2022
Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea.
Cortese R, Adams T, Cataldo K, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea. European Respiratory Journal 2022, 61: 2201465. PMID: 36356973, DOI: 10.1183/13993003.01465-2022.Peer-Reviewed Original ResearchConceptsObstructive sleep apnoeaSleep apnoeaImpact of OSASystemic immune functionMononuclear cell compositionMolecular signaturesCell-specific markersSystemic inflammationCardiovascular dysfunctionImmune cellsImmune functionSingle-cell transcriptomic analysisPaediatric sleep apnoeaUndescribed cell typePrevalent diseaseMajor causeCellular compositionApnoeaCell compositionRNA expression datasetsDiagnostic settingCell typesCell lineagesMolecular diagnostic settingScRNA-seq
2021
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children
Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children. Immunity 2021, 54: 1083-1095.e7. PMID: 33891889, PMCID: PMC8043654, DOI: 10.1016/j.immuni.2021.04.003.Peer-Reviewed Original ResearchConceptsMIS-C patientsDisease severityInflammatory syndromeTCR repertoireSARS-CoV-2-associated multisystem inflammatory syndromeAsymptomatic SARS-CoV-2 infectionSARS-CoV-2 infectionAdult COVID-19Post-infectious complicationsMultisystem inflammatory syndromeCytotoxicity genesHealthy pediatricImmune dysregulationMemory TActive infectionMyeloid dysfunctionPatientsSingle-cell RNA sequencingFlow cytometrySerum proteomicsRepertoire analysisElevated expressionSeverityAlarminsCOVID-19
2020
Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics
Steinman JB, Lum FM, Ho PP, Kaminski N, Steinman L. Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 24620-24626. PMID: 32883878, PMCID: PMC7547272, DOI: 10.1073/pnas.2012358117.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptorT helper 2 (Th2) immune responsesCross-reactive humoral immunityCOVID-19T cell immunityT helper 2SARS-CoV-2Cell immunityCommon coronavirusesHelper 2Humoral immunityInflammatory cytokinesRespiratory tractImmune responseCommon coldPandemic virusPotential therapeuticsChildrenPathogenesisImmunityReduced developmentMolecular checkpointsCoronavirusLow levelsEosinophiliaSARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Ziegler C, Allon S, Nyquist S, Mbano I, Miao V, Tzouanas C, Cao Y, Yousif A, Bals J, Hauser B, Feldman J, Muus C, Wadsworth M, Kazer S, Hughes T, Doran B, Gatter G, Vukovic M, Taliaferro F, Mead B, Guo Z, Wang J, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre J, Taylor C, Lin B, Waghray A, Mitsialis V, Dwyer D, Buchheit K, Boyce J, Barrett N, Laidlaw T, Carroll S, Colonna L, Tkachev V, Peterson C, Yu A, Zheng H, Gideon H, Winchell C, Lin P, Bingle C, Snapper S, Kropski J, Theis F, Schiller H, Zaragosi L, Barbry P, Leslie A, Kiem H, Flynn J, Fortune S, Berger B, Finberg R, Kean L, Garber M, Schmidt A, Lingwood D, Shalek A, Ordovas-Montanes J, Network H, Banovich N, Barbry P, Brazma A, Desai T, Duong T, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kropski J, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic M, Ordovas-Montanes J, Pe’er D, Powell J, Quake S, Rajagopal J, Tata P, Rawlins E, Regev A, Reyfman P, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schiller H, Schultze J, Seibold M, Shalek A, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Theis F, Tsankov A, van den Berge M, von Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi L, Zhang K. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell 2020, 181: 1016-1035.e19. PMID: 32413319, PMCID: PMC7252096, DOI: 10.1016/j.cell.2020.04.035.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAlveolar Epithelial CellsAngiotensin-Converting Enzyme 2AnimalsBetacoronavirusCell LineCells, CulturedChildCoronavirus InfectionsCOVID-19EnterocytesGoblet CellsHIV InfectionsHumansInfluenza, HumanInterferon Type ILungMacaca mulattaMiceMycobacterium tuberculosisNasal MucosaPandemicsPeptidyl-Dipeptidase APneumonia, ViralReceptors, VirusSARS-CoV-2Serine EndopeptidasesSingle-Cell AnalysisTuberculosisUp-RegulationConceptsSARS-CoV-2Interferon-stimulated genesAirway epithelial cellsCell subsetsSingle-cell RNA sequencing datasetsRNA sequencing datasetsSARS-CoV-2 receptor ACE2Human interferon-stimulated genesTransmembrane serine protease 2Human airway epithelial cellsEpithelial cellsSevere acute respiratory syndrome coronavirus clade 2SARS-CoV-2 spike proteinType II pneumocytesSerine protease 2Clade 2Putative targetsNon-human primatesSpecific cell subsetsCo-expressing cellsDisease COVID-19ACE2 expressionLung injuryLung type II pneumocytesAbsorptive enterocytes
2019
Integrating multiomics longitudinal data to reconstruct networks underlying lung development
Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l556-l568. PMID: 31432713, PMCID: PMC6879899, DOI: 10.1152/ajplung.00554.2018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornChildChild, PreschoolDNA MethylationEpigenesis, GeneticFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksHigh-Throughput Nucleotide SequencingHumansImmunity, InnateInfantInfant, NewbornLungMaleMiceMice, Inbred C57BLMicroRNAsOrganogenesisProteomicsPulmonary AlveoliRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsSingle-cell RNA-seq dataLung developmentDynamic regulatory networksOmics data setsRNA-seq dataIndividual cell typesHuman lung developmentRegulatory networksDNA methylationLaser capture microdissectionEpigenetic changesExpression trajectoriesKey pathwaysCell typesActive pathwaysCapture microdissectionRegulatorKey eventsInnate immunityNew insightsSpecific key eventsPathwayComprehensive understandingProteomicsMethylation
2018
The aging lung: tissue telomere shortening in health and disease
Everaerts S, Lammertyn EJ, Martens DS, De Sadeleer LJ, Maes K, van Batenburg AA, Goldschmeding R, van Moorsel CHM, Dupont LJ, Wuyts WA, Vos R, Gayan-Ramirez G, Kaminski N, Hogg JC, Janssens W, Verleden GM, Nawrot TS, Verleden SE, McDonough JE, Vanaudenaerde BM. The aging lung: tissue telomere shortening in health and disease. Respiratory Research 2018, 19: 95. PMID: 29751799, PMCID: PMC5948770, DOI: 10.1186/s12931-018-0794-z.Peer-Reviewed Original ResearchConceptsBronchiolitis obliterans syndromeRestrictive allograft syndromeRelative telomere lengthRegional disease severityShorter RTLNormal lungDisease severityLung agePrior transplantationLung tissueDiseased lungsChronic obstructive pulmonary diseaseChronic hypersensitivity pneumonitisObstructive pulmonary diseaseTelomere lengthNormal human lungPeripheral blood leucocytesDiseased lung tissueDistinct lung regionsAverage relative telomere lengthExplant lungsObliterans syndromeUnused donorPulmonary diseaseHypersensitivity pneumonitis
2017
Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis
Vukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, Stefanovic B, Kaminski N. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis. BMC Pulmonary Medicine 2017, 17: 15. PMID: 28081703, PMCID: PMC5228096, DOI: 10.1186/s12890-016-0356-4.Peer-Reviewed Original ResearchConceptsPaired-end sequencingTranscript profilingHuman genomeRNA sequencingTranscriptomic profilingFFPE lung tissuesSequencing readsLung tissueTotal RNABackgroundIdiopathic pulmonary fibrosisLethal lung diseaseSequencingReadsProfilingPulmonary fibrosisLung diseaseUnknown etiologyIPF tissueGenomeHiSeqTissueTopHat2GenesIPFRNA
1994
Acute bacterial diarrhoea in the emergency room: therapeutic implications of stool culture results.
Kaminski N, Bogomolski V, Stalnikowicz R. Acute bacterial diarrhoea in the emergency room: therapeutic implications of stool culture results. Emergency Medicine Journal 1994, 11: 168. PMID: 7804582, PMCID: PMC1342424, DOI: 10.1136/emj.11.3.168.Peer-Reviewed Original ResearchMeSH KeywordsAcute DiseaseAdolescentAdultAgedAged, 80 and overAmpicillinBacterial InfectionsBacteriological TechniquesChildChild, PreschoolCiprofloxacinDiarrheaDrug Resistance, MicrobialDysentery, BacillaryEmergency Service, HospitalEscherichia coli InfectionsFecesHumansInfantMicrobial Sensitivity TestsMiddle AgedSalmonella InfectionsTrimethoprim, Sulfamethoxazole Drug CombinationConceptsTrimethoprim-sulfamethoxazoleEmergency roomStool culture resultsTreatment of choiceAcute diarrhoeal diseaseAcute bacterial diarrheaEmergence of resistanceEmpiric treatmentAcute diarrheaStool culturesShigella isolatesBacterial diarrheaNew quinolonesSick patientsTherapeutic implicationsDiarrhoeal diseaseCulture resultsDrug resistanceShigella speciesPatientsStudy periodShigella sonneiAntimicrobial resistanceAntimicrobial drugsDiarrhea