2022
Characterization of the COPD alveolar niche using single-cell RNA sequencing
Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nature Communications 2022, 13: 494. PMID: 35078977, PMCID: PMC8789871, DOI: 10.1038/s41467-022-28062-9.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingRNA sequencingCell-specific mechanismsChronic obstructive pulmonary diseaseAdvanced chronic obstructive pulmonary diseaseTranscriptomic network analysisSingle-cell RNA sequencing profilesCellular stress toleranceAberrant cellular metabolismStress toleranceRNA sequencing profilesTranscriptional evidenceCellular metabolismAlveolar nicheSequencing profilesHuman alveolar epithelial cellsChemokine signalingAlveolar epithelial type II cellsObstructive pulmonary diseaseSitu hybridizationType II cellsEpithelial type II cellsSequencingCOPD pathobiologyHuman lung tissue samples
2021
Microvascular fluid flow in ex vivo and engineered lungs
Raredon MSB, Engler AJ, Yuan Y, Greaney AM, Niklason LE. Microvascular fluid flow in ex vivo and engineered lungs. Journal Of Applied Physiology 2021, 131: 1444-1459. PMID: 34554016, PMCID: PMC8616606, DOI: 10.1152/japplphysiol.00286.2020.Peer-Reviewed Original ResearchIntegrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.Peer-Reviewed Original ResearchConceptsDifferential expression analysisPrimary lung endothelial cellsLung endothelial cellsCell typesMarker genesExpression analysisSingle-cell RNA sequencing dataCross-species analysisVenous endothelial cellsEndothelial marker genesSingle-cell atlasMarker gene setsRNA sequencing dataEndothelial cellsSubsequent differential expression analysisDifferent lung cell typesResident cell typesLung cell typesCellular diversityEndothelial cell typesCapillary endothelial cellsHuman lung endothelial cellsPhenotypic diversityEndothelial diversityIndistinguishable populations
2020
Bioengineering the Blood‐gas Barrier
Leiby KL, Raredon MSB, Niklason LE. Bioengineering the Blood‐gas Barrier. 2020, 10: 415-452. PMID: 32163210, PMCID: PMC7366783, DOI: 10.1002/cphy.c190026.Peer-Reviewed Original ResearchPlatform 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
2019
Single-cell connectomic analysis of adult mammalian lungs
Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. Science Advances 2019, 5: eaaw3851. PMID: 31840053, PMCID: PMC6892628, DOI: 10.1126/sciadv.aaw3851.Peer-Reviewed Original ResearchConceptsTissue homeostasisMammalian lungSingle-cell RNA sequencing techniquesAdult mammalian lungRNA sequencing techniquesCell-cell interactionsSequencing techniquesKey pathwaysAlveolar type IFunctional roleCell typesCell populationsRegenerative medicineHomeostatic mechanismsHomeostasisFine architectureFunctional lung tissueIncomplete understandingMajor roleType ITissueRegulationPathwayAlveolar cell populationsDistal lungNon-invasive and real-time measurement of microvascular barrier in intact lungs
Engler AJ, Raredon MSB, Le AV, Yuan Y, Oczkowicz YA, Kan EL, Baevova P, Niklason LE. Non-invasive and real-time measurement of microvascular barrier in intact lungs. Biomaterials 2019, 217: 119313. PMID: 31280072, PMCID: PMC6863174, DOI: 10.1016/j.biomaterials.2019.119313.Peer-Reviewed Original ResearchEpac agonist improves barrier function in iPSC-derived endothelial colony forming cells for whole organ tissue engineering
Yuan Y, Engler AJ, Raredon MS, Le A, Baevova P, Yoder MC, Niklason LE. Epac agonist improves barrier function in iPSC-derived endothelial colony forming cells for whole organ tissue engineering. Biomaterials 2019, 200: 25-34. PMID: 30754017, DOI: 10.1016/j.biomaterials.2019.02.005.Peer-Reviewed Original Research
2017
Lung regeneration
Calle EA, Leiby KL, Raredon MB, Niklason LE. Lung regeneration. Current Opinion In Anaesthesiology 2017, 30: 23-29. PMID: 27922848, PMCID: PMC5283945, DOI: 10.1097/aco.0000000000000425.Peer-Reviewed Original Research
2010
Tissue-Engineered Lungs for in Vivo Implantation
Petersen TH, Calle EA, Zhao L, Lee EJ, Gui L, Raredon MB, Gavrilov K, Yi T, Zhuang ZW, Breuer C, Herzog E, Niklason LE. Tissue-Engineered Lungs for in Vivo Implantation. Science 2010, 329: 538-541. PMID: 20576850, PMCID: PMC3640463, DOI: 10.1126/science.1189345.Peer-Reviewed Original ResearchConceptsLung tissueLung matrixAcellular lung matrixNative lung tissueTissue-engineered lungsLung transplantationPrimary therapyAdult lung tissueAdult ratsPulmonary epitheliumVascular endotheliumFunctional lungLung regenerationVascular compartmentLungSeeded endothelial cellsMechanical characteristicsEndothelial cellsVivo implantationRatsEpitheliumTissueCellular componentsExtracellular matrixGas exchange