2025
Macroporous scaffolds based on biomass polymers and their applications in wound healing
Gao D, Shipman W, Sun Y, Glahn J, Beraki L, Hsia H. Macroporous scaffolds based on biomass polymers and their applications in wound healing. Journal Of Bioresources And Bioproducts 2025, 10: 14-31. DOI: 10.1016/j.jobab.2024.12.001.Peer-Reviewed Original ResearchMacroporous scaffoldsTissue engineeringMacroporous tissue engineering scaffoldsTissue engineering scaffoldsBiomass materialsPetroleum-based polymersEngineering scaffoldsBiomedical polymersBicontinuous macroporesBiomass-based materialsPolymer wasteMacroporous constructsMicroparticle assemblyEnvironmental friendlinessPolymerTissue regenerationMacroporesBiomass polymersScaffoldsMaterialsEngineeringMedical applicationsCell behaviorBioprintingWaste
2024
Notch signaling regulates UNC5B to suppress endothelial proliferation, migration, junction activity, and retinal plexus branching
Raza Q, Nadeem T, Youn S, Swaminathan B, Gupta A, Sargis T, Du J, Cuervo H, Eichmann A, Ackerman S, Naiche L, Kitajewski J. Notch signaling regulates UNC5B to suppress endothelial proliferation, migration, junction activity, and retinal plexus branching. Scientific Reports 2024, 14: 13603. PMID: 38866944, PMCID: PMC11169293, DOI: 10.1038/s41598-024-64375-z.Peer-Reviewed Original ResearchConceptsNotch signalingEndothelial cell behaviorEndothelial junctionsCell behaviorMultiple endothelial cell typesStabilization of endothelial junctionsNotch activationEndothelial Notch signalingTarget of Notch signalingTranscriptional activation complexEndothelial cell typesPlexus branchesVascular densityEndothelial proliferationBrain endotheliumMouse retinaIn vivo targetingEffector proteinsVascular outgrowthJunction activityNotch proteinsEndothelial cellsExcessive vascularizationDownstream effectorsEndothelial gene expression
2023
Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation
Meyer K, Lammers N, Bugaj L, Garcia H, Weiner O. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nature Communications 2023, 14: 6929. PMID: 37903793, PMCID: PMC10616176, DOI: 10.1038/s41467-023-42643-2.Peer-Reviewed Original ResearchConceptsCell fateYAP levelsControlling gene activityCell fate analysisPluripotency regulators Oct4Stem cell fateEffector genesTranscriptional regulationGene activationControl pluripotencyYAP activityNative dynamicsCellular differentiationRegulators Oct4Developmental decision-makingControl proliferationMolecular logicCell behaviorYAPFate analysisDynamic decoderOptogenetic controlOct4 expressionCellsFateChemical interactions modulate λ6‐85 stability in cells
Knab E, Davis C. Chemical interactions modulate λ6‐85 stability in cells. Protein Science 2023, 32: e4698. PMID: 37313657, PMCID: PMC10288553, DOI: 10.1002/pro.4698.Peer-Reviewed Original ResearchAutomated time-lapse data segmentation reveals in vivo cell state dynamics
Genuth M, Kojima Y, Jülich D, Kiryu H, Holley S. Automated time-lapse data segmentation reveals in vivo cell state dynamics. Science Advances 2023, 9: eadf1814. PMID: 37267354, PMCID: PMC10413672, DOI: 10.1126/sciadv.adf1814.Peer-Reviewed Original ResearchConceptsCell statesSingle-cell RNA sequencing dataCell state dynamicsCell behaviorEmbryonic development proceedsCell state transitionsRNA sequencing dataCollective cell behaviorIndividual cell behaviorsZebrafish tailbudLeft-right asymmetryCell tracking dataCollective cell motionGene expressionSequencing dataMolecular processesIndividual embryosDevelopment proceedsEmbryosCell motionParallel identificationBilateral symmetryReproducible patternTailbudState transitionsTunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior (Adv. Mater. 16/2023)
Nguyen R, Cabral A, Rossello‐Martinez A, Zulli A, Gong X, Zhang Q, Yan J, Mak M. Tunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior (Adv. Mater. 16/2023). Advanced Materials 2023, 35 DOI: 10.1002/adma.202370115.Peer-Reviewed Original ResearchTissue engineeringHydrogel fabrication methodHydrogel mechanical propertiesCollagen I hydrogelScaffold materialsMechanical propertiesFabrication methodModulating stem cell behaviorExtracellular matrix architectureMatrix architectureEngineeringStem cell behaviorMesoscopic featuresCell behaviorHydrogelsFabricationTunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior
Nguyen R, Cabral A, Rossello‐Martinez A, Zulli A, Gong X, Zhang Q, Yan J, Mak M. Tunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior. Advanced Materials 2023, 35: e2207882. PMID: 36895051, PMCID: PMC10166061, DOI: 10.1002/adma.202207882.Peer-Reviewed Original ResearchConceptsStem cell behaviorCell behaviorPluripotent stem cellsMesenchymal stem cell behaviorMammalian cellsMesodermal differentiationCell migrationExtracellular matrixStem cellsOsteogenic differentiationRegional enrichmentCollagen-based hydrogelsPhysiological tissuesBioactive cuesDifferentiationBiophysical environmentCollagen hydrogelsCellsIslandsComplex architectureTissue engineering applicationsTissueCollagen architectureEnrichmentGel
2022
Self-assembly of mesoscale collagen architectures and applications in 3D cell migration
Liu C, Nguyen R, Pizzurro G, Zhang X, Gong X, Martinez A, Mak M. Self-assembly of mesoscale collagen architectures and applications in 3D cell migration. Acta Biomaterialia 2022, 155: 167-181. PMID: 36371004, PMCID: PMC9805527, DOI: 10.1016/j.actbio.2022.11.011.Peer-Reviewed Original ResearchConceptsNano-scale topographyCollagen-based scaffoldsBiomimetic scaffoldsMicroscale topographyMechanical agitationCollagen networkGelation processCollagen scaffoldsMatrix structureCollagen architectureMesoscale featuresCell behaviorScaffoldsLarge scaleTopographySoftnessLocal propertiesExtracellular matrix structureBehaviorECM architectureMicroCurrent methodsProcessMethodInterplay between substrate rigidity and tissue fluidity regulates cell monolayer spreading
Staddon M, Murrell M, Banerjee S. Interplay between substrate rigidity and tissue fluidity regulates cell monolayer spreading. Soft Matter 2022, 18: 7877-7886. PMID: 36205535, PMCID: PMC9700261, DOI: 10.1039/d2sm00757f.Peer-Reviewed Original ResearchConceptsSubstrate rigidityCollective cell motionSubstrate stiffnessTissue fluidityStiff substratesCell-matrix adhesionTraction force generationCell-cell interactionsCell motionTissue morphogenesisSoft elastic matrixCell collectivesEmbryonic developmentCell crawlingCell spreadingCell monolayersSolid tissuesCell behaviorMechanical behaviorPredictive understandingMechanical propertiesCancer invasionCell aggregatesElastic matrixCell propertiesLive imaging and conditional disruption of native PCP activity using endogenously tagged zebrafish sfGFP-Vangl2
Jussila M, Boswell C, Griffiths N, Pumputis P, Ciruna B. Live imaging and conditional disruption of native PCP activity using endogenously tagged zebrafish sfGFP-Vangl2. Nature Communications 2022, 13: 5598. PMID: 36151137, PMCID: PMC9508082, DOI: 10.1038/s41467-022-33322-9.Peer-Reviewed Original ResearchConceptsPlanar cell polarityVertebrate planar cell polarityTissue-specific functionsNon-canonical Wnt/planar cell polarityWnt/planar cell polarityCore PCP componentsLoss of vangl2Polarity proteinsCell polarityPCP componentsMembrane localizationCytoskeletal organizationGenome editingPowerful experimental paradigmCRISPR/Live imagingDynamic regulationCell lineagesAuthentic regulationPCP activityVangl2Fluorescent reportersEpendymal cell ciliaCell behaviorNormal developmentNew insights into the role of dipeptidyl peptidase 8 and dipeptidyl peptidase 9 and their inhibitors
Cui C, Tian X, Wei L, Wang Y, Wang K, Fu R. New insights into the role of dipeptidyl peptidase 8 and dipeptidyl peptidase 9 and their inhibitors. Frontiers In Pharmacology 2022, 13: 1002871. PMID: 36172198, PMCID: PMC9510841, DOI: 10.3389/fphar.2022.1002871.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsDipeptidyl peptidase 8Peptidase 8Dipeptidyl peptidase 9Serine proteolytic enzymesBiological processesNew potential targetsPhysiological functionsSpecific substratesCell behaviorNormal developmentEnergy metabolismEssential roleChronic kidney diseaseN-terminal dipeptidePenultimate positionPotential targetOrgan fibrosisPathological rolePathological processesNew insightsTreatment of tumorsProteolytic enzymesRecent research advancesKidney diseaseCell pyroptosisDecomposing a deterministic path to mesenchymal niche formation by two intersecting morphogen gradients
Qu R, Gupta K, Dong D, Jiang Y, Landa B, Saez C, Strickland G, Levinsohn J, Weng PL, Taketo MM, Kluger Y, Myung P. Decomposing a deterministic path to mesenchymal niche formation by two intersecting morphogen gradients. Developmental Cell 2022, 57: 1053-1067.e5. PMID: 35421372, PMCID: PMC9050909, DOI: 10.1016/j.devcel.2022.03.011.Peer-Reviewed Original ResearchConceptsMorphogen gradientsCell fate specificationWnt/β-cateninFate specificationShape tissuesOrgan formationCell fateDermal condensatesGenetic perturbationsNiche formationDifferentiation processSpatiotemporal patterningCell behaviorΒ-cateninMore intermediatesComputational approachProliferationMorphogenesisScRNAOrganogenesisShhKey componentProgenitorsCritical transitionDKK1
2021
Multi-omics analysis to identify susceptibility genes for colorectal cancer
Yuan Y, Bao J, Chen Z, Villanueva A, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu X, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Human Molecular Genetics 2021, 30: 321-330. PMID: 33481017, PMCID: PMC8485221, DOI: 10.1093/hmg/ddab021.Peer-Reviewed Original ResearchMeSH KeywordsCarcinogenesisCell Line, TumorCell ProliferationColorectal NeoplasmsDNA MethylationGene Expression Regulation, NeoplasticGenetic Association StudiesGenetic Predisposition to DiseaseGenomeGenome-Wide Association StudyHumansNerve Tissue ProteinsPolymorphism, Single NucleotideRepressor ProteinsRisk FactorsTranscriptomeConceptsGenome-wide association studiesMulti-omics analysisSusceptibility genesTarget genesPutative target genesGWAS-identified variantsMost genetic variantsDNA methylation dataNovel susceptibility genesGenotype-Tissue ExpressionGenetic risk lociPutative susceptibility genesGene regulationIntergenic regionPathogenic dysregulationCancer Genome AtlasEpithelial-mesenchymal transitionRisk lociGene expressionMethylation dataAssociation studiesGenesCell behaviorGenetic variantsGenome Atlas
2019
Endophilin-A2 dependent VEGFR2 endocytosis promotes sprouting angiogenesis
Genet G, Boyé K, Mathivet T, Ola R, Zhang F, Dubrac A, Li J, Genet N, Henrique Geraldo L, Benedetti L, Künzel S, Pibouin-Fragner L, Thomas JL, Eichmann A. Endophilin-A2 dependent VEGFR2 endocytosis promotes sprouting angiogenesis. Nature Communications 2019, 10: 2350. PMID: 31138815, PMCID: PMC6538628, DOI: 10.1038/s41467-019-10359-x.Peer-Reviewed Original ResearchMeSH KeywordsAcyltransferasesAnimalsCell MovementCell PolarityCell ProliferationCell SurvivalEndocytosisEndothelial CellsIntercellular Signaling Peptides and ProteinsMAP Kinase Signaling SystemMiceMice, KnockoutNeovascularization, PhysiologicNerve Tissue Proteinsp21-Activated KinasesReceptors, ImmunologicRetinal VesselsVascular Endothelial Growth Factor Receptor-2ConceptsEndophilin A2Endothelial cell migrationSprouting angiogenesisCell migrationFront-rear polarityBAR domain proteinsFront-rear polarizationClathrin-independent internalizationSpecific endocytic pathwaysVEGFR2 endocytosisEndocytic pathwayAngiogenesis defectsEffector PAKTip cellsSlit-RoboActivation of VEGFR2Downstream activationVEGFR2 internalizationCell behaviorPathological angiogenesisCritical mediatorEndocytosisPathological conditions
2018
Cell circuits between B cell progenitors and IL-7+ mesenchymal progenitor cells control B cell development
Fistonich C, Zehentmeier S, Bednarski JJ, Miao R, Schjerven H, Sleckman BP, Pereira JP. Cell circuits between B cell progenitors and IL-7+ mesenchymal progenitor cells control B cell development. Journal Of Experimental Medicine 2018, 215: 2586-2599. PMID: 30158115, PMCID: PMC6170173, DOI: 10.1084/jem.20180778.Peer-Reviewed Original ResearchConceptsB cell progenitorsCell progenitorsUnrepaired double-strand DNA breaksDouble-strand DNA breaksB cell developmentMesenchymal progenitor cellsInterleukin-7IL-7R signalingFocal adhesion kinase expressionBone marrow stromal cellsCell movementMarrow stromal cellsDNA breaksPreB cellsCell developmentParacrine signalsCell behaviorAcute lymphoblastic leukemic cellsProgenitor cellsKinase expressionProgenitorsIL-7RCell exposureStromal cellsLow-adhesion stateHierarchical Micro- and Nanopatterning of Metallic Glass to Engineer Cellular Responses
Wang J, Loye A, Ketkaew J, Schroers J, Kyriakides T. Hierarchical Micro- and Nanopatterning of Metallic Glass to Engineer Cellular Responses. ACS Applied Bio Materials 2018, 1: 51-58. DOI: 10.1021/acsabm.8b00007.Peer-Reviewed Original ResearchHierarchical microNano/micro levelTopographical length scalesLength scalesMechanical propertiesMultiple length scalesPt-BMGMetallic glassesWetting abilityRelevant length scalesForeign body responseNanotopographical featuresCellular responsesAmorphous natureEngineering sciencesSpecific cell responsesMicroSubstrateCell behaviorCell typesMorphology of macrophagesMacrophage fusionCell morphologyNanopatterningBiomaterialsHoming in: Mechanisms of Substrate Targeting by Protein Kinases
Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends In Biochemical Sciences 2018, 43: 380-394. PMID: 29544874, PMCID: PMC5923429, DOI: 10.1016/j.tibs.2018.02.009.Peer-Reviewed Original ResearchConceptsProtein kinaseReversible post-translational modificationKinase substrate specificityCellular signaling networksPost-translational modificationsSimilar catalytic domainsMode of regulationSignaling outputsSubstrate repertoireSubstrate targetingSignaling networksPhosphorylation sitesProtein phosphorylationCatalytic domainSubstrate specificityKinaseCell behaviorEukaryotesRecent progressPhosphorylationAnticancer drugsSitesRegulationMechanismTargeting
2016
Epidermal growth factor receptor targeting alters gene expression and restores the adhesion function of cancerous cells as measured by single cell force spectroscopy
Azadi S, Tafazzoli-Shadpour M, Omidvar R, Moradi L, Habibi-Anbouhi M. Epidermal growth factor receptor targeting alters gene expression and restores the adhesion function of cancerous cells as measured by single cell force spectroscopy. Molecular And Cellular Biochemistry 2016, 423: 129-139. PMID: 27696309, DOI: 10.1007/s11010-016-2831-x.Peer-Reviewed Original ResearchConceptsCell-cell adhesionE-cadherin expressionEpidermal growth factor receptorGrowth factor receptorAdhesion functionCell-cell adhesion forcesCell-cell adhesion functionSingle-cell force spectroscopyFactor receptorAlters gene expressionCell force spectroscopyE-cadherin geneTime PCR analysisBlockade of EGFRTreatment of cellsForce spectroscopy techniquesHuman epithelial cancer cell linesEpithelial cancer cell linesCancerous cellsCell mechanical propertiesEGFR activityGene expressionCell behaviorInhibition of metastasisCancer progressionCarcinogenesis: UV Radiation
Brash D, Heffernan T, Nghiem P, Cho R. Carcinogenesis: UV Radiation. 2016, 887-902. DOI: 10.1007/978-3-662-47398-6_56.ChaptersLarge-scale sequencing projectsUV-damaged cellsSequencing projectsDNA repairTumor suppressorSomatic point mutationsSurveillance mechanismClonal growthLow-frequency mutationsDNA damageBase changesCell behaviorPoint mutationsMutationsSomatic mutationsFree radical clearanceHuman skin cancerFrequency mutationsSpecific somatic mutationsUltraviolet radiationPTCH mutationsGenetic factorsNOTCH1 mutationsCellsVast numberAbelson kinase acts as a robust, multifunctional scaffold in regulating embryonic morphogenesis
Rogers EM, Spracklen AJ, Bilancia CG, Sumigray KD, Allred SC, Nowotarski SH, Schaefer KN, Ritchie BJ, Peifer M. Abelson kinase acts as a robust, multifunctional scaffold in regulating embryonic morphogenesis. Molecular Biology Of The Cell 2016, 27: 2613-2631. PMID: 27385341, PMCID: PMC4985262, DOI: 10.1091/mbc.e16-05-0292.Peer-Reviewed Original ResearchConceptsF-actin-binding domainCell biological rolesCell shape changesDifferent protein motifsSeries of mutantsTyrosine kinase domainAbl functionActin regulationDrosophila morphogenesisEmbryonic morphogenesisProtein motifsAbelson familyPXXP motifInteraction domainKinase domainAbelson kinaseLinker regionKey regulatorAbl SH3Biological roleCellular behaviorMorphogenesisCell behaviorNormal developmentSH3
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