2017
Application of “Omics” and Systems Biology to Sarcoidosis Research
Crouser ED, Fingerlin TE, Yang IV, Maier LA, Nana-Sinkam P, Collman RG, Kaminski N. Application of “Omics” and Systems Biology to Sarcoidosis Research. Annals Of The American Thoracic Society 2017, 14: s445-s451. PMID: 29053026, PMCID: PMC5822413, DOI: 10.1513/annalsats.201707-567ot.Peer-Reviewed Original ResearchConceptsSystems biology researchBiology researchSystems biologyDistinct genetic mechanismsNumerous genetic mutationsField of sarcoidosisGenetic mechanismsDiverse clinical phenotypesOmicsMechanistic underpinningsComprehensive profilingPolygenic diseaseGenetic mutationsDiverse diseasesBiologyAdvanced computational approachesEnormous data setsComputational approachClinical phenotypeOrganismsPolygenicMutationsDisease-related mortalityPhenotypeLife-altering symptomsMicrobes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis
Huang Y, Ma SF, Espindola MS, Vij R, Oldham JM, Huffnagle GB, Erb-Downward JR, Flaherty KR, Moore BB, White ES, Zhou T, Li J, Lussier YA, Han MK, Kaminski N, Garcia JG, Hogaboam CM, Martinez FJ, Noth I. Microbes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2017, 196: 208-219. PMID: 28157391, PMCID: PMC5519968, DOI: 10.1164/rccm.201607-1525oc.Peer-Reviewed Original ResearchConceptsProgression-free survivalMicrobial diversityRegulated signaling pathwaysNOD-like receptor signalingRNA sequencing dataGene expression dataMicroarray gene expression dataImmune response pathwaysMicrobial interactionsMicrobial communitiesHost innate immune responseResponse pathwaysLung microbial communityLeukocyte phenotypeImmune responseSequencing dataNetwork analysisShannon indexSignaling pathwaysToll-like receptor 9 stimulationExpression associationsExpression dataIndividual generaIdiopathic pulmonary fibrosis progressionOligomerization domain
2015
Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol
Moller DR, Koth LL, Maier LA, Morris A, Drake W, Rossman M, Leader JK, Collman RG, Hamzeh N, Sweiss NJ, Zhang Y, O’Neal S, Senior RM, Becich M, Hochheiser HS, Kaminski N, Wisniewski SR, Gibson KF, Group* F. Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol. Annals Of The American Thoracic Society 2015, 12: 1561-1571. PMID: 26193069, PMCID: PMC4627423, DOI: 10.1513/annalsats.201503-172ot.Peer-Reviewed Original ResearchConceptsAlpha-1 antitrypsin deficiencyClinical courseLung microbiomeAntitrypsin deficiencyClinical heterogeneityPathobiology of sarcoidosisTremendous clinical heterogeneityObservational cohort studyPulmonary function testsSystemic inflammatory responsePeripheral blood changesDiagnosis of sarcoidosisSelf-administered questionnaireCohort studyBaseline visitBronchoalveolar lavageFunction testsGranulomatous inflammationSystemic diseaseSarcoidosis phenotypesUrine testingClinical bronchoscopyInflammatory responseSarcoidosis StudyPrognostic biomarkerRationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol
Strange C, Senior RM, Sciurba F, O’Neal S, Morris A, Wisniewski SR, Bowler R, Hochheiser HS, Becich MJ, Zhang Y, Leader JK, Methé BA, Kaminski N, Sandhaus RA, Group* F. Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol. Annals Of The American Thoracic Society 2015, 12: 1551-1560. PMID: 26153726, PMCID: PMC4627425, DOI: 10.1513/annalsats.201503-143oc.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlpha 1-Antitrypsin DeficiencyBronchoalveolar LavageCross-Sectional StudiesExercise ToleranceFemaleGenomicsGenotypeHumansMaleMicrobiotaMiddle AgedPhenotypeProspective StudiesPulmonary Disease, Chronic ObstructivePulmonary EmphysemaResearch DesignRespiratory Function TestsSarcoidosisTomography, X-Ray ComputedConceptsAlpha-1 antitrypsin deficiencyAugmentation therapyBronchoalveolar lavageAntitrypsin deficiencyClinical presentationPiZZ individualsAlpha-1-antitrypsin augmentation therapyAlpha-1 antitrypsin genotypeChronic obstructive pulmonary disease phenotypesPulmonary function testingAge 35 yearsVariable clinical presentationCross-sectional studyAlpha-1 antitrypsinIntermediate outcome measuresPulmonary disease phenotypesUnique genetic causeExercise capacityTherapeutic trialsChest tomographyClinical symptomsCOPD pathogenesisCOPD phenotypesFunction testingCOPD Study