2024
Fibrotic cocktail treated human precision lung slices replicate the cellular diversity of the IPF lung
Justet A, Pineda H, Adams T, Balayev A, Mitash N, Ishizuka M, Kim H, Khoury J, Cala-García J, Flint J, Schupp J, Ahangari F, Yan X, Rosas I, Kaminski N, Königshoff M. Fibrotic cocktail treated human precision lung slices replicate the cellular diversity of the IPF lung. Revue Des Maladies Respiratoires 2024, 41: 218. DOI: 10.1016/j.rmr.2024.01.074.Peer-Reviewed Original ResearchCellular repertoireCell typesSingle cell platformsSequence readsCDNA libraryIllumina platformHuman genomeNucleus transcriptomicsCellular diversityIPF lungsPulmonary fibrosisEMT markersAirway epithelial cellsBasaloid cellsCellular populationsEpithelial cellsFibrotic fibroblastsCell platformLung slicesLung cell populationsHuman precision-cut lung slicesCell populationsSenescence markersCellsBasal markers
2023
An integrated cell atlas of the lung in health and disease
Sikkema L, Ramírez-Suástegui C, Strobl D, Gillett T, Zappia L, Madissoon E, Markov N, Zaragosi L, Ji Y, Ansari M, Arguel M, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung M, Collin A, Gay A, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos T, Kole T, Leroy S, Mayr C, Oliver A, von Papen M, Peter L, Taylor C, Walzthoeni T, Xu C, Bui L, De Donno C, Dony L, Faiz A, Guo M, Gutierrez A, Heumos L, Huang N, Ibarra I, Jackson N, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini K, Wilbrey-Clark A, Worlock K, Yoshida M, van den Berge M, Bossé Y, Desai T, Eickelberg O, Kaminski N, Krasnow M, Lafyatis R, Nikolic M, Powell J, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold M, Sheppard D, Shepherd D, Sin D, Timens W, Tsankov A, Whitsett J, Xu Y, Banovich N, Barbry P, Duong T, Falk C, Meyer K, Kropski J, Pe’er D, Schiller H, Tata P, Schultze J, Teichmann S, Misharin A, Nawijn M, Luecken M, Theis F. An integrated cell atlas of the lung in health and disease. Nature Medicine 2023, 29: 1563-1577. PMID: 37291214, PMCID: PMC10287567, DOI: 10.1038/s41591-023-02327-2.Peer-Reviewed Original ResearchConceptsCell atlasGene modulesCell typesCell type definitionsHuman Cell AtlasSingle-cell technologiesSingle-cell datasetsUndescribed cell typeMultiple lung diseasesCell statesMarker genesMonocyte-derived macrophagesDistal axisStudy of diseasesHuman tissuesAnnotationAtlasGenesSPP1DiversityExpressionTreesLimited numberCellsNew dataThe Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During Aging
Yuan Y, Khoury J, Ramachandra A, Singh I, Tellides G, Humphrey J, Kaminski N, Manning E. The Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During Aging. 2023, a2680-a2680. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2680.Peer-Reviewed Original ResearchEmergence of division of labor in tissues through cell interactions and spatial cues
Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams T, Kaminski N, Macosko E, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports 2023, 42: 112412. PMID: 37086403, PMCID: PMC10242439, DOI: 10.1016/j.celrep.2023.112412.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingMost cell typesCell-type populationsCell-cell interactionsDistinguishable expression patternsCell population levelSpatial transcriptomics dataCell interactionsLigand-receptor networkMulticellular organismsTranscriptomic dataRNA sequencingInstructive signalsExpression patternsSpecialist cellsCell typesIndividual cellsDivision of laborMultiple functionsTissue environmentSame cellsDifferent functionsPopulation levelCellsDivision
2021
Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis
Chandran RR, Xie Y, Gallardo-Vara E, Adams T, Garcia-Milian R, Kabir I, Sheikh AQ, Kaminski N, Martin KA, Herzog EL, Greif DM. Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis. Nature Communications 2021, 12: 7179. PMID: 34893592, PMCID: PMC8664937, DOI: 10.1038/s41467-021-27499-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell ProliferationDisease Models, AnimalDown-RegulationExtracellular MatrixFemaleFibroblastsFibrosisHumansKruppel-Like Factor 4LungLung InjuryMaleMesenchymal Stem CellsMiceMice, Inbred C57BLMyofibroblastsReceptor, Platelet-Derived Growth Factor betaRespiratory Tract DiseasesSignal TransductionTransforming Growth Factor betaConceptsMesenchymal cell typesPlatelet-derived growth factor receptorSmooth muscle actinLung fibrosisKruppel-like factor 4Forkhead box M1Growth factor receptorCell transitionCell typesExtracellular matrixDistinct rolesKLF4Box M1C chemokine ligandMesenchymal cell subtypesFactor receptorPro-fibrotic effectsFactor 4PDGFRMesenchymeCellsMacrophage accumulationKLF4 levelsChemokine ligandLung fibrogenesisCutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19
Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19. The Journal Of Immunology 2021, 206: 2785-2790. PMID: 34049971, PMCID: PMC8627528, DOI: 10.4049/jimmunol.2100135.Peer-Reviewed Original ResearchConceptsSevere COVID-19Mild COVID-19B cell responsesMemory B cellsB cell repertoireB cellsCell repertoireCOVID-19Cell responsesExtrafollicular B cell responsesLong-term immunitySymptomatic COVID-19Onset of symptomsB cell populationsGerminal center reactionProtective immunityPlasma cellsSingle-cell RNA sequencingCenter reactionPatientsCell populationsImmunityRNA sequencingCellsPostvaccination
2020
Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics
Blumental-Perry A, Jobava R, Bederman I, Degar A, Kenche H, Guan B, Pandit K, Perry N, Molyneaux N, Wu J, Prendergas E, Ye Z, Zhang J, Nelson C, Ahangari F, Krokowski D, Guttentag S, Linden P, Townsend D, Miron A, Kang M, Kaminski N, Perry Y, Hatzoglou M. Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics. Communications Biology 2020, 3: 626. PMID: 33127975, PMCID: PMC7603330, DOI: 10.1038/s42003-020-01322-4.Peer-Reviewed Original ResearchConceptsMitochondrial genomeNuclear-encoded genesCell type-specific mannerNon-coding RNASteady-state transcriptionMitochondrial energy metabolismControl regionPositive regulationMitochondrial bioenergeticsMitochondria stressMitochondrial functionSpecific mannerAlveolar epithelial type II cellsEnergy metabolismType II cellsEpithelial type II cellsGenomePhysiological stressRNAII cellsCellsMouse lungTranscriptionGenesMitochondriaCollagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis
Tsukui T, Sun KH, Wetter JB, Wilson-Kanamori JR, Hazelwood LA, Henderson NC, Adams TS, Schupp JC, Poli SD, Rosas IO, Kaminski N, Matthay MA, Wolters PJ, Sheppard D. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis. Nature Communications 2020, 11: 1920. PMID: 32317643, PMCID: PMC7174390, DOI: 10.1038/s41467-020-15647-5.Peer-Reviewed Original ResearchConceptsCollagen-producing cellsSitu hybridization showDisease-relevant phenotypesCell atlasDistinct localizationExpression of CTHRC1Fibrotic lungsDifferent compartmentsPulmonary fibrosisDistinct anatomical localizationCellsCTHRC1Murine lungFibroblastsIdiopathic pulmonary fibrosisAdoptive transfer experimentsLocalizationSubpopulationsComplex architectureTransfer experimentsFibroblastic fociPathologic fibrosisPathologic scarringScleroderma patientsSimilar heterogeneity
2019
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Braga F, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis F, Regev A, Kaminski N, Rajagopal J, Teichmann S, Misharin A, Nawijn M. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. American Journal Of Respiratory Cell And Molecular Biology 2019, 61: 31-41. PMID: 30995076, PMCID: PMC6604220, DOI: 10.1165/rcmb.2018-0416tr.Peer-Reviewed Original ResearchConceptsCell atlasHuman Cell Atlas consortiumCell typesCell-cell interactionsHigh-throughput techniquesFunction of geneticsLung cell typesTranscriptomic analysisDevelopmental processesIndividual cellsMolecular descriptionReference mapTissue microenvironmentDisease mechanismsCellular neighborhoodsHealthy human bodyMolecular profilePersonalized therapeutic regimensCellsLung diseaseTherapeutic regimensImmune cellsLung tissueRecent progressTissue matrix
2018
Evolving Genomics of Pulmonary Fibrosis
Ibarra G, Herazo-Maya J, Kaminski N. Evolving Genomics of Pulmonary Fibrosis. Respiratory Medicine 2018, 207-239. DOI: 10.1007/978-3-319-99975-3_9.Peer-Reviewed Original ResearchTranscript profiling approachesProfiling approachPotential drug targetsNonspecific interstitial pneumoniaIdiopathic pulmonary fibrosisFibrotic lung diseaseGenomic profiling studiesLung diseaseDrug targetsPulmonary fibrosisHypersensitivity pneumonitisKey moleculesProfiling studiesCells of patientsUnbiased viewDifferent interstitial lung diseasesInterstitial lung diseaseInterstitial pneumoniaLung fibrosisAnimal modelsTranscriptomeCellsGenomicsFibrosisDiseaseReconstructing differentiation networks and their regulation from time series single-cell expression data
Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Research 2018, 28: 383-395. PMID: 29317474, PMCID: PMC5848617, DOI: 10.1101/gr.225979.117.Peer-Reviewed Original ResearchTranscription factorsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataDiverse cell populationsGene expression levelsDifferent cell typesStages of organogenesisCell fateDescendant cellsDifferentiation networkExpression similarityKey regulatorRegulatory informationExpression dataCell typesProgenitor cellsCell trajectoriesExpression levelsCell populationsDevelopmental dataCellsLineagesOrganogenesisRegulator
2015
Mesenchymal stem cells use extracellular vesicles to outsource mitophagy and shuttle microRNAs
Phinney DG, Di Giuseppe M, Njah J, Sala E, Shiva S, St Croix CM, Stolz DB, Watkins SC, Di YP, Leikauf GD, Kolls J, Riches DW, Deiuliis G, Kaminski N, Boregowda SV, McKenna DH, Ortiz LA. Mesenchymal stem cells use extracellular vesicles to outsource mitophagy and shuttle microRNAs. Nature Communications 2015, 6: 8472. PMID: 26442449, PMCID: PMC4598952, DOI: 10.1038/ncomms9472.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArrestinsBlotting, WesternCell-Derived MicroparticlesExosomesExtracellular VesiclesFlow CytometryHumansMacrophagesMesenchymal Stem CellsMiceMicroRNAsMicroscopy, ElectronMitochondriaMitophagyMyeloid Differentiation Factor 88Oxidative StressReceptors, ImmunologicSignal TransductionSilicosisToll-Like Receptor 4Toll-Like Receptor 9Toll-Like ReceptorsConceptsMesenchymal stem cellsStem cellsDomain-containing protein 1Stem cell nicheHealthy mitochondrial functionHaematopoietic stem cellsCell nichePlasma membraneToll-like receptor signalingIntracellular oxidative stressMitochondrial functionExtracellular vesiclesMicro RNAsReceptor signalingProtein 1MitophagyMSC survivalMitochondriaOxidative stressMacrophage functionVesiclesCellsRecent studiesMacrophage activationMacrophages
2013
Evolving Genomics of Pulmonary Fibrosis
Herazo-Maya J, Kaminski N. Evolving Genomics of Pulmonary Fibrosis. Respiratory Medicine 2013, 379-402. DOI: 10.1007/978-1-62703-682-5_19.Peer-Reviewed Original ResearchTranscript profiling approachesProfiling approachField of genomicsNonspecific interstitial pneumoniaFibrotic lung diseasePotential drug targetsLung diseaseGenomic profiling studiesHypersensitivity pneumonitisDrug targetsKey moleculesProfiling studiesDifferent interstitial lung diseasesCells of patientsUnbiased viewGenomicsInterstitial lung diseaseStudy of lungInterstitial pneumoniaPulmonary fibrosisLung fibrosisAnimal modelsTranscriptomeCellsDisease
2012
Global Gene Expression Of Bronchoalveolar Lavage (BAL) Cells And Peripheral Blood Mononuclear Cells (PBMCs) In IPF Patients
Vuga L, Richards T, Tedrow J, Sciurba J, Autore K, Kaminski N, Prasse A. Global Gene Expression Of Bronchoalveolar Lavage (BAL) Cells And Peripheral Blood Mononuclear Cells (PBMCs) In IPF Patients. 2012, a2661-a2661. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2661.Peer-Reviewed Original Research
2009
Pluripotency genes overexpressed in primate embryonic stem cells are localized on homologues of human chromosomes 16, 17, 19, and X
Ben-Yehudah A, Navara CS, Redinger CJ, Mich-Basso JD, Castro CA, Oliver S, Chensny LJ, Richards TJ, Kaminski N, Schatten G. Pluripotency genes overexpressed in primate embryonic stem cells are localized on homologues of human chromosomes 16, 17, 19, and X. Stem Cell Research 2009, 4: 25-37. PMID: 19854689, PMCID: PMC2818202, DOI: 10.1016/j.scr.2009.09.003.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsEmbryonic stem cellsChromosome 16Chromosome 17Human chromosome 16Human chromosome 17Stem cellsDifferentiated parental cellsPrimate embryonic stem cellsPluripotency genesDifferentiated progenySpecific genesGene expressionGenesParental cellsTeratoma cellsHomologuesEmbryosCellsSkin fibroblastsPluripotencySpecific candidatesESCsProgenyOverexpression
2005
Ha-rasval12 induces HSP70b transcription via the HSE/HSF1 system, but HSP70b expression is suppressed in Ha-rasval12-transformed cells
Stanhill A, Levin V, Hendel A, Shachar I, Kazanov D, Arber N, Kaminski N, Engelberg D. Ha-rasval12 induces HSP70b transcription via the HSE/HSF1 system, but HSP70b expression is suppressed in Ha-rasval12-transformed cells. Oncogene 2005, 25: 1485-1495. PMID: 16278678, DOI: 10.1038/sj.onc.1209193.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsCell Line, TransformedDNA-Binding ProteinsGene Expression RegulationGenes, ReporterHeat Shock Transcription FactorsHeLa CellsHSP70 Heat-Shock ProteinsHumansMiceMice, NudeNIH 3T3 CellsOncogene Protein p21(ras)Oxidation-ReductionPhosphorylationRatsTranscription FactorsTranscription, GeneticConceptsCellular protective responseHeat shock factor 1Shock factor 1Fibroblast expressionProtective responseHeat shock proteinsHSP70 expressionFactor 1Promoter-driven reporter geneSoft agarTumorsHeat shock elementShock proteinsHSF1 activationCellsDirect effectExpressionHsp70 transcriptionPoint mutationsFrom signatures to models: understanding cancer using microarrays
Segal E, Friedman N, Kaminski N, Regev A, Koller D. From signatures to models: understanding cancer using microarrays. Nature Genetics 2005, 37: s38-s45. PMID: 15920529, DOI: 10.1038/ng1561.Peer-Reviewed Original ResearchConceptsTranscriptional networksModel organismsRegulatory mechanismsBiological processesMolecular underpinningsMechanistic understandingModular organizationDisease mechanismsComputational analysisComprehensive viewGenomicsRobust signatureOrganismsMicroarrayComparative analysisMechanismSignaturesCellsCancerManagement of cancer