Low tumor purity is associated with poor prognosis, heavy mutation burden, and intense immune phenotype in colon cancer

References

• SiegelRLMillerKDJemalACancer statistics, 2018CA Cancer J Clin201868173029313949
   PubMed Web of Science ®Google Scholar
• HanahanDWeinbergRAHallmarks of cancer: the next generationCell2011144564667421376230
   PubMed Web of Science ®Google Scholar
• QuailDFJoyceJAMicroenvironmental regulation of tumor progression and metastasisNat Med201319111423143724202395
   PubMed Web of Science ®Google Scholar
• JunttilaMRde SauvageFJInfluence of tumour micro-environment heterogeneity on therapeutic responseNature2013501746734635424048067
   PubMed Web of Science ®Google Scholar
• AranDSirotaMButteAJSystematic pan-cancer analysis of tumour purityNat Commun20156897126634437
   PubMed Web of Science ®Google Scholar
• MeskerWEJunggeburtJMSzuhaiKThe carcinoma-stromal ratio of colon carcinoma is an independent factor for survival compared to lymph node status and tumor stageCell Oncol200729538739817726261
   PubMed Web of Science ®Google Scholar
• WestNPDattaniMMcShanePThe proportion of tumour cells is an independent predictor for survival in colorectal cancer patientsBr J Cancer2010102101519152320407439
   PubMed Web of Science ®Google Scholar
• HuijbersATollenaarRAv PeltGWThe proportion of tumorstroma as a strong prognosticator for stage II and III colon cancer patients: validation in the VICTOR trialAnn Oncol201324117918522865778
   PubMed Web of Science ®Google Scholar
• ParkJHRichardsCHMcMillanDCHorganPGRoxburghCSThe relationship between tumour stroma percentage, the tumour microenvironment and survival in patients with primary operable colorectal cancerAnn Oncol201425364465124458470
   PubMed Web of Science ®Google Scholar
• DanielsenHEHveemTSDomingoEPrognostic markers for colorectal cancer; estimating ploidy and stromaAnn Oncol201829361662329293881
   PubMed Web of Science ®Google Scholar
• MarisaLde ReynièsADuvalAGene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic valuePLoS Med2013105e100145323700391
   PubMed Web of Science ®Google Scholar
• FreemanTJSmithJJChenXSmad4-mediated signaling inhibits intestinal neoplasia by inhibiting expression of β-cateninGastroenterology20121423562571.e222115830
   PubMed Web of Science ®Google Scholar
• SmithJJDeaneNGWuFExperimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancerGastroenterology2010138395896819914252
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas NetworkComprehensive molecular characterization of human colon and rectal cancerNature2012487740733033722810696
   PubMed Web of Science ®Google Scholar
• YoshiharaKShahmoradgoliMMartínezEInferring tumour purity and stromal and immune cell admixture from expression dataNat Commun20134261224113773
   PubMed Web of Science ®Google Scholar
• ZhangCChengWRenXTumor purity as an underlying key factor in gliomaClin Cancer Res201723206279629128754819
   PubMed Web of Science ®Google Scholar
• BarretinaJCaponigroGStranskyNThe Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivityNature2012483739160360722460905
   PubMed Web of Science ®Google Scholar
• MayakondaAKoefflerHPMaftools: efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studiesbioRxiv2016
   Google Scholar
• HuangWShermanBTLempickiRASystematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesNat Protoc200941445719131956
   PubMed Web of Science ®Google Scholar
• HuangWShermanBTLempickiRABioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene listsNucleic Acids Res200937111319033363
   PubMed Web of Science ®Google Scholar
• MermelCHSchumacherSEHillBMeyersonMLBeroukhimRGetzGGISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancersGenome Biol2011124R4121527027
   PubMed Web of Science ®Google Scholar
• RobinsonMDMcCarthyDJSmythGKedgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics201026113914019910308
   PubMed Web of Science ®Google Scholar
• MoothaVKLindgrenCMErikssonKFPGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetesNat Genet200334326727312808457
   PubMed Web of Science ®Google Scholar
• SubramanianATamayoPMoothaVKGene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profilesProc Natl Acad Sci U S A200510243155451555016199517
   PubMed Web of Science ®Google Scholar
• CampRLDolled-FilhartMRimmDLX-tile: a new bio-informatics tool for biomarker assessment and outcome-based cut-point optimizationClin Cancer Res200410217252725915534099
   PubMed Web of Science ®Google Scholar
• YuanTLCantleyLCPI3K pathway alterations in cancer: variations on a themeOncogene200827415497551018794884
   PubMed Web of Science ®Google Scholar
• RheeJKJungYCKimKRImpact of tumor purity on immune gene expression and clustering analyses across multiple cancer typesCancer Immunol Res201861879729141981
   PubMed Web of Science ®Google Scholar
• CarterSLCibulskisKHelmanEAbsolute quantification of somatic DNA alterations in human cancerNat Biotechnol201230541342122544022
   PubMed Web of Science ®Google Scholar
• ZhengXZhaoQWuHJMethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomesGenome Biol201415841925103624
   PubMed Web of Science ®Google Scholar
• LiYXieXDeconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosityBioinformatics201430152121212924695406
   PubMed Web of Science ®Google Scholar
• LeeMSMenterDGKopetzSRight versus left colon cancer biology: integrating the consensus molecular subtypesJ Natl Compr Canc Netw201715341141928275039
   PubMed Web of Science ®Google Scholar
• GalloisCPernotSZaananATaiebJColorectal cancer: why does side matter?Drugs201878878979829790124
   PubMed Web of Science ®Google Scholar
• HalamaNZoernigIBerthelATumoral immune cell exploitation in colorectal cancer metastases can be targeted effectively by anti-CCR5 therapy in cancer patientsCancer Cell201629458760127070705
   PubMed Web of Science ®Google Scholar
• ZouWWolchokJDChenLPD-L1 (B7-H1) and PD-1 pathway blockade for cancer therapy: Mechanisms, response biomarkers, and combinationsSci Transl Med20168328328rv4
   PubMed Web of Science ®Google Scholar
• WuTDaiYTumor microenvironment and therapeutic responseCancer Lett2017387616826845449
   PubMed Web of Science ®Google Scholar
• LuPWeaverVMWerbZThe extracellular matrix: a dynamic niche in cancer progressionJ Cell Biol2012196439540622351925
   PubMed Web of Science ®Google Scholar
• Papadatos-PastosDRabbieRRossPSarkerDThe role of the PI3K pathway in colorectal cancerCrit Rev Oncol Hematol2015941183025591826
   PubMed Web of Science ®Google Scholar
• TsafrirDBacolodMSelvanayagamZRelationship of gene expression and chromosomal abnormalities in colorectal cancerCancer Res20066642129213716489013
   PubMed Web of Science ®Google Scholar
• AlonsoMHAussóSLopez-DorigaAComprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal componentBr J Cancer2017117342143128683472
   PubMed Web of Science ®Google Scholar
• NoyRPollardJWTumor-associated macrophages: from mechanisms to therapyImmunity2014411496125035953
   PubMed Web of Science ®Google Scholar
• OstuniRKratochvillFMurrayPJNatoliGMacrophages and cancer: from mechanisms to therapeutic implicationsTrends Immunol201536422923925770924
   PubMed Web of Science ®Google Scholar
• DroeserRAHirtCEppenberger-CastoriSHigh myeloperoxidase positive cell infiltration in colorectal cancer is an independent favorable prognostic factorPLoS One201385e6481423734221
   PubMed Web of Science ®Google Scholar
• GaldieroMRBianchiPGrizziFOccurrence and significance of tumor-associated neutrophils in patients with colorectal cancerInt J Cancer2016139244645626939802
   PubMed Web of Science ®Google Scholar
• RaoHLChenJWLiMIncreased intratumoral neutrophil in colorectal carcinomas correlates closely with malignant phenotype and predicts patients’ adverse prognosisPLoS One201271e3080622295111
   PubMed Web of Science ®Google Scholar
• ZhouGPengKSongYCD177+ neutrophils suppress epithelial cell tumourigenesis in colitis-associated cancer and predict good prognosis in colorectal cancerCarcinogenesis201839227228229228136
   PubMed Web of Science ®Google Scholar