Taylor Adams
Research Associate 2 MSCards
About
Research
Publications
2026
Single-cell atlas of human lung aging identifies cell type dyssynchrony and increased transcriptional entropy
De Man R, McDonough J, Adams T, Nikola F, Rangel R, Anderson S, Manning E, Cala Garcia J, Moss B, Waich A, Poli F, Cardenas R, Coarfa C, Song Q, Bar-Joseph Z, Vanaudenaerde B, Wuyts W, Niklason L, Raredon M, Yan X, Rosas I, Kaminski N. Single-cell atlas of human lung aging identifies cell type dyssynchrony and increased transcriptional entropy. Nature Communications 2026, 17: 2095. PMID: 41571679, PMCID: PMC12953888, DOI: 10.1038/s41467-026-68810-9.Peer-Reviewed Original ResearchConceptsGenomic landscapeLung ageSingle-cell atlasAlveolar epithelialIndependent predictorsAnalysis of somatic mutationsSingle-cell dataSingle-cell RNA sequencingEndothelial cellsLoss of differentiationAlveolar epithelial cellsRNA sequencingTranscriptional changesCell-typeEndothelial cell typesSomatic mutationsMutational burdenAT2 cellsLung diseaseCell typesAge-related changesEpithelial cellsRisk factorsSenescence signatureEpithelial
2025
Keratinocytes as active regulators of cutaneous and mucosal immunity: a systematic review across inflammatory epithelial disorders
Klimitz F, Shen Y, Repetto F, Brown S, Knoedler L, Ko C, Abu Hussein N, Crisler W, Adams T, Kaminski N, Lian C, Murphy G, Hsia H, Pomahac B, Kauke-Navarro M. Keratinocytes as active regulators of cutaneous and mucosal immunity: a systematic review across inflammatory epithelial disorders. Frontiers In Immunology 2025, 16: 1694066. PMID: 41479908, PMCID: PMC12753988, DOI: 10.3389/fimmu.2025.1694066.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsThis study investigates how keratinocytes, key skin cells, regulate immune responses in inflammatory disorders like psoriasis and lupus, revealing shared and disease-specific pathways critical for targeted therapies.A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases
Zheng Y, Schupp J, Adams T, Clair G, Justet A, Ahangari F, Yan X, Hansen P, Carlon M, Cortesi E, Vermant M, Vos R, De Sadeleer L, Rosas I, Pineda R, Sembrat J, Königshoff M, McDonough J, Vanaudenaerde B, Wuyts W, Kaminski N, Ding J. A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases. Nature Biomedical Engineering 2025, 9: 2155-2180. PMID: 40542107, PMCID: PMC12705450, DOI: 10.1038/s41551-025-01423-7.Peer-Reviewed Original ResearchComplex cellular dynamicsCellular dynamicsSingle-cell transcriptomic dataIn silico drug discoverySingle-cell transcriptomicsTranscriptome dataPotential therapeutic drug candidateComplex diseasesHuman diseasesIdiopathic pulmonary fibrosisTherapeutic drug candidateCell embeddingDrug discoveryPulmonary fibrosisDrug candidatesDisease progressionHuman tissuesHuman precision-cut lung slicesDynamic analysisPrecision-cut lung slicesPathological landscapeComputational toolsAnti-fibrotic effectsUnagiTranscriptomeMolecular and Spatial Transcriptomics Analysis in Silica-Induced Pulmonary Fibrosis
Abu Hussein N, Adams T, Anderson S, Kramer M, Nikola F, Homer R, Najjar A, Sharma P, Yang L, Zhang Y, Yan X, Perzov B, Kaminski N. Molecular and Spatial Transcriptomics Analysis in Silica-Induced Pulmonary Fibrosis. 2025, tp230. DOI: 10.1183/23120541.lsc-2025.tp230.Peer-Reviewed Original ResearchEpigenetic age acceleration in idiopathic pulmonary fibrosis revealed by DNA methylation clocks
Kurbanov D, Ahangari F, Adams T, De Man R, Tang J, Carlon M, Abu Hussein N, Cortesi E, Zapata M, De Sadelaar L, Wuyts W, Vanaudenaerde B, Kaminski N, McDonough J. Epigenetic age acceleration in idiopathic pulmonary fibrosis revealed by DNA methylation clocks. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2025, 328: l456-l462. PMID: 39970931, PMCID: PMC12169420, DOI: 10.1152/ajplung.00171.2024.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisIdiopathic pulmonary fibrosis tissuePulmonary fibrosisLung tissueEpigenetic clocksPotential of DNA methylationDNA methylation levelsDebilitating lung diseaseIllumina MethylationEPIC arrayHuman lung tissueEpigenetic ageDNA methylation clocksBiological ageAffected lung tissueIPF casesClinical prognosisMethylation patternsDNA methylationLung diseaseHealthy controlsAcceleration of biological agingMethylation levelsMethylationEPIC arrayAge accelerationClinical assessmentCD103+ dendritic cell — fibroblast crosstalk via TLR9, TDO2, and AHR signaling drives lung fibrogenesis
Carter H, Costa R, Adams T, Gilchrist T, Emch C, Bame M, Oldham J, Huang S, Linderholm A, Noth I, Kaminski N, Moore B, Gurczynski S. CD103+ dendritic cell — fibroblast crosstalk via TLR9, TDO2, and AHR signaling drives lung fibrogenesis. JCI Insight 2025, 10 PMID: 39964756, PMCID: PMC11949071, DOI: 10.1172/jci.insight.177072.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDBasic Helix-Loop-Helix Transcription FactorsBleomycinDendritic CellsDisease Models, AnimalFibroblastsHumansIdiopathic Pulmonary FibrosisIntegrin alpha ChainsInterleukin-6LungMaleMiceMice, Inbred C57BLReceptors, Aryl HydrocarbonSignal TransductionToll-Like Receptor 9Tryptophan OxygenaseConceptsIdiopathic pulmonary fibrosisAhR signalingMice treated with BLMIL-17+ cellsCD103+ DCLoss of lung functionStudies of human samplesLimited treatment optionsTreated ex vivoProduction of IL-6Inflammatory cytokine productionExon 2 deletionExpression of TDO2IL-6 productionAdoptive transferCD11c-CreCD11c+ cellsImmunological changesPulmonary fibrosisTLR agonistsProgressive scarringTreatment optionsCytokine productionLung fibrogenesisAryl hydrocarbon receptor
2024
Predicting lung aging using scRNA-Seq data
Song Q, Singh A, McDonough J, Adams T, Vos R, De Man R, Myers G, Ceulemans L, Vanaudenaerde B, Wuyts W, Yan X, Schupp J, Hagood J, Kaminski N, Bar-Joseph Z. Predicting lung aging using scRNA-Seq data. PLOS Computational Biology 2024, 20: e1012632. PMID: 39700255, PMCID: PMC11741621, DOI: 10.1371/journal.pcbi.1012632.Peer-Reviewed Original ResearchSingle-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis.
Zhao A, Unterman A, Abu Hussein N, Sharma P, Nikola 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, 210: 1252-1266. PMID: 38924775, PMCID: PMC11568434, 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 transcriptomicsSDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Wei H, Justet A, Adams T, Homer R, Amei A, Rosas I, Kaminski N, Wang Z, Yan X. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 2024, 25: 271. PMID: 39402626, PMCID: PMC11475911, DOI: 10.1186/s13059-024-03416-2.Peer-Reviewed Original ResearchIdentification of FGFR4 as a regulator of myofibroblast differentiation in pulmonary fibrosis
Ghanem M, Justet A, Jaillet M, Vasarmidi E, Boghanim T, Hachem M, Vadel A, Joannes A, Mordant P, Balayev A, Adams T, Mal H, Cazes A, Poté N, Mailleux A, Crestani B. Identification of FGFR4 as a regulator of myofibroblast differentiation in pulmonary fibrosis. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2024, 327: l818-l830. PMID: 39350729, DOI: 10.1152/ajplung.00184.2023.Peer-Reviewed Original ResearchWild type littermatesFibroblast growth factorMurine embryonic fibroblastsEndothelin-1Pulmonary fibrosisFGFR4 inhibitionBleomycin-Induced Pulmonary FibrosisIn vitroMyofibroblast differentiationBleomycin-induced lung fibrosisPulmonary fibrosis in vivoTGF-bLung fibroblastsPro-fibrotic propertiesProtein levelsIn vivoAnti-fibrotic propertiesFibrosis in vivoRegulation of myofibroblast differentiationDevelopment of bleomycin-induced lung fibrosisWT miceTherapeutic optionsHuman lung fibroblastsIPF lungsLung fibrosis