2025
Adding insult to injury: the spectrum of tubulointerstitial responses in acute kidney injury
Baker M, Cantley L. Adding insult to injury: the spectrum of tubulointerstitial responses in acute kidney injury. Journal Of Clinical Investigation 2025, 135: e188358. PMID: 40091836, PMCID: PMC11910233, DOI: 10.1172/jci188358.Peer-Reviewed Original ResearchConceptsAcute kidney injuryTubular epithelial cellsKidney injuryTubular cellsCases of acute kidney injuryImmune-mediated processPersistence of inflammationBiphasic immune responseChronic kidney diseaseCell deathTubular cell injuryLymphocyte subsetsTubular repairCell cycle arrestOutflow obstructionTEC differentiationPreclinical findingsLymphocytic infiltrationProinflammatory macrophagesKidney diseaseModulate inflammationImmune responseActivated macrophagesMetabolic reprogrammingTubular castsImpact 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 ResearchMeSH KeywordsAgingComputational BiologyEpithelial CellsHumansLungRNA-SeqSequence Analysis, RNASingle-Cell Gene Expression AnalysisStress 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 studyA spatial expression atlas of the adult human proximal small intestine
Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T, Korem Kohanim Y, Egozi A, Golani O, Addadi Y, Kedmi M, Keidar Haran T, Levin Y, Savidor A, Keren-Shaul H, Mayer C, Pencovich N, Pery R, Shouval D, Tirosh I, Nachmany I, Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature 2024, 632: 1101-1109. PMID: 39112711, DOI: 10.1038/s41586-024-07793-3.Peer-Reviewed Original ResearchConceptsExpression atlasSingle-molecule fluorescence in situ hybridizationLipid droplet assemblyAdult human gutFluorescence in situ hybridizationHuman proximal small intestineHuman small intestineHuman gutSpatial proteomicsProximal small intestineTip cellsGene expressionSmall intestineIron uptakeSpatial transcriptomicsVillus tip cellsImmune cell typesMouse small intestineCell typesDroplet assemblyImmunosuppressive rolePro-immunogenicAdult human small intestineT cellsZonated expressionIn silico model development and optimization of in vitro lung cell population growth
Mostofinejad A, Romero D, Brinson D, Marin-Araujo A, Bazylak A, Waddell T, Haykal S, Karoubi G, Amon C. In silico model development and optimization of in vitro lung cell population growth. PLOS ONE 2024, 19: e0300902. PMID: 38748626, PMCID: PMC11095723, DOI: 10.1371/journal.pone.0300902.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCell ProliferationComputer SimulationEpithelial CellsGlucoseHumansLungModels, BiologicalOxygenTissue EngineeringA common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma
Everman J, Sajuthi S, Liegeois M, Jackson N, Collet E, Peters M, Chioccioli M, Moore C, Patel B, Dyjack N, Powell R, Rios C, Montgomery M, Eng C, Elhawary J, Mak A, Hu D, Huntsman S, Salazar S, Feriani L, Fairbanks-Mahnke A, Zinnen G, Michel C, Gomez J, Zhang X, Medina V, Chu H, Cicuta P, Gordon E, Zeitlin P, Ortega V, Reisdorph N, Dunican E, Tang M, Elicker B, Henry T, Bleecker E, Castro M, Erzurum S, Israel E, Levy B, Mauger D, Meyers D, Sumino K, Gierada D, Hastie A, Moore W, Denlinger L, Jarjour N, Schiebler M, Wenzel S, Woodruff P, Rodriguez-Santana J, Pearson C, Burchard E, Fahy J, Seibold M. A common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma. Nature Communications 2024, 15: 3900. PMID: 38724552, PMCID: PMC11082194, DOI: 10.1038/s41467-024-48034-5.Peer-Reviewed Original ResearchConceptsAirway epithelial cellsIntelectin-1Mucus pluggingGene expressionAirways of severe asthmaticsEpithelial cellsHuman airway epithelial cellsAirway epithelial brushingsMucus secretory cellsT2-high asthmaFormation of mucus plugsAssociated with protectionC-terminusGenetic variantsAirway mucus pluggingMolecular roleSecretory cellsSecreted componentsEpithelial brushingsT2-lowIL-13Mucus obstructionTarget pathwaysSevere asthmaticsClinical significanceLytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells
Zamora P, Reidy T, Armbruster C, Sun M, Van Tyne D, Turner P, Koff J, Bomberger J. Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells. PLOS Biology 2024, 22: e3002566. PMID: 38652717, PMCID: PMC11037538, DOI: 10.1371/journal.pbio.3002566.Peer-Reviewed Original ResearchConceptsLytic phagesLytic bacteriophagesPhage therapyAirway epithelial cellsPseudomonas aeruginosa phagesEpithelial cellsMultidrug resistanceAirway epitheliumCystic fibrosisProinflammatory cytokinesHuman respiratory epithelial cellsPhage exposurePhage familiesMammalian cell responsesHuman airway epithelial cellsInternalized phageTreat multidrug-resistantPhageBacterial isolatesTranscriptional profilesRespiratory epithelial cellsHuman hostChronic respiratory disordersBacterial biofilmsBacteriophageDHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells
Ren X, Liu Q, Zhou P, Zhou T, Wang D, Mei Q, Flavell R, Liu Z, Li M, Pan W, Zhu S. DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells. Nature Communications 2024, 15: 3080. PMID: 38594251, PMCID: PMC11004185, DOI: 10.1038/s41467-024-47235-2.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseIntestinal stem cellsIntestinal epithelial cellsEpithelial homeostasisSusceptibility to experimental colitisIncreased susceptibility to experimental colitisImpaired ISC functionStem cellsEpithelial barrier dysfunctionGenomic instabilityInflammatory bowel disease patientsPathogenesis of inflammatory bowel diseaseR-loop-mediated genome instabilityHallmarks of inflammatory bowel diseaseContinuous self-renewalBarrier dysfunctionExperimental colitisCrypt destructionEpithelial cellsInflammatory responseSelf-renewalBowel diseaseRisk factorsIntestinal epitheliumProtein levelsMulti-omics analysis reveals immune features associated with immunotherapy benefit in squamous cell lung cancer patients from Phase III Lung-MAP S1400I trial
Parra E, Zhang J, Duose D, Gonzalez-Kozlova E, Redman M, Chen H, Manyam G, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli M, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang H, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray J, Herbst R, Wistuba I, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee J, Zhang J, Haymaker C. Multi-omics analysis reveals immune features associated with immunotherapy benefit in squamous cell lung cancer patients from Phase III Lung-MAP S1400I trial. Clinical Cancer Research 2024, 30: 1655-1668. PMID: 38277235, PMCID: PMC11016892, DOI: 10.1158/1078-0432.ccr-23-0251.Peer-Reviewed Original ResearchConceptsChromosome copy-number variationsOverall survivalMultiplex immunofluorescenceMulti-omics analysisAssociated with superior progression-free survivalNCounter PanCancer Immune Profiling PanelSquamous cell lung cancer patientsSuperior progression-free survivalTreated with nivolumab monotherapyAssociated with worse overall survivalNon-small cell carcinomaAssociated with worse survivalCell lung cancer patientsCold immune microenvironmentProgression-free survivalImmune Profiling PanelRegulatory T cellsPhase III trialsResponse to ICIImmune cell infiltrationHigher immune scoresImmune cell densityLung cancer patientsWhole-exome sequencingImmune gene expression profiles
2023
Heterogeneous murine peribiliary glands orchestrate compartmentalized epithelial renewal
Singh S, Lian Q, Budiman T, Taketo M, Simons B, Gupta V. Heterogeneous murine peribiliary glands orchestrate compartmentalized epithelial renewal. Developmental Cell 2023, 58: 2732-2745.e5. PMID: 37909044, PMCID: PMC10842076, DOI: 10.1016/j.devcel.2023.10.004.Peer-Reviewed Original ResearchThe cellular states and fates of shed intestinal cells
Bahar Halpern K, Korem Kohanim Y, Biram A, Harnik Y, Egozi A, Yakubovsky O, Shulman Z, Itzkovitz S. The cellular states and fates of shed intestinal cells. Nature Metabolism 2023, 5: 1858-1869. PMID: 37857731, DOI: 10.1038/s42255-023-00905-9.Peer-Reviewed Original ResearchIFN-λ derived from nonsusceptible enterocytes acts on tuft cells to limit persistent norovirus
Ingle H, Makimaa H, Aggarwal S, Deng H, Foster L, Li Y, Kennedy E, Peterson S, Wilen C, Lee S, Suthar M, Baldridge M. IFN-λ derived from nonsusceptible enterocytes acts on tuft cells to limit persistent norovirus. Science Advances 2023, 9: eadi2562. PMID: 37703370, PMCID: PMC10499323, DOI: 10.1126/sciadv.adi2562.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntiviral AgentsEnterocytesEnterovirus InfectionsEpithelial CellsInterferon LambdaMiceNorovirusSignal TransductionConceptsIntestinal epithelial cellsTuft cellsUninfected bystander cellsIFN-λ signalingSource of IFNImmune cellsIntestinal infectionsLeading causeViral gastroenteritisMNoVNorovirus pathogenesisCellular tropismPotent antiviralEpidemic viral gastroenteritisEpithelial cellsBystander cellsIFNNorovirusAntiviralsInfectionMurine norovirusIntercellular communicationPersistent strainsCellsVivoS-nitrosylation of EMMPRIN influences the migration of HSCs and MMP activity in liver fibrosis
Zhu X, Tang Z, Li W, Li X, Iwakiri Y, Liu F. S-nitrosylation of EMMPRIN influences the migration of HSCs and MMP activity in liver fibrosis. Acta Biochimica Et Biophysica Sinica 2023, 55: 1640-1649. PMID: 37700592, PMCID: PMC10577453, DOI: 10.3724/abbs.2023141.Peer-Reviewed Original ResearchConceptsExtracellular matrix metalloproteinase inducerLiver fibrosisLevels of EMMPRINMMP activitySinus epithelial cellsHSC migrationMatrix metalloproteinase inducerNormal control liversActivity of MMP2Matrix metalloproteinase activityS-nitrosylationStellate cell migrationHepatic stellate cell migrationTissue microarrayFibrotic liverFibrosisMouse liver tissueControl liversECM accumulationLiver tissueMetalloproteinase activityEMMPRIN mRNALiver areaEpithelial cellsProtein levelsEpithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis
Reyes E, Castillo-Azofeifa D, Rispal J, Wald T, Zwick R, Palikuqi B, Mujukian A, Rabizadeh S, Gupta A, Gardner J, Boffelli D, Gartner Z, Klein O. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. Journal Of Clinical Investigation 2023, 133: e163591. PMID: 37643009, PMCID: PMC10575728, DOI: 10.1172/jci163591.Peer-Reviewed Original ResearchConceptsCystic fibrosis transmembrane conductance regulatorTumor necrosis factorInflammatory bowel diseaseCell differentiationRegulate mucin productionCystic fibrosis transmembrane conductance regulator inhibitionCystic fibrosis transmembrane conductance regulator activityTumor necrosis factor treatmentInflammatory cytokine tumor necrosis factorAnti-TNF therapyAbsence of tumor necrosis factorTransmembrane conductance regulatorCytokine tumor necrosis factorMucus-producing goblet cellsGenetic mouse modelsUpstream regulatorIncreased mucus accumulationAdult intestineConductance regulatorEpithelial signalsSignaling axisProgenitor cellsMouse modelNecrosis factorGut transit timeAlveolar type II epithelial cell FASN maintains lipid homeostasis in experimental COPD
Fan L, McConn K, Plataki M, Kenny S, Williams N, Kim K, Quirke J, Chen Y, Sauler M, Möbius M, Chung K, Gomez E, Choi A, Xu J, Cloonan S. Alveolar type II epithelial cell FASN maintains lipid homeostasis in experimental COPD. JCI Insight 2023, 8: e163403. PMID: 37606038, PMCID: PMC10543729, DOI: 10.1172/jci.insight.163403.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseAEC2 cellsFatty acid synthaseCigarette smokeExperimental chronic obstructive pulmonary diseaseBronchoalveolar lavage fluid neutrophilsLipid metabolismDisease-chronic obstructive pulmonary diseaseObstructive pulmonary diseaseAlveolar epithelial type II cellsEpithelial type II cellsType II cellsCOPD developmentPulmonary diseaseAirspace enlargementBALF proteinLipogenesis enzymesFerroptosis markersHigh-throughput lipidomic analysisSurfactant phospholipidsMiceSurfactant synthesisLipid homeostasisII cellsCell functionInactivation of Invs/Nphp2 in renal epithelial cells drives infantile nephronophthisis like phenotypes in mouse
Li Y, Xu W, Makova S, Brueckner M, Sun Z. Inactivation of Invs/Nphp2 in renal epithelial cells drives infantile nephronophthisis like phenotypes in mouse. ELife 2023, 12: e82395. PMID: 36920028, PMCID: PMC10154023, DOI: 10.7554/elife.82395.Peer-Reviewed Original ResearchConceptsFlox/Valproic acidRenal fibrosisCyst formationEnd-stage renal diseaseMutant miceHistone deacetylase inhibitor valproic acidKidney function declineStage renal diseaseCell proliferationInhibitor valproic acidEpithelial-stromal crosstalkKnockout mouse modelRenal cyst formationCyst burdenRenal diseaseFunction declineInterstitial fibrosisDisease progressionStromal fibrosisTargeted therapyInfantile nephronophthisisMouse modelMyofibroblast activationRenal epithelial cellsLow CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity.
Li X, Guerra S, Ledford JG, Kraft M, Li H, Hastie AT, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Meyers DA, Bleecker ER. Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 438-451. PMID: 36066606, PMCID: PMC9940145, DOI: 10.1164/rccm.202206-1230oc.Peer-Reviewed Original ResearchMeSH KeywordsAsthmaBiomarkersEpithelial CellsHumansInflammationProspective StudiesRetrospective StudiesRNA, MessengerUteroglobinConceptsBronchial epithelial cellsMRNA expression levelsAsthma severityT2 biomarkersAsthma susceptibilityT2 inflammationExpression levelsSevere Asthma Research ProgramSystemic corticosteroid useLower pulmonary functionEpithelial cellsAsthma-related phenotypesCorticosteroid useAsthma exacerbationsPulmonary functionAsthma developmentAsthma endotypesAsthma progressionInflammation biomarkersInflammation genesHost defenseCC16Th2 genesSeverityBiomarkersUnique DUOX2+ACE2+ small cholangiocytes are pathogenic targets for primary biliary cholangitis
Li X, Li Y, Xiao J, Wang H, Guo Y, Mao X, Shi P, Hou Y, Zhang X, Zhao N, Zheng M, He Y, Ding J, Tan Y, Liao M, Li L, Peng Y, Li X, Pan Q, Xie Q, Li Q, Li J, Li Y, Chen Z, Huang Y, Assis D, Cai S, Boyer J, Huang X, Tang C, Liu X, Peng S, Chai J. Unique DUOX2+ACE2+ small cholangiocytes are pathogenic targets for primary biliary cholangitis. Nature Communications 2023, 14: 29. PMID: 36759512, PMCID: PMC9911648, DOI: 10.1038/s41467-022-34606-w.Peer-Reviewed Original ResearchMeSH KeywordsAngiotensin-Converting Enzyme 2AnimalsDual OxidasesEpithelial CellsHumansLiver Cirrhosis, BiliaryMiceConceptsPrimary biliary cholangitisPrimary biliary cholangitis patientsBiliary cholangitisEtiology of primary biliary cholangitisScRNA-seqPathogenic targetsSeverity of diseaseSingle-cell RNA sequencingAMA-M2PBC patientsAutoantibody levelsPolymeric immunoglobulin receptorMemory BMultiplex immunofluorescenceCholangiocyte injuryPlasma cellsAutoimmune diseasesRNAscope analysisCholangiocytesImmunoglobulin receptorBile formationPatientsTherapeutic interventionsMultiplexed IFRNA sequencing
2022
Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury
Palikuqi B, Rispal J, Reyes E, Vaka D, Boffelli D, Klein O. Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury. Cell Stem Cell 2022, 29: 1262-1272.e5. PMID: 35931034, PMCID: PMC9387209, DOI: 10.1016/j.stem.2022.07.007.Peer-Reviewed Original ResearchMeSH KeywordsCell ProliferationEndothelial CellsEpithelial CellsIntestinal MucosaIntestinesStem CellsConceptsLymphatic endothelial cellsIntestinal stem cellsCytotoxic injuryEndothelial cellsIntestinal stem cell nicheWnt signalingProliferation of intestinal stem cellsCrypt epithelial cellsSource of Wnt signalingNiche cellsEpithelial renewalProgenitor cellsIntestinal recoveryIntestinal repairEpithelial cellsNiche componentsStem cellsInjury statesIntestinal epitheliumInjurySecreted moleculesSmall intestineCellsRepair
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply