinaLamb, AndrewAndrewLambZhou, WandingWandingZhouShen, HuiHuiShenChoueiri, Toni KToni KChoueiriWeinstein, John NJohn NWeinsteinGuinney, JustinJustinGuinneySaltz, JoelJoelSaltzHolt, Robert ARobert AHoltRabkin, Charles ECharles ERabkinLazar, Alexander JAlexander JLazarSerody, Jonathan SJonathan SSerodyDemicco, Elizabeth GElizabeth GDemiccoDisis, Mary LMary LDisisVincent, Benjamin GBenjamin GVincentShmulevich, LlyaLlyaShmulevich2024-10-082024-10-082018-04-17https://boris-portal.unibe.ch/handle/20.500.12422/64150We 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-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 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.encancer genomics immune subtypes immuno-oncology immunomodulatory immunotherapy integrative network analysis tumor immunology tumor microenvironment600 - Technology::610 - Medicine & healtharticle10.7892/boris.1263662962829010.1016/j.immuni.2018.03.023