2025
High-content image-based pooled screens reveal regulators of synaptogenesis
Le A, Biederer T, Blainey P. High-content image-based pooled screens reveal regulators of synaptogenesis. Cell Reports 2025, 44: 115889. PMID: 40560725, DOI: 10.1016/j.celrep.2025.115889.Peer-Reviewed Original ResearchNeuroligin-1High-content screening approachPresynaptic assemblyCell-cell interactionsCytoskeletal dynamicsRegulation of synaptogenesisPhosphatase PTENPooled screeningSynapse inductionCell adhesionSynapse formationSynapse typesScreening platformPhenotypic profileDAG1Adhesion moleculesMolecular interactionsScreening approachSynaptogenesisRegulationSynapseNeuroliginInhibitory synapsesNervous systemPTENMAP kinase phosphatases in metabolic diseases
Hota A, Bennett A. MAP kinase phosphatases in metabolic diseases. Trends In Endocrinology And Metabolism 2025 PMID: 40555575, DOI: 10.1016/j.tem.2025.05.002.Peer-Reviewed Original ResearchMitogen-activated protein kinaseInactivate mitogen-activated protein kinasesMAP kinase phosphatasesRegulation of MAPK signaling pathwaysMetabolic diseasesMAPK signaling pathwayRegulatory residuesInsulin signalingProtein kinaseSignaling pathwayCellular responsesKey pathwaysLipid metabolismGlucose homeostasisTherapeutic targetPathwayMetabolismKinaseResiduesHomeostasisMKPRegulationPhosphataseMetabolic switches in cell death regulation
Galluzzi L. Metabolic switches in cell death regulation. Cell Metabolism 2025, 37: 1252-1254. PMID: 40466623, DOI: 10.1016/j.cmet.2025.04.017.Peer-Reviewed Original ResearchNeuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators
Malone T, Wu J, Zhang Y, Licznerski P, Chen R, Nahiyan S, Pedram M, Jonas E, Kaczmarek L. Neuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators. Science Advances 2025, 11: eadv3140. PMID: 40435242, PMCID: PMC12118559, DOI: 10.1126/sciadv.adv3140.Peer-Reviewed Original ResearchConceptsMRNA translationTranslational regulationInitiation of mRNA translationInitiation of translationSevere intellectual disabilityRegulation of translationMRNA translation regulationNeurites of cortical neuronsB-actinChannel activityIntellectual disabilityPotassium channel activityNeuronal activityMolecular mechanismsInhibit initiationMutationsCell linesPharmacological stimulationCortical neuronsMRNABindingRegulationTranslationEIF4ECYFIP1Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides
Kabonick S, Verma K, Modesto J, Pearce V, Winokur K, Groisman E, Townsend G. Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides. Nature Communications 2025, 16: 4488. PMID: 40368925, PMCID: PMC12078602, DOI: 10.1038/s41467-025-59704-3.Peer-Reviewed Original ResearchConceptsFructose-1,6-bisphosphateMammalian gutGut BacteroidesBacterial phylumGut microbiomeIntestinal colonizationTranscription factorsGlycolytic pathwayBacteroides speciesCarbohydrate utilizationHost immunomodulationGutCarbohydrateCurIntestinal disordersFructoseHostRegulationAbundant amountSugarPhylumBacteroidetesMicrobiomeBacteroidesTranscriptionExploring the complexity of MECP2 function in Rett syndrome
Liu Y, Whitfield T, Bell G, Guo R, Flamier A, Young R, Jaenisch R. Exploring the complexity of MECP2 function in Rett syndrome. Nature Reviews Neuroscience 2025, 26: 379-398. PMID: 40360671, DOI: 10.1038/s41583-025-00926-1.Peer-Reviewed Original ResearchConceptsMethylated DNA binding protein MeCP2Neuronal gene regulationReview recent insightsChromatin structureTranscriptional regulationGene regulationInteraction hubProtein MeCP2Cofactor interactionsTranscription factorsEpigenetic regulationRett syndromeProteomic studiesDiverse processesMolecular mechanismsMeCP2 functionTherapeutic designMeCP2Neuronal functionRegulationModel systemNeurodevelopmental disordersRepressorChromatinMechanistic studiesVAC14 oligomerization is essential for the function of the FAB1/PIKfyve-VAC14-FIG4 complex.
Zhang L, Uygun T, Hahn H, Liu Y, Rivero-Ríos P, Li D, Navratna V, Bristow E, Luo G, Kovarzin A, Bo Y, Gadde S, Côté M, Ko D, Mosalaganti S, Reinisch K, Weisman L. VAC14 oligomerization is essential for the function of the FAB1/PIKfyve-VAC14-FIG4 complex. Molecular Biology Of The Cell 2025, 36: ar78. PMID: 40305106, DOI: 10.1091/mbc.e24-11-0490.Peer-Reviewed Original ResearchMeSH KeywordsCryoelectron MicroscopyFlavoproteinsHexosyltransferasesHumansIntracellular Signaling Peptides and ProteinsMembrane ProteinsMutationPhosphatidylinositol 3-KinasesPhosphatidylinositol PhosphatesPhosphoric Monoester HydrolasesPhosphotransferases (Alcohol Group Acceptor)Protein BindingProtein MultimerizationSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsVesicular Transport ProteinsConceptsPatient mutationsFluorescence-detection size-exclusion chromatographyPI(3,5)P<sub>2</sub>Phosphatidylinositol 3,5-bisphosphatePull-down assaysMedium-resolution structureYeast mutationsPediatric neurodegenerative diseaseVac14Signaling lipidsCell lysatesMutationsOligomerizationNeurodegenerative diseasesElectron microscopy mappingKnockoutFab1/PIKfyveYeastEndosomesFIG4PIKfyveLysatesColocalizationComplexRegulationA Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function
Jiménez-Jiménez V, Sánchez-Cabo F, Schwartz M, Sánchez-Álvarez M, del Pozo M. A Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function. International Journal Of Molecular Sciences 2025, 26: 3789. PMID: 40332409, PMCID: PMC12027754, DOI: 10.3390/ijms26083789.Peer-Reviewed Original ResearchConceptsGenotype-Tissue ExpressionTranscript levelsProtein-coding genesRNA-seq datasetsUpstream regulatory networkCell type proportionsInter-species comparisonsTissue-specific correlationsChromatin modifiersRegulatory networksPRC2 complexTissue-specific influencesCav1Complexity of human tissuesPhysiological regulationHuman tissuesPhysiological conditionsRegulationMetabolic stimuliCAV1 levelsDisease statesTissue dataInfiltration of immune cellsCellsChromatinReflections on Advocacy as a Foundation of Global Health Law
Gonsalves G. Reflections on Advocacy as a Foundation of Global Health Law. The Journal Of Law, Medicine & Ethics 2025, 53: 59-59. DOI: 10.1017/jme.2025.9.Peer-Reviewed Original ResearchDissecting the stress granule RNA world: dynamics, strategies and data
Biancon G, Busarello E, Cheng M, Halene S, Tebaldi T. Dissecting the stress granule RNA world: dynamics, strategies and data. RNA 2025, 31: rna.080409.125. PMID: 40086831, PMCID: PMC12084887, DOI: 10.1261/rna.080409.125.Peer-Reviewed Original ResearchConceptsStress granulesRNA worldRegulation of gene expressionRNA-binding proteinsCytoplasmic ribonucleoprotein granulesRibonucleoprotein granulesTranscriptome dataRNA componentSG dynamicsCell signalingSG compositionSG componentsGene expressionCellular adaptationHuman diseasesStress conditionsExperimental strategiesRNAProteinComprehensive understandingMRNAGranulesRegulationNongenetic adaptation by collective migration
Vo L, Avgidis F, Mattingly H, Edmonds K, Burger I, Balasubramanian R, Shimizu T, Kazmierczak B, Emonet T. Nongenetic adaptation by collective migration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2423774122. PMID: 39970001, PMCID: PMC11874451, DOI: 10.1073/pnas.2423774122.Peer-Reviewed Original ResearchConceptsGene regulationCollective migrationPhenotype distributionPhenotypic compositionStress response pathwaysSwimming phenotypeCell populationsBacterial populationsStress responseAbundance distributionMultidimensional phenotypesGenetic mutationsPhenotypeDiverse environmentsEnvironmental conditionsGenesMutationsSwimming behaviorChanging environmentDoubling timeMigrating populationCellsRegulationMigrationAdaptationA Selective Review of Network Analysis Methods for Gene Expression Data
Li R, Yi H, Ma S. A Selective Review of Network Analysis Methods for Gene Expression Data. Methods In Molecular Biology 2025, 2880: 293-307. PMID: 39900765, DOI: 10.1007/978-1-0716-4276-4_14.Peer-Reviewed Original ResearchConceptsGene expression dataGene expression networksExpression dataDownstream analysisExpression networksGene expressionBiological processesGenesMolecular mechanismsBiological implicationsHigh-throughput profiling techniquesBiological findingsGlobal viewComplex interactionsProfiling techniquesRegulationcSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling
Deng H, Rukhlenko O, Joshi D, Hu X, Junk P, Tuliakova A, Kholodenko B, Schwartz M. cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling. Science Advances 2025, 11: eado9970. PMID: 39752487, PMCID: PMC11698091, DOI: 10.1126/sciadv.ado9970.Peer-Reviewed Original ResearchConceptsShear stressCell cycle-dependent kinasesHigh shear stressLow shear stressOscillatory shear stressPhysiological shear stressFluid shear stressCell cycle arrestRegulatory networksTranscriptomic statesResponse to drug treatmentCycle arrestCell cycleEndothelial cell cycleDisease susceptibilityRegulatory mechanismsVessel behaviorCDK2Endothelial cellsIn vitroStressRegulationVascular endothelial cellsRemodelingCells
2024
Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation
Bierman R, Dave J, Greif D, Salzman J. Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation. ELife 2024, 12: rp87517. PMID: 39699003, PMCID: PMC11658768, DOI: 10.7554/elife.87517.Peer-Reviewed Original ResearchConceptsSubcellular localizationUntranslated regionAlternative poly-adenylationSubcellular RNA localizationCell-type specific regulationLow-throughput studiesUntranslated region lengthRNA subcellular localizationSingle-cell resolutionSpatial transcriptomics techniquesRNA localizationFunction predictionPoly-adenylationTranscriptomic techniquesCellular functionsMouse brainSpecific regulationStatistical frameworkIsoform expressionMouse liverRegulationMiceUntranslatedLocalizationRNAStatistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation
Bierman R, Dave J, Greif D, Salzman J. Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation. ELife 2024, 12 DOI: 10.7554/elife.87517.2.Peer-Reviewed Original ResearchSubcellular localizationUntranslated regionAlternative poly-adenylationSubcellular RNA localizationCell-type specific regulationLow-throughput studiesUntranslated region lengthRNA subcellular localizationSingle-cell resolutionSpatial transcriptomics techniquesRNA localizationFunction predictionPoly-adenylationTranscriptomic techniquesCellular functionsMouse brainSpecific regulationStatistical frameworkIsoform expressionMouse liverRegulationNXPH1MiceUntranslatedLocalizationEpiGePT: a pretrained transformer-based language model for context-specific human epigenomics
Gao Z, Liu Q, Zeng W, Jiang R, Wong W. EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics. Genome Biology 2024, 25: 310. PMID: 39696471, PMCID: PMC11657395, DOI: 10.1186/s13059-024-03449-7.Peer-Reviewed Original ResearchConceptsTranscription factor activityChromatin interactionsEpigenomic signalsGenomic interactionsHuman epigenomeGene regulationVariant impactBiological sequencesCellular contextInteraction predictionFactor activityGenomeChromatinEpigenomeTranscriptionGenesHttp://healthSequenceRegulationTransformer-based modelsInteractionPhase separation of microtubule-binding proteins - implications for neuronal function and disease.
Duan D, Koleske A. Phase separation of microtubule-binding proteins - implications for neuronal function and disease. Journal Of Cell Science 2024, 137 PMID: 39679446, PMCID: PMC11795294, DOI: 10.1242/jcs.263470.Peer-Reviewed Original ResearchConceptsMT-binding proteinsLiquid-liquid phase separationRegulation of MT dynamicsProtein liquid-liquid phase separationNeuronal developmentTau neurofibrillary tanglesCytoskeletal regulationMT dynamicsNeurofibrillary tanglesBinding domainMT nucleationBiological functionsDisordered regionsAlzheimer's diseaseNeurodegenerative diseasesIn vivo studiesMaintains homeostasisMicrotubulesNeuronal functionMature neuronsProteinRegulationIn vitroFormation of aggregatesIn vitro studiesInferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation
Shao W, Liu Y, Zhang S, Chen S, Liu Q, Zhou J, Zeng W. Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation. 2024, 00: 451-456. DOI: 10.1109/bibm62325.2024.10822868.Peer-Reviewed Original ResearchGene regulatory networksGene regulatory network inferenceGene regulationScATAC-seqRegulatory networksConstruction of gene regulatory networksAccurate gene regulatory networksInferring gene regulatory networksSingle-cell ATAC-seqChromatin accessibility dataDynamic regulatory landscapeATAC-seqChromatin accessibilityGene perturbationsComplex biological systemsRegulatory relationshipsBiological processesGenesRegulatory landscapeRegulationIntricate interactionsBiological systemsChromatinPost-perturbationAccess dataAn integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
Li C, Bonder M, Syed S, Jensen M, Consortium H, Group H, Gerstein M, Zody M, Chaisson M, Talkowski M, Marschall T, Korbel J, Eichler E, Lee C, Shi X. An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Research 2024, 34: 2304-2318. PMID: 39638559, PMCID: PMC11694747, DOI: 10.1101/gr.279419.124.Peer-Reviewed Original ResearchConceptsTopologically associating domainsTopologically associating domains boundariesImpact of structural variantsLymphoblastoid cell linesStructural variantsHuman genomeGene regulationAdjacent TADsHuman lymphoblastoid cell linesCell linesSub-TADGenomic structureInsulate genesChromatin architectureImpact of deletionChromatin structureGenomeAberrant regulationAnalysis pipelineMammalian speciesGenesCCREsFunctional impactChromatinRegulationMechanistic Insights of Gamma Sensory Stimulation: CSF Proteomic Analyses Reveal Changes in Myelin and Synaptic Proteins
Shpokayte M, Pandey K, Singer A, Doung D, Lah J, Levey A, Seyfried N, Malchano Z, Kern R, Hajos M. Mechanistic Insights of Gamma Sensory Stimulation: CSF Proteomic Analyses Reveal Changes in Myelin and Synaptic Proteins. Alzheimer's & Dementia 2024, 20: e087390. PMCID: PMC11715388, DOI: 10.1002/alz.087390.Peer-Reviewed Original ResearchCell surface receptorsAlzheimer's diseaseSurface receptorsCo-expression modulesDifferential expression analysisAD-related pathologyContext of ADProteome databasePost-synaptic densityProteomic analysisExpression analysisSynaptic proteinsCerebrospinal fluid proteomeCerebrospinal fluidProteinSignificance thresholdMyelin-related proteinsSynaptic regulationMechanism of actionSensory stimulationCellsPrecursor cellsRegulationCerebrospinal fluid samplesCerebrospinal fluid protein
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply