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Featured Publications
SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection
Greaney A, Raredon M, Kochugaeva M, Niklason L, Levchenko A. SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection. IScience 2023, 26: 106175. PMID: 36788793, PMCID: PMC9912025, DOI: 10.1016/j.isci.2023.106175.Peer-Reviewed Original ResearchSingle-cell RNA sequencing datasetsCell-cell communicationRNA sequencing datasetsViral infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infectionEarly SARS-CoV-2 infectionSequencing datasetsSARS-CoV-2 infectionRepair mechanismsEarly viral entryTissue repair mechanismsMature ciliated cellsAlternative therapeutic approachSARS-CoV-2 virusResponse mechanismsFeedforward loopCell precursorsRapid differentiationViral entryBronchial epitheliumTherapeutic approachesBarrier tissuesKey mechanismCiliated cellsInfectionDecellularization compromises mechanical and structural properties of the native trachea
Greaney A, Ramachandra A, Yuan Y, Korneva A, Humphrey J, Niklason L. Decellularization compromises mechanical and structural properties of the native trachea. Biomaterials And Biosystems 2023, 9: 100074. PMID: 36967724, PMCID: PMC10036236, DOI: 10.1016/j.bbiosy.2023.100074.Peer-Reviewed Original ResearchMechanical behaviorGraft failureNative tracheaMechanical failureTissue engineering technologyDepletion of proteoglycansAirway narrowingAirway replacementClinical interventionsWestern blotTracheaMajor causeTracheal graftsEngineering technologyHistological stainingTracheal replacementDifferent decellularization protocolsSignificant differencesClinical implantationTissue repairCollagen IStructural deteriorationStructural propertiesDecellularization protocolGreat potentialThe History of Engineered Tracheal Replacements: Interpreting the Past and Guiding the Future
Greaney A, Niklason L. The History of Engineered Tracheal Replacements: Interpreting the Past and Guiding the Future. Tissue Engineering Part B Reviews 2021, 27: 341-352. PMID: 33045942, PMCID: PMC8390779, DOI: 10.1089/ten.teb.2020.0238.Peer-Reviewed Original ResearchConceptsFailure modesTracheal graftsTracheal replacementGraft mechanicsDesign criteriaInert materialLong segment defectType of graftRecent preclinical workClinical care prioritiesRigid tubeLeuven protocolTracheal allograftsClinical followAirway reconstructionCadaveric allograftsCircumferential defectsTissue analysis techniquesEngineersPreclinical workReplacement graftsCare prioritiesGraft performanceHuman patientsGraftPlatform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing
Greaney AM, Adams TS, Raredon M, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing. Cell Reports 2020, 30: 4250-4265.e6. PMID: 32209482, PMCID: PMC7175071, DOI: 10.1016/j.celrep.2020.03.004.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingBasal marker expressionBasal cellsChronic pulmonary diseaseRat tracheal epitheliumPulmonary diseaseRNA sequencingCell-based therapiesRat tracheaAir-liquid interfaceTissue graftMarker expressionTracheal epitheliumRegenerative outcomesTracheaEpithelial progenitorsDifferential outcomesEpitheliumOutcomesWhole organPopulation level
2026
20 years of Progress in Stem Cells, Cell Therapy, and Bioengineering in Lung Biology and Diseases
Greaney A, Orr J, Moore S, Ikonomou L, Weiss D, Ryan A. 20 years of Progress in Stem Cells, Cell Therapy, and Bioengineering in Lung Biology and Diseases. American Journal Of Respiratory Cell And Molecular Biology 2026, aanag126. PMID: 42286350, DOI: 10.1093/ajrcmb/aanag126.Peer-Reviewed Original ResearchPreclinical evidenceCell therapyLung biologyCell-free therapeutic strategyStem cellsPluripotent stem cell technologyLung progenitor cellsInflammatory lung diseasesStem cell technologyTissue engineering strategiesStem cell biologyRelevant in vitroEx vivo modelDiverse cell populationsLung lineagesCell-based approachesLung-on-chipDecellularized lung scaffoldsLung diseaseLung homeostasisMatrix compositesProgenitor cellsLung regenerationPulmonary biologyTherapeutic strategiesEngineering function in lung biology: integrating imaging, regenerative constructs, and functional biodesign
Girard R, Tran J, Cai Y, Farach-Carson M, Nia H, Greaney A, Niklason L, Hurley K, Blanco E, Koc-Günel S, Karmouty-Quintana H. Engineering function in lung biology: integrating imaging, regenerative constructs, and functional biodesign. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2026, 330: l653-l660. PMID: 42030197, PMCID: PMC13198914, DOI: 10.1152/ajplung.00066.2026.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsEpithelial Reprogramming and Transition during Pulmonary Bioengineering.
Mizoguchi S, Lee V, Kim H, Edelstein SE, Wang N, Gracia MT, Danelski C, Haynes C, Rivero R, Stitelman D, Obata T, Greaney AM, Tsuchiya T, Kyriakides TR, Kaminski N, Raredon MSB. Epithelial Reprogramming and Transition during Pulmonary Bioengineering. BioRxiv 2026 PMID: 41659587, DOI: 10.64898/2026.01.24.701406.Peer-Reviewed Original Research
2023
Rational engineering of lung alveolar epithelium
Leiby K, Yuan Y, Ng R, Raredon M, Adams T, Baevova P, Greaney A, Hirschi K, Campbell S, Kaminski N, Herzog E, Niklason L. Rational engineering of lung alveolar epithelium. Npj Regenerative Medicine 2023, 8: 22. PMID: 37117221, PMCID: PMC10147714, DOI: 10.1038/s41536-023-00295-2.Peer-Reviewed Original Research
2022
Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome. Scientific Reports 2022, 12: 4187. PMID: 35264704, PMCID: PMC8906120, DOI: 10.1038/s41598-022-07959-x.Peer-Reviewed Original ResearchExpression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids
Cakir B, Tanaka Y, Kiral FR, Xiang Y, Dagliyan O, Wang J, Lee M, Greaney AM, Yang WS, duBoulay C, Kural MH, Patterson B, Zhong M, Kim J, Bai Y, Min W, Niklason LE, Patra P, Park IH. Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids. Nature Communications 2022, 13: 430. PMID: 35058453, PMCID: PMC8776770, DOI: 10.1038/s41467-022-28043-y.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsHuman cortical organoidsTranscription factor PUSingle-cell RNA sequencingMicroglia-like cellsSingle-cell transcriptomicsEmbryonic stem cellsDisease stage IIIRole of microgliaAD-associated genesExpression of genesCortical organoidsNeurodegenerative disordersRNA sequencingMolecular damageIntact complementStem cellsDysfunction of microgliaFunctional microgliaReduced expressionGenesCell clustersExpressionChemokine systemHuman microglia
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