2023
Sputum alarmins delineate distinct T2 cytokine pathways and unique subtypes of patients with asthma
Gautam S, Chu J, Cohen A, Kaur R, Lee S, Wilson G, Liu Q, Gomez J, Rajaveen H, Yan X, Cohn L, Clark B, Chupp G. Sputum alarmins delineate distinct T2 cytokine pathways and unique subtypes of patients with asthma. Allergy 2023, 78: 3274-3277. PMID: 37874609, PMCID: PMC10842366, DOI: 10.1111/all.15915.Peer-Reviewed Original ResearchDeep learning prediction of hospital readmissions for asthma and COPD
Lopez K, Li H, Lipkin-Moore Z, Kay S, Rajeevan H, Davis J, Wilson F, Rochester C, Gomez J. Deep learning prediction of hospital readmissions for asthma and COPD. Respiratory Research 2023, 24: 311. PMID: 38093373, PMCID: PMC10720134, DOI: 10.1186/s12931-023-02628-7.Peer-Reviewed Original Research
2021
Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma
Chen A, Diaz-Soto MP, Sanmamed MF, Adams T, Schupp JC, Gupta A, Britto C, Sauler M, Yan X, Liu Q, Nino G, Cruz CSD, Chupp GL, Gomez JL. Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma. Respiratory Research 2021, 22: 122. PMID: 33902571, PMCID: PMC8074196, DOI: 10.1186/s12931-021-01709-9.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsSevere asthmaEffector T cellsBlood mononuclear cellsT cellsHealthy controlsPoly IDendritic cellsMononuclear cellsUnstimulated peripheral blood mononuclear cellsInterferon responseTLR3 agonist poly IImpaired interferon responseMain cell subsetsNatural killer cellsPro-inflammatory profilePro-inflammatory pathwaysC stimulationCyTOF profilingHigh CD8Cell typesEffector cellsKiller cellsCell subsetsMain cell types
2020
Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients
Spakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients. Genome Biology 2020, 21: 150. PMID: 32571363, PMCID: PMC7310008, DOI: 10.1186/s13059-020-02033-z.Peer-Reviewed Original ResearchA Network of Sputum MicroRNAs is Associated with Neutrophilic Airway Inflammation in Asthma
Gomez JL, Chen A, Diaz MP, Zirn N, Gupta A, Britto C, Sauler M, Yan X, Stewart E, Santerian K, Grant N, Liu Q, Fry R, Rager J, Cohn L, Alexis N, Chupp GL. A Network of Sputum MicroRNAs is Associated with Neutrophilic Airway Inflammation in Asthma. American Journal Of Respiratory And Critical Care Medicine 2020, 0: 51-64. PMID: 32255668, PMCID: PMC7328332, DOI: 10.1164/rccm.201912-2360oc.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulum stressAirway inflammationNeutrophil countClinical featuresT-helper cell type 17Neutrophilic airway inflammationReticulum stressSputum of subjectsLung function impairmentHistory of hospitalizationNumber of neutrophilsPeripheral blood neutrophilsSputum of patientsMicroRNA expressionAsthma severityTh17 pathwayFunction impairmentAirway samplesMicroRNA networkBlood neutrophilsOzone exposureAsthmaSputumCellular sourceClinical phenotypeAn endothelial microRNA-1–regulated network controls eosinophil trafficking in asthma and chronic rhinosinusitis
Korde A, Ahangari F, Haslip M, Zhang X, Liu Q, Cohn L, Gomez JL, Chupp G, Pober JS, Gonzalez A, Takyar SS. An endothelial microRNA-1–regulated network controls eosinophil trafficking in asthma and chronic rhinosinusitis. Journal Of Allergy And Clinical Immunology 2020, 145: 550-562. PMID: 32035607, PMCID: PMC8440091, DOI: 10.1016/j.jaci.2019.10.031.Peer-Reviewed Original ResearchConceptsMiR-1 levelsAllergic airway inflammationChronic rhinosinusitisP-selectin levelsEndothelium-specific overexpressionLung endotheliumAirway eosinophiliaAirway inflammationAsthmatic patientsTissue eosinophiliaMiR-1House dust mite modelEndothelial cellsThymic stromal lymphopoietinNumber of hospitalizationsHuman lung endotheliumIL-13 stimulationCRS cohortQuantitative RT-PCRSputum eosinophiliaAirway obstructionAsthma modelAsthma phenotypesLentiviral vector deliveryMurine model
2019
Epigenetics in Asthma
Gomez JL. Epigenetics in Asthma. Current Allergy And Asthma Reports 2019, 19: 56. PMID: 31776749, PMCID: PMC6986424, DOI: 10.1007/s11882-019-0886-y.BooksConceptsChildhood asthmaCommon chronic respiratory diseasePurpose of ReviewAsthmaChronic respiratory diseasesUnderlying pathophysiological processesHuman asthmaAllergic inflammationAsthma endotypesHealthcare utilizationAsthma pathogenesisEpigenetic mechanismsImmune cellsRespiratory diseaseAsthmaHuman studiesPathophysiological processesSummaryThis reviewSpecific methylation signaturesNovel findingsMethylation signaturesCurrent literatureAdditional researchFuture studiesRegulatory roleEndotypes
2018
Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations
Gomez JL, Diaz MP, Nino G, Britto CJ. Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations. BMC Medical Genomics 2018, 11: 21. PMID: 29486764, PMCID: PMC5830339, DOI: 10.1186/s12920-018-0340-3.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsAsthma exacerbationsInterferon-stimulated genesRespiratory infectionsIL-15Vivo cohortToll-like receptor 2STAT1 responseRecurrent asthma exacerbationsAcute asthma exacerbationPro-inflammatory moleculesType I interferon regulationBlood mononuclear cellsPro-inflammatory signatureTranscriptomic signaturesType I interferonFold changeAdult asthmaAcute phaseMononuclear cellsImmunologic genesExacerbationIndependent cohortReceptor 2I interferon
2017
Characterisation of asthma subgroups associated with circulating YKL-40 levels
Gomez JL, Yan X, Holm CT, Grant N, Liu Q, Cohn L, Nezgovorova V, Meyers DA, Bleecker ER, Crisafi GM, Jarjour NN, Rogers L, Reibman J, Chupp GL. Characterisation of asthma subgroups associated with circulating YKL-40 levels. European Respiratory Journal 2017, 50: 1700800. PMID: 29025889, PMCID: PMC5967238, DOI: 10.1183/13993003.00800-2017.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAge of OnsetAirway ObstructionAsthmaChitinase-3-Like Protein 1Cluster AnalysisCross-Sectional StudiesDisease ProgressionFemaleGene Expression ProfilingHumansInflammationMaleMiddle AgedReproducibility of ResultsRespiratory SystemSeverity of Illness IndexSputumStatistics as TopicSymptom Flare UpConceptsSerum YKL-40 levelsYKL-40 levelsHigher serum YKL-40 levelsAirflow obstructionAsthma phenotypesElevated serum YKL-40 levelsSevere Asthma Research ProgramClinical asthma phenotypesExacerbation-prone asthmaIrreversible airway obstructionSevere airflow obstructionFrequent exacerbationsSevere exacerbationsAirway inflammationAirway obstructionAsthma exacerbationsAirway diseaseAsthma patientsAsthma severitySerum levelsInflammatory pathwaysAsthma subgroupsAdult onsetIdentification of individualsUnsupervised cluster analysisA novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression
Yan X, Liang A, Gomez J, Cohn L, Zhao H, Chupp GL. A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. BMC Bioinformatics 2017, 18: 309. PMID: 28637421, PMCID: PMC5480187, DOI: 10.1186/s12859-017-1727-4.Peer-Reviewed Original ResearchToward Precision Medicine of Symptom Control in Asthma
Gomez JL, Kaminski N. Toward Precision Medicine of Symptom Control in Asthma. American Journal Of Respiratory And Critical Care Medicine 2017, 195: 147-148. PMID: 28084831, PMCID: PMC5394790, DOI: 10.1164/rccm.201608-1600ed.Commentaries, Editorials and Letters
2015
Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma
Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma. American Journal Of Respiratory And Critical Care Medicine 2015, 191: 1116-1125. PMID: 25763605, PMCID: PMC4451618, DOI: 10.1164/rccm.201408-1440oc.Peer-Reviewed Original ResearchConceptsHistory of intubationNitric oxide levelsOxide levelsClinical phenotypeMost subjectsHigher bronchodilator responseNormal lung functionBlood of patientsCohort of childrenLogistic regression analysisSputum gene expressionBlood of childrenAirway transcriptomeMilder asthmaPathophysiologic heterogeneityPrebronchodilator FEV1Steroid requirementsLung functionBronchodilator responseGene expressionPhenotype of diseaseAsthmaBlood samplesGene signatureIntubationGenetic variation in chitinase 3-like 1 (CHI3L1) contributes to asthma severity and airway expression of YKL-40
Gomez JL, Crisafi GM, Holm CT, Meyers DA, Hawkins GA, Bleecker ER, Jarjour N, Investigators S, Cohn L, Chupp GL. Genetic variation in chitinase 3-like 1 (CHI3L1) contributes to asthma severity and airway expression of YKL-40. Journal Of Allergy And Clinical Immunology 2015, 136: 51-58.e10. PMID: 25592985, PMCID: PMC4494869, DOI: 10.1016/j.jaci.2014.11.027.Peer-Reviewed Original ResearchConceptsYKL-40 levelsYKL-40 expressionSerum YKL-40 levelsAsthma severityYKL-40Airway expressionAirway diseaseLung functionSingle nucleotide polymorphismsChitinase 3Severe Asthma Research ProgramHigh YKL-40 expressionOnly single nucleotide polymorphismRisk allele APostbronchodilator FEV1Airflow obstructionFEV1 percentSevere asthmaAsthmatic subjectsAsthma prevalenceHaplotype analysisGene polymorphismsG alleleCHI3L1 geneAsthma