2025
Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells.
D'Mello A, Murphy T, Wade M, Kirkham C, Kong Y, Tettelin H, Pettigrew M. Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells. MSphere 2025, e0024225. PMID: 40492732, DOI: 10.1128/msphere.00242-25.Peer-Reviewed Original ResearchRegulation of quorum sensingTranscriptome profilingBioinformatics analysisCell culture modelBiological pathwaysIron-sulfur metabolismHost-pathogen interactionsHost biological pathwaysHost cell pathwaysIscR regulonChronic obstructive pulmonary diseaseEpithelial cellsQuorum sensingEpithelial cell infectionRNA-seqH292 cell lineHost pathwaysExacerbation of chronic obstructive pulmonary diseaseNontypeable Haemophilus influenzaeRNA sequencingHost cellsDifferential regulationCulture modelBronchial epithelial cellsMono-infectionEvidence of secondary Notch signaling within the rat small intestine.
Zagoren E, Dias N, Santos A, Smith Z, Ameen N, Sumigray K. Evidence of secondary Notch signaling within the rat small intestine. Development 2025, 152 PMID: 40371707, PMCID: PMC12188240, DOI: 10.1242/dev.204277.Peer-Reviewed Original ResearchConceptsSecretory lineageRegulate luminal pHSecretory cellsNotch signalingSecretory cell typesSmall intestinal epithelial cellsRNA sequencing dataIntestinal epithelial cellsIntestinal stem cellsSmall intestineFate in vivoFibrosis pathophysiologyRat small intestineCrypt progenitorsTranscription factorsEpithelial cellsRat jejunumStem cellsPseudotime trajectory analysisRare populationLuminal pHRatsHigher expressionIntestinal functionIn vitroSuppression of Autosomal Dominant Polycystic Kidney Disease Influences Epithelial Cell Transcription Program
Rai V, Failli M, Fiusco M, Reyna-Neyra A, Onuchic L, di Bernardo D, Craft J, Caplan M. Suppression of Autosomal Dominant Polycystic Kidney Disease Influences Epithelial Cell Transcription Program. Physiology 2025, 40: 0966. DOI: 10.1152/physiol.2025.40.s1.0966.Peer-Reviewed Original ResearchC-terminal tailCystic phenotypeTranscriptional programsAutosomal dominant polycystic kidney diseaseScRNA-seqTranscriptional differencesAmino acid C-terminal tailAcidic C-terminal tailPolycystin-1 proteinCell transcriptional programDifferentiated cell stateEpithelial cellsSingle cell RNA sequencingDoxycycline-inducible mouse modelCell RNA sequencingNovel transcriptsLibrary preparationCell transcriptional profilingChromium technologyPKD1 geneBiological replicatesRNA velocityCDNA synthesisRNA sequencingTranscriptional profilesProinflammatory Pulmonary Effects of SARS-CoV-2 Main Protease in Mice and Human Bronchial Epithelial Cells
Caceres A, Jabba S, Jordt S. Proinflammatory Pulmonary Effects of SARS-CoV-2 Main Protease in Mice and Human Bronchial Epithelial Cells. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a6597-a6597. DOI: 10.1164/ajrccm.2025.211.abstracts.a6597.Peer-Reviewed Original ResearchCompartmentalization of the Endoplasmic Reticulum in Mouse Kidney Proximal Tubule Epithelial Cells
Reyna-Neyra A, Pandya R, Lackner E, Pang S, Li W, Xu C, Zugates C, Burdyniuk M, Pandya V, Weisz O, Caplan M. Compartmentalization of the Endoplasmic Reticulum in Mouse Kidney Proximal Tubule Epithelial Cells. Physiology 2025, 40: 1280. DOI: 10.1152/physiol.2025.40.s1.1280.Peer-Reviewed Original ResearchPT cellsProximal tubulesEndoplasmic reticulumER structureKidney proximal tubule epithelial cellsProximal tubule epithelial cellsER proteinsRenal proximal tubulesProximal tubule cellsKidney proximal tubulesTubule epithelial cellsBasolateral plasma membraneOuter membrane proteinsCalcium ATPaseTubule cellsSolute reabsorptionCalcium ion storageMouse kidney tissuesK-ATPaseMean volumeEpithelial cellsER lumenCLIMP-63ER volumeMouse kidneySpatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis
Gao Y, Li B, Jin Y, Cheng J, Tian W, Ying L, Hong L, Xin S, Lin B, Liu C, Sun X, Zhang J, Zhang H, Xie J, Deng X, Dai X, Liu L, Zheng Y, Zhao P, Yu G, Fang W, Bao X. Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis. Oncogene 2025, 44: 2268-2282. PMID: 40234722, DOI: 10.1038/s41388-025-03388-y.Peer-Reviewed Original ResearchConceptsLung metastasesTumor microenvironmentBreast cancerImaging mass cytometryHLA-DR+Primary BCTME componentsEndothelial cellsTumour microenvironment of BCEpithelial cellsPaired lung metastasesExhausted T cellsTriple-negative subtypeMultiplex immunofluorescence analysisPrimary breast cancerAnti-angiogenic therapyDevelopment of therapeutic optionsFormalin-fixed paraffin-embedded (FFPEParaffin-embedded (FFPELung-specific metastasisOligo-metastasisMetastatic tumorsSurgical specimensMultiplex immunofluorescenceT cellsApplying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis
Justet A, Mitash N, Pineda R, Adams T, Balayev A, Abu Hussein N, Ishizuka M, Kim H, Khoury J, Cala-García J, Ahangari F, Yan X, Kaminski N, Königshoff M. Applying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis. Revue Des Maladies Respiratoires 2025, 42: 223. DOI: 10.1016/j.rmr.2025.02.083.Peer-Reviewed Original ResearchAbnormal cell populationsAlveolar epithelial cellsTreated with drugsAnti-fibrotic propertiesSingle cell platformsSingle nuclear RNA sequencingLigand-receptor analysisPreclinical evidencePulmonary fibrosisBasaloid cellsFibrotic propertiesReceptor analysisFibrotic pathwaysCell signaturesClinical trialsProfibrotic genesAnti-fibroticFDA-approved drugsGene signatureAnimal modelsEpithelial cellsGene expression changesDay 5Drug efficacyCell profilesEnhanced paracrine action of FGF21 in stromal cells delays thymic aging
Youm Y, Gliniak C, Zhang Y, Dlugos T, Scherer P, Dixit V. Enhanced paracrine action of FGF21 in stromal cells delays thymic aging. Nature Aging 2025, 5: 576-587. PMID: 39972172, PMCID: PMC12003152, DOI: 10.1038/s43587-025-00813-5.Peer-Reviewed Original ResearchThymic epithelial cellsThymic agingNaive CD8 T cellsCD8 T cellsAge-related thymic involutionT cell diversityThymic functionImmune dysfunctionThymic stromaT cellsThymic lymphopoiesisThymic involutionActions of FGF21Immune agingAged miceStromal cellsEpithelial cellsAged animalsCo-receptorHepatic overexpressionElevation of FGF21FGF21AgeCellsAdipocytesPhysiologic mechanisms underlying polycystic kidney disease
Boletta A, Caplan M. Physiologic mechanisms underlying polycystic kidney disease. Physiological Reviews 2025, 105: 1553-1607. PMID: 39938884, PMCID: PMC12174308, DOI: 10.1152/physrev.00018.2024.Peer-Reviewed Original ResearchPrimary ciliaPolycystic kidney diseaseTrafficking of proteinsHuman ciliopathiesExtracellular signalsMultiple genesKidney diseaseProtein productionMolecular basisCell biologyMonogenic disordersCyst formationGenesRenal epithelial cellsProteinCiliaBiochemical informationApical surfaceEpithelial cellsFunctional expressionPhysiological propertiesWealth of informationPhysiological mechanismsCellsFibrocystinInvestigation of ferroptosis and mTOR signaling in chromophobe renal cell carcinoma (ChRCC).
Madsen K, Labaki C, Saad E, Alchoueiry M, Bi K, Hobeika C, Bakouny Z, Priolo C, Khabibullin D, Schindler N, Camp S, Saliby R, Heng D, Van Allen E, Shukla S, Henske E, Choueiri T, Braun D. Investigation of ferroptosis and mTOR signaling in chromophobe renal cell carcinoma (ChRCC). Journal Of Clinical Oncology 2025, 43: 583-583. DOI: 10.1200/jco.2025.43.5_suppl.583.Peer-Reviewed Original ResearchInternational Metastatic RCC Database ConsortiumMetastatic clear cell RCCProgression-free survivalOverall survivalClear cell RCCCell of originMTOR inhibitorsTumor cellsChRCC tumorsEpithelial cellsScRNA-seq analysisCell RCCMetastatic ChRCCResponse to immune checkpoint inhibitorsDistal tubulesMechanisms of therapeutic responseChromophobe renal cell carcinomaTreated with mTOR inhibitorsResponse to mTOR inhibitorsImmune checkpoint inhibitorsScRNA-seqA intercalated cellsB intercalated cellsImproved overall survivalEvaluate survival outcomesHarnessing the tumor microenvironment: targeted cancer therapies through modulation of epithelial-mesenchymal transition
Glaviano A, Lau H, Carter L, Lee E, Lam H, Okina E, Tan D, Tan W, Ang H, Carbone D, Yee M, Shanmugam M, Huang X, Sethi G, Tan T, Lim L, Huang R, Ungefroren H, Giovannetti E, Tang D, Bruno T, Luo P, Andersen M, Qian B, Ishihara J, Radisky D, Elias S, Yadav S, Kim M, Robert C, Diana P, Schalper K, Shi T, Merghoub T, Krebs S, Kusumbe A, Davids M, Brown J, Kumar A. Harnessing the tumor microenvironment: targeted cancer therapies through modulation of epithelial-mesenchymal transition. Journal Of Hematology & Oncology 2025, 18: 6. PMID: 39806516, PMCID: PMC11733683, DOI: 10.1186/s13045-024-01634-6.Peer-Reviewed Original ResearchConceptsEpithelial-mesenchymal transitionTumor microenvironmentCancer progressionTherapeutic resistanceCancer therapyTumor microenvironment componentsTumor microenvironment modulationModulation of epithelial-mesenchymal transitionPromote tumor growthImprove treatment efficacyTumor microenvironment signalsTargeted cancer therapyTarget various componentsTherapeutic challengeTreatment responseTumor growthPromote metastasisTherapeutic strategiesTreatment efficacyEpithelial cellsMesenchymal traitsCancer cellsExtracellular matrix componentsCancerResistance mechanismsImpact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research
Merrill S, Konwar C, Fatima F, Dever K, MacIsaac J, Letourneau N, Giesbrecht G, Dewey D, England-Mason G, Lewis C, Wang D, Teh A, Meaney M, Gonzalez A, Noll J, De Weerth C, Bush N, O’Donnell K, Stewart S, Kobor M. Impact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research. Nature Communications 2025, 16: 609. PMID: 39800776, PMCID: PMC11725590, DOI: 10.1038/s41467-025-55909-8.Peer-Reviewed Original ResearchConceptsBuccal epithelial cellsAge-related changesObsessive-compulsive disorderEpithelial cellsDiurnal cortisol slopeCheek swabsImpact of age-related changesCortisol slopeAssociated with ageOral cellsDevelopmental rangeAge accelerationDNA methylation studiesHeterogeneous sampleNeutrophil proportionBiomarker researchMethylation studiesAgeSwabsWeak associationEpigenetic age
2024
Predicting lung aging using scRNA-Seq data
Song Q, Singh A, McDonough J, Adams T, Vos R, De Man R, Myers G, Ceulemans L, Vanaudenaerde B, Wuyts W, Yan X, Schupp J, Hagood J, Kaminski N, Bar-Joseph Z. Predicting lung aging using scRNA-Seq data. PLOS Computational Biology 2024, 20: e1012632. PMID: 39700255, PMCID: PMC11741621, DOI: 10.1371/journal.pcbi.1012632.Peer-Reviewed Original ResearchGlucosamine mitigates ischemia-reperfusion-induced acute kidney injury through anti-inflammatory mechanisms
Zhang G, Jin S, Fan X, Qi J, Liu J, Yin S, Cao Y, Du Y, Dong X, Wang Z, Tan X, Yan S. Glucosamine mitigates ischemia-reperfusion-induced acute kidney injury through anti-inflammatory mechanisms. Frontiers In Materials 2024, 11: 1438610. DOI: 10.3389/fmats.2024.1438610.Peer-Reviewed Original ResearchAcute kidney injuryTubular epithelial cellsKidney injuryI/R injuryRenal tissueEpithelial cellsInflammatory responseRenal ischemia-reperfusion (I/R) injuryIschemia-reperfusion-induced acute kidney injuryI/R-induced acute kidney injuryEndoplasmic reticulumIschemia-reperfusion (I/R) injuryProximal tubular epithelial cellsMarkers of oxidative stressEfficacy of glucosaminePotential therapeutic efficacyProximal convoluted tubular epithelial cellsRenal interstitial fibrosisI/R injury modelAnti-inflammatory actionMitigate ER stressAnti-inflammatory mechanismsAssessed in vitroOxidative stress levelsReduced oxidative stress levelsInterleukin‐5 as a pleiotropic cytokine orchestrating airway type 2 inflammation: Effects on and beyond eosinophils
Buchheit K, Shaw D, Chupp G, Lehtimaki L, Heffler E, Finney‐Hayward T, Zangrilli J, Kwiatek J, Siddiqui S, Roufosse F, Thamboo A, West N, Vichiendilokkul A, Hellings P, Peters A, Howarth P. Interleukin‐5 as a pleiotropic cytokine orchestrating airway type 2 inflammation: Effects on and beyond eosinophils. Allergy 2024, 79: 2662-2679. PMID: 39359069, DOI: 10.1111/all.16303.Peer-Reviewed Original ResearchConceptsAnti-IL-5 therapyType 2 inflammationIL-5Airway type 2 inflammationT regulatory cellsInnate lymphoid cellsInterleukin (IL)-5Relevant to disease pathogenesisSurvival of eosinophilsLower airway diseaseEosinophil-associated diseasesEffector cellsEosinophil depletionTargeted therapyClinical benefitLymphoid cellsPlasma cellsAirway diseaseInterleukin-5Epithelial cellsTherapeutic effectMast cellsDisease pathogenesisEosinophilsTissue damageGAD65 tunes the functions of Best1 as a GABA receptor and a neurotransmitter conducting channel
Wang J, Owji A, Kittredge A, Clark Z, Zhang Y, Yang T. GAD65 tunes the functions of Best1 as a GABA receptor and a neurotransmitter conducting channel. Nature Communications 2024, 15: 8051. PMID: 39277606, PMCID: PMC11401937, DOI: 10.1038/s41467-024-52039-5.Peer-Reviewed Original ResearchConceptsCl- currentsRetinal pigment epithelial cellsIsoform of glutamic acid decarboxylasePigment epithelial cellsGlutamic acid decarboxylaseG-aminobutyric acidBestrophin-1BEST1GABA receptorsTransport metabolonEpithelial cellsGAD65Glutamate metabolizing enzymesAcid decarboxylaseGAD67Bestrophin channelsGABAExtracellular sitesNo effectAnion channelMetabolic enzymesPhysiological roleGlutamateCellsBestrophinStress increases sperm respiration and motility in mice and men
Moon N, Morgan C, Marx-Rattner R, Jeng A, Johnson R, Chikezie I, Mannella C, Sammel M, Epperson C, Bale T. Stress increases sperm respiration and motility in mice and men. Nature Communications 2024, 15: 7900. PMID: 39261485, PMCID: PMC11391062, DOI: 10.1038/s41467-024-52319-0.Peer-Reviewed Original ResearchConceptsEpididymal epithelial cellsIncreased mitochondrial respirationIn vitro stress modelsCells secrete extracellular vesiclesSperm RNASperm respirationMouse spermSperm maturationDNA regionsSperm functionTranslational signaling pathwaysSperm motilitySemen qualitySpermMitochondrial respirationMetabolic pathwaysSignaling pathwayEnvironmental stressorsExtracellular vesiclesHuman cohort studiesEpithelial cellsMotilityCellular mechanismsEmbryo developmentCohort studyProteomic Profile of Circulating Extracellular Vesicles in the Brain after Δ9-Tetrahydrocannabinol Inhalation
Lallai V, Lam T, Garcia-Milian R, Chen Y, Fowler J, Manca L, Piomelli D, Williams K, Nairn A, Fowler C. Proteomic Profile of Circulating Extracellular Vesicles in the Brain after Δ9-Tetrahydrocannabinol Inhalation. Biomolecules 2024, 14: 1143. PMID: 39334909, PMCID: PMC11430348, DOI: 10.3390/biom14091143.Peer-Reviewed Original ResearchConceptsImmediate early gene c-fosChronic THC exposureEarly gene c-fosCannabinoid 1 receptorGene c-fosSex-specific mannerTHC exposurePsychoactive componentExtracellular vesiclesCentral signaling mechanismDrug effectsTHCChoroid plexus epithelial cellsFemale ratsC-fosPlexus epithelial cellsBrainCannabisRelease of EVsRegulate intercellular communicationCerebrospinal fluidEpithelial cellsIntercellular signaling mediatorsEV signalingIntercellular communicationSpatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma
Yasumizu Y, Kinoshita M, Zhang M, Motooka D, Suzuki K, Nojima S, Koizumi N, Okuzaki D, Funaki S, Shintani Y, Ohkura N, Morii E, Okuno T, Mochizuki H. Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma. Cell Reports 2024, 43: 114677. PMID: 39180749, DOI: 10.1016/j.celrep.2024.114677.Peer-Reviewed Original ResearchMyasthenia gravisMedullary thymic epithelial cellsGerminal center responseRegulatory T cellsImmune cell compositionMigratory dendritic cellsThymic epithelial cellsCortico-medullary junctionImmune microenvironmentDendritic cellsT cellsChemokine patternsThymus abnormalitiesHyperplasia samplesThymomaSpatial transcriptomic analysisEpithelial cellsMG pathologyMedullary regionCenter responseMedullaCell compositionCortical regionsPathologyCellsChitinase 3-like-1 (CHI3L1) in the pathogenesis of epidermal growth factor receptor mutant non-small cell lung cancer
Kamle S, Ma B, Schor G, Bailey M, Pham B, Cho I, Khan H, Azzoli C, Hofstetter M, Sadanaga T, Herbst R, Politi K, Lee C, Elias J. Chitinase 3-like-1 (CHI3L1) in the pathogenesis of epidermal growth factor receptor mutant non-small cell lung cancer. Translational Oncology 2024, 49: 102108. PMID: 39178575, PMCID: PMC11388375, DOI: 10.1016/j.tranon.2024.102108.Peer-Reviewed Original ResearchNon-small cell lung cancerEpidermal growth factor receptorTyrosine kinase inhibitorsEpidermal growth factor receptor mutant non-small cell lung cancerMutant non-small cell lung cancerEpidermal growth factor receptor axisCell lung cancerLung cancerTherapeutic resistanceDownstream targets of EGFRResistance to TKI therapyEpithelial cellsStimulated epidermal growth factor receptorWild type epidermal growth factor receptorTargeting of epidermal growth factor receptorActivating EGFR mutationsChitinase 3-like 1Progression free survivalInduce tumor cell deathEpidermal growth factor receptor activationEffects of EGFR activationInhibited pulmonary metastasisTumor cell deathResponse to treatmentGrowth factor receptor
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