2024
Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma.
Aung T, Warrell J, Martinez-Morilla S, Gavrielatou N, Vathiotis I, Yaghoobi V, Kluger H, Gerstein M, Rimm D. Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical Cancer Research 2024, 30: 3520-3532. PMID: 38837895, PMCID: PMC11326985, DOI: 10.1158/1078-0432.ccr-23-3932.Peer-Reviewed Original ResearchGene signatureResistance to immunotherapyResponse to immunotherapyPrediction of treatment outcomeResistant to treatmentAccurate prediction of treatment outcomePredictive of responseImmunotherapy outcomesMelanoma patientsMelanoma specimensValidation cohortPatient stratificationDiscovery cohortTreatment outcomesImmunotherapyMelanomaTumorPatientsCohortS100BOutcomesGene expression dataGenesCD68+macrophagesExpression data
2022
133 Spatially defined gene signatures uncover the association of extracellular matrix genes with immunotherapy resistance in head and neck squamous cell carcinoma
Gavrielatou N, Warrell J, Aung T, Vathiotis L, Economopoulou P, Burtness B, Psyrri A, Rimm D. 133 Spatially defined gene signatures uncover the association of extracellular matrix genes with immunotherapy resistance in head and neck squamous cell carcinoma. 2022, a146-a146. DOI: 10.1136/jitc-2022-sitc2022.0133.Peer-Reviewed Original Research
2011
A Pathway for the Control of Anoikis Sensitivity by E-Cadherin and Epithelial-to-Mesenchymal Transition
Kumar S, Park SH, Cieply B, Schupp J, Killiam E, Zhang F, Rimm DL, Frisch SM. A Pathway for the Control of Anoikis Sensitivity by E-Cadherin and Epithelial-to-Mesenchymal Transition. Molecular And Cellular Biology 2011, 31: 4036-4051. PMID: 21746881, PMCID: PMC3187352, DOI: 10.1128/mcb.01342-10.Peer-Reviewed Original ResearchConceptsRegulation of anoikisE-cadherin complexMesenchymal transitionE-cadherinAnoikis sensitivityNuclear localizationInappropriate matrixAnoikis resistanceApoptotic responseOncogenic EMTAnoikisNRAGECellular sensitivityNovel pathwayUnknown mechanismAnkyrinEpithelial cellsEMTPathwayP14ARFCellsTbx2ComplexesGenesCytoplasmProinvasion Metastasis Drivers in Early-Stage Melanoma Are Oncogenes
Scott KL, Nogueira C, Heffernan TP, van Doorn R, Dhakal S, Hanna JA, Min C, Jaskelioff M, Xiao Y, Wu CJ, Cameron LA, Perry SR, Zeid R, Feinberg T, Kim M, Woude G, Granter SR, Bosenberg M, Chu GC, DePinho RA, Rimm DL, Chin L. Proinvasion Metastasis Drivers in Early-Stage Melanoma Are Oncogenes. Cancer Cell 2011, 20: 92-103. PMID: 21741599, PMCID: PMC3176328, DOI: 10.1016/j.ccr.2011.05.025.Peer-Reviewed Original ResearchMeSH KeywordsAcid PhosphataseAnimalsCell LineageConserved SequenceEvolution, MolecularGene Expression ProfilingGene Expression Regulation, NeoplasticGenomeHumansIsoenzymesKaplan-Meier EstimateMelanomaMiceNeoplasm InvasivenessNeoplasm MetastasisNeoplasm StagingOncogenesPhosphorylationReproducibility of ResultsSkin NeoplasmsTartrate-Resistant Acid PhosphataseTissue Array AnalysisConceptsFunctional genetic screensGenetic screenGlobal transcriptomeMetastatic potentialSuch genesGenomic evidenceExpression selectionTranscriptomic profilesHuman melanoma tissuesMetastasis driverCell invasionKey pathwaysOncogenic capabilitiesMelanoma tissuesGenesHuman melanomaHuman primary melanomasTranscriptomeMouse modelSpontaneous metastasisOncogeneEnhancerACP5PathwayInvasion
2009
Analysis of Drosophila Segmentation Network Identifies a JNK Pathway Factor Overexpressed in Kidney Cancer
Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. Analysis of Drosophila Segmentation Network Identifies a JNK Pathway Factor Overexpressed in Kidney Cancer. Science 2009, 323: 1218-1222. PMID: 19164706, PMCID: PMC2756524, DOI: 10.1126/science.1157669.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsApoptosisCarcinoma, Renal CellCell LineCompound Eye, ArthropodDrosophila melanogasterDrosophila ProteinsEmbryo, NonmammalianFushi Tarazu Transcription FactorsGene Expression ProfilingGene Regulatory NetworksHomeodomain ProteinsHumansJanus KinasesKidneyKidney NeoplasmsMolecular Sequence DataNervous SystemNuclear ProteinsPhosphoprotein PhosphatasesPhosphorylationRepressor ProteinsSignal TransductionTranscription FactorsTranscription, GeneticConceptsTranscription factorsClear cell renal cell carcinomaCell renal cell carcinomaKey transcription factorDrosophila segmentation networkConserved roleEmbryonic segmentationDrosophila melanogasterUbiquitin E3JNK signalingDependent apoptosisSPOPRenal cell carcinomaSPOP expressionKidney cancerTumor necrosis factorNew roleDrosophilaMelanogasterPuckeredGenesSignalingOverexpressedIdentificationApoptosis
2005
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005, 436: 117-122. PMID: 16001072, DOI: 10.1038/nature03664.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorCell LineageCell SurvivalChromosomes, Human, Pair 3Disease ProgressionDNA-Binding ProteinsGene AmplificationGene DosageGene Expression Regulation, NeoplasticGenomicsHumansIn Situ Hybridization, FluorescenceMelanomaMicrophthalmia-Associated Transcription FactorOncogenesPolymerase Chain ReactionPolymorphism, Single NucleotideTranscription FactorsConceptsMITF gene expressionDNA amplification eventsIntegrative genomic analysisLineage-survival oncogenePossible drug targetsGenomics effortsGenomic analysisGenetic dataGene expressionMelanoma formationAmplification eventsMelanoma genesDrug targetsCancer cell linesGenetic alterationsCell linesMITFMelanoma cellsHuman melanomaMalignant melanomaGenesMelanomaOncogeneExpressionCells
2004
Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas
Hoek K, Rimm DL, Williams KR, Zhao H, Ariyan S, Lin A, Kluger HM, Berger AJ, Cheng E, Trombetta ES, Wu T, Niinobe M, Yoshikawa K, Hannigan GE, Halaban R. Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas. Cancer Research 2004, 64: 5270-5282. PMID: 15289333, DOI: 10.1158/0008-5472.can-04-0731.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiomarkers, TumorCell Transformation, NeoplasticCohort StudiesDown-RegulationGene Expression ProfilingGene Expression Regulation, NeoplasticHumansLymphatic MetastasisMelanocytesMelanomaMiceNuclear ProteinsOligonucleotide Array Sequence AnalysisPrognosisSignal TransductionSkin NeoplasmsSurvival RateTranscription FactorsTransfectionTwist-Related Protein 1Ubiquitin ThiolesteraseConceptsGlobal differential gene expressionMembrane trafficking eventsNovel pathwayNormal melanocytesHelix protein TwistAdditional transcriptional regulatorsDifferential gene expressionMelanoma cellsTransformation of melanocytesCpG promoter methylationNormal human melanocytesTrafficking eventsTranscriptional regulatorsEmbryonic developmentGrowth suppressorChromosomal regionsExpression profilingGene expressionNotch pathwayOligonucleotide microarraysMelanoma tissue microarrayDifferential expressionGenesHuman melanocytesGrowth advantage
1991
Analysis of cDNA clones for Acanthamoeba profilin‐I and profilin‐II shows end to end homology with vertebrate profilins and a small family of profilin genes
Pollard T, Rimm D. Analysis of cDNA clones for Acanthamoeba profilin‐I and profilin‐II shows end to end homology with vertebrate profilins and a small family of profilin genes. Cytoskeleton 1991, 20: 169-177. PMID: 1751969, DOI: 10.1002/cm.970200209.Peer-Reviewed Original ResearchConceptsProfilin IIDNA sequencesProtein sequencesAcanthamoeba profilinGenomic DNA fragmentsFull-length cDNAFamily of proteinsProfilin geneAncestral precursorDifferent phylaInvariant residuesAdditional genesCDNA clonesLength cDNAConservative substitutionsPairwise identityDNA fragmentsSouthern blotNorthern blotGenesProfilinAmino acidsSmall familyCDNAConsiderable divergence
1988
Resolution of Acanthamoeba castellanii chromosomes by pulsed field gel electrophoresis and construction of the initial linkage map
Rimm D, Pollard T, Hieter P. Resolution of Acanthamoeba castellanii chromosomes by pulsed field gel electrophoresis and construction of the initial linkage map. Chromosoma 1988, 97: 219-223. PMID: 3219918, DOI: 10.1007/bf00292964.Peer-Reviewed Original ResearchConceptsChromosome-sized DNA moleculesMyosin II geneGel electrophoresisDNA moleculesField gel electrophoresisNon-allelic genesProtozoan Acanthamoeba castellaniiDifferent chromosomal bandsLower eukaryotesLinkage mapSmall chromosomesLarge chromosomesLinkage groupsElectrophoretic karyotypeChromosomal bandsChromosome bandsMyosin IBChromosomesAcanthamoeba castellaniiGenesBiochemical researchElectrophoresisEukaryotesDictyosteliumFungi
1984
Structural analysis of the murine IgG3 constant region gene.
Wels J, Word C, Rimm D, Der-Balan G, Martinez H, Tucker P, Blattner F. Structural analysis of the murine IgG3 constant region gene. The EMBO Journal 1984, 3: 2041-6. PMID: 6092053, PMCID: PMC557641, DOI: 10.1002/j.1460-2075.1984.tb02089.x.Peer-Reviewed Original ResearchConceptsConstant region genesMembrane exonsMRNA precursorsHeavy chain constant region genesAmino acid sequenceRegion genesSwitch recombination regionC gamma 3 geneGamma 3 chainCarbohydrate addition sitesProtein domainsC deltaCarboxyl terminusComplete sequenceAcid sequenceRemarkable homologyGamma 3 geneAddition siteSwitch sitesSecondary structureMembrane formClass switch mechanismExonsGenesC mu