2021
Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets
Reichmann MT, Tezera LB, Vallejo AF, Vukmirovic M, Xiao R, Reynolds J, Jogai S, Wilson S, Marshall B, Jones MG, Leslie A, D'Armiento JM, Kaminski N, Polak ME, Elkington P. Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets. Journal Of Clinical Investigation 2021, 131 PMID: 34128839, PMCID: PMC8321576, DOI: 10.1172/jci148136.Peer-Reviewed Original ResearchConceptsTherapeutic targetTB granulomasHuman TB diseaseHuman tuberculosis granulomasNoninfectious granulomatous diseasesPathological host responsesSarcoidosis lymph nodesInflammatory immune responseSphingosine kinase 1 inhibitionInflammatory mediator secretionPotential therapeutic targetHuman TB granulomasKinase 1 inhibitionHuman cell culture modelsInfected granulomasTB diseaseLymph nodesTB outcomesTuberculosis granulomasStandard treatmentSphingosine kinase 1Granulomatous diseaseLaser capture microdissectionMediator secretionExtensive infection
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