2023
An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model
Charkoftaki G, Aalizadeh R, Santos-Neto A, Tan W, Davidson E, Nikolopoulou V, Wang Y, Thompson B, Furnary T, Chen Y, Wunder E, Coppi A, Schulz W, Iwasaki A, Pierce R, Cruz C, Desir G, Kaminski N, Farhadian S, Veselkov K, Datta R, Campbell M, Thomaidis N, Ko A, Thompson D, Vasiliou V. An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model. Human Genomics 2023, 17: 80. PMID: 37641126, PMCID: PMC10463861, DOI: 10.1186/s40246-023-00521-4.Peer-Reviewed Original ResearchConceptsCOVID-19 patientsDisease severityViral outbreaksFuture viral outbreaksLength of hospitalizationIntensive care unitWorse disease prognosisLife-threatening illnessEffective medical interventionsCOVID-19Clinical decision treeGlucuronic acid metabolitesNew potential biomarkersHospitalization lengthCare unitComorbidity dataSerotonin levelsDisease progressionHealthy controlsPatient outcomesDisease prognosisPatient transferPatientsHealthcare resourcesPotential biomarkersHumanized mouse liver reveals endothelial control of essential hepatic metabolic functions
Kaffe E, Roulis M, Zhao J, Qu R, Sefik E, Mirza H, Zhou J, Zheng Y, Charkoftaki G, Vasiliou V, Vatner D, Mehal W, AlcHepNet, Kluger Y, Flavell R. Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions. Cell 2023, 186: 3793-3809.e26. PMID: 37562401, PMCID: PMC10544749, DOI: 10.1016/j.cell.2023.07.017.Peer-Reviewed Original ResearchConceptsMetabolic functionsSpecies-specific interactionsKey metabolic functionsCell-autonomous mechanismsNon-alcoholic fatty liver diseaseMajor metabolic hubNon-parenchymal cellsMetabolic hubHuman hepatocytesMicroenvironmental regulationHuman diseasesHuman-specific aspectsHuman pathologiesHomeostatic processesSpecies mismatchCholesterol uptakeFatty liver diseaseParacrine mannerHuman immuneBile acid conjugationSinusoidal endothelial cellsHepatic metabolic functionMouse liverEndothelial cellsCellsIntegrated Analysis of Tracheobronchial Fluid from Before and After Cardiopulmonary Bypass Reveals Activation of the Integrated Stress Response and Altered Pulmonary Microvascular Permeability
Habet V, Li N, Qi J, Peng G, Charkoftaki G, Vasiliou V, Sharma L, Pober J, Dela Cruz C, Yan X, Pierce R. Integrated Analysis of Tracheobronchial Fluid from Before and After Cardiopulmonary Bypass Reveals Activation of the Integrated Stress Response and Altered Pulmonary Microvascular Permeability. The Yale Journal Of Biology And Medicine 2023, 96: 23-42. PMID: 37009190, PMCID: PMC10052603, DOI: 10.59249/kfyz8002.Peer-Reviewed Original ResearchConceptsIntegrated stress responseProteomic analysisTranscriptional activityStress responseSingle-cell RNA sequencingCell RNA sequencingHuman pulmonary microvascular endothelial cellsMulti-omics approachCell type annotationRespiratory transport chainUnbiased proteomic analysisUpregulation of proteinsIngenuity Pathway AnalysisCardiopulmonary bypassCell clusteringProtective cellular responseFunctional cellular assaysDistinct cell populationsDEG analysisCellular phenotypesRNA sequencingPathway analysisTransport chainCellular responsesImmune cells
2022
Proteomic profiling reveals an association between ALDH and oxidative phosphorylation and DNA damage repair pathways in human colon adenocarcinoma stem cells
Wang Y, Chen Y, Garcia-Milian R, Golla JP, Charkoftaki G, Lam TT, Thompson DC, Vasiliou V. Proteomic profiling reveals an association between ALDH and oxidative phosphorylation and DNA damage repair pathways in human colon adenocarcinoma stem cells. Chemico-Biological Interactions 2022, 368: 110175. PMID: 36162455, PMCID: PMC9891852, DOI: 10.1016/j.cbi.2022.110175.Peer-Reviewed Original ResearchConceptsCancer stem cellsProteomic profilingOxidative phosphorylationLabel-free quantitative proteomic analysisDNA damage repair pathwaysQuantitative proteomic analysisAldehyde dehydrogenase familyColon cancer stem cellsCOLO320DM cellsStem cellsNucleotide excision repairDamage repair pathwaysIngenuity Pathway AnalysisCell populationsProteomic analysisProteomic datasetsDehydrogenase familyMetabolic switchProteomic studiesRepair pathwaysCellular pathwaysALDH enzymatic activityCellular survivalExcision repairALDH activity
2021
Population pharmacokinetics of cyclophosphamide and 4-hydroxycyclophosphamide metabolite in patients with autoimmune glomerulonephritis
Iliopoulou VN, Charkoftaki G, Cooper JC, Dokoumetzidis A, Joy MS. Population pharmacokinetics of cyclophosphamide and 4-hydroxycyclophosphamide metabolite in patients with autoimmune glomerulonephritis. Journal Of Pharmacy And Pharmacology 2021, 73: 1683-1692. PMID: 34480477, DOI: 10.1093/jpp/rgab135.Peer-Reviewed Original ResearchConceptsPopulation pharmacokinetic modelPharmacokinetic modelAutoimmune glomerulonephritisCentral volumeSimultaneous population pharmacokinetic modelInitiation of therapyVisual predictive checkProportional error modelElimination rate constantDose regimensPopulation pharmacokineticsTotal clearancePatient variablesPlasma concentrationsCyclophosphamidePharmacokinetic evaluationPharmacokinetic parametersPatientsPlasma samplingPotential covariatesGlomerulonephritisSignificant covariatesPredictive checksFinal modelCovariatesAn evaluation of a novel nanoformulation of imatinib mesylate in a mouse model of lupus nephritis
Fogueri U, Charkoftaki G, Roda G, Tuey S, Ibrahim M, Persaud I, Wempe MF, Brown JM, Thurman JM, Anchordoquy TJ, Joy MS. An evaluation of a novel nanoformulation of imatinib mesylate in a mouse model of lupus nephritis. Drug Delivery And Translational Research 2021, 12: 1445-1454. PMID: 34322850, DOI: 10.1007/s13346-021-01022-4.Peer-Reviewed Original ResearchConceptsSystemic lupus erythematosus nephritisKidney depositionImatinib mesylateMouse modelMRL/MpJ miceT-testStudent's t-testDose-toxicity relationshipLupus nephritisSystemic exposureRenal excretionMesangial locationsPharmacokinetic parametersPotential treatmentNaked drugPharmacokineticsNephritisNovel nanoformulationMiceMesylateFuture strategiesCurrent studyNanoformulationsEncouraging resultsKidneyInfluence of vitamin D treatment on functional expression of drug disposition pathways in human kidney proximal tubule cells during simulated uremia
Tuey S, Atilano-Roque A, Charkoftaki G, Thurman J, Nolin T, Joy M. Influence of vitamin D treatment on functional expression of drug disposition pathways in human kidney proximal tubule cells during simulated uremia. Xenobiotica 2021, 51: 657-667. PMID: 33870862, DOI: 10.1080/00498254.2021.1909783.Peer-Reviewed Original ResearchConceptsHuman kidney proximal tubule epithelial cellsUraemic serumProtein expressionHuman kidney proximal tubule cellsVitamin D treatmentEffect of cholecalciferolProximal tubule epithelial cellsKidney proximal tubule epithelial cellsKidney proximal tubule cellsDrug transport pathwaysProximal tubule cellsDrug disposition pathwaysEffect of treatmentTubule epithelial cellsMajor vitamin DVitD treatmentVitamin DFunctional assessmentTubule cellsNM dosesEthanol vehicleFunctional expressionCYP enzymesMRNA expressionDisposition pathwaysNetwork machine learning maps phytochemically rich “Hyperfoods” to fight COVID-19
Laponogov I, Gonzalez G, Shepherd M, Qureshi A, Veselkov D, Charkoftaki G, Vasiliou V, Youssef J, Mirnezami R, Bronstein M, Veselkov K. Network machine learning maps phytochemically rich “Hyperfoods” to fight COVID-19. Human Genomics 2021, 15: 1. PMID: 33386081, PMCID: PMC7775839, DOI: 10.1186/s40246-020-00297-x.Peer-Reviewed Original Research
2019
Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells
Charkoftaki G, Thompson DC, Golla JP, Garcia-Milian R, Lam TT, Engel J, Vasiliou V. Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells. Chemico-Biological Interactions 2019, 304: 88-96. PMID: 30851239, PMCID: PMC7988342, DOI: 10.1016/j.cbi.2019.02.030.Peer-Reviewed Original ResearchUpdate on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an “evolutionary bloom”
Charkoftaki G, Wang Y, McAndrews M, Bruford EA, Thompson DC, Vasiliou V, Nebert DW. Update on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an “evolutionary bloom”. Human Genomics 2019, 13: 11. PMID: 30782214, PMCID: PMC6381713, DOI: 10.1186/s40246-019-0191-9.Peer-Reviewed Original ResearchConceptsMajor urinary protein genesKingdoms of lifeLipocalin gene familyGene familyMUP genesMouse genomeHuman genomeProtein geneChromosome 4Regulation of glucoseBarrel structurePhysiological processesΒ-strandsPhysiological functionsSecretory tissueGenesScent marksPseudogenesGenomeLipid metabolismBloomsEvidence pointsSyntenicImportant roleSteroid hormones
2018
Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level
Charkoftaki G, Rattray NJW, Andrén PE, Caprioli RM, Castellino S, Duncan MW, Goodwin RJA, Schey KL, Shahidi-Latham SK, Veselkov KA, Johnson CH, Vasiliou V. Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level. Human Genomics 2018, 12: 10. PMID: 29482659, PMCID: PMC5828306, DOI: 10.1186/s40246-018-0142-x.Peer-Reviewed Original Research