2023
Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer
de Miguel F, Gentile C, Feng W, Silva S, Sankar A, Exposito F, Cai W, Melnick M, Robles-Oteiza C, Hinkley M, Tsai J, Hartley A, Wei J, Wurtz A, Li F, Toki M, Rimm D, Homer R, Wilen C, Xiao A, Qi J, Yan Q, Nguyen D, Jänne P, Kadoch C, Politi K. Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer. Cancer Cell 2023, 41: 1516-1534.e9. PMID: 37541244, PMCID: PMC10957226, DOI: 10.1016/j.ccell.2023.07.005.Peer-Reviewed Original ResearchConceptsMammalian SWI/SNF chromatinSWI/SNF chromatinMSWI/SNF complexesGenome-wide localizationGene regulatory signaturesNon-genetic mechanismsEpithelial cell differentiationEGFR-mutant cellsChromatin accessibilitySNF complexCellular programsRegulatory signaturesTKI-resistant lung cancerGene targetsKinase inhibitor resistanceCell differentiationMesenchymal transitionTKI resistancePharmacologic disruptionTyrosine kinase inhibitor resistanceCell proliferationChromatinInhibitor resistanceEGFR-mutant lungKinase inhibitorsFailure to Detect Influenza A H1N1 Highlights the Need for Multiple Gene Targets in Influenza Molecular Tests
Landry M, Owen M. Failure to Detect Influenza A H1N1 Highlights the Need for Multiple Gene Targets in Influenza Molecular Tests. Journal Of Clinical Microbiology 2023, 61: e00448-23. PMID: 37338345, PMCID: PMC10358165, DOI: 10.1128/jcm.00448-23.Peer-Reviewed Original ResearchHigh Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States
Hislop M, Allicock O, Thammavongsa D, Mbodj S, Nelson A, Shaw A, Weinberger D, Wyllie A. High Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States. Microbiology Spectrum 2023, 11: e05207-22. PMID: 37067447, PMCID: PMC10269540, DOI: 10.1128/spectrum.05207-22.Peer-Reviewed Original ResearchIntegrative miRNA–mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy
Andelic M, Salvi E, Marcuzzo S, Marchi M, Lombardi R, Cartelli D, Cazzato D, Mehmeti E, Gelemanovic A, Paolini M, Pardo C, D'Amato I, Hoeijmakers J, Dib-Hajj S, Waxman S, Faber C, Lauria G. Integrative miRNA–mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy. Brain 2023, 146: 3049-3062. PMID: 36730021, PMCID: PMC10316770, DOI: 10.1093/brain/awad025.Peer-Reviewed Original ResearchConceptsNeuropathic painPain-related mechanismsCohort of patientsSmall nerve fibersUnmet clinical needPainful neuropathyTargeted molecular profilingNeuropathy painPathophysiological mechanismsAvailable therapiesPreclinical modelsNerve fibersLimited efficacyHealthy individualsPersonalized managementPotential drug candidatesTranslational gapPainClinical needGene targetsPatientsImmunofluorescence assaysMolecular profilingMiR-30 familyProtein expression
2022
Distinct non‐coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages
Pantazi P, Clements T, Venø M, Abrahams V, Holder B. Distinct non‐coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages. Journal Of Extracellular Vesicles 2022, 11: 12293. PMID: 36544271, PMCID: PMC9772496, DOI: 10.1002/jev2.12293.Peer-Reviewed Original ResearchConceptsNon-coding RNAsSmall non-coding RNAsY RNA fragmentsTRNA fragmentsRNA cargoExtracellular vesiclesFull-length tRNASmall RNA sequencingPrimary macrophagesSmall RNA cargoHigh relative abundanceHuman primary macrophagesRNA sequencingEnrichment analysisGene targetsGene expressionFirst comprehensive analysisSignaling pathwaysFunctional cargoRelative abundanceLow abundancePutative roleRNASnoRNAsInflammatory signaling pathwaysA translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility
Voloudakis G, Vicari J, Venkatesh S, Hoffman G, Dobrindt K, Zhang W, Beckmann N, Higgins C, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee K, Bian J, Lee J, Iyengar S, Luoh S, Akbarian S, Striker R, Assimes T, Schadt E, Lynch J, Merad M, tenOever B, Charney A, Brennand K, Fullard J, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. Npj Genomic Medicine 2022, 7: 52. PMID: 36064543, PMCID: PMC9441828, DOI: 10.1038/s41525-022-00324-x.Peer-Reviewed Original ResearchCandidate gene targetsGene targetsTranslational genomics approachesHost susceptibilityGenomic approachesGenetic susceptibility variantsGenetic lociDruggable genesGene expressionMolecular pathwaysSusceptibility variantsCOVID-19 susceptibilityGenetic findingsApproach identifiesExpressionCOVID-19 patient bloodCritical next stepGenesLociOverexpressionTargetPathwaySusceptibilityIL10RBRecent efforts
2021
Krüppel-like factor 5 regulates wound repair and the innate immune response in human airway epithelial cells
Paranjapye A, NandyMazumdar M, Browne JA, Leir SH, Harris A. Krüppel-like factor 5 regulates wound repair and the innate immune response in human airway epithelial cells. Journal Of Biological Chemistry 2021, 297: 100932. PMID: 34217701, PMCID: PMC8353497, DOI: 10.1016/j.jbc.2021.100932.Peer-Reviewed Original ResearchConceptsKrüppel-like factor 5Lung epithelial cell lineEpithelial cell lineHistone modification H3K27acEpithelial cell identityDirect gene targetsSiRNA-mediated depletionHuman airway epithelial cellsCCAAT enhancer-binding protein betaEnhancer-binding protein betaCell linesSecretion of cytokinesAirway epithelial cellsHuman lung diseasesInnate immune responseHuman airway epitheliumPseudomonas aeruginosa lipopolysaccharideFactor 5Cell identityCalu-3 cellsChIP-seqTranscription factorsRNA-seqGene targetsIL-1βApplying stem cells and CRISPR engineering to uncover the etiology of schizophrenia
Michael Deans P, Brennand K. Applying stem cells and CRISPR engineering to uncover the etiology of schizophrenia. Current Opinion In Neurobiology 2021, 69: 193-201. PMID: 34010781, PMCID: PMC8387340, DOI: 10.1016/j.conb.2021.04.003.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsCell type-specific fashionStem cell biologyType-specific fashionDisease-associated variantsNeural cell typesCommon genetic variantsMore genesCell biologyCRISPR engineeringGene manipulationGene targetsCRISPR technologyMolecular geneticsInvaluable advancesCell typesHiPSC technologyGenetic variantsStem cellsIndividual variantsEtiology of diseasePolygenic disorderVariantsComplex interactionsRecent advancesEtiology of schizophreniaAP-2α Regulates S-Phase and Is a Marker for Sensitivity to PI3K Inhibitor Buparlisib in Colon Cancer
Beck AC, Cho E, White JR, Paemka L, Li T, Gu VW, Thompson DT, Koch KE, Franke C, Gosse M, Wu VT, Landers SR, Pamatmat AJ, Kulak MV, Weigel RJ. AP-2α Regulates S-Phase and Is a Marker for Sensitivity to PI3K Inhibitor Buparlisib in Colon Cancer. Molecular Cancer Research 2021, 19: 1156-1167. PMID: 33753551, PMCID: PMC8254761, DOI: 10.1158/1541-7786.mcr-20-0867.Peer-Reviewed Original ResearchMeSH KeywordsAminopyridinesAnimalsBiomarkers, TumorCell Line, TumorCell SurvivalColonic NeoplasmsGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockout TechniquesHCT116 CellsHumansMiceMorpholinesPhosphoinositide-3 Kinase InhibitorsRNA InterferenceRNA-SeqS PhaseTranscription Factor AP-2Xenograft Model Antitumor AssaysConceptsAP-2αPI3K inhibitorsColon cancer cell linesCell cycleS phasePrimary gene targetsK inhibitorsChromatin immunoprecipitation sequencingCancer cell linesPI3K cascadeProlonged S phaseCell linesActivation of AktShort hairpin RNAPhosphorylation of AktHistone H3Immunoprecipitation sequencingRNA sequencingPI3K inhibitionTarget genesK cascadeGene targetsTumor suppressorHairpin RNAColon cancer
2020
In-Depth Analysis of Genetic Variation Associated with Severe West Nile Viral Disease
Cahill ME, Loeb M, Dewan AT, Montgomery RR. In-Depth Analysis of Genetic Variation Associated with Severe West Nile Viral Disease. Vaccines 2020, 8: 744. PMID: 33302579, PMCID: PMC7768385, DOI: 10.3390/vaccines8040744.Peer-Reviewed Original ResearchAdditional novel variantsWest Nile virusNovel genetic variantsComprehensive genetic studiesGenetic Variation AssociatedGenetic architectureGene-gene interaction analysisNovel lociGene targetsLocus analysisBiological roleGenetic studiesGenetic variantsVirus datasetCell linesVariation AssociatedSevere West Nile neuroinvasive diseaseNovel variantsMosquito-borne virusViable targetViral diseasesNile virusInteraction analysisGenesLoci
2018
A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs
Wang Z, Gearhart MD, Lee YW, Kumar I, Ramazanov B, Zhang Y, Hernandez C, Lu AY, Neuenkirchen N, Deng J, Jin J, Kluger Y, Neubert TA, Bardwell VJ, Ivanova NB. A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs. Cell Stem Cell 2018, 22: 235-251.e9. PMID: 29337181, PMCID: PMC5797497, DOI: 10.1016/j.stem.2017.12.002.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationChromatinF-Box ProteinsHistonesHuman Embryonic Stem CellsHumansJumonji Domain-Containing Histone DemethylasesLysineMethylationMultiprotein ComplexesPolycomb Repressive Complex 1Polycomb Repressive Complex 2Promoter Regions, GeneticProtein DomainsProto-Oncogene ProteinsRepressor ProteinsConceptsEmbryonic stem cellsHuman embryonic stem cellsPolycomb domainsNon-canonical PRC1 complexesKey developmental lociNon-canonical complexesPolycomb group (PcG) proteinsE3 ubiquitin ligasesStem cell systemInitiation of differentiationDevelopmental lociPRC1 complexesRepressive chromatinRepressor functionPRC1.1 complexMesoderm lineageGroup proteinsCo-repressorAccessory subunitsDifferentiation programCanonical complexDevelopmental systemsC-terminusGene targetsN-terminus
2017
Using In Vivo and Tissue and Cell Explant Approaches to Study the Morphogenesis and Pathogenesis of the Embryonic and Perinatal Aorta.
Misra A, Feng Z, Zhang J, Lou ZY, Greif DM. Using In Vivo and Tissue and Cell Explant Approaches to Study the Morphogenesis and Pathogenesis of the Embryonic and Perinatal Aorta. Journal Of Visualized Experiments 2017 PMID: 28930997, PMCID: PMC5752224, DOI: 10.3791/56039.Peer-Reviewed Original ResearchConceptsSmooth muscle cellsAortic smooth muscle cellsPregnant micePharmacological agentsAortic wallAortaLarge arteriesAdult aortaMuscle cellsEndothelial cellsPathological modelsHypothesis-generating experimentsContinuous exposureCell explantsTissue explantsPathogenesisFate mappingSpecific gene targetsClonal analysisNormal developmentVivoGene targetsExtracellular matrixClonal architectureCellsCorrelations of Abdominal Fat and Colonic Sulfidogenic Bacteria in African Americans and Non‐Hispanic Whites with Newly Diagnosed Colorectal Cancer
Gomez‐Perez S, Yazici C, Wolf P, Braunschweig C, Xicola R, Llor X, Ellis N, Tussing‐Humphreys L, Mutlu E, Gaskins R. Correlations of Abdominal Fat and Colonic Sulfidogenic Bacteria in African Americans and Non‐Hispanic Whites with Newly Diagnosed Colorectal Cancer. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.138.7.Peer-Reviewed Original ResearchAbdominal fat distributionNon-Hispanic whitesNational Cancer InstituteColonic mucosaAbdominal fatWaist circumferenceColorectal cancerCancer InstitutePreoperative abdominal computed tomography scansAfrican AmericansAbdominal computed tomography scanIncident colorectal cancerComputed tomography scanGene targetsIncident CRCMean ageFat distributionTomography scanColonic tissueGut microbiotaAbundance of DesulfovibrioL3 vertebraMucosaSignificant correlationCancer
2015
Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein
Londono-Renteria B, Troupin A, Conway MJ, Vesely D, Ledizet M, Roundy CM, Cloherty E, Jameson S, Vanlandingham D, Higgs S, Fikrig E, Colpitts TM. Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein. PLOS Pathogens 2015, 11: e1005202. PMID: 26491875, PMCID: PMC4619585, DOI: 10.1371/journal.ppat.1005202.Peer-Reviewed Original ResearchConceptsDENV infectionVirus infectionDengue virusCysteine-rich venom proteinsSpecific antiviral therapyDengue virus infectionMosquito-borne flavivirusAedes aegypti cellsAntiviral therapyFlavivirus infectionMultiple flavivirusesTherapeutic measuresNew treatmentsAedes aegyptiInfectionGene targetsSerious human diseasesAegypti cellsMosquito vectorsVaccineVenom proteinsFlavivirusesHuman diseasesMosquitoesAntiserum inhibitsEffects of Alcohol metabolism on Hepatocellular carcinoma progression
Puszyk W, Hlady R, Tiedemann R, Robertson K, Liu C. Effects of Alcohol metabolism on Hepatocellular carcinoma progression. The FASEB Journal 2015, 29 DOI: 10.1096/fasebj.29.1_supplement.45.8.Peer-Reviewed Original ResearchHepatocellular carcinomaTumor progressionModel of HCCRisk of developmentHepatocellular carcinoma progressionEffects of alcoholCancer deathCommon causeAlcohol consumptionCell culture modelCarcinoma progressionCIMP cancersAlcohol metabolismEthanol metabolismTumor developmentProgressionCancerCulture modelPrimary tissuesDNA methylationMethylation abnormalitiesGene targetsMetabolismCarcinomaAbnormalities
2014
Genistein Disrupts Glucocorticoid Receptor Signaling in Human Uterine Endometrial Ishikawa Cells
Whirledge S, Senbanjo LT, Cidlowski JA. Genistein Disrupts Glucocorticoid Receptor Signaling in Human Uterine Endometrial Ishikawa Cells. Environmental Health Perspectives 2014, 123: 80-87. PMID: 25136773, PMCID: PMC4286279, DOI: 10.1289/ehp.1408437.Peer-Reviewed Original ResearchConceptsTarget genesWhole-genome microarray analysisIshikawa cellsGlucocorticoid receptorGenome microarray analysisCommon gene targetsGR target genesTranscriptional responseNumerous genesDisruption of GRTranscriptional antagonismGlucocorticoid receptor signalingEnvironmental estrogen exposureRegulation of stressGene targetsSelect genesGene expressionCoadministration of genisteinEndometrial Ishikawa cellsMicroarray analysisReal-time reverse transcription-polymerase chain reactionFemale reproductive tractReverse transcription-polymerase chain reactionGenesQuantitative real-time reverse transcription-polymerase chain reaction
2011
Identification of Mirnas and Their Gene Targets Differentially Expressed in Microsatellite Stable and Unstable Colorectal Cancers Through an Integrated Analysis
Xicola R, Mu W, Huang L, Sohn V, Doyle B, Jover R, Carracedo A, Andreu M, Bessa X, Castells A, Boland C, Goel A, Investigators E, Dai Y, Llor X. Identification of Mirnas and Their Gene Targets Differentially Expressed in Microsatellite Stable and Unstable Colorectal Cancers Through an Integrated Analysis. Gastroenterology 2011, 140: s-819. DOI: 10.1016/s0016-5085(11)63391-x.Peer-Reviewed Original Research
2008
Linking Notch signaling to ischemic stroke
Arboleda-Velasquez JF, Zhou Z, Shin HK, Louvi A, Kim HH, Savitz SI, Liao JK, Salomone S, Ayata C, Moskowitz MA, Artavanis-Tsakonas S. Linking Notch signaling to ischemic stroke. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 4856-4861. PMID: 18347334, PMCID: PMC2290794, DOI: 10.1073/pnas.0709867105.Peer-Reviewed Original ResearchConceptsVascular smooth muscle cellsSmooth muscle cellsGenetic rescue experimentsUnderlying cellular pathwaysSpecific gene targetsKnockout mouse modelCellular pathwaysIschemic strokeGene targetsRescue experimentsSMC functionLong-term neurological disabilityMolecular analysisPathophysiology of strokeIschemic phenotypeMuscle cellsNotch-3Neurological disabilityCommon causeMouse modelStriking susceptibilityParaloguesStrokeNotchPhenotypeGenomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression
Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP. Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Molecular Systems Biology 2008, 4: msb200825. PMID: 18414489, PMCID: PMC2394496, DOI: 10.1038/msb.2008.25.Peer-Reviewed Original ResearchConceptsHistone variant H2A.ZVariant H2A.ZBreast cancer progressionTranscription factor-binding sitesTranscriptional regulatory cascadeCancer progressionGenome tiling arraysWhole-genome mappingFactor-binding sitesRegulatory cascadeTiling arraysChromatin immunoprecipitationGenome mappingGenomic analysisH2A.Z levelsRNA interferenceGene targetsGene expressionEpigenetic factorsMicroarray screeningH2A.ZCell proliferationLymph node metastasisBreast cancer survivalHigh expression
2001
Infection of Mice with the Agent of Human Granulocytic Ehrlichiosis after Different Routes of Inoculation
Hodzic E, Feng S, Fish D, Leutenegger C, Freet K, Barthold S. Infection of Mice with the Agent of Human Granulocytic Ehrlichiosis after Different Routes of Inoculation. The Journal Of Infectious Diseases 2001, 183: 1781-1786. PMID: 11372031, DOI: 10.1086/320735.Peer-Reviewed Original ResearchConceptsBone marrow samplesReal-time polymerase chain reactionPolymerase chain reactionHuman granulocytic ehrlichiosisMarrow samplesDay 20Granulocytic ehrlichiosisInfection of miceRate of infectionKinetics of infectionLymph nodesGene targetsInfected miceC3H miceEarly disseminationVascular perfusionDay 10Experimental infectionInfectionMiceNeedle inoculationChain reactionBloodEhrlichiosisInoculation
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