2023
Spatial transcriptomic analysis reveals similar gene expression patterns in the Long COVID and IPF lungs.
Justet A, Ravaglia C, Zhao A, Al Hussein N, Adams T, Balayev A, Deluliis J, Kaminski N, Tomassetti S, Poletti V. Spatial transcriptomic analysis reveals similar gene expression patterns in the Long COVID and IPF lungs. 2023, oa4198. DOI: 10.1183/13993003.congress-2023.oa4198.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
2022
From COVID to fibrosis: lessons from single-cell analyses of the human lung
Justet A, Zhao AY, Kaminski N. From COVID to fibrosis: lessons from single-cell analyses of the human lung. Human Genomics 2022, 16: 20. PMID: 35698166, PMCID: PMC9189802, DOI: 10.1186/s40246-022-00393-0.Peer-Reviewed Original ResearchConceptsSingle-cell RNA-sequencing technologySingle-cell RNA sequencingRNA-sequencing technologyGene expression patternsMonocyte-derived macrophage populationSingle-cell analysisCell populationsLung diseaseCellular phenotypesRNA sequencingExpression patternsGene expressionAberrant repairMultiple tissuesPulmonary fibrosisMechanisms of diseaseFibrotic interstitial lung diseaseLife-threatening complicationsProgressive lung diseaseCOVID-19 pneumoniaInterstitial lung diseaseParenchymal lung diseaseAcute viral diseaseMacrophage populationsNovel cellSingle-Cell RNAseq Reveals Cell Composition and Gene Expression Patterns in the Peripheral Blood of Pediatric Obstructive Sleep Apnea
Cortese R, Adams T, Hohensee K, Kaminski N, Gozal L, Gozal D. Single-Cell RNAseq Reveals Cell Composition and Gene Expression Patterns in the Peripheral Blood of Pediatric Obstructive Sleep Apnea. 2022, a2565-a2565. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2565.Peer-Reviewed Original Research
2021
Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis
Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. European Respiratory Journal 2021, 58: 2002950. PMID: 34083402, PMCID: PMC9759791, DOI: 10.1183/13993003.02950-2020.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisGene co-expression network analysisCo-expression network analysisGene expression programsGene expression patternsDistinct transcriptional programsImmune response pathwaysIon Torrent ProtonMicroarray expression datasetsExpression programsTranscriptional programsPhenotypic traitsGene modulesResponse pathwaysRNA sequencingMolecular endotypesExpression patternsGene expressionHilar lymphadenopathyOrgan involvementGenomic researchMechanistic targetExpression datasetsT helper type 1T cell immune responses
2020
Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency
Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency. Thorax 2020, 76: 134-143. PMID: 33303696, PMCID: PMC10794043, DOI: 10.1136/thoraxjnl-2019-214301.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisAlpha-1 antitrypsin deficiencyGene modulesGene co-expression network analysisDifferential gene expression analysisCo-expression network analysisPeripheral blood mononuclear cellsGene expression patternsPBMC gene expression patternsGene coexpression networksAATD individualsGene expression profilesGene expression analysisBronchoalveolar lavageAugmentation therapyClinical variablesAntitrypsin deficiencyGene expression assaysRNA-seqCoexpression networkGene validationExpression analysisExpression assaysWGCNA modulesExpression patterns
2018
Spatial distribution of marker gene activity in the mouse lung during alveolarization
Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data In Brief 2018, 22: 365-372. PMID: 30596133, PMCID: PMC6307338, DOI: 10.1016/j.dib.2018.10.150.Peer-Reviewed Original ResearchRNA-seq expression profilesMarker gene activityGene expression patternsLung developmentLung Development ProgramGene activityRNA-seqMolecular atlasCellular differentiationDifferent genesExpression patternsExpression profilesNormal lung developmentMouse lungMRNA transcriptsMammalian lungMRNA probesProbe sequencesAbnormal lung developmentCurated CollectionGenesSpatial distributionTranscriptsE16.5E18.5
2014
Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways
Modena BD, Tedrow JR, Milosevic J, Bleecker ER, Meyers DA, Wu W, Bar-Joseph Z, Erzurum SC, Gaston BM, Busse WW, Jarjour NN, Kaminski N, Wenzel SE. Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 1363-1372. PMID: 25338189, PMCID: PMC4294630, DOI: 10.1164/rccm.201406-1099oc.Peer-Reviewed Original ResearchConceptsEpithelial cell gene expressionCell gene expressionGene expressionAirway epithelial cell gene expressionGene expression patternsSevere Asthma Research ProgramActin cytoskeletonGene clusterGenomic studiesGene transcriptionGene pathwaysMolecular basisExpression patternsAsthma phenotypesWnt pathwayMicroarray platformGenesNovel pathwayPhenotypeBiomolecular pathwaysNeuronal functionPathwayUnadjusted p-valuesExpressionBiological characteristics
2011
Peripheral Blood Monuclear Cells Gene Expression Patterns Predict Mortality In Patients With Idiopathic Pulmonary Fibrosis
Herazo J, Gibson K, Juan-Guardela B, Ma S, Richards T, Lussier Y, Duncan S, Tseng G, Lindell K, Garcia J, Noth I, Kaminski N. Peripheral Blood Monuclear Cells Gene Expression Patterns Predict Mortality In Patients With Idiopathic Pulmonary Fibrosis. 2011, a5306-a5306. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5306.Peer-Reviewed Original Research
2009
Gene Expression Patterns of Peripheral Blood Mononuclear Cells in Patients with Idiopathic Pulmonary Fibrosis.
Herazo J, Juan B, Chensny L, Richards T, Konishi K, leJeune M, Ravinovich E, Lindell K, Gibson K, Kaminski N. Gene Expression Patterns of Peripheral Blood Mononuclear Cells in Patients with Idiopathic Pulmonary Fibrosis. 2009, a2731. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2731.Peer-Reviewed Original Research
2008
Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs
Wu W, Dave NB, Yu G, Strollo PJ, Kovkarova-Naumovski E, Ryter SW, Reeves SR, Dayyat E, Wang Y, Choi AM, Gozal D, Kaminski N. Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs. Physiological Genomics 2008, 36: 24-34. PMID: 18826996, PMCID: PMC2604785, DOI: 10.1152/physiolgenomics.00258.2007.Peer-Reviewed Original ResearchConceptsSystems biology approachEstrogen receptor 1Lung responseQuantitative real-time PCRRat lungBiology approachIntermittent hypoxiaExpression patternsSustained hypoxiaReal-time PCRDistinct gene expression patternsDifferent temporal expression patternsDownstream physiological effectsGene expression patternsTemporal expression patternsSteroid hormone receptor activityGene expression profilesTemporal expression changesRegulatory networksHormone receptor activityPulmonary hypertensionKey proteinsGene expressionMolecular networksExpression changesMolecular Staging of Epithelial Maturation Using Secretory Cell–Specific Genes as Markers
Zemke AC, Snyder JC, Brockway BL, Drake JA, Reynolds SD, Kaminski N, Stripp BR. Molecular Staging of Epithelial Maturation Using Secretory Cell–Specific Genes as Markers. American Journal Of Respiratory Cell And Molecular Biology 2008, 40: 340-348. PMID: 18757308, PMCID: PMC2645532, DOI: 10.1165/rcmb.2007-0380oc.Peer-Reviewed Original ResearchConceptsCell-specific genesCategories of genesUnique gene expression profileDevelopmental expression patternsSecretory cellsGene expression profilesCell marker genesExpression of FMO3Messenger RNA abundanceUnique developmental expression patternTransgenic approachesClara cell markerRNA abundanceMarker genesClara cellsExpression patternsExpression profilesMolecular markersEpithelial maturationPhenotypic changesFlavin monooxygenase 3GenesTemporal inductionBronchiolar Clara cellsEmbryonic day
2007
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies
Kaminski N, Bar-Joseph Z. A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. Journal Of Computational Biology 2007, 14: 324-338. PMID: 17563314, DOI: 10.1089/cmb.2007.0001.Peer-Reviewed Original ResearchConceptsClinical studiesResponse ratePatient expression dataDisease progressionPatient levelPatient responseExpression profilesResponse patternsBaseline expressionPatient dataCommon response patternExpression levelsPatientsCell linesSpecific response patternsTemporal expression levelsLab animalsExpression patternsGene levelSpecific expression patternsImportant pathwayLevelsTemporal expression profiles
2006
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies
Kaminski N, Bar-Joseph Z. A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. Lecture Notes In Computer Science 2006, 3909: 69-82. DOI: 10.1007/11732990_6.Peer-Reviewed Original ResearchClinical studiesResponse ratePatient expression dataDisease progressionPatient levelPatient responseResponse patternsExpression profilesBaseline expressionPatient dataCommon response patternExpression levelsPatientsCell linesSpecific response patternsTemporal expression levelsLab animalsExpression patternsGene levelSpecific expression patternsImportant pathwayLevelsInterferonTemporal expression profiles
2005
Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis
Selman M, Pardo A, Barrera L, Estrada A, Watson SR, Wilson K, Aziz N, Kaminski N, Zlotnik A. Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2005, 173: 188-198. PMID: 16166619, PMCID: PMC2662988, DOI: 10.1164/rccm.200504-644oc.Peer-Reviewed Original ResearchConceptsGene expression signaturesExpression signaturesCustom oligonucleotide microarrayGene expression patternsOligonucleotide DNA microarrayStandard Affymetrix protocolGene clusterDNA microarraysExpression patternsGene expressionOligonucleotide microarraysComplementary ribonucleic acidTranscriptional signatureProbe setsCustom arrayT cell activationTissue remodelingNonspecific interstitial pneumoniaRibonucleic acidGenesMicroarrayInterstitial lung diseaseHypersensitivity pneumonitisPathogenic mechanismsExpressionCan Blood Gene Expression Predict Which Patients with Multiple Sclerosis Will Respond to Interferon?
Kaminski N, Achiron A. Can Blood Gene Expression Predict Which Patients with Multiple Sclerosis Will Respond to Interferon? PLOS Medicine 2005, 2: e33. PMID: 15736992, PMCID: PMC549584, DOI: 10.1371/journal.pmed.0020033.Peer-Reviewed Original Research
2004
Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease
Ning W, Li CJ, Kaminski N, Feghali-Bostwick CA, Alber SM, Di YP, Otterbein SL, Song R, Hayashi S, Zhou Z, Pinsky DJ, Watkins SC, Pilewski JM, Sciurba FC, Peters DG, Hogg JC, Choi AM. Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 14895-14900. PMID: 15469929, PMCID: PMC522001, DOI: 10.1073/pnas.0401168101.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseGene expressionObstructive pulmonary diseaseEgr-1 DNA-binding activityComprehensive gene expression profilesUnreported candidate genesMatrix metalloproteinase-2Gene expression patternsDNA-binding activityGene expression profilesEgr1-null miceExtracellular matrix proteinsEgr-1 protein expressionPulmonary diseaseEpithelial cellsGOLD 2Transcription factorsSAGE analysisPotential molecular targetsReal-time quantitative RT-PCRMolecular basisCandidate genesHuman lung fibroblast cellsRelated proteinsExpression patternsGene expression profiling of in vivo UVB‐irradiated human epidermis
Enk CD, Shahar I, Amariglio N, Rechavi G, Kaminski N, Hochberg M. Gene expression profiling of in vivo UVB‐irradiated human epidermis. Photodermatology Photoimmunology & Photomedicine 2004, 20: 129-137. PMID: 15144390, DOI: 10.1111/j.1600-0781.2004.00097.x.Peer-Reviewed Original ResearchConceptsGlobal gene expression analysisGene expression patternsGene expression analysisGene expression profilingIntact human epidermisOligonucleotide microarray technologyNumerous genesFunctional categoriesExpression analysisExpression profilingExpression patternsGene expressionBiological processesMicroarray profilingDifferential expressionDifferential regulationMicroarray technologyGenesMolecular pathwaysCultured cellsRNA samplesHuman epidermisUV-induced photodamageSemi-quantitative reverse transcriptase-polymerase chain reactionIntact tissue
2002
Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans
Zuo F, Kaminski N, Eugui E, Allard J, Yakhini Z, Ben-Dor A, Lollini L, Morris D, Kim Y, DeLustro B, Sheppard D, Pardo A, Selman M, Heller RA. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2002, 99: 6292-6297. PMID: 11983918, PMCID: PMC122942, DOI: 10.1073/pnas.092134099.Peer-Reviewed Original ResearchConceptsPulmonary fibrosisFibrotic lungsHuman pulmonary fibrosisPotential therapeutic targetGene expression analysisClinical diseaseSmooth muscleKnockout miceTherapeutic targetFibrosisHuman tissue samplesUntreatable groupLungTissue samplesMolecular pathwaysGlobal gene expression analysisExtracellular matrix formationMiceExpression analysisMatrilysinMolecular mechanismsKey regulatorGene expression patternsExpression patternsOligonucleotide microarraysEngraftment and differentiation of human metanephroi into functional mature nephrons after transplantation into mice is accompanied by a profile of gene expression similar to normal human kidney development.
Dekel B, Amariglio N, Kaminski N, Schwartz A, Goshen E, Arditti FD, Tsarfaty I, Passwell JH, Reisner Y, Rechavi G. Engraftment and differentiation of human metanephroi into functional mature nephrons after transplantation into mice is accompanied by a profile of gene expression similar to normal human kidney development. Journal Of The American Society Of Nephrology 2002, 13: 977-990. PMID: 11912257, DOI: 10.1681/asn.v134977.Peer-Reviewed Original ResearchConceptsHuman kidney developmentKidney developmentNormal human kidney developmentSpecific genesGene expressionGlobal gene expression patternsGlobal gene expressionMature nephronsGene expression patternsCell cycle regulatorsExtracellular matrix moleculesResult of hybridizationMolecular regulationCDNA arraysEmbryonic precursorsExpression patternsCycle regulatorsExpression profilesGenesMatrix moleculesExpression levelsAdult kidneyGrowth factorMetanephroiDevelopment of strategies