2023
Myocardial Recovery in Recent Onset Dilated Cardiomyopathy: Role of CDCP1 and Cardiac Fibrosis
Liu D, Wang M, Murthy V, McNamara D, Nguyen T, Philips T, Vyas H, Gao H, Sahni J, Starling R, Cooper L, Skime M, Batzler A, Jenkins G, Barlera S, Pileggi S, Mestroni L, Merlo M, Sinagra G, Pinet F, Krejčí J, Chaloupka A, Miller J, de Groote P, Tschumperlin D, Weinshilboum R, Pereira N. Myocardial Recovery in Recent Onset Dilated Cardiomyopathy: Role of CDCP1 and Cardiac Fibrosis. Circulation Research 2023, 133: 810-825. PMID: 37800334, PMCID: PMC10746262, DOI: 10.1161/circresaha.123.323200.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesRecent-onset dilated cardiomyopathyGenome-wide association study signalsLeft ventricular ejection fractionVentricular ejection fractionDilated CardiomyopathyHuman cardiac fibroblastsCardiac fibrosisMyocardial recoveryEjection fractionHeart failureAssociated with improved cardiac functionTranscriptome profilingCDCP1 expressionStandard drug therapyMolecular mechanismsVariant allelesAttenuated cardiac fibrosisHeart failure patientsCellular modelKnockdownDecreased AktStudy signalsCDCP1Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering
Abel A, Sozen B. Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering. Current Opinion In Genetics & Development 2023, 81: 102069. PMID: 37392541, PMCID: PMC10530566, DOI: 10.1016/j.gde.2023.102069.Peer-Reviewed Original ResearchContributions of circadian clock genes to cell survival in fibroblast models of lithium-responsive bipolar disorder
Mishra H, Wei H, Rohr K, Ko I, Nievergelt C, Maihofer A, Shilling P, Alda M, Berrettini W, Brennand K, Calabrese J, Coryell W, Frye M, Gage F, Gershon E, McInnis M, Nurnberger J, Oedegaard K, Zandi P, Kelsoe J, McCarthy M. Contributions of circadian clock genes to cell survival in fibroblast models of lithium-responsive bipolar disorder. European Neuropsychopharmacology 2023, 74: 1-14. PMID: 37126998, PMCID: PMC11801370, DOI: 10.1016/j.euroneuro.2023.04.009.Peer-Reviewed Original ResearchConceptsCell survival genesCircadian clockSurvival genesCell survivalCircadian clock genesCircadian rhythmGenetic variationClock genesKnockdown studiesCaspase activityCell deathMolecular pathwaysPrimary fibroblastsCellular modelGenesMouse fibroblastsFibroblast modelApoptosisStaurosporinePER1FibroblastsOpposite mannerLithium responsivenessDistinct patternsClock
2022
A nomenclature consensus for nervous system organoids and assembloids
Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Muotri AR, Park IH, Reiner O, Song H, Studer L, Temple S, Testa G, Treutlein B, Vaccarino FM. A nomenclature consensus for nervous system organoids and assembloids. Nature 2022, 609: 907-910. PMID: 36171373, PMCID: PMC10571504, DOI: 10.1038/s41586-022-05219-6.Peer-Reviewed Original ResearchControl of cell state transitions
Rukhlenko O, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher N, Kolch W, Kholodenko B. Control of cell state transitions. Nature 2022, 609: 975-985. PMID: 36104561, PMCID: PMC9644236, DOI: 10.1038/s41586-022-05194-y.Peer-Reviewed Original ResearchConceptsCell state transitionsCell fateCell statesCell fate transitionsCell fate decisionsSingle-cell dataNew biological insightsFate transitionsMovement of cellsFate decisionsWaddington landscapePhenotypic dataBiological insightsOmics datasetsOmics dataCellular modelMechanistic modelLandscape1FateCellsDevelopment pathwaysLandscapeBiologyState transitionsTherapeutic interventions
2021
Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons
Gowrishankar S, Lyons L, Rafiq NM, Roczniak-Ferguson A, De Camilli P, Ferguson SM. Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons. Molecular Biology Of The Cell 2021, 32: 1094-1103. PMID: 33788575, PMCID: PMC8351540, DOI: 10.1091/mbc.e20-06-0382.Peer-Reviewed Original ResearchConceptsAxonal transportAlzheimer's disease-related amyloid precursor proteinAmyloidogenic APP processingAmyloid precursor proteinDependence of neuronsHuman iPSCNeuronal cell biologyAPP processingAxonal lysosomesNeuronsLoss of JIP3Lysosome abundanceMovement of lysosomesPrecursor proteinCellular modelCritical regulatorStem cellsPluripotent stem cellsAβ42 peptideIPSCsLysosome transportLysosomesOverlapping rolePathology
2020
Discernment between candidate mechanisms for KRAS G13D colorectal cancer sensitivity to EGFR inhibitors
McFall T, Schomburg N, Rossman K, Stites E. Discernment between candidate mechanisms for KRAS G13D colorectal cancer sensitivity to EGFR inhibitors. Cell Communication And Signaling 2020, 18: 179. PMID: 33153459, PMCID: PMC7643456, DOI: 10.1186/s12964-020-00645-3.Peer-Reviewed Original ResearchConceptsKRAS mutationsKRAS G13DEGFR inhibitorsColorectal cancerSensitivity to EGFR inhibitorsRas-GTP levelsSensitivity to cetuximabClinical trial evidenceWild-type RasGTPase activityKRAS G13D mutationBind NF1Tumor suppressor NF1EGFR inhibitionG13D mutationKRASCetuximabBiophysical studiesTrial evidenceG13DWild-typeNF1MutationsCellular modelEGFRCellular and animal models for facioscapulohumeral muscular dystrophy
DeSimone AM, Cohen J, Lek M, Lek A. Cellular and animal models for facioscapulohumeral muscular dystrophy. Disease Models & Mechanisms 2020, 13: dmm046904. PMID: 33174531, PMCID: PMC7648604, DOI: 10.1242/dmm.046904.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsFacioscapulohumeral muscular dystrophyMicrosatellite repeat arraysNon-primate animalsRepeat arrayFSHD pathologyCellular pathwaysChromosome 4Myogenic differentiationExpression patternsMosaic expression patternMuscular dystrophyNew disease modelsHuman diseasesCellular modelMolecular factorsHumeral musclesSkeletal muscleDisease modelsMisexpressionDUX4GenesDrug candidatesTransgenicDifferentiationPathwaySevere respiratory viral infection induces procalcitonin in the absence of bacterial pneumonia
Gautam S, Cohen AJ, Stahl Y, Toro P, Young GM, Datta R, Yan X, Ristic NT, Bermejo SD, Sharma L, Restrepo M, Dela Cruz CS. Severe respiratory viral infection induces procalcitonin in the absence of bacterial pneumonia. Thorax 2020, 75: 974-981. PMID: 32826284, DOI: 10.1136/thoraxjnl-2020-214896.Peer-Reviewed Original ResearchConceptsPure viral infectionBacterial coinfectionViral infectionInfluenza infectionSevere respiratory viral infectionsAbility of procalcitoninRetrospective cohort studyViral respiratory infectionsRespiratory viral infectionsMarker of severityRespiratory viral illnessSevere viral infectionsSpecificity of procalcitoninCharacteristic curve analysisCellular modelHigher procalcitoninProcalcitonin expressionElevated procalcitoninCohort studyViral illnessRespiratory infectionsAntibiotic administrationBacterial pneumoniaSevere diseaseProcalcitoninComprehensive proteomic analysis of murine terminal erythroid differentiation
Gautier EF, Leduc M, Ladli M, Schulz VP, Lefèvre C, Boussaid I, Fontenay M, Lacombe C, Verdier F, Guillonneau F, Hillyer CD, Mohandas N, Gallagher PG, Mayeux P. Comprehensive proteomic analysis of murine terminal erythroid differentiation. Blood Advances 2020, 4: 1464-1477. PMID: 32282884, PMCID: PMC7160260, DOI: 10.1182/bloodadvances.2020001652.Peer-Reviewed Original ResearchConceptsTerminal erythroid differentiationErythroid differentiationProteomic dataMurine terminal erythroid differentiationTerminal differentiationOverall cellular contentComprehensive proteomic dataComprehensive proteomic analysisMurine erythroid cellsTerminal differentiation processMost biologic processesProteome levelComparison of murineHuman proteomeProteomic analysisTranscriptomic changesChromatin condensationProteomeErythroid cellsFundamental mechanismsRed cell disordersDifferentiation processErythroid progenitorsFriend erythroleukemiaCellular model
2019
BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications
Weathington N, O’Brien M, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie A, Jarjour N, Meyers D, Milosevic J, Moore W, Tedrow J, Trudeau J, Wong H, Wu W, Kaminski N, Wenzel S, Modena B. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. American Journal Of Respiratory And Critical Care Medicine 2019, 200: 837-856. PMID: 31161938, PMCID: PMC6812436, DOI: 10.1164/rccm.201811-2221oc.Peer-Reviewed Original ResearchMeSH KeywordsAdrenergic beta-AgonistsAdultAsthmaBronchoalveolar Lavage FluidCase-Control StudiesCyclic AMPEosinophilsEpithelial CellsFemaleGene ExpressionHumansIn Vitro TechniquesLymphocytesMacrophages, AlveolarMaleNeutrophilsSequence Analysis, RNASeverity of Illness IndexSignal TransductionTHP-1 CellsConceptsCell gene expressionGene expressionAirway epithelial cell gene expressionEpithelial cell gene expressionGlobal gene expressionCellular gene expressionCell expression profilesAsthma susceptibility lociProtein levelsSystem-wide analysisExpression networksImportant disease mechanismCoexpression networkCellular milieuExpression changesExpression profilesSusceptibility lociCellular modelDisease mechanismsBiomolecular mechanismsNew targetsRobust upregulationSample traitsGenesExpressionEverything You Always Wanted to Know about β3-AR * (* But Were Afraid to Ask)
Schena G, Caplan MJ. Everything You Always Wanted to Know about β3-AR * (* But Were Afraid to Ask). Cells 2019, 8: 357. PMID: 30995798, PMCID: PMC6523418, DOI: 10.3390/cells8040357.Peer-Reviewed Original ResearchConceptsNovel pharmacological approachesCurrent clinical practiceNovel therapeutic targetAR signalingΒ3-ARPharmacological approachesOcular diseasesTherapeutic targetAdrenergic receptorsClinical practiceFindings translateClinical areasCellular modelSuitable animalAppealing targetInter-species differencesDiseaseReceptors
2017
Guidelines on experimental methods to assess mitochondrial dysfunction in cellular models of neurodegenerative diseases
Connolly NMC, Theurey P, Adam-Vizi V, Bazan NG, Bernardi P, Bolaños JP, Culmsee C, Dawson VL, Deshmukh M, Duchen MR, Düssmann H, Fiskum G, Galindo MF, Hardingham GE, Hardwick JM, Jekabsons MB, Jonas EA, Jordán J, Lipton SA, Manfredi G, Mattson MP, McLaughlin B, Methner A, Murphy AN, Murphy MP, Nicholls DG, Polster BM, Pozzan T, Rizzuto R, Satrústegui J, Slack RS, Swanson RA, Swerdlow RH, Will Y, Ying Z, Joselin A, Gioran A, Moreira Pinho C, Watters O, Salvucci M, Llorente-Folch I, Park DS, Bano D, Ankarcrona M, Pizzo P, Prehn JHM. Guidelines on experimental methods to assess mitochondrial dysfunction in cellular models of neurodegenerative diseases. Cell Death & Differentiation 2017, 25: 542-572. PMID: 29229998, PMCID: PMC5864235, DOI: 10.1038/s41418-017-0020-4.Peer-Reviewed Original ResearchConceptsNeurodegenerative diseasesMitochondrial dysfunctionCellular modelSpectrum of chronicDeath of neuronsViable therapeutic targetPrimary neuron culturesMost neurodegenerative diseasesMitochondrial bioenergetic dysfunctionProgressive degenerationConsensus articleTherapeutic targetNeuron culturesDysfunctionSuch dysfunctionDiseaseHuntington's diseaseNeurodegenerative disease phenotypesBioenergetic dysfunctionDistinct molecular mechanismsCross-disease analysisDisease phenotypeMitochondrial functionCellular bioenergeticsMolecular mechanismsQuantitative study of zinc and metallothioneins in the human retina and RPE cells by mass spectrometry-based methodologies
Rodríguez-Menéndez S, Fernández B, García M, Álvarez L, Fernández M, Sanz-Medel A, Coca-Prados M, Pereiro R, González-Iglesias H. Quantitative study of zinc and metallothioneins in the human retina and RPE cells by mass spectrometry-based methodologies. Talanta 2017, 178: 222-230. PMID: 29136815, DOI: 10.1016/j.talanta.2017.09.024.Peer-Reviewed Original ResearchAdding dimension to cellular mechanotransduction: Advances in biomedical engineering of multiaxial cell-stretch systems and their application to cardiovascular biomechanics and mechano-signaling
Friedrich O, Schneidereit D, Nikolaev Y, Nikolova-Krstevski V, Schürmann S, Wirth-Hücking A, Merten A, Fatkin D, Martinac B. Adding dimension to cellular mechanotransduction: Advances in biomedical engineering of multiaxial cell-stretch systems and their application to cardiovascular biomechanics and mechano-signaling. Progress In Biophysics And Molecular Biology 2017, 130: 170-191. PMID: 28647645, DOI: 10.1016/j.pbiomolbio.2017.06.011.Peer-Reviewed Original ResearchConceptsFocal adhesion complexesCell-substrate junctionLive-cell imagingMechanosensitive ion channelsDirect mechanistic studiesAdhesion complexesCellular mechanotransductionMembrane junctionsIntracellular signalingMechanotransduction researchCellular stretchCellular modelIon channelsCellular levelCell membraneMechanotransductionIndividual cardiomyocytesBiomedical engineeringMechanical wall stressMembraneMechanistic studiesCellsStretch deviceCardiomyocytesElastomeric membrane
2016
The zinc‐metallothionein redox system in human retina and RPE
Alvarez L, García M, Rodríguez S, Fernández B, Pereiro R, Sanz‐Medel A, Coca‐Prados M, González‐Iglesias H. The zinc‐metallothionein redox system in human retina and RPE. Acta Ophthalmologica 2016, 94 DOI: 10.1111/j.1755-3768.2016.0560.Peer-Reviewed Original ResearchHuman RPE cellsInflammatory cytokinesNeuroprotective functionOxidative stress processesEye sectionsNeural retinaHuman donorsRPE cellsRetinaHuman retinaHuman eyeRPEMT proteinExogenous zincCellular zinc homeostasisCellular modelZinc homeostasisMain regulatorStoichiometric transitionsEyesBinding profileProtein binding profileProtein synthesisLesser levelsMetallothionein
2015
STEP61 is a substrate of the E3 ligase parkin and is upregulated in Parkinson’s disease
Kurup PK, Xu J, Videira RA, Ononenyi C, Baltazar G, Lombroso PJ, Nairn AC. STEP61 is a substrate of the E3 ligase parkin and is upregulated in Parkinson’s disease. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 1202-1207. PMID: 25583483, PMCID: PMC4313846, DOI: 10.1073/pnas.1417423112.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCorpus StriatumCyclic AMP Response Element-Binding ProteinDown-RegulationGene Expression Regulation, EnzymologicHEK293 CellsHumansMAP Kinase Signaling SystemMiceMice, KnockoutMitogen-Activated Protein Kinase 3MPTP PoisoningProtein Tyrosine Phosphatases, Non-ReceptorRatsRats, Sprague-DawleyUbiquitin-Protein LigasesUbiquitinationUp-RegulationConceptsE3 ubiquitin ligase ParkinSubstantia nigra pars compactaPathophysiology of PDProtein tyrosine phosphataseUbiquitin ligase ParkinSporadic Parkinson's diseaseE3 ligase ParkinRegulation of ParkinParkinson's diseaseTyrosine phosphataseParkin mutantsE3 ligaseProteasome systemDopaminergic neuronsDownstream targetsAutosomal recessive juvenile parkinsonismNovel substrateSTEP61ParkinCellular modelSTEP61 levelsSNc dopaminergic neuronsProtein levelsFunction contributesERK1/2
2013
Bicarbonate-Dependent Secretion and Proteolytic Processing of Recombinant Myocilin
Aroca-Aguilar JD, Martínez-Redondo F, Martín-Gil A, Pintor J, Coca-Prados M, Escribano J. Bicarbonate-Dependent Secretion and Proteolytic Processing of Recombinant Myocilin. PLOS ONE 2013, 8: e54385. PMID: 23342144, PMCID: PMC3547000, DOI: 10.1371/journal.pone.0054385.Peer-Reviewed Original ResearchConceptsIrreversible visual lossElevated intraocular pressureIntracellular accumulationC-terminal fragmentVisual lossOptic neuropathyIntraocular pressureIntracellular proteolytic processingProteolytic processingOcular tissuesRecombinant myocilinCalpain IICellular modelMyocilinSecretionPossible factorsExtracellular glycoproteinNeuropathyGlaucomaIntegration of Cell Line and Clinical Trial Genome-Wide Analyses Supports a Polygenic Architecture of Paclitaxel-Induced Sensory Peripheral Neuropathy
Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, B F, Cox NJ, Dolan ME. Integration of Cell Line and Clinical Trial Genome-Wide Analyses Supports a Polygenic Architecture of Paclitaxel-Induced Sensory Peripheral Neuropathy. Clinical Cancer Research 2013, 19: 491-499. PMID: 23204130, PMCID: PMC3549006, DOI: 10.1158/1078-0432.ccr-12-2618.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociSingle nucleotide polymorphismsPolygenic architectureGenome-wide association study resultsLymphoblastoid cell line (LCL) modelGenome-wide analysisSignificant enrichmentQuantitative trait lociRegulatory factor X (RFX) familyAssociation study resultsRelevant genetic variantsGWAS resultsTrait lociAllelic directionCell line modelsRelated traitsHapMap projectEnrichment resultsPaclitaxel-induced cytotoxicityCellular modelReduced neurite outgrowthGenetic variantsRFX2Neurite outgrowthCell lines
2012
Cerulein hyperstimulation decreases AMP-activated protein kinase levels at the site of maximal zymogen activation
Shugrue C, Alexandre M, de Villalvilla A, Kolodecik TR, Young LH, Gorelick FS, Thrower EC. Cerulein hyperstimulation decreases AMP-activated protein kinase levels at the site of maximal zymogen activation. AJP Gastrointestinal And Liver Physiology 2012, 303: g723-g732. PMID: 22821946, PMCID: PMC3468535, DOI: 10.1152/ajpgi.00082.2012.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAminoimidazole CarboxamideAMP-Activated Protein KinasesAnimalsCells, CulturedCeruletideCyclic AMP-Dependent Protein KinasesEnzyme PrecursorsGene Expression RegulationMaleMetforminOctoxynolPancreasPhosphorylationPyrazolesPyrimidinesRatsRats, Sprague-DawleyRibonucleotidesSodium Dodecyl SulfateConceptsAdenosine monophosphate-activated protein kinaseZymogen activationAMPK activityPancreatic acinar cellsMonophosphate-activated protein kinaseVacuolar ATPase activityAMPK levelsDigestive enzyme zymogensAMPK effectsProtein kinaseProtein kinase levelsE subunitAcinar cellsTime-dependent translocationCompound CCellular modelPancreatitis responsesATPase activityDifferential centrifugationPremature activationChymotrypsin activityActivationInitiating eventSoluble fractionCerulein hyperstimulation
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