2025
Decreased T helper 1 cell function underlies recurrent sinopulmonary infections in the 17q12 deletion syndrome
Shin J, Shin H, Gutierrez A, Yoo N, Par-Young J, Osmani L, Shin M, Sanchez-Lara P, Bucala R, Soffer G, Kang I. Decreased T helper 1 cell function underlies recurrent sinopulmonary infections in the 17q12 deletion syndrome. EBioMedicine 2025, 112: 105578. PMID: 39891996, PMCID: PMC11840234, DOI: 10.1016/j.ebiom.2025.105578.Peer-Reviewed Original ResearchConceptsCD4<sup>+</sup> T cellsRecurrent sinopulmonary infectionsT cell functionRNA-seq analysisT cellsHealthy controlsSinopulmonary infectionsRNA-seqT-betIFN-gFrequency of CD4<sup>+</sup> T cellsCD4<sup>+</sup> T cell functionTh1 transcription factor T-betDeletion syndromeFlow cytometryCompared to age-matched healthy controlsTranscription factor T-betDecreased T-betUrinary tract abnormalitiesAge-matched healthy controlsMultiplex assayDownstream effector cytokinesEffector cytokinesRecurrent infectionsTh17 cytokines
2024
Comparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes
Sura G, Tran K, Trevarton A, Marczyk M, Fu C, Du L, Qu J, Lau R, Tasto A, Gould R, Tinnirello A, Sinn B, Pusztai L, Hatzis C, Symmans W. Comparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes. Journal Of The American Society Of Cytopathology 2024, 14: 91-101. PMID: 39668068, DOI: 10.1016/j.jasc.2024.11.001.Peer-Reviewed Original ResearchRNA integrity numberRNA qualityRNA-seqMeasurement of gene expressionRNA-seq analysisMetastatic breast cancerFicoll-Hypaque methodDensity gradient enrichmentSequence dataRead-basedVariant detectionMalignant effusionsCytospin slidesFresh frozen samplesRNA fragmentsTranscript abundanceSequencing outcomesSequencing methodsBreast cancerRNA sequencingFicoll-HypaqueUMI-basedGene expressionRNAMalignant effusion specimensUnraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies
Biancon G, Busarello E, Cheng M, Sidoli S, VanOudenhove J, Bucciarelli G, Tebaldi T, Halene S. Unraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies. Blood 2024, 144: 4117. DOI: 10.1182/blood-2024-211265.Peer-Reviewed Original ResearchRNA-binding proteinsStress granulesRNA-seqArsenite stressSF mutationsAcute myeloid leukemiaSplicing factorsSG proteinsStress responseClonal advantageSG coresMulti-omicsDeregulated genesMyelodysplastic syndromeEnhances SG formationU2AF1 S34F mutationSingle-cell RNA-seqWT cellsMegakaryocyte-erythroid progenitorsRegulation of translationTranslation initiation factorsImprove cell fitnessRNA-seq analysisPost-translational modificationsU2AF1 mutationsLung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations.
Lu R, Gregory A, Suryadevara R, Xu Z, Jain D, Morrow J, Hobbs B, Yun J, Lichtblau N, Chase R, Curtis J, Sauler M, Bartholmai B, Silverman E, Hersh C, Castaldi P, Boueiz A. Lung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations. American Journal Of Respiratory And Critical Care Medicine 2024, 211: 75-90. PMID: 38935868, PMCID: PMC11755365, DOI: 10.1164/rccm.202305-0793oc.Peer-Reviewed Original ResearchRNA sequencing dataAlternative splicingExpressed genesFunctional pathwaysCell typesBiological pathwaysGene expressionTranscriptomic featuresGene regulatory processesDysregulated pathwaysSingle-cell RNA sequencing dataRNA-seq analysisLung cell typesLung Tissue Research ConsortiumTranscriptome analysisGenesCell-typeDifferential expressionMultiple lung cell typesPathway activationTranscriptomic signaturesPathway dysregulationRegulatory processesSplicingPathwayInterleukin-7-based identification of liver lymphatic endothelial cells reveals their unique structural features
Yang Y, Jeong J, Su T, Lai S, Zhang P, Garcia-Milian R, Graham M, Liu X, McConnell M, Utsumi T, Pereira J, Iwakiri Y. Interleukin-7-based identification of liver lymphatic endothelial cells reveals their unique structural features. JHEP Reports 2024, 6: 101069. PMID: 38966234, PMCID: PMC11222939, DOI: 10.1016/j.jhepr.2024.101069.Peer-Reviewed Original ResearchCell surface structuresLymphatic endothelial cellsPublished single-cell RNA-sequencingRNA-seq analysisScRNA-seq analysisSingle-cell RNA sequencingLymphatic systemEndothelial cellsInterleukin-7RNA-seqScRNA-seqExpressed genesRNA sequencingTranscriptomic changesLow abundanceI/R liver injuryGenesIsolation protocolLiver cell typesCell typesIsolation methodLiver of miceHuman liver specimensHeterozygous miceMouse liver
2023
Novel hippocampal genes involved in enhanced susceptibility to chronic pain-induced behavioral emotionality
Garman A, Ash A, Kokkinos E, Nerland D, Winter L, Langreck C, Forgette M, Girgenti M, Banasr M, Duric V. Novel hippocampal genes involved in enhanced susceptibility to chronic pain-induced behavioral emotionality. European Journal Of Pharmacology 2023, 964: 176273. PMID: 38135263, DOI: 10.1016/j.ejphar.2023.176273.Peer-Reviewed Original ResearchBlood-brain barrier integrityChronic pain statesBehavioral emotionalityHippocampal genesPain statesGenome-wide RNA-seq analysisStress responseBarrier integrityCommon stress responseRNA-seq analysisAurora kinase BChronic inflammatory painDepressive-like behaviorChronic pain conditionsRodent stress modelsLimbic brain regionsTight junction proteinsBioinformatics analysisInflammatory painAstrocyte activationPain groupPain conditionsTranscriptomic profilesAltered moodKinase BDifferential regulation of hair cell actin cytoskeleton mediated by SRF and MRTFB
Zhou L, Jin C, Wang W, Song L, Shin J, Du T, Wu H. Differential regulation of hair cell actin cytoskeleton mediated by SRF and MRTFB. ELife 2023, 12: e90155. PMID: 37982489, PMCID: PMC10703445, DOI: 10.7554/elife.90155.Peer-Reviewed Original ResearchConceptsActin cytoskeletonRegulation of actin cytoskeletonMRTF-SRF pathwayModulating actin dynamicsCell actin cytoskeletonCuticular plateActin cytoskeleton organizationActin cytoskeleton activityTranscriptional regulation mechanismRNA-seq analysisF-actin intensityHair cell developmentProfiles of genesActin dynamicsCytoskeleton organizationTranscriptional regulationF-actinCalponin 2Cytoskeleton activityHair bundle morphologyTranscriptome analysisDifferential regulationCell developmentCell-specific deletionCytoskeletonThe importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer
Al Assaad M, Gundem G, Liechty B, Sboner A, Medina J, Papaemmanuil E, Sternberg C, Marks A, Souweidane M, Greenfield J, Tran I, Snuderl M, Elemento O, Imielinski M, Pisapia D, Mosquera J. The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer. Molecular Case Studies 2023, 9: a006275. PMID: 37652664, PMCID: PMC10815291, DOI: 10.1101/mcs.a006275.Peer-Reviewed Original ResearchConceptsPediatric brain cancerPilocytic astrocytomaTargeted next-generation sequencingCase of pilocytic astrocytomaTumor size reductionLow-grade neoplasmsBrain cancerPediatric brain tumorsInternal tandem duplicationImpact treatment decisionsWhole-genome sequencingMolecular diagnosticsRNA-seq analysisRAS pathway activationNext-generation sequencingThalamic tumorsStable diseaseSuprasellar tumorsDabrafenib treatmentMultiple resectionsImprove patient outcomesTumor progressionWhole genomeRNA-seqTumorA systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension
Gunawardhana K, Hong L, Rugira T, Uebbing S, Kucharczak J, Mehta S, Karunamuni D, Cabera-Mendoza B, Gandotra N, Scharfe C, Polimanti R, Noonan J, Mani A. A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension. Journal Of Clinical Investigation 2023, 133: e160036. PMID: 36602864, PMCID: PMC9927944, DOI: 10.1172/jci160036.Peer-Reviewed Original ResearchConceptsDevelopment of hypertensionParallel reporter assaysRenin inhibitor aliskirenNeural crest-derived cellsRenin-producing cellsSystems biology approachRNA-seq analysisCell-specific disruptionCrest-derived cellsSmooth muscle cellsMuscle cell proteinsSystemic hypertensionBlood pressureWT miceAntihypertensive drugsBiology approachSuper enhancersFine mappingWT littermatesThird intronMultiple GWASCollagen depositionMouse aortaReporter assaysFate mappingIncreased length-dependent activation of human engineered heart tissue after chronic α1A-adrenergic agonist treatment: testing a novel heart failure therapy
Rupert C, López J, Cortez-Toledo E, De la Cruz Cabrera O, Chesler N, Simpson P, Campbell S, Baker A. Increased length-dependent activation of human engineered heart tissue after chronic α1A-adrenergic agonist treatment: testing a novel heart failure therapy. AJP Heart And Circulatory Physiology 2023, 324: h293-h304. PMID: 36637971, PMCID: PMC9886349, DOI: 10.1152/ajpheart.00279.2022.Peer-Reviewed Original ResearchConceptsHuman heart failureHeart failureAR stimulationChronic stimulationLength-dependent activationVehicle treatmentHeart tissueAdrenergic receptorsHuman EHTsAnimal heart failure modelNovel heart failure therapiesHeart failure therapyHeart failure modelMultiple preclinical modelsFailure therapyAgonist treatmentSeparate control experimentsPreclinical modelsDrug washoutTherapeutic effectTranslational significanceHuman myocardiumBaseline testingRNA-seq analysisPig myocardium
2022
Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas
Zhang H, Li B, Huang Q, López-Giráldez F, Tanaka Y, Lin Q, Mehta S, Wang G, Graham M, Liu X, Park I, Eichmann A, Min W, Zhou J. Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas. Nature Communications 2022, 13: 7637. PMID: 36496409, PMCID: PMC9741628, DOI: 10.1038/s41467-022-35262-w.Peer-Reviewed Original ResearchConceptsMitochondrial dysfunctionThioredoxin 2Single-cell RNA-seq analysisRNA-seq analysisMutant miceNuclear genesMitochondrial proteinsMitochondrial localizationHuman retinal diseasesTranscriptional factorsGene expressionMutant retinasMitochondrial activityExtracellular matrixNovel mechanismVascular maturationArteriovenous malformationsGenetic deficiencyVessel growthSmad2Mouse retinaVascular malformationsMechanistic studiesBasement membraneRetinal vascular malformationsHijacking of transcriptional condensates by endogenous retroviruses
Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses. Nature Genetics 2022, 54: 1238-1247. PMID: 35864192, PMCID: PMC9355880, DOI: 10.1038/s41588-022-01132-w.Peer-Reviewed Original ResearchConceptsTranscriptional condensatesEndogenous retrovirusesMurine embryonic stem cellsSingle-cell RNA-seq analysisKnockout mouse embryosRNA-seq analysisEmbryonic stem cellsMost endogenous retrovirusesERV RNAsPhase-separated dropletsNascent RNAPluripotency genesPluripotent lineageRNA polymeraseTranscription factorsReconstitution systemTriggers dissociationERV lociMouse embryosMediator coactivatorSelective degradationDisease contextsStem cellsRNASpecific depletionMFN2 Deficiency Impairs Mitochondrial Functions and PPAR Pathway During Spermatogenesis and Meiosis in Mice
Wang T, Xiao Y, Hu Z, Gu J, Hua R, Hai Z, Chen X, Zhang J, Yu Z, Wu T, Yeung W, Liu K, Guo C. MFN2 Deficiency Impairs Mitochondrial Functions and PPAR Pathway During Spermatogenesis and Meiosis in Mice. Frontiers In Cell And Developmental Biology 2022, 10: 862506. PMID: 35493072, PMCID: PMC9046932, DOI: 10.3389/fcell.2022.862506.Peer-Reviewed Original ResearchConditional knock-outMitochondrial functionPPAR pathwayMale germ cellsRNA-seq analysisGenes up-regulatedGenes down-regulatedPathway enrichment analysisImpaired mitochondrial functionDynamic organellesMitochondrial dynamicsRNA-seqMitochondrial fusionDisrupted spermatogenesisMfn2 deficiencyGerm cellsPachytene stageOxidative phosphorylationSpermatogenesisTranscriptome profilingEnrichment analysisMfn2Cellular differentiationMolecular mechanismsLipid dropletsInternode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids
Yanagui K, Camargo ELO, Abreu LGF, Nagamatsu ST, Fiamenghi MB, Silva NV, Carazzolle MF, Nascimento LC, Franco SF, Bressiani JA, Mieczkowski PA, Grassi MCB, Pereira GAG. Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids. Gene 2022, 828: 146476. PMID: 35413393, DOI: 10.1016/j.gene.2022.146476.Peer-Reviewed Original ResearchConceptsInternode elongationSaccharum hybridsSecondary cell wall formationDetailed transcriptome analysisCell wall formationDevelopment of plantsMolecular regulatory mechanismsEnergy caneRNA-seq analysisGrowth-related genesDifferent biological processesGene expression analysisCell wall characterizationDivision zoneTranscriptional regulationUnique genesCellulose synthesisTranscriptome analysisHigh biomass productionKey genesCell divisionWall formationBreeding programsBiomass biosynthesisExpression analysisPrdm6 controls heart development by regulating neural crest cell differentiation and migration
Hong L, Li N, Gasque V, Mehta S, Ye L, Wu Y, Li J, Gewies A, Ruland J, Hirschi KK, Eichmann A, Hendry C, van Dijk D, Mani A. Prdm6 controls heart development by regulating neural crest cell differentiation and migration. JCI Insight 2022, 7: e156046. PMID: 35108221, PMCID: PMC8876496, DOI: 10.1172/jci.insight.156046.Peer-Reviewed Original ResearchConceptsCardiac NCCNeural crest cell fateNeural crest cell differentiationSingle-cell RNA-seq analysisRNA-seq analysisDorsal neural tubeG1-S progressionFate-mapping approachCNCC migrationSpecification genesH4K20 monomethylationCell fateTranscriptomic analysisEpigenetic modifiersHeart developmentRegulated networkTranscript levelsKey regulatorMolecular mechanismsCell differentiationNeural tubePRDM6Ductus arteriosusPotential targetDifferentiation
2021
Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function
Thompson B, Chen Y, Davidson EA, Garcia-Milian R, Golla JP, Apostolopoulos N, Orlicky DJ, Schey K, Thompson DC, Vasiliou V. Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function. The Ocular Surface 2021, 22: 190-203. PMID: 34425299, PMCID: PMC8560581, DOI: 10.1016/j.jtos.2021.08.010.Peer-Reviewed Original ResearchConceptsHEK293T cellsEye developmentGSH biosynthesisTransactivation activityPax6 functionReactive oxygen speciesSubsequent gene ontologyCell identity genesButhionine sulfoximineEpithelial cell identityRNA-seq analysisIngenuity Pathway AnalysisKey upstream regulatorIdentity genesCell identityGene OntologyRNA-seqImmune response genesBioinformatics analysisResponse genesGlutathione biosynthesisLens morphogenesisMolecular consequencesUpstream regulatorMicrophthalmia phenotypeYAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion
Feliciano D, Ott CM, Espinosa-Medina I, Weigel AV, Benedetti L, Milano KM, Tang Z, Lee T, Kliman HJ, Guller SM, Lippincott-Schwartz J. YAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion. Nature Communications 2021, 12: 4502. PMID: 34301937, PMCID: PMC8302681, DOI: 10.1038/s41467-021-24708-2.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAMP-Activated Protein KinasesAnimalsBiological TransportCell FusionCell LineCell Line, TumorCell MembraneCell NucleusCells, CulturedGiant CellsHEK293 CellsHumansMembrane GlycoproteinsMiceRNA-SeqSignal TransductionTranscription FactorsTranscription, GeneticViral Envelope ProteinsYAP-Signaling ProteinsConceptsCell cycle arrestCell fusionNew cellular statesPlasma membrane surface areaRNA-seq analysisCell fusion systemTranscriptional programsNutrient stressCellular statesTranscriptional changesNuclear effluxCytoplasmic glucoseExtrinsic cuesUndifferentiated cellsGlucose transporterFused cellsMechanistic insightsMembrane surface areaNew functionsEndocytosisYAP1 inhibitionEnergetic stateSyncytiaCellsVSVDeficiency of histone lysine methyltransferase SETDB2 in hematopoietic cells promotes vascular inflammation and accelerates atherosclerosis
Zhang X, Sun J, Canfrán-Duque A, Aryal B, Tellides G, Chang YJ, Suárez Y, Osborne TF, Fernández-Hernando C. Deficiency of histone lysine methyltransferase SETDB2 in hematopoietic cells promotes vascular inflammation and accelerates atherosclerosis. JCI Insight 2021, 6: e147984. PMID: 34003795, PMCID: PMC8262461, DOI: 10.1172/jci.insight.147984.Peer-Reviewed Original ResearchConceptsHematopoietic cellsHistone methylation/acetylationSingle-cell RNA-seq analysisMethylation/acetylationHistone H3 Lys9RNA-seq analysisProgression of atherosclerosisEpigenetic marksLysine methyltransferasesH3 Lys9Epigenetic modificationsDNA methylationNoncoding RNAsCell regulatorsSETDB2Vascular inflammationAtherosclerotic lesionsAtherosclerotic plaquesMyeloid cell recruitmentGenetic deletionLDLR knockout miceEnhanced expressionHepatic lipid metabolismMurine atherosclerotic lesionsGenesIsolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis
Santoro F, Chien K, Sahara M. Isolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis. STAR Protocols 2021, 2: 100339. PMID: 33644774, PMCID: PMC7887647, DOI: 10.1016/j.xpro.2021.100339.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cell differentiationEmbryonic stem cell differentiationSingle-cell RNA-seq analysisSingle-cell RNA sequencing analysisComprehensive transcriptional analysisRNA-seq analysisStem cell differentiationRNA sequencing analysisCardiac derivativesFluorescence-activated cell sortingSmart-seq2Developmental tissuesTranscriptional analysisCombination of populationCDNA libraryMolecular atlasHuman embryogenesisHuman ESCsCell differentiationSequencing analysisComplete detailsCell sortingPowerful approachEmbryonic heart cellsDifferentiationQuantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter
Psifidi A, Kranis A, Rothwell L, Bremner A, Russell K, Robledo D, Bush S, Fife M, Hocking P, Banos G, Hume D, Kaufman J, Bailey R, Avendano S, Watson K, Kaiser P, Stevens M. Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter. Scientific Reports 2021, 11: 1623. PMID: 33436657, PMCID: PMC7804197, DOI: 10.1038/s41598-020-79005-7.Peer-Reviewed Original ResearchConceptsQuantitative trait lociTrait lociMajor histocompatibility complexConsumption of contaminated poultry meatFrequency of resistance-associated allelesCis-acting variationGenome-wide genotypingRNA-seq analysisInbred chicken linesResistance-associated allelesBacterial foodborne gastroenteritisCis-QTLsTranscribed genesColonisation phenotypeRNA-seqTrait heritabilityChromosome 14Chromosome 16Non-genetic factorsChromosome 19Campylobacter colonisationFoodborne gastroenteritisBG genesChicken linesHeritable resistance
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