2024
Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology
Tan W, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Current Issues In Molecular Biology 2024, 46: 6533-6565. PMID: 39057032, PMCID: PMC11276574, DOI: 10.3390/cimb46070390.Peer-Reviewed Original ResearchCell-free DNA liquid biopsyCell-free DNALiquid biopsy technologiesLiquid biopsyBiopsy technologyEarly cancer detectionClinical applicationCfDNA-based liquid biopsyMonitoring residual diseaseEarly detection testsCancer detectionPotential of epigeneticsPersonalized cancer treatmentImprove cancer outcomesTissue of originFragmentation pattern analysisResidual diseaseDNA methylationMulti-cancer early detection testTreatment responseBiopsyCancer outcomesCancer preventionEpigeneticsPrecision oncologyA host–microbiota interactome reveals extensive transkingdom connectivity
Sonnert N, Rosen C, Ghazi A, Franzosa E, Duncan-Lowey B, González-Hernández J, Huck J, Yang Y, Dai Y, Rice T, Nguyen M, Song D, Cao Y, Martin A, Bielecka A, Fischer S, Guan C, Oh J, Huttenhower C, Ring A, Palm N. A host–microbiota interactome reveals extensive transkingdom connectivity. Nature 2024, 628: 171-179. PMID: 38509360, DOI: 10.1038/s41586-024-07162-0.Peer-Reviewed Original ResearchNiche colonizationHost–microorganism interactionsHost-microbiota interactionsInvade host tissuesStrain-specific interactionsHost cells in vitroConspecific strainsEffect of indigenous microorganismsHost biologyHost proteinsSecreted proteinsCommensal microorganismsExoproteinsBacterial strainsDiverse phylogenyMolecular basisMyriad microorganismsTissue of originTissue isolationCells in vitroInteractomeBinding patternsHost tissuesBiological logicHost immune system in vivo
2022
Developmental Deconvolution for Classification of Cancer Origin
Moiso E, Farahani A, Marble H, Hendricks A, Mildrum S, Levine S, Lennerz J, Garg S. Developmental Deconvolution for Classification of Cancer Origin. Cancer Discovery 2022, 12: 2566-2585. PMID: 36041084, PMCID: PMC9627133, DOI: 10.1158/2159-8290.cd-21-1443.Peer-Reviewed Original Research
2021
Discovering dominant tumor immune archetypes in a pan-cancer census
Combes A, Samad B, Tsui J, Chew N, Yan P, Reeder G, Kushnoor D, Shen A, Davidson B, Barczak A, Adkisson M, Edwards A, Naser M, Barry K, Courau T, Hammoudi T, Argüello R, Rao A, Olshen A, Consortium T, Spitzer M, Fong L, Nelson A, Kumar R, Lee J, Burra A, Hsu J, Hackett C, Tolentino K, Sjarif J, Johnson P, Shao E, Abrau D, Lupin L, Shaw C, Collins Z, Lea T, Corvera C, Nakakura E, Carnevale J, Alvarado M, Loo K, Chen L, Chow M, Grandis J, Ryan W, El-Sayed I, Jablons D, Woodard G, Meng M, Porten S, Okada H, Tempero M, Ko A, Kirkwood K, Vandenberg S, Guevarra D, Oropeza E, Cyr C, Glenn P, Bolen J, Morton A, Eckalbar W, Cai C, Zhan J, Davis K, Kelley R, Chapman J, Atreya C, Patel A, Daud A, Ha P, Diaz A, Kratz J, Collisson E, Fragiadakis G, Erle D, Boissonnas A, Asthana S, Chan V, Krummel M. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell 2021, 185: 184-203.e19. PMID: 34963056, PMCID: PMC8862608, DOI: 10.1016/j.cell.2021.12.004.Peer-Reviewed Original ResearchConceptsTumor immune microenvironmentIndividual tumorsTumor gene expression patternsCancer immunityImmune microenvironmentImmune compositionImmune systemTumor biologyUnique immuneTissue of originFlow cytometryCancer typesDriver mutationsImmune organizationDominant patternStandardized protocolTumorsSignificant heterogeneityCancerUniversity of CaliforniaTissueGene expression patternsCommon patternTherapyImmune
2020
Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care
Penson A, Camacho N, Zheng Y, Varghese A, Al-Ahmadie H, Razavi P, Chandarlapaty S, Vallejo C, Vakiani E, Gilewski T, Rosenberg J, Shady M, Tsui D, Reales D, Abeshouse A, Syed A, Zehir A, Schultz N, Ladanyi M, Solit D, Klimstra D, Hyman D, Taylor B, Berger M. Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care. JAMA Oncology 2020, 6: 84-91. PMID: 31725847, PMCID: PMC6865333, DOI: 10.1001/jamaoncol.2019.3985.Peer-Reviewed Original ResearchConceptsTumor typesTissue of originGenomic analysis of plasma cell-free DNADNA sequence dataPlasma cell-free DNAClinical DNA sequencingOncology practiceAnalysis of plasma cell-free DNAMetastatic breast cancerTumor biological characteristicsCohort of patientsTargeted tumor sequencingCell-free DNASequence dataSite of originGenomic analysisDNA sequencesClinical responseHistologic reviewTumor originMutant geneTherapeutic sensitivityBreast cancerMolecular alterationsDiverse clinical settings
2017
Regulatory network changes between cell lines and their tissues of origin
Lopes-Ramos C, Paulson J, Chen C, Kuijjer M, Fagny M, Platig J, Sonawane A, DeMeo D, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics 2017, 18: 723. PMID: 28899340, PMCID: PMC5596945, DOI: 10.1186/s12864-017-4111-x.Peer-Reviewed Original ResearchConceptsLymphoblastoid cell linesCell linesTranscription factor (TFChIP-seq dataRegulatory network changesRNA-seq dataTissue of originRegulatory network analysisCell cycle genesPrimary tissuesGene expression analysisEpstein-Barr virus-transformed lymphoblastoid cell linesChIP-seqVirus-transformed lymphoblastoid cell linesTF-targetRNA-seqGTEx projectTF regulationCycle genesTranscriptomic differencesBackgroundCell linesTranscript levelsExpression analysisFibroblast cell lineNetwork analysis
2014
Establishment of Human cell Type-Specific iPS cells with Enhanced Chondrogenic Potential
Guzzo RM, Scanlon V, Sanjay A, Xu RH, Drissi H. Establishment of Human cell Type-Specific iPS cells with Enhanced Chondrogenic Potential. Stem Cell Reviews And Reports 2014, 10: 820-829. PMID: 24958240, DOI: 10.1007/s12015-014-9538-8.Peer-Reviewed Original ResearchConceptsIPS cellsCell typesVivo functional analysisSpecialized cell typesNew cellular toolsSomatic cell typesChondrogenic potentialDelivery of Oct4Pluripotent differentiation capacityCell linesPluripotent stem cellsArticular chondrocytesHuman articular chondrocytesFate potentialEnhanced chondrogenic potentialHigh chondrogenic potentialSpecific lineagesFibroblast cell lineTissue of originCellular toolsGene expressionFunctional analysisDermal fibroblast cell lineChondrogenic differentiationDifferentiation capacity
2012
Gene expression array analysis to determine tissue of origin of carcinoma of unknown primary
Dolled‐Filhart M, Rimm DL. Gene expression array analysis to determine tissue of origin of carcinoma of unknown primary. Cancer Cytopathology 2012, 121: 129-135. PMID: 22927160, DOI: 10.1002/cncy.21228.Peer-Reviewed Original Research
2008
The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells
Chou YF, Chen HH, Eijpe M, Yabuuchi A, Chenoweth JG, Tesar P, Lu J, McKay RD, Geijsen N. The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells. Cell 2008, 135: 449-461. PMID: 18984157, PMCID: PMC2767270, DOI: 10.1016/j.cell.2008.08.035.Peer-Reviewed Original ResearchConceptsStem cell linesGrowth factor environmentPluripotent stateTissue of originCell linesEmbryonic stem cell linesPluripotent ground stateBlastocyst embryosStem cell identityCell-cell interactionsGrowth factor conditionsStem cell typesFactor environmentPostimplantation epiblastCell identityES cellsDevelopmental stagesCell typesStem cellsFunctional differencesCritical roleEmbryosGrowth factorGrowth factor milieuEpiSCs
2005
"Lineage Addiction" in Human Cancer: Lessons from Integrated Genomics
GARRAWAY L, WEIR B, ZHAO X, WIDLUND H, BEROUKHIM R, BERGER A, RIMM D, RUBIN M, FISHER D, MEYERSON M, SELLERS W. "Lineage Addiction" in Human Cancer: Lessons from Integrated Genomics. Cold Spring Harbor Symposia On Quantitative Biology 2005, 70: 25-34. PMID: 16869735, DOI: 10.1101/sqb.2005.70.016.Peer-Reviewed Original ResearchMeSH KeywordsChromosomes, Human, Pair 3Cluster AnalysisDNA, NeoplasmGene AmplificationGene DosageGene Expression ProfilingGenomicsHumansIn Situ Hybridization, FluorescenceMelanomaMicrophthalmia-Associated Transcription FactorNeoplasmsOligonucleotide Array Sequence AnalysisOncogenesPolymorphism, Single NucleotideConceptsLineage addictionGenome-scale data setsHigh-density single nucleotide polymorphism arraysNovel cancer genesSingle nucleotide polymorphism arrayDNA microarray platformCell line collectionCell linesAdditional functional studiesTumor survival mechanismsSNP array dataDetailed genomic characterizationGene expression dataDistinct tissue typesIntegrated GenomicCopy number alterationsTissue of originGenome characterizationSurvival mechanismCancer genesGenomic characterizationMelanoma cell linesSurvival pathwaysExpression dataProgression of tumors
2004
Plasticity of Bone Marrow–Derived Stem Cells
Grove JE, Bruscia E, Krause DS. Plasticity of Bone Marrow–Derived Stem Cells. Stem Cells 2004, 22: 487-500. PMID: 15277695, DOI: 10.1634/stemcells.22-4-487.Peer-Reviewed Original ResearchConceptsBone marrow stem cellsHematopoietic stem cellsStem cellsCell plasticityMesenchymal stem cellsStem cell plasticityGene expression profilesAdult stem cellsAdult bone marrow cellsMature lineagesAdult bone marrow stem cellsTissue of originExpression profilesMature cellsMarrow stem cellsBone marrow cellsNonhematopoietic tissuesMature phenotypePlasticityMarrow cellsCellsLineagesBone marrowPhenotypeTissue
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply