2015
Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR
Hinske L, Galante P, Limbeck E, Möhnle P, Parmigiani R, Ohno-Machado L, Camargo A, Kreth S. Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR. PLOS ONE 2015, 10: e0121507. PMID: 25799583, PMCID: PMC4370670, DOI: 10.1371/journal.pone.0121507.Peer-Reviewed Original ResearchConceptsHost genesAlternative polyadenylationIntronic miRNAsMiR-579Protein-coding host genesPotential miRNA binding sitesHost gene expressionMiRNA binding sitesIntronic miRNAMiRNA genesNegative feedback loopRNA-seqPolyadenylation signalPolyadenylation sitesBioinformatics analysisCell line modelsGene expressionSilico analysisDifferential targetingPolyadenylationGenesMiRNAsZFRBinding sitesNegative feedback
2011
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Galante P, Parmigiani R, Zhao Q, Caballero O, de Souza J, Navarro F, Gerber A, Nicolás M, Salim A, Silva A, Edsall L, Devalle S, Almeida L, Ye Z, Kuan S, Pinheiro D, Tojal I, Pedigoni R, de Sousa R, Oliveira T, de Paula M, Ohno-Machado L, Kirkness E, Levy S, da Silva W, Vasconcelos A, Ren B, Zago M, Strausberg R, Simpson A, de Souza S, Camargo A. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research 2011, 39: 6056-6068. PMID: 21493686, PMCID: PMC3152357, DOI: 10.1093/nar/gkr221.Peer-Reviewed Original ResearchConceptsTumor genomesSomatic alterationsProtein-protein interaction analysisSynonymous substitutionsKEGG analysisEndogenous mutagensGenomeTumorigenic transformationNucleotide substitutionsBreast tumor cell linesReplication errorsTumor cell linesGenetic alterationsFrequency of mutationsCell linesTumorigenesisMutationsSynergistic functionDistinct patternsInteraction analysisLymphoblastoidAlterationsGenesSame individualPathwayTwist1-Induced Invadopodia Formation Promotes Tumor Metastasis
Eckert M, Lwin T, Chang A, Kim J, Danis E, Ohno-Machado L, Yang J. Twist1-Induced Invadopodia Formation Promotes Tumor Metastasis. Cancer Cell 2011, 19: 372-386. PMID: 21397860, PMCID: PMC3072410, DOI: 10.1016/j.ccr.2011.01.036.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Vesicular TransportAnimalsBase SequenceBreast NeoplasmsCell LineCell Line, TumorCell MovementCell Surface ExtensionsElectrophoresis, Polyacrylamide GelEpithelial-Mesenchymal TransitionFemaleHEK293 CellsHumansMiceMice, NudeNeoplasm MetastasisNeoplasmsNuclear ProteinsReceptor, Platelet-Derived Growth Factor alphaReverse Transcriptase Polymerase Chain ReactionRNA InterferenceSignal TransductionSrc Homology DomainsTwist-Related Protein 1ConceptsInvadopodia formationTumor metastasisFormation of invadopodiaDirect transcriptional targetTwist1 transcription factorEMT-inducing signalsMatrix degradationPromotes Tumor MetastasisMembrane protrusionsExtracellular matrix degradationTranscriptional targetsTranscription factorsInvadopodiaPDGFRα expressionMesenchymal transitionTwist1Central mediatorPDGFRαKey functionsSnail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis
Casas E, Kim J, Bendesky A, Ohno-Machado L, Wolfe C, Yang J. Snail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis. Cancer Research 2011, 71: 245-254. PMID: 21199805, PMCID: PMC3025803, DOI: 10.1158/0008-5472.can-10-2330.Peer-Reviewed Original Research
2008
Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications
Hasina R, Whipple M, Martin L, Kuo W, Ohno-Machado L, Lingen M. Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications. Laboratory Investigation 2008, 88: 342-353. PMID: 18283272, PMCID: PMC2614382, DOI: 10.1038/labinvest.2008.6.Peer-Reviewed Original Research