2023
Nmes1 is a novel regulator of mucosal response influencing intestinal healing potential
Hamley M, Leyk S, Casar C, Liebold I, Al Jawazneh A, Lanzloth C, Böttcher M, Haas H, Richardt U, Rothlin C, Jacobs T, Huber S, Adlung L, Pelczar P, Henao‐Mejia J, Bosurgi L. Nmes1 is a novel regulator of mucosal response influencing intestinal healing potential. European Journal Of Immunology 2023, 54: e2350434. PMID: 37971166, DOI: 10.1002/eji.202350434.Peer-Reviewed Original ResearchMucosal healingSchistosoma mansoni infectionCytokines IL-4Innovative therapeutic approachesDifferent intestinal diseasesWound-healing potentialIntestinal damageMucosal responsesMansoni infectionInflamed colonIL-4Intestinal disordersIntestinal diseaseNormal mucosaMurine modelTherapeutic approachesNovel regulatorType 2Advanced stageTherapy efficacyMacrophage responseCell therapyHealing potentialNew targetsIntestinal regenerationDYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner
Strine M, Cai W, Wei J, Alfajaro M, Filler R, Biering S, Sarnik S, Chow R, Patil A, Cervantes K, Collings C, DeWeirdt P, Hanna R, Schofield K, Hulme C, Konermann S, Doench J, Hsu P, Kadoch C, Yan Q, Wilen C. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLOS Biology 2023, 21: e3002097. PMID: 37310920, PMCID: PMC10263356, DOI: 10.1371/journal.pbio.3002097.Peer-Reviewed Original ResearchConceptsGenome-wide CRISPR/Cas9 screenCRISPR/Cas9 screenPathogenic human coronavirusesKinase-independent mannerRegulated kinase 1AProviral host factorNovel drug targetsMultiple cell typesDNA accessibilityHost factorsKinase functionHuman coronavirusesHost genesDistal enhancerNovel regulatorCas9 screenKinase 1AGene expressionNeuronal developmentDYRK1ADrug targetsDiverse coronavirusesProviral activityCell typesSevere acute respiratory syndrome coronavirus 2
2021
Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription
Ogawa LM, Buhagiar AF, Abriola L, Leland BA, Surovtseva YV, Baserga SJ. Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription. Molecular Biology Of The Cell 2021, 32: 956-973. PMID: 33689394, PMCID: PMC8108525, DOI: 10.1091/mbc.e20-10-0670.Peer-Reviewed Original ResearchConceptsRNA polymerase INumber of nucleoliRibosome biogenesisNucleolar organizer regionsPolymerase ICell cycleRNA polymerase I transcriptionPolymerase I transcriptionCell cycle regulationHigh-throughput quantitative imagingHuman diploid genomeIdentification of proteinsEukaryotic cellsG2/M phaseDiploid genomeNuclear condensatesRibosomal DNACycle regulationHuman breast epithelial cell lineBreast epithelial cell lineI transcriptionNovel regulatorEpithelial cell lineCycle progressionFunctional analysisLong noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state
Omote N, Sakamoto K, Li Q, Schupp JC, Adams T, Ahangari F, Chioccioli M, DeIuliis G, Hashimoto N, Hasegawa Y, Kaminski N. Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state. Physiological Reports 2021, 9: e14727. PMID: 33527707, PMCID: PMC7851438, DOI: 10.14814/phy2.14727.Peer-Reviewed Original ResearchConceptsTerminal differentiation-induced lncRNANormal human bronchial epithelial cellsTINCR overexpressionCell differentiationNotch genesTissue developmentBronchial epithelial cellsExtracellular matrix organizationCell phenotypeRNA sequencing analysisNumerous biological functionsRole of lncRNAsCell differentiation stateEpithelial cellsHuman bronchial epithelial cellsCiliated cell differentiationStaufen1 proteinNovel regulatorBasal cell phenotypeDownstream regulatorsRNA immunoprecipitationBiological functionsCritical regulatorDifferential expressionDifferentiation state
2020
FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo
Duprey A, Groisman EA. FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo. MBio 2020, 11: 10.1128/mbio.01053-20. PMID: 32723920, PMCID: PMC7387798, DOI: 10.1128/mbio.01053-20.Peer-Reviewed Original ResearchConceptsDNA supercoilingFluorescent proteinDNA supercoiling resultsBacterial DNA supercoilingSingle-cell heterogeneityGreen fluorescent proteinRed fluorescent proteinCellular physiologyDNA processesHigh-throughput methodConstitutive promoterNovel regulatorNucleotide sequenceGenetic informationRegulatory loopHigh-throughput measurementsSupercoilingForms of lifeGenesSingle cellsTranscriptionPromoterProteinChemical supportNovel fluorescence
2019
Rhomboid-Like-2 Intramembrane Protease Mediates Metalloprotease-Independent Regulation of Cadherins
Battistini C, Rehman M, Avolio M, Arduin A, Valdembri D, Serini G, Tamagnone L. Rhomboid-Like-2 Intramembrane Protease Mediates Metalloprotease-Independent Regulation of Cadherins. International Journal Of Molecular Sciences 2019, 20: 5958. PMID: 31783481, PMCID: PMC6928865, DOI: 10.3390/ijms20235958.Peer-Reviewed Original ResearchConceptsE-cadherin extracellular domainIntramembrane proteasesExtracellular domainPost-translational regulationSame functional pathwayRhomboid familyRHBDL2Tissue homeostasisNovel regulatorCell motilityNegative regulatorFunctional pathwaysCadherinMajor familiesCell migrationAdhesive receptorsFunctional roleNovel mechanismVE-cadherinNovel MMPsE-cadherinCancer cellsRegulatorProteaseEndothelial cellsProteomic Detection and Validation of Translated Small Open Reading Frames
Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Current Protocols In Chemical Biology 2019, 11: e77. PMID: 31750990, PMCID: PMC6878975, DOI: 10.1002/cpch.77.Peer-Reviewed Original ResearchConceptsSiRNA-based silencingSmall open reading framesNon-AUG start codonsOpen reading frameStandard proteomic methodsSpecific transcript isoformsCultured human cellsUnique tryptic peptidesGenomic lociShorter proteinTranscript isoformsProtein databaseProteomic methodsNovel regulatorReading frameProteomic detectionStart codonFunctional characterizationMass spectrometry-based detectionComplete annotationSmall proteinsHuman cellsTryptic peptidesProtein extractionSmORFs
2018
LRG1 is a novel regulator of endothelial activation and is shear dependent: A Potential therapeutic target?
Pang K, Fhu C, Ghim M, Tay H, Hou H, Lu Q, Warboys C, Wang X, Weinberg P. LRG1 is a novel regulator of endothelial activation and is shear dependent: A Potential therapeutic target? Atherosclerosis 2018, 275: e37. DOI: 10.1016/j.atherosclerosis.2018.06.094.Peer-Reviewed Original Research53LRG1 is a novel regulator of endothelial activation and is shear dependent: a potential therapeutic target?
Pang K, Fhu C, Ghim M, Tay H, Hou H, Lu Q, Warboys C, Wang X, Weinberg P. 53LRG1 is a novel regulator of endothelial activation and is shear dependent: a potential therapeutic target? Cardiovascular Research 2018, 114: s13-s14. DOI: 10.1093/cvr/cvy060.023.Peer-Reviewed Original ResearchHigh throughput discovery of novel regulators of human ribosome biogenesis
Baserga S, Farley‐Barnes K, McCann K, Ogawa L, Merkel J, Surovtseva Y. High throughput discovery of novel regulators of human ribosome biogenesis. The FASEB Journal 2018, 32: 526.25-526.25. DOI: 10.1096/fasebj.2018.32.1_supplement.526.25.Peer-Reviewed Original ResearchRibosome biogenesisNucleolar functionNumber of nucleoliMammalian cellsGenome-wide siRNA screenRNA polymerase I transcriptionHuman ribosome biogenesisPre-ribosomal RNAPolymerase I transcriptionExperimental Biology 2018 MeetingHigh-throughput discoveryNucleolar proteinsRibosomal DNAProtein regulatorsI transcriptionNew regulatorNovel regulatorSiRNA screenBiogenesisHuman cellsProteinRegulatorNucleoliFASEB JournalThroughput discoveryChitinase-3-like Protein 1: A Progranulin Downstream Molecule and Potential Biomarker for Gaucher Disease
Jian J, Chen Y, Liberti R, Fu W, Hu W, Saunders-Pullman R, Pastores G, Chen Y, Sun Y, Grabowski G, Liu C. Chitinase-3-like Protein 1: A Progranulin Downstream Molecule and Potential Biomarker for Gaucher Disease. EBioMedicine 2018, 28: 251-260. PMID: 29396296, PMCID: PMC5835567, DOI: 10.1016/j.ebiom.2018.01.022.Peer-Reviewed Original ResearchConceptsGD patientsHealthy controlsGaucher diseaseDownstream moleculesExpression of CHI3L1Serum CHI3L1Serum levelsPGRN levelsTherapeutic effectClinical biomarkersPatientsPotential biomarkersNull miceCHI3L1ProgranulinElevated levelsBiomarkersWhole-genome microarraysDiseaseCHIT1Genome microarraysNovel regulatorImmunohistochemistryLevelsMice
2017
TRAK2, a novel regulator of ABCA1 expression, cholesterol efflux and HDL biogenesis
Lake N, Taylor R, Trahair H, Harikrishnan K, Curran J, Almeida M, Kulkarni H, Mukhamedova N, Hoang A, Low H, Murphy A, Johnson M, Dyer T, Mahaney M, Göring H, Moses E, Sviridov D, Blangero J, Jowett J, Bozaoglu K. TRAK2, a novel regulator of ABCA1 expression, cholesterol efflux and HDL biogenesis. European Heart Journal 2017, 38: 3579-3587. PMID: 28655204, PMCID: PMC6251650, DOI: 10.1093/eurheartj/ehx315.Peer-Reviewed Original ResearchConceptsNovel regulatorLiver X receptorHDL biogenesisCholesterol effluxTranscription of ABCA1ABCA1 expressionSan Antonio Family Heart StudyAbsence of ABCA1Novel associationsSiRNA-mediated knockdownTrafficking proteinsTranscriptomic dataABCA1 promoterMolecular basisTRAK2RegulatorKnockdownBiogenesisHuman macrophagesMember 1Protein expressionEfflux pathwayX receptorHDL metabolismFamily Heart Study
2016
The neuropilin-like protein ESDN regulates insulin signaling and sensitivity
Li X, Jung JJ, Nie L, Razavian M, Zhang J, Samuel V, Sadeghi MM. The neuropilin-like protein ESDN regulates insulin signaling and sensitivity. AJP Heart And Circulatory Physiology 2016, 310: h1184-h1193. PMID: 26921437, PMCID: PMC4867389, DOI: 10.1152/ajpheart.00782.2015.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsAntigens, CDAorta, ThoracicCell MovementCell ProliferationCells, CulturedDose-Response Relationship, DrugEnzyme ActivationFemaleGenotypeGRB10 Adaptor ProteinInsulinInsulin ResistanceMaleMice, Inbred C57BLMice, KnockoutMitogen-Activated Protein KinasesMuscle, Smooth, VascularMyocytes, Smooth MuscleNeuropilinsPhenotypePhosphorylationProto-Oncogene Proteins c-aktReceptor, InsulinSignal TransductionTime FactorsUbiquitinationConceptsSignal transductionNovel regulatorSmooth muscle cell-derived neuropilin-like proteinInsulin receptorInsulin receptor signal transductionMitogen-activated protein kinase activationSrc homology 2Novel regulatory mechanismReceptor signal transductionProtein kinase BInsulin signal transductionProtein kinase activationInsulin receptor phosphorylationPleckstrin homologyHomology 2Adaptor proteinTransmembrane proteinGrowth factor receptorKinase activationVascular smooth muscle cell proliferationRegulatory mechanismsKinase BInsulin signalingReceptor phosphorylationNovel therapeutic avenues
2015
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency
Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Sui S, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell 2015, 162: 412-424. PMID: 26186193, PMCID: PMC4511597, DOI: 10.1016/j.cell.2015.06.016.Peer-Reviewed Original ResearchConceptsInduced pluripotencyHuman cellsEmbryonic patterning genesComplementary functional analysesPre-implantation stagesPatterning genesDevelopmental regulatorsEpigenomic analysisMolecular principlesNovel regulatorFunctional analysisIntegrative analysisIntercellular heterogeneityMolecular underpinningsPluripotencyDisease modelingCell platformRegulatorCellsDistinct wavesDonor variabilityGenesNemo-like kinase is a novel regulator of spinal and bulbar muscular atrophy
Todd TW, Kokubu H, Miranda HC, Cortes CJ, La Spada AR, Lim J. Nemo-like kinase is a novel regulator of spinal and bulbar muscular atrophy. ELife 2015, 4: e08493. PMID: 26308581, PMCID: PMC4577982, DOI: 10.7554/elife.08493.Peer-Reviewed Original ResearchConceptsNemo-like kinaseMuscular atrophyExact pathogenic mechanismProgressive neuromuscular diseaseAndrogen receptor proteinSBMA phenotypePathogenic mechanismsDisease pathogenesisNeuromuscular diseaseGene transcriptionTherapy developmentAtrophySBMAAR fragmentReceptor proteinPolyglutamine expansionMolecular mechanismsNovel regulatorNovel avenuesToxicityPathogenesisDiseaseMice
2014
Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response
Pulloor NK, Nair S, McCaffrey K, Kostic AD, Bist P, Weaver JD, Riley AM, Tyagi R, Uchil PD, York JD, Snyder SH, García-Sastre A, Potter BV, Lin R, Shears SB, Xavier RJ, Krishnan MN. Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response. PLOS Pathogens 2014, 10: e1003981. PMID: 24586175, PMCID: PMC3937324, DOI: 10.1371/journal.ppat.1003981.Peer-Reviewed Original ResearchConceptsInositol pyrophosphatesHuman genome-wide RNAi screenGenome-wide RNAi screenNovel regulatory proteinPattern recognition receptor RIGActivation of IRF3RNAi screenPositive regulatorTranscription factorsType I interferon responseType I interferon productionNovel regulatorRegulatory proteinsKinase activityBiochemical experimentsPhosphoryl transferIntact cellsInnate immune responseMetabolic pathwaysInterferon transcriptionGlobal regulationIRF3 activationCellular infectionPPIP5K2PPIP5K1
2012
microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma
Genovese G, Ergun A, Shukla SA, Campos B, Hanna J, Ghosh P, Quayle SN, Rai K, Colla S, Ying H, Wu CJ, Sarkar S, Xiao Y, Zhang J, Zhang H, Kwong L, Dunn K, Wiedemeyer WR, Brennan C, Zheng H, Rimm DL, Collins JJ, Chin L. microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma. Cancer Discovery 2012, 2: 736-749. PMID: 22750848, PMCID: PMC3911772, DOI: 10.1158/2159-8290.cd-12-0111.Peer-Reviewed Original ResearchConceptsMultidimensional cancer genomic dataPromoter enrichment analysisCancer genomic dataNovel regulatorGenomic dataContext likelihoodEnrichment analysisPutative regulatory networksFunctional genetic screensDifferent genetic elementsGenetic screenTGF-β signalingTranscriptional networksPlatelet-derived growth factorMRNA nodesGenome spaceRegulatory networksTranscriptomic networksBiology of cancerNovel regulationGenetic elementsTumor suppressorSilico analysisDirect regulationNew pathogenetic insights
2011
Functional and Structural Insights into ASB2α, a Novel Regulator of Integrin-dependent Adhesion of Hematopoietic Cells*
Lamsoul I, Burande CF, Razinia Z, Houles TC, Menoret D, Baldassarre M, Erard M, Moog-Lutz C, Calderwood DA, Lutz PG. Functional and Structural Insights into ASB2α, a Novel Regulator of Integrin-dependent Adhesion of Hematopoietic Cells*. Journal Of Biological Chemistry 2011, 286: 30571-30581. PMID: 21737450, PMCID: PMC3162417, DOI: 10.1074/jbc.m111.220921.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAmino Acid MotifsAnimalsCarrier ProteinsCell AdhesionFibronectinsGene Expression RegulationHeLa CellsHematopoietic Stem CellsHumansIntegrinsMiceMusclesNIH 3T3 CellsProtein BindingProtein Structure, TertiarySubstrate SpecificitySuppressor of Cytokine Signaling ProteinsConceptsN-terminal regionHematopoietic cellsE3 ubiquitin ligase complexE3 ubiquitin ligase functionShort N-terminal regionUbiquitin ligase complexUbiquitin ligase functionAcid-responsive genesIntegrin-dependent adhesionRetinoic acid-responsive geneCell fateLigase complexSpecificity subunitLigase functionResponsive genesLeukemia cellsProteasomal degradationNovel regulatorFilamin A.Myogenic differentiationStructural insightsASB2αΒ-integrinAcute promyelocytic leukemia cellsStructural homologyWNK2 Kinase Is a Novel Regulator of Essential Neuronal Cation-Chloride Cotransporters*
Rinehart J, Vázquez N, Kahle KT, Hodson CA, Ring AM, Gulcicek EE, Louvi A, Bobadilla NA, Gamba G, Lifton RP. WNK2 Kinase Is a Novel Regulator of Essential Neuronal Cation-Chloride Cotransporters*. Journal Of Biological Chemistry 2011, 286: 30171-30180. PMID: 21733846, PMCID: PMC3191056, DOI: 10.1074/jbc.m111.222893.Peer-Reviewed Original ResearchConceptsCation-chloride cotransportersSerine-threonine phosphorylationKinase-dependent mannerMammalian brainCell volume regulationSer-383Protein complexesRegulatory cascadeCotransporter regulationXenopus laevis oocytesNovel regulatorWNK2KinaseLaevis oocytesVolume regulationCl accumulationRecognition sitesWNKIntracellular concentrationRegulationSPAKAdult brainThalamic relay cellsThiazide-sensitive NCCMass spectrometry studies
2009
FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1
Norrmén C, Ivanov KI, Cheng J, Zangger N, Delorenzi M, Jaquet M, Miura N, Puolakkainen P, Horsley V, Hu J, Augustin HG, Ylä-Herttuala S, Alitalo K, Petrova TV. FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. Journal Of Cell Biology 2009, 185: 439-457. PMID: 19398761, PMCID: PMC2700385, DOI: 10.1083/jcb.200901104.Peer-Reviewed Original ResearchConceptsLymphatic vessel maturationGenome-wide mapsVessel maturationLymphatic endothelial cellsTranscription factor NFATc1Blood vessel maturationLymphatic developmentNovel regulatorLymphatic maturationUnsuspected linkFOXC2Control formationLymphatic collecting vesselsBlood vasculatureNFATc1Potential targetMaturationIntense investigationEndothelial cellsLymphatic vesselsLymphatic dysfunctionMorphological characterizationRegulatorEnhancerTherapeutic interventions
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