2024
Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis.
Unterman A, Zhao A, Neumark N, Schupp J, Ahangari F, Cosme C, Sharma P, Flint J, Stein Y, Ryu C, Ishikawa G, Sumida T, Gomez J, Herazo-Maya J, Dela Cruz C, Herzog E, Kaminski N. Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2024, 210: 484-496. PMID: 38717443, DOI: 10.1164/rccm.202306-0979oc.Peer-Reviewed Original ResearchStable idiopathic pulmonary fibrosisIdiopathic pulmonary fibrosisPeripheral blood mononuclear cellsProgressive idiopathic pulmonary fibrosisPeripheral immune systemT cellsPulmonary fibrosisCohort of IPF patientsAssociated with decreased survivalIdiopathic pulmonary fibrosis patientsPeripheral blood mononuclear cell samplesPeripheral blood cell populationsImmune systemFraction of TregsRegulatory T cellsBlood mononuclear cellsBlood cell populationsFlow cytometry analysisImmune aberrationsIPF patientsTregsMononuclear cellsSingle-cell RNA sequencingLung homogenatesMonocyte chemoattractantSingle Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis.
Zhao A, Unterman A, Abu Hussein N, Sharma P, Nekola F, Flint J, Yan X, Adams T, Justet A, Sumida T, Zhao J, Schupp J, Raredon M, Ahangari F, Deluliis G, Zhang Y, Buendia-Roldan I, Adegunsoye A, Sperling A, Prasse A, Ryu C, Herzog E, Selman M, Pardo A, Kaminski N. Single Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2024 PMID: 38924775, DOI: 10.1164/rccm.202401-0078oc.Peer-Reviewed Original ResearchFibrotic hypersensitivity pneumonitisIdiopathic pulmonary fibrosisPeripheral blood mononuclear cellsBronchoalveolar lavage cellsBlood mononuclear cellsClassical monocytesHypersensitivity pneumonitisPulmonary fibrosisT cellsImmune perturbationsLavage cellsMononuclear cellsCD8+ T cellsCytotoxic T cellsInterstitial lung diseaseHypersensitivity pneumonitis patientsCytotoxic CD4Immune aberrationsPneumonic patientsPneumonitisLung diseaseHealthy controlsImmune mechanismsPatient cellsSingle-cell transcriptomics
2021
Prediction of Survival after Chronic Lung Allograft Dysfunction in Lung Transplant Recipients by Blood Profiling Using a Predefined 52 Gene Signature
Luijk B, Krebber M, Li Q, Kardol-Hoefnagel T, Budding K, van Kessel D, Grutters J, Otten H, Kaminski N, Maya J. Prediction of Survival after Chronic Lung Allograft Dysfunction in Lung Transplant Recipients by Blood Profiling Using a Predefined 52 Gene Signature. The Journal Of Heart And Lung Transplantation 2021, 40: s155-s156. DOI: 10.1016/j.healun.2021.01.470.Peer-Reviewed Original ResearchChronic lung allograft dysfunctionDiagnosis of CLADPeripheral blood mononuclear cellsLung allograft dysfunctionAllograft dysfunctionLTx recipientsRisk groupsHigh riskRisk scoreIdiopathic pulmonary fibrosis patientsLung transplant recipientsHigh-risk patientsKaplan-Meier analysisPulmonary fibrosis patientsBlood mononuclear cellsHigh-risk groupLow-risk groupLow-risk scoresPrediction of survivalLong-term survivalCLAD onsetCLAD patientsLung transplantationTransplant recipientsOverall survival
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
S100A12 as a marker of worse cardiac output and mortality in pulmonary hypertension
Tzouvelekis A, Herazo‐Maya J, Ryu C, Chu J, Zhang Y, Gibson KF, Adonteng‐Boateng P, Li Q, Pan H, Cherry B, Ahmad F, Ford HJ, Herzog EL, Kaminski N, Fares WH. S100A12 as a marker of worse cardiac output and mortality in pulmonary hypertension. Respirology 2018, 23: 771-779. PMID: 29611244, PMCID: PMC6047907, DOI: 10.1111/resp.13302.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsPH patientsPH cohortCardiac outputWorld Health Organization group 1Idiopathic pulmonary fibrosis patientsPulmonary hypertension patientsPulmonary fibrosis patientsBlood mononuclear cellsProtein serum concentrationsHigher S100A12Pulmonary hypertensionS100A12 levelsOverall mortalityHypertension patientsPrognostic valueValidation cohortMononuclear cellsPeripheral bloodSerum concentrationsInflammatory diseasesGroup 1PatientsFibrosis patientsS100A12
2017
Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study
Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N. Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study. The Lancet Respiratory Medicine 2017, 5: 857-868. PMID: 28942086, PMCID: PMC5677538, DOI: 10.1016/s2213-2600(17)30349-1.Peer-Reviewed Original ResearchMeSH KeywordsAgedCohort StudiesFemaleGene Expression ProfilingGenetic MarkersGenetic TestingHumansIdiopathic Pulmonary FibrosisLeukocytes, MononuclearLinear ModelsMaleMiddle AgedOligonucleotide Array Sequence AnalysisPrognosisProportional Hazards ModelsRisk AssessmentRisk FactorsTime FactorsVital CapacityConceptsIdiopathic pulmonary fibrosisTransplant-free survivalRisk profilePulmonary fibrosisAntifibrotic drugsPeripheral blood mononuclear cellsCox proportional hazards modelClinical prediction toolGroup of patientsBlood mononuclear cellsHigh-risk groupProportional hazards modelPulmonary Fibrosis FoundationPittsburgh cohortUntreated patientsCohort studyClinical courseIPF diagnosisBlood InstituteProspective studyVital capacityMononuclear cellsPeripheral bloodUS National InstitutesNational Heart
2015
A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Huang Y, Ma SF, Vij R, Oldham JM, Herazo-Maya J, Broderick SM, Strek ME, White SR, Hogarth DK, Sandbo NK, Lussier YA, Gibson KF, Kaminski N, Garcia JG, Noth I. A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis. BMC Pulmonary Medicine 2015, 15: 147. PMID: 26589497, PMCID: PMC4654815, DOI: 10.1186/s12890-015-0142-8.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPrognostic indexIPF patientsPulmonary fibrosisValidation cohortTraining cohortMultivariate Cox regression survival analysisPrognostic modelPeripheral blood mononuclear cellsUnivariate Cox regression analysisCox regression survival analysisLow-risk patientsWeighted gene co-expression network analysisCox regression analysisBlood mononuclear cellsCourse of diseaseIndependent validation cohortRegression survival analysisNovel prognostic modelPredictor genesT cell biologyT cell receptorCurrent prognostic toolsFunctional pathway analysisFold change
2014
Blockade of the Programmed Death-1 Pathway Restores Sarcoidosis CD4+ T-Cell Proliferative Capacity
Braun NA, Celada LJ, Herazo-Maya JD, Abraham S, Shaginurova G, Sevin CM, Grutters J, Culver DA, Dworski R, Sheller J, Massion PP, Polosukhin VV, Johnson JE, Kaminski N, Wilkes DS, Oswald-Richter KA, Drake WP. Blockade of the Programmed Death-1 Pathway Restores Sarcoidosis CD4+ T-Cell Proliferative Capacity. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 560-571. PMID: 25073001, PMCID: PMC4214083, DOI: 10.1164/rccm.201401-0188oc.Peer-Reviewed Original ResearchConceptsPD-1 pathway blockadeT cell proliferative capacityPeripheral blood mononuclear cellsPD-L1 expressionPD-1 pathwayBlood mononuclear cellsT cell functionPathway blockadePD-L1Clinical outcomesLung diseaseMononuclear cellsControl subjectsProliferative capacityT cellsImmunohistochemistry analysisPD-1/PD-L1 expressionControl peripheral blood mononuclear cellsHealthy control peripheral blood mononuclear cellsHealthy control lungsIdiopathic lung diseaseSpontaneous clinical resolutionChronic lung diseaseHealthy control subjectsEffective therapeutic interventionsWnt Coreceptor Lrp5 Is a Driver of Idiopathic Pulmonary Fibrosis
Lam AP, Herazo-Maya JD, Sennello JA, Flozak AS, Russell S, Mutlu GM, Budinger GR, DasGupta R, Varga J, Kaminski N, Gottardi CJ. Wnt Coreceptor Lrp5 Is a Driver of Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 185-195. PMID: 24921217, PMCID: PMC4226053, DOI: 10.1164/rccm.201401-0079oc.Peer-Reviewed Original ResearchMeSH KeywordsAgedAnimalsBeta CateninBiomarkersDisease ProgressionFemaleHumansIdiopathic Pulmonary FibrosisLeukocytes, MononuclearLow Density Lipoprotein Receptor-Related Protein-5Low Density Lipoprotein Receptor-Related Protein-6MaleMiceMice, KnockoutMiddle AgedProspective StudiesSeverity of Illness IndexSignal TransductionTransforming Growth Factor betaWnt ProteinsConceptsIdiopathic pulmonary fibrosisPeripheral blood mononuclear cellsBlood mononuclear cellsLung fibrosisPulmonary fibrosisDisease progressionMononuclear cellsDisease severityNull miceAlveolar type 2 cellsTGF-β productionWild-type miceActivation of TGFType 2 cellsWnt pathway inhibitorsWnt/β-catenin signalingWnt coreceptors LRP5Role of LRP5Bone marrow cellsLrp5 lossΒ-catenin signalingPatient selectionSmall molecular inhibitorsAdditional cohortFibrosisThe Mitochondrial Cardiolipin Remodeling Enzyme Lysocardiolipin Acyltransferase Is a Novel Target in Pulmonary Fibrosis
Huang LS, Mathew B, Li H, Zhao Y, Ma SF, Noth I, Reddy SP, Harijith A, Usatyuk PV, Berdyshev EV, Kaminski N, Zhou T, Zhang W, Zhang Y, Rehman J, Kotha SR, Gurney TO, Parinandi NL, Lussier YA, Garcia JG, Natarajan V. The Mitochondrial Cardiolipin Remodeling Enzyme Lysocardiolipin Acyltransferase Is a Novel Target in Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2014, 189: 1402-1415. PMID: 24779708, PMCID: PMC4098083, DOI: 10.1164/rccm.201310-1917oc.Peer-Reviewed Original ResearchMeSH Keywords1-Acylglycerol-3-Phosphate O-AcyltransferaseAcyltransferasesAnimalsBiomarkersCardiolipinsCohort StudiesDisease Models, AnimalHumansIdiopathic Pulmonary FibrosisIn Situ HybridizationLeukocytes, MononuclearMiceMitochondriaPredictive Value of TestsPulmonary FibrosisRNA, MessengerSensitivity and SpecificitySeverity of Illness IndexConceptsPeripheral blood mononuclear cellsIdiopathic pulmonary fibrosisPulmonary fibrosisMurine modelAlveolar epithelial cellsOverall survivalReactive oxygen species generationLysocardiolipin acyltransferaseOxygen species generationCarbon monoxide diffusion capacityRadiation-induced pulmonary fibrosisPulmonary function outcomesEpithelial cellsBlood mononuclear cellsPreclinical murine modelsNovel therapeutic approachesSpecies generationBleomycin challengeLung inflammationLung protectionPulmonary functionFunction outcomesLung fibrosisMononuclear cellsFibrotic lungs
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
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
2004
Autoimmunity gene expression portrait: specific signature that intersects or differentiates between multiple sclerosis and systemic lupus erythematosus
MANDEL M, GUREVICH M, PAUZNER R, KAMINSKI N, ACHIRON A. Autoimmunity gene expression portrait: specific signature that intersects or differentiates between multiple sclerosis and systemic lupus erythematosus. Clinical & Experimental Immunology 2004, 138: 164-170. PMID: 15373920, PMCID: PMC1809188, DOI: 10.1111/j.1365-2249.2004.02587.x.Peer-Reviewed Original ResearchConceptsSystemic lupus erythematosusPeripheral blood mononuclear cellsMultiple sclerosisHealthy subjectsAutoimmune signatureSLE patientsLupus erythematosusAutoimmune diseasesRelapsing-remitting MS patientsBlood mononuclear cellsMatrix metalloproteinase pathwayAdditional blood samplesDisease-specific signaturesDisease-associated signaturesTIMP1 gene expressionGene expression signaturesMS patientsMononuclear cellsSpecific therapyGene expression findingsMetalloproteinase pathwayNuclear autoantibodiesBlood samplesMMP activityPatientsBlood transcriptional signatures of multiple sclerosis: Unique gene expression of disease activity
Achiron A, Gurevich M, Friedman N, Kaminski N, Mandel M. Blood transcriptional signatures of multiple sclerosis: Unique gene expression of disease activity. Annals Of Neurology 2004, 55: 410-417. PMID: 14991819, DOI: 10.1002/ana.20008.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsMultiple sclerosisMS patientsTranscriptional signatureCentral nervous system diseaseBlood transcriptional signaturesBlood mononuclear cellsNervous system diseasesT cell activationAcute relapseDisease activityImmunomodulatory treatmentMS pathogenesisActive demyelinationMononuclear cellsUnpredictable courseImmune surveillanceCellular recruitmentSystem diseasesTherapeutic strategiesDisease processDisease pathogenesisUnique gene expressionSclerosisPatients