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
Integrated 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
Single-Cell and Population Transcriptomics Reveal Pan-epithelial Remodeling in Type 2-High Asthma
Jackson ND, Everman JL, Chioccioli M, Feriani L, Goldfarbmuren KC, Sajuthi SP, Rios CL, Powell R, Armstrong M, Gomez J, Michel C, Eng C, Oh SS, Rodriguez-Santana J, Cicuta P, Reisdorph N, Burchard EG, Seibold MA. Single-Cell and Population Transcriptomics Reveal Pan-epithelial Remodeling in Type 2-High Asthma. Cell Reports 2020, 32: 107872. PMID: 32640237, PMCID: PMC8046336, DOI: 10.1016/j.celrep.2020.107872.Peer-Reviewed Original ResearchConceptsIL-13Single-cell RNA sequencingHuman airway epithelial cell culturesCell typesIL-13 effectsAirway epithelial cell culturesNasal airway epitheliumCandidate therapeutic targetTranscriptional statesAsthmatic childrenAsthma endotypesRNA sequencingMucus obstructionAirway epitheliumSecretory programMucin productionNormal epithelial functionTherapeutic targetEpithelial cell culturesCellular remodelingER stressCell deathEpithelial functionMetaplastic stateSecretory cells
2017
Phototaxis beyond turning: persistent accumulation and response acclimation of the microalga Chlamydomonas reinhardtii
Arrieta J, Barreira A, Chioccioli M, Polin M, Tuval I. Phototaxis beyond turning: persistent accumulation and response acclimation of the microalga Chlamydomonas reinhardtii. Scientific Reports 2017, 7: 3447. PMID: 28615673, PMCID: PMC5471259, DOI: 10.1038/s41598-017-03618-8.Peer-Reviewed Original ResearchMeSH KeywordsAcclimatizationAlgorithmsChlamydomonas reinhardtiiLightModels, BiologicalPhototaxisSingle-Cell AnalysisConceptsChlamydomonas reinhardtiiModel organism Chlamydomonas reinhardtiiMicroalga Chlamydomonas reinhardtiiPhototactic motilityEukaryotic microalgaeChlorophyll fluorescenceFlagellar activitySingle cellsReinhardtiiPhototaxisPhototactic responsePopulation levelAdaptation dynamicsCell steeringMicroorganismsPersistent accumulationLight exposure historyStriking quantitative agreementCellsFirst quantitative studyChlamydomonasPhotosynthesisAcclimationMicroalgaeMotility