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 biomarkersAlzheimer’s disease: using gene/protein network machine learning for molecule discovery in olive oil
Rita L, Neumann N, Laponogov I, Gonzalez G, Veselkov D, Pratico D, Aalizadeh R, Thomaidis N, Thompson D, Vasiliou V, Veselkov K. Alzheimer’s disease: using gene/protein network machine learning for molecule discovery in olive oil. Human Genomics 2023, 17: 57. PMID: 37420280, PMCID: PMC10327379, DOI: 10.1186/s40246-023-00503-6.Peer-Reviewed Original Research
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
2020
COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission
Godri Pollitt KJ, Peccia J, Ko AI, Kaminski N, Dela Cruz CS, Nebert DW, Reichardt JKV, Thompson DC, Vasiliou V. COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission. Human Genomics 2020, 14: 17. PMID: 32398162, PMCID: PMC7214856, DOI: 10.1186/s40246-020-00267-3.Peer-Reviewed Original Research
2019
Genetics and functions of the retinoic acid pathway, with special emphasis on the eye
Thompson B, Katsanis N, Apostolopoulos N, Thompson DC, Nebert DW, Vasiliou V. Genetics and functions of the retinoic acid pathway, with special emphasis on the eye. Human Genomics 2019, 13: 61. PMID: 31796115, PMCID: PMC6892198, DOI: 10.1186/s40246-019-0248-9.Peer-Reviewed Original ResearchConceptsRequirement of RAEmbryonic developmentRetinoic acidAnterior segment formationRetinoic acid pathwayRas signalingPotent morphogenEye developmentOptic cup formationPostnatal lethalitySegment formationAcid pathwayCup formationNormal developmentOptic vesicleMultistep processParacrine fashionPathwayRecent advancesMorphogensGenesGeneticsMutationsVesiclesLethalityExpression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1
Pantouris G, Dioletis E, Chen Y, Thompson DC, Vasiliou V, Lolis EJ. Expression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1. Chemico-Biological Interactions 2019, 304: 168-172. PMID: 30894314, PMCID: PMC6746316, DOI: 10.1016/j.cbi.2019.03.009.Peer-Reviewed Original ResearchConceptsAldehyde dehydrogenaseCritical Cys residuesPreliminary crystallographic analysisGenomic analysisSf9 cellsCys residuesALDH16A1Novel familyLower animalsSize exclusion chromatographyActive siteStructure determinationMetabolomics studiesCrystallographic analysisCellsMammalsHomologuesGenesExclusion chromatographyFishStructural characteristicsFrogsPathogenesis of goutUnique structural characteristicsResiduesIntegrated 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
Glutathione and Transsulfuration in Alcohol-Associated Tissue Injury and Carcinogenesis
Chen Y, Han M, Matsumoto A, Wang Y, Thompson DC, Vasiliou V. Glutathione and Transsulfuration in Alcohol-Associated Tissue Injury and Carcinogenesis. Advances In Experimental Medicine And Biology 2018, 1032: 37-53. PMID: 30362089, PMCID: PMC6743726, DOI: 10.1007/978-3-319-98788-0_3.ChaptersConceptsGSH biosynthesisAbundant non-protein thiolEpigenetic gene regulationNon-protein thiolsGlutathione S-transferase (GST) familyGene regulationPeroxidase familyExogenous electrophilesCellular methylationReactive oxygen speciesGSH functionsCellular concentrationRelated enzymesTranssulfuration pathwayCancer developmentOxygen speciesBiosynthesisExogenous chemicalsEnzymeTransmethylation pathwayEnhanced susceptibilityPathological conditionsIntimate involvementMillimolar rangePathwayEvaluation of potential carcinogenicity of organic chemicals in synthetic turf crumb rubber
Perkins AN, Inayat-Hussain SH, Deziel NC, Johnson CH, Ferguson SS, Garcia-Milian R, Thompson DC, Vasiliou V. Evaluation of potential carcinogenicity of organic chemicals in synthetic turf crumb rubber. Environmental Research 2018, 169: 163-172. PMID: 30458352, PMCID: PMC6396308, DOI: 10.1016/j.envres.2018.10.018.Peer-Reviewed Original ResearchConceptsSynthetic turf fieldsCrumb rubber infillEuropean Chemicals AgencyOrganic chemicalsUS EPAADMET PredictorRubber infillUnited States Environmental Protection AgencyFuture exposure studiesChemical constituentsStates Environmental Protection AgencyHazardous chemicalsComputational toxicologyChemical componentsVinyl chlorideChemicalsPriority carcinogensTurf fieldsToxicology assessmentEnvironmental Protection AgencyCarcinogenic chemicalsChemicals AgencyExposure studiesECHA databasePotential carcinogenicity
2017
Aldehyde dehydrogenase 1B1: a novel immunohistological marker for colorectal cancer
Matsumoto A, Arcaroli J, Chen Y, Gasparetto M, Neumeister V, Thompson DC, Singh S, Smith C, Messersmith W, Vasiliou V. Aldehyde dehydrogenase 1B1: a novel immunohistological marker for colorectal cancer. British Journal Of Cancer 2017, 117: 1537-1543. PMID: 28881356, PMCID: PMC5680456, DOI: 10.1038/bjc.2017.304.Peer-Reviewed Original ResearchConceptsCRC markersTumor tissueNormal tissuesCell linesHuman CRC explantsCRC cell linesColorectal cancer markersAldehyde dehydrogenase 1A1CRC explantsImmunohistological biomarkersColorectal cancerCRC biomarkersImmunohistological markersTissue microarraySolid tumorsLow expressionMicroarray findingsGenetic alterationsALDH isozymesCell populationsALDH1A1CRCMRNA analysisCancer markersMarkers
2016
Roles of defective ALDH2 polymorphism on liver protection and cancer development
Matsumoto A, Thompson DC, Chen Y, Kitagawa K, Vasiliou V. Roles of defective ALDH2 polymorphism on liver protection and cancer development. Environmental Health And Preventive Medicine 2016, 21: 395-402. PMID: 27714678, PMCID: PMC5112207, DOI: 10.1007/s12199-016-0579-2.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSerum transaminasesLiver protectionSerum alanine aminotransferase levelsExcessive drinkingAlanine aminotransferase levelsAlcohol-related cancersUseful biological markerAldehyde dehydrogenase 2 geneAminotransferase levelsLiver injuryAlcohol intakeAlcohol dosePotential cancer riskCancer riskALDH2 polymorphismEthanol loadHealthy individualsBiological markersCancer developmentMultiple studiesFurther studiesALDH2TransaminaseDrinkingRiskLetter to the editor for “Update of the human and mouse Fanconi anemia genes”
Nebert DW, Dong H, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Letter to the editor for “Update of the human and mouse Fanconi anemia genes”. Human Genomics 2016, 10: 25. PMID: 27377885, PMCID: PMC4932714, DOI: 10.1186/s40246-016-0081-3.Peer-Reviewed Original ResearchALDH3A1 Plays a Functional Role in Maintenance of Corneal Epithelial Homeostasis
Koppaka V, Chen Y, Mehta G, Orlicky DJ, Thompson DC, Jester JV, Vasiliou V. ALDH3A1 Plays a Functional Role in Maintenance of Corneal Epithelial Homeostasis. PLOS ONE 2016, 11: e0146433. PMID: 26751691, PMCID: PMC4708999, DOI: 10.1371/journal.pone.0146433.Peer-Reviewed Original ResearchConceptsCorneal cell proliferationCorneal epithelial homeostasisCell proliferationALDH3A1 expressionEpithelial homeostasisHuman corneal epithelial cell lineDouble knockout miceAnti-proliferation effectCorneal epithelial cell lineCorneal epithelial proliferationAldehyde dehydrogenase 1A1Epithelial cell lineCorneal differentiation markersInner ocular tissuesInverse associationFunctional roleEpithelial proliferationKnockout miceP53 expressionCorneal epitheliumOcular tissuesMouse corneaCalcium concentrationMRNA levelsEpithelial differentiationAldehyde Dehydrogenase 1B1 as a Modulator of Pancreatic Adenocarcinoma
Singh S, Arcaroli JJ, Orlicky DJ, Chen Y, Messersmith WA, Bagby S, Purkey A, Quackenbush KS, Thompson DC, Vasiliou V. Aldehyde Dehydrogenase 1B1 as a Modulator of Pancreatic Adenocarcinoma. Pancreas 2016, 45: 117-122. PMID: 26566217, PMCID: PMC5175203, DOI: 10.1097/mpa.0000000000000542.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde DehydrogenaseAldehyde Dehydrogenase 1 FamilyAldehyde Dehydrogenase, MitochondrialAnimalsBiomarkers, TumorCarcinoma, Pancreatic DuctalCell Line, TumorCell ProliferationFemaleGene Expression Regulation, EnzymologicGene Expression Regulation, NeoplasticHumansImmunohistochemistryMice, NudeNeoplasm InvasivenessPancreatic NeoplasmsRNA InterferenceSignal TransductionTissue Array AnalysisTransfectionTumor BurdenUp-RegulationConceptsALDH1B1 expressionPancreatic cancerPancreatic adenocarcinomaTissue microarrayHuman pancreatic cancer cell linesPancreatic cancer cell linesPancreatic cancer patientsPancreatic ductal carcinomaHuman pancreatic cancerAldehyde dehydrogenase 1B1Potential modulatory rolePancreatic cancer cellsNormal human pancreasCell linesCancer cell linesDuctal carcinomaCancer patientsModulatory roleHuman pancreasGlandular cellsTumor cellsProtein expressionCancer cellsGreater expressionAdenocarcinoma
2015
Update of the human and mouse Fanconi anemia genes
Dong H, Nebert DW, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Update of the human and mouse Fanconi anemia genes. Human Genomics 2015, 9: 32. PMID: 26596371, PMCID: PMC4657327, DOI: 10.1186/s40246-015-0054-y.Peer-Reviewed Original ResearchConceptsHUGO Gene Nomenclature CommitteeDNA repair pathwaysFanconi anemiaFanconi anemia (FA) complementation group proteinsRepair pathwaysFA DNA repair pathwayCommon DNA repair pathwaySet of genesFanconi anemia genesGene Nomenclature CommitteeNumber of genesFANC genesFA pathogenesisGenomic integrityEvolutionary phylogenyGroup proteinsMutant proteinsMouse orthologRoot symbolFA pathwayPhysiological functionsGenesBone marrow failureGenetic diseasesEvolutionary perspectiveDead enzymes in the aldehyde dehydrogenase gene family: role in drug metabolism and toxicology
Jackson BC, Thompson DC, Charkoftaki G, Vasiliou V. Dead enzymes in the aldehyde dehydrogenase gene family: role in drug metabolism and toxicology. Expert Opinion On Drug Metabolism & Toxicology 2015, 11: 1839-1847. PMID: 26558415, PMCID: PMC4937717, DOI: 10.1517/17425255.2016.1108406.Peer-Reviewed Original ResearchConceptsAldehyde dehydrogenase gene familiesDehydrogenase gene familyDead enzymesGene familyActive enzymeProtein-protein interactionsTotal enzyme populationNon-enzymatic functionsALDH proteinsAvailability of substratesSubcellular spaceGene productsKey residuesProtein recordsCatalytic activityEnzyme populationPathophysiological functionsAllosteric modulationEnzymeBiological actionsProteinBiological activityComputational analysisALDHFamilyALDH1B1 Is Crucial for Colon Tumorigenesis by Modulating Wnt/β-Catenin, Notch and PI3K/Akt Signaling Pathways
Singh S, Arcaroli J, Chen Y, Thompson DC, Messersmith W, Jimeno A, Vasiliou V. ALDH1B1 Is Crucial for Colon Tumorigenesis by Modulating Wnt/β-Catenin, Notch and PI3K/Akt Signaling Pathways. PLOS ONE 2015, 10: e0121648. PMID: 25950950, PMCID: PMC4423958, DOI: 10.1371/journal.pone.0121648.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde DehydrogenaseAldehyde Dehydrogenase 1 FamilyAldehyde Dehydrogenase, MitochondrialAnimalsCell Line, TumorColonic NeoplasmsGene Expression Regulation, NeoplasticHCT116 CellsHT29 CellsHumansMiceNeoplasm TransplantationPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktReceptors, NotchRNA, Small InterferingSignal TransductionSpheroids, CellularWnt Signaling PathwayConceptsWnt/β-cateninPI3K/AktΒ-cateninSW-480 cellsColon cancer tumorigenesisWnt reporter activityPattern of expressionPI3K/Akt Signaling PathwayDual-luciferase reporterPI3K/Akt signal pathwayAkt Signaling PathwayTranscription factorsAkt signal pathwayNude mouse xenograft tumor modelColon tumorigenesisGene promoterColon adenocarcinoma cell lineMouse xenograft tumor modelALDH1B1 expressionAldehyde dehydrogenase 1B1Signaling pathwaysLuciferase reporterSize of spheroidsAdenocarcinoma cell lineXenograft tumor model
2014
Human ALDH1B1 Polymorphisms may Affect the Metabolism of Acetaldehyde and All-trans retinaldehyde—In Vitro Studies and Computational Modeling
Jackson BC, Reigan P, Miller B, Thompson DC, Vasiliou V. Human ALDH1B1 Polymorphisms may Affect the Metabolism of Acetaldehyde and All-trans retinaldehyde—In Vitro Studies and Computational Modeling. Pharmaceutical Research 2014, 32: 1648-1662. PMID: 25413692, PMCID: PMC4382438, DOI: 10.1007/s11095-014-1564-3.Peer-Reviewed Original ResearchAcetaldehydeAldehyde DehydrogenaseAldehyde Dehydrogenase 1 FamilyAldehyde Dehydrogenase, MitochondrialAldehydesAmino Acid SequenceComputer SimulationHumansModels, BiologicalModels, MolecularMolecular Sequence DataNitroglycerinPolymorphism, GeneticProtein ConformationRetinaldehydeSubstrate SpecificityTransgenic Mouse Models for Alcohol Metabolism, Toxicity, and Cancer
Heit C, Dong H, Chen Y, Shah YM, Thompson DC, Vasiliou V. Transgenic Mouse Models for Alcohol Metabolism, Toxicity, and Cancer. Advances In Experimental Medicine And Biology 2014, 815: 375-387. PMID: 25427919, PMCID: PMC4323349, DOI: 10.1007/978-3-319-09614-8_22.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsReactive oxygen speciesAldehyde dehydrogenasesCritical biological functionsAlcohol dehydrogenaseFormation of proteinHuman genesBiological functionsMolecular mechanismsVariety of cancersPrimary enzymeGenetic defectsOxygen speciesEnzymeNitrogen speciesEthanol metabolismTransgenic mouse modelOxidative stressSpeciesCytochrome P450Pathogenic eventsMetabolismGenetic polymorphismsAntioxidant mechanismsAlcohol-induced toxicityAlcohol-metabolizing enzymes