2022
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAgedAntibodies, Monoclonal, HumanizedCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCells, CulturedCOVID-19COVID-19 Drug TreatmentFemaleGene Expression ProfilingGene Expression RegulationHumansImmunity, InnateMaleReceptors, Antigen, B-CellReceptors, Antigen, T-CellRNA-SeqSARS-CoV-2Single-Cell AnalysisConceptsProgressive COVID-19B cell clonesSingle-cell analysisT cellsImmune responseMulti-omics single-cell analysisCOVID-19Cell clonesAdaptive immune interactionsSevere COVID-19Dynamic immune responsesGene expressionSARS-CoV-2 virusAdaptive immune systemSomatic hypermutation frequenciesCellular effectsProtein markersEffector CD8Immune signaturesProgressive diseaseHypermutation frequencyProgressive courseClassical monocytesClonesImmune interactionsLung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis.
De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2022, 205: 60-74. PMID: 34724391, PMCID: PMC8865586, DOI: 10.1164/rccm.202103-0569oc.Peer-Reviewed Original ResearchConceptsFibrotic hypersensitivity pneumonitisIdiopathic pulmonary fibrosisHypersensitivity pneumonitisLung zonesMolecular traitsUnused donor lungsInterstitial lung diseaseLocal disease extentProgression of fibrosisSevere fibrosis groupGene co-expression network analysisCo-expression network analysisExplant lungsDonor lungsLung involvementEndothelial functionLung findingsDisease extentPulmonary fibrosisLung diseaseFibrosis groupLung microenvironmentClinical behaviorDisease progressionBAL samples
2021
FeV1 and BMI influence King’s Sarcoidosis Questionnaire score in sarcoidosis patients
Frye B, Potasso L, Farin-Glattacker E, Birring S, Müller-Quernheim J, Schupp J. FeV1 and BMI influence King’s Sarcoidosis Questionnaire score in sarcoidosis patients. BMC Pulmonary Medicine 2021, 21: 395. PMID: 34861850, PMCID: PMC8643005, DOI: 10.1186/s12890-021-01761-7.Peer-Reviewed Original ResearchConceptsKing's Sarcoidosis QuestionnaireBody mass indexSarcoidosis patientsQuality of lifeSerological parametersHigher body mass indexGerman Clinical Trials RegisterLife style modificationClinical Trials RegisterEffect of obesitySteroid-sparing therapiesLung functional parametersGeneral health statusOrgan-specific domainsConclusionThis observationKSQ scoresTrials RegisterClinical chartsMethodsClinical dataOrgan manifestationsLung functionMass indexClinical parametersStyle modificationTRIAL REGISTRATIONSingle-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Muus C, Luecken M, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav E, Subramanian A, Smillie C, Jagadeesh K, Duong E, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber A, Chung H, Montoro D, Adams T, Aliee H, Allon S, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui L, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon T, Cuoco M, Cuomo A, Deprez M, Duclos G, Fine D, Fischer D, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez A, Habermann A, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos T, Kuo C, Larsson L, Leney-Greene M, Lim K, Litviňuková M, Ludwig L, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr C, Mbano I, McAdams A, Nabhan A, Nyquist S, Penland L, Poirion O, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp J, Shea C, Shi X, Sinha R, Sit R, Slowikowski K, Slyper M, Smith N, Sountoulidis A, Strunz M, Sullivan T, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini K, Tucker N, Vernon K, Wadsworth M, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler C. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine 2021, 27: 546-559. PMID: 33654293, PMCID: PMC9469728, DOI: 10.1038/s41591-020-01227-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlveolar Epithelial CellsAngiotensin-Converting Enzyme 2Cathepsin LCOVID-19Datasets as TopicDemographyFemaleGene Expression ProfilingHost-Pathogen InteractionsHumansLungMaleMiddle AgedOrgan SpecificityRespiratory SystemSARS-CoV-2Sequence Analysis, RNASerine EndopeptidasesSingle-Cell AnalysisVirus InternalizationConceptsSingle-cell RNA-sequencing studiesRNA-sequencing studiesSpecific expression patternsExpression programsKey immune functionsExpression patternsSARS-CoV-2 entry genesSpecific expressionAlveolar type 2 cellsMolecular pathwaysLung parenchyma samplesCoronavirus disease 2019 (COVID-19) transmissionDifferent tissuesCellular entryGenesRespiratory epithelial cellsAirway secretory cellsSecretory cellsTumor necrosis factorEntry genesExpression levelsType 2 cellsEpithelial cellsGut tissueSpecific subset
2020
Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.
Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2020, 202: 1419-1429. PMID: 32603604, PMCID: PMC7667912, DOI: 10.1164/rccm.202004-0991oc.Peer-Reviewed Original ResearchConceptsCF lung diseaseHealthy control subjectsImmune dysfunctionLung diseaseCystic fibrosisControl subjectsSputum cellsAbnormal chloride transportLung mononuclear phagocytesInnate immune dysfunctionDivergent clinical coursesImmune cell repertoireMonocyte-derived macrophagesCF monocytesAirway inflammationClinical courseProinflammatory featuresCell survival programInflammatory responseTissue injuryCell repertoireImmune functionTranscriptional profilesAlveolar macrophagesMononuclear phagocytes
2019
Translation and psychometric properties of the King’s Sarcoidosis Questionnaire (KSQ) in German language
Farin E, Heyduck K, Frye BC, Birring SS, Müller-Quernheim J, Schupp JC. Translation and psychometric properties of the King’s Sarcoidosis Questionnaire (KSQ) in German language. Health And Quality Of Life Outcomes 2019, 17: 62. PMID: 30975148, PMCID: PMC6460543, DOI: 10.1186/s12955-019-1131-z.Peer-Reviewed Original ResearchConceptsKing's Sarcoidosis QuestionnaireGood psychometric propertiesGerman Clinical Trials RegisterGerman versionResultsOne hundred ninetyClinical Trials RegisterHealth-related qualityPsychometric propertiesGeneral health statusRasch model fitStructural validityInternal consistencyConstruct validityTrials RegisterConsecutive patientsSarcoidosis patientsOutpatient clinicInterventional studyLife QuestionnaireHealth statusSarcoidosisPatientsMeasurement propertiesCronbach's alphaStructured interviewsBAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis
Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2019, 199: 622-630. PMID: 30141961, PMCID: PMC6396865, DOI: 10.1164/rccm.201712-2551oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAirway basal cellsChronic obstructive pulmonary diseaseObstructive pulmonary diseasePulmonary diseaseBAL cellsBasal cellsPulmonary fibrosisControl subjectsCell gene expressionIndependent IPF cohortsNine-gene signatureIPF cohortDerivation cohortClinical parametersRetrospective studyUnivariate analysisUnpredictable courseCell involvementDiscovery cohortGene expressionHealthy volunteersCox modelStage IIIFatal disease
2018
Phenotypes of organ involvement in sarcoidosis
Schupp J, Freitag-Wolf S, Bargagli E, Mihailović-Vučinić V, Rottoli P, Grubanovic A, Müller A, Jochens A, Tittmann L, Schnerch J, Olivieri C, Fischer A, Jovanovic D, Filipovic S, Videnovic-Ivanovic J, Bresser P, Jonkers R, O'Reilly K, Ho L, Gaede K, Zabel P, Dubaniewicz A, Marshall B, Kieszko R, Milanowski J, Günther A, Weihrich A, Petrek M, Kolek V, Keane M, O'Beirne S, Donnelly S, Haraldsdottir S, Jorundsdottir K, Costabel U, Bonella F, Wallaert B, Grah C, Peroš-Golubičić T, Luisetti M, Kadija Z, Pabst S, Grohé C, Strausz J, Vašáková M, Sterclova M, Millar A, Homolka J, Slováková A, Kendrick Y, Crawshaw A, Wuyts W, Spencer L, Pfeifer M, Valeyre D, Poletti V, Wirtz H, Prasse A, Schreiber S, Krawczak M, Müller-Quernheim J. Phenotypes of organ involvement in sarcoidosis. European Respiratory Journal 2018, 51: 1700991. PMID: 29371378, DOI: 10.1183/13993003.00991-2017.Peer-Reviewed Original ResearchConceptsOrgan involvementIntrathoracic lymph node involvementAbdominal organ involvementLymph node involvementEuropean multicentre studySystemic granulomatous diseaseNew clinical phenotypeHitherto unknown etiologyAcute onsetExtrapulmonary involvementNode involvementSkin involvementFemale patientsMulticentre studyDisease involvementUnknown etiologyCaucasian patientsGranulomatous diseaseHomogenous cohortSarcoidosisPatientsClinical phenotypeStudy centersStandardised protocolDisease phenotype
2017
Preferential Reduction of Circulating Innate Lymphoid Cells Type 2 in Patients with Common Variable Immunodeficiency with Secondary Complications Is Part of a Broader Immune Dysregulation
Friedmann D, Keller B, Harder I, Schupp J, Tanriver Y, Unger S, Warnatz K. Preferential Reduction of Circulating Innate Lymphoid Cells Type 2 in Patients with Common Variable Immunodeficiency with Secondary Complications Is Part of a Broader Immune Dysregulation. Journal Of Clinical Immunology 2017, 37: 759-769. PMID: 28936778, DOI: 10.1007/s10875-017-0444-0.Peer-Reviewed Original ResearchConceptsInnate lymphoid cellsCommon variable immunodeficiencyTh1-like T cellsCD21low B cellsCVID patientsT cellsSecondary complicationsVariable immunodeficiencyILC phenotypesB cellsInnate lymphoid cells type 2T helper cell subsetsBroad immune dysregulationThird of patientsCD4 T cellsCell type 2Helper cell subsetsInflammatory organ diseaseAdaptive immune systemAutoimmune manifestationsImmune dysregulationTh1 shiftCell subsetsImmunological phenotypePeripheral blood
2016
Usefulness of Cyclophosphamide Pulse Therapy in Interstitial Lung Diseases
Schupp J, Köhler T, Müller-Quernheim J. Usefulness of Cyclophosphamide Pulse Therapy in Interstitial Lung Diseases. Respiration 2016, 91: 296-301. PMID: 27082957, DOI: 10.1159/000445031.Peer-Reviewed Original ResearchConceptsNon-specific interstitial pneumoniaInterstitial lung diseaseLymphocytic interstitial pneumoniaCyclophosphamide pulse therapyLung functionPulse therapyInterstitial pneumoniaLung diseaseRheumatoid arthritis-associated interstitial lung diseaseIdiopathic non-specific interstitial pneumoniaFibrotic interstitial lung diseaseProgressive lung function declineBetter survival outcomesLung function declineIdiopathic pulmonary fibrosisBronchoalveolar lavage cytologyGroup of disordersILD patientsMost patientsSystemic sclerosisTotal cohortFunction declineLavage cytologyPulmonary fibrosisCyclophosphamide treatment
2015
Macrophage Activation in Acute Exacerbation of Idiopathic Pulmonary Fibrosis
Schupp J, Binder H, Jäger B, Cillis G, Zissel G, Müller-Quernheim J, Prasse A. Macrophage Activation in Acute Exacerbation of Idiopathic Pulmonary Fibrosis. PLOS ONE 2015, 10: e0116775. PMID: 25590613, PMCID: PMC4295887, DOI: 10.1371/journal.pone.0116775.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAcute exacerbationBAL cellsMacrophage activationPulmonary fibrosisIL-8M2 cytokinesAE of IPFBAL differential cell countsFuture acute exacerbationsM2 macrophage activationCytokine production levelsDifferential cell countsHigher baseline levelsPatients wSerial lavagesBAL neutrophilsCytokine profileNeutrophil countStable patientsDisease accelerationCCL18 levelsInitial diagnosisIL-1raIL-1β