2025
Integrating gut microbiome and neuroplasticity genomics in alcohol use disorder therapy
Koutromanos I, Legaki E, Dovrolis N, Vassilopoulos E, Stem A, Vasiliou V, Tzavellas E, Gazouli M. Integrating gut microbiome and neuroplasticity genomics in alcohol use disorder therapy. Human Genomics 2025, 19: 78. PMID: 40646629, PMCID: PMC12255058, DOI: 10.1186/s40246-025-00793-y.Peer-Reviewed Original ResearchConceptsGut microbiotaShort-chain fatty acid (SCFA)-producing bacteriaMetabolic pathwaysStress-related metabolic pathwaysHost-microbiota interactionsMicrobial metabolic pathwaysMulti-omics approachGut barrier integrityGene expression changesGene expression profilesNeuroplasticity-related genesRRNA sequencingGut microbiomeFamily genesGenomic signaturesMicrobiome compositionMicrobial compositionAUD patientsMicrobial dysbiosisTreatment responseFunctional pathwaysGene expressionMicrobiomeGenesExpression changes1647-P: Coenzyme A Synthase Knockdown Increases Hepatic Mitochondrial Fat Oxidation and Reduces Hepatic Steatosis and Hepatic Insulin Resistance
GASPAR R, SAKUMA I, HUBBARD B, LAMOIA T, ZHENG J, PARIKH S, KAHN M, SILVEIRA L, DUFOUR S, NASIRI A, PERELIS M, PETERSEN K, SAMUEL V, SHULMAN G. 1647-P: Coenzyme A Synthase Knockdown Increases Hepatic Mitochondrial Fat Oxidation and Reduces Hepatic Steatosis and Hepatic Insulin Resistance. Diabetes 2025, 74 DOI: 10.2337/db25-1647-p.Peer-Reviewed Original ResearchHFD-fed miceAcetyl-CoAHepatic insulin resistanceHFD-fedHepatic acetyl-CoA contentMalonyl-CoA levelsCoenzyme A synthaseFatty acid synthesisHepatic acetyl-CoAAcetyl-CoA contentSteatotic liver diseasePathogenesis of type 2 diabetesHigh-fat dietTCA cycleMitochondrial fat oxidationWhole-body energy expenditureCoA biosynthesisHepatic steatosisAcid synthesisMetabolic pathwaysInsulin resistanceReduced hepatic steatosisDecreased hepatic steatosisCOASYTriacylglycerol contentTranscriptomic and epigenomic signatures of liver metabolism and insulin sensitivity in aging mice
González J, Scharfman O, Zhu W, Kasamoto J, Gould V, Perry R, Higgins-Chen A. Transcriptomic and epigenomic signatures of liver metabolism and insulin sensitivity in aging mice. Mechanisms Of Ageing And Development 2025, 225: 112068. PMID: 40324540, PMCID: PMC12151592, DOI: 10.1016/j.mad.2025.112068.Peer-Reviewed Original ResearchConceptsDNA methylation modulesHepatic insulin resistanceRNA modulesProtein-protein interaction network analysisMetabolic pathwaysMethylation modulatorsPyruvate carboxylase fluxInteraction network analysisCitrate synthase fluxDNA methylation analysisCanonical metabolic pathwaysLipid metabolic pathwaysDecreased fatty acid oxidationComprehensive phenotypic characterizationMZF-1Fatty acid oxidationEpigenomic signaturesInsulin-stimulated conditionsModule genesNetwork analysisPhenotypic characterizationMitochondrial metabolic defectsInsulin resistanceLiver insulin resistanceMethylation analysisSex differences in proteomics of cardiovascular disease – Results from the Yale-CMD registry
Liu Y, Wang Z, Collins S, Testani J, Safdar B. Sex differences in proteomics of cardiovascular disease – Results from the Yale-CMD registry. IJC Heart & Vasculature 2025, 58: 101667. PMID: 40224648, PMCID: PMC11987697, DOI: 10.1016/j.ijcha.2025.101667.Peer-Reviewed Original ResearchCMD patientsUpregulation of immune pathwaysCardiovascular diseaseProximity extension assayBody mass indexRegulation of blood flowSex differencesProteomic profilingIschemic symptomsCAD patientsMass indexIncreased angiogenesisGlucose metabolic pathwaysDifferential protein expressionPatientsSex-specific pathwaysProtein expressionImmune pathwaysBlood flowBlood samplesPrecision medicineINSL3Metabolic pathwaysPathway analysisExtension assayOptical photothermal infrared imaging using metabolic probes in live biological systems
Shuster S, Curtis A, Davis C. Optical photothermal infrared imaging using metabolic probes in live biological systems. Progress In Biomedical Optics And Imaging 2025, 13332: 1333208-1333208-6. DOI: 10.1117/12.3040983.Peer-Reviewed Original ResearchSpectrally resolved imagesLiving cellsImaging of living cellsReduce imaging timeMultifrequency imagesBiological systemsProtein localizationSite-specific probeDynamic imaging of live cellsMetabolic pathwaysConformational changes of biomoleculesSpatial resolutionInfrared spectraConformational changesReaction mechanismCell linesWater backgroundIdentifying biomoleculesInfrared SpectroscopyPolyamine metabolism is dysregulated in COXFA4-related mitochondrial disease
Marquez J, Viviano S, Beckman E, Thies J, Friedland-Little J, Lam C, Deniz E, Shelkowitz E. Polyamine metabolism is dysregulated in COXFA4-related mitochondrial disease. Human Genetics And Genomics Advances 2025, 6: 100418. PMID: 39967265, PMCID: PMC11946867, DOI: 10.1016/j.xhgg.2025.100418.Peer-Reviewed Original ResearchOrnithine decarboxylase pathwayCytochrome c oxidaseMitochondrial diseaseCause of mitochondrial diseaseAnalysis of cellular gene expressionSubunits of cytochrome c oxidaseC oxidaseTissue-specific diseasesCellular gene expressionDeficiency of cytochrome c oxidaseLeigh-like diseaseElectron donor NADHDownstream deficienciesMitochondrial membraneProtein complexesCellular functionsOxidative phosphorylationProtein subunitsGene expressionMetabolic pathwaysPolyamine metabolismPathwayProteinPoor growthAdenosine triphosphateDrug interactions in people with HIV treated with antivirals for other viral illnesses
Okoli A, Ogbuagu O. Drug interactions in people with HIV treated with antivirals for other viral illnesses. Expert Opinion On Drug Metabolism & Toxicology 2025, 21: 383-397. PMID: 39836520, PMCID: PMC12169512, DOI: 10.1080/17425255.2025.2455401.Peer-Reviewed Original ResearchDrug-drug interactionsDrug interactionsManagement of drug interactionsTreatment of HIVViral coinfectionAntiviral therapyHepatitis CViral illnessHIV treatmentIncreased riskPrescribing informationEffective treatmentViral infectionHIVAntiviral agentsConference abstractsPWHPatient outcomesARVDrug prescribing informationTreatmentCoinfectionGoogle ScholarDrugMetabolic pathways
2024
Microbial metabolism of host-derived antioxidants
Zhou Z, Hatzios S. Microbial metabolism of host-derived antioxidants. Current Opinion In Chemical Biology 2024, 84: 102565. PMID: 39721219, PMCID: PMC11863140, DOI: 10.1016/j.cbpa.2024.102565.Peer-Reviewed Original ResearchIntracellular endothelial cell metabolism in vascular function and dysfunction
Citrin K, Chaube B, Fernández-Hernando C, Suárez Y. Intracellular endothelial cell metabolism in vascular function and dysfunction. Trends In Endocrinology And Metabolism 2024, 36: 744-755. PMID: 39672762, PMCID: PMC12159263, DOI: 10.1016/j.tem.2024.11.004.Peer-Reviewed Original ResearchFatty acid oxidationEndothelial cellsIntracellular metabolic pathwaysInner lining of blood vesselsVascular functionCell metabolismMetabolic pathwaysEndothelial cell metabolismLipid handlingDesign new therapiesRegulate vascular toneInfluence disease progressionAcid oxidationMetabolic signaturesVascular toneNew therapiesLining of blood vesselsDisease progressionLeukocyte adhesionMetabolic changesVascular diseaseOxidative stressBlood vesselsIncreased permeabilityWound healingAedes aegypti adiponectin receptor-like protein signaling facilitates Zika virus infection
Chen T, Marín-López A, Raduwan H, Fikrig E. Aedes aegypti adiponectin receptor-like protein signaling facilitates Zika virus infection. MBio 2024, 15: e02433-24. PMID: 39373507, PMCID: PMC11559040, DOI: 10.1128/mbio.02433-24.Peer-Reviewed Original ResearchReceptor-like proteinZika virus infectionVirus infectionDevelopment of effective control strategiesSignificant public health challengeTranscriptome analysisTrypsin genesMetabolic pathwaysProtein signalingPublic health challengeViral infectionTransmission of viral diseasesAedes aegypti</i>InfectionBlood digestionZika virusProteinSignificance of signalsComplex interactionsVirusEffective control strategiesViral diseasesZikaMosquitoesPathwayThe Association of the Oral Microbiota with Cognitive Functioning in Adolescence
Naumova O, Dobrynin P, Khafizova G, Grigorenko E. The Association of the Oral Microbiota with Cognitive Functioning in Adolescence. Genes 2024, 15: 1263. PMID: 39457387, PMCID: PMC11507344, DOI: 10.3390/genes15101263.Peer-Reviewed Original ResearchOral microbiotaKaufman Assessment Battery for Children IIHealthy oral microbiomeCognitive functionMetabolic pathwaysBacterial cell divisionAbundance of BacteroidetesAfrican-American originClinical phenotypeOral microbiomeAssociated with cognitive functionGut microbiomeMicrobiome diversityMicrobial communitiesBacterial speciesCell divisionGABA metabolismMicrobiomeMicrobiotaPopulation-based researchIndicators of general intelligenceMiddle-agedImprove cognitive healthAmerican originAssociationBeyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation
Holendová B, Šalovská B, Benáková Š, Plecitá-Hlavatá L. Beyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation. Metabolism 2024, 161: 156027. PMID: 39260557, DOI: 10.1016/j.metabol.2024.156027.Peer-Reviewed Original ResearchPost-translational modificationsReactive oxygen speciesEndoplasmic reticulumTricarboxylic acidRedox signalingPancreatic B-cellsGlucose stimulationModification of proteinsB-cell metabolismRedox signaling pathwaysReversible cysteine oxidationIncreased ROS levelsProduction of reactive oxygen speciesB cell functionInsulin secretionB cellsProtein functionProtein processingCysteine thiol modificationsGlucose-induced increaseOxidative phosphorylationPyruvate metabolismProtein activityRegulatory mechanismsMetabolic pathwaysStress increases sperm respiration and motility in mice and men
Moon N, Morgan C, Marx-Rattner R, Jeng A, Johnson R, Chikezie I, Mannella C, Sammel M, Epperson C, Bale T. Stress increases sperm respiration and motility in mice and men. Nature Communications 2024, 15: 7900. PMID: 39261485, PMCID: PMC11391062, DOI: 10.1038/s41467-024-52319-0.Peer-Reviewed Original ResearchConceptsEpididymal epithelial cellsIncreased mitochondrial respirationIn vitro stress modelsCells secrete extracellular vesiclesSperm RNASperm respirationMouse spermSperm maturationDNA regionsSperm functionTranslational signaling pathwaysSperm motilitySemen qualitySpermMitochondrial respirationMetabolic pathwaysSignaling pathwayEnvironmental stressorsExtracellular vesiclesHuman cohort studiesEpithelial cellsMotilityCellular mechanismsEmbryo developmentCohort studyExpanding the repertoire of GalNAc analogues for cell-specific bioorthogonal tagging of glycoproteins
Zafar A, Sridhar S, Bineva-Todd G, Cioce A, Abdulla N, Chang V, Malaker S, Hewings D, Schumann B. Expanding the repertoire of GalNAc analogues for cell-specific bioorthogonal tagging of glycoproteins. RSC Chemical Biology 2024, 5: 1002-1009. PMID: 39238612, PMCID: PMC11369666, DOI: 10.1039/d4cb00093e.Peer-Reviewed Original ResearchModeling Glucose, Insulin, C-Peptide, and Lactate Interplay in Adolescents During an Oral Glucose Tolerance Test.
Bonet J, Barbieri E, Santoro N, Dalla Man C. Modeling Glucose, Insulin, C-Peptide, and Lactate Interplay in Adolescents During an Oral Glucose Tolerance Test. Journal Of Diabetes Science And Technology 2024, 19322968241266825. PMID: 39076151, PMCID: PMC11572107, DOI: 10.1177/19322968241266825.Peer-Reviewed Original ResearchOral glucose tolerance testArea under the curveGlucose tolerance testC-peptideTolerance testStandard oral glucose tolerance testPathological conditionsTime coursePopulation of adolescentsClinical dataLactate metabolism pathwaysLiver diseaseSteatotic liver diseaseModel glucoseMetabolic diseasesIntersubject variabilityObesityLactate metabolismAnaerobic glycolysisInsulinLactate kineticsDiseaseAdolescentsLactateMetabolic pathwaysFolate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium
Metayer C, Spector L, Scheurer M, Jeon S, Scott R, Takagi M, Clavel J, Manabe A, Ma X, Hailu E, Lupo P, Urayama K, Bonaventure A, Kato M, Meirhaeghe A, Chiang C, Morimoto L, Wiemels J. Folate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium. Cancer Epidemiology Biomarkers & Prevention 2024, 33: 1248-1252. PMID: 38904462, PMCID: PMC11369612, DOI: 10.1158/1055-9965.epi-24-0189.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsGenome-wide dataAncestry groupsFolate metabolic pathwayGenetic variantsChildhood cancerMetabolic pathwaysGenetic pathway analysisRisk of childhood ALLRisk of childhood acute lymphoblastic leukemiaGene-folate interactionsChildhood ALL riskCase-control studyDNA methylationMETAL softwareGenetic studiesNucleotide polymorphismsPathway analysisMeta-analysis of original dataALL riskGenetic effectsAncestryFolate pathwayMaternal genetic effectsFolate intakeGrowth characteristics of HCT116 xenografts lacking asparagine synthetase vary according to sex
Aladelokun O, Lu L, Zheng J, Yan H, Jain A, Gibson J, Khan S, Johnson C. Growth characteristics of HCT116 xenografts lacking asparagine synthetase vary according to sex. Human Genomics 2024, 18: 67. PMID: 38886847, PMCID: PMC11184737, DOI: 10.1186/s40246-024-00635-3.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAspartate-Ammonia LigaseCarbon-Nitrogen Ligases with Glutamine as Amide-N-DonorCell ProliferationColorectal NeoplasmsFemaleGene Expression Regulation, NeoplasticHCT116 CellsHeterograftsHumansMaleMiceReceptors, EstrogenReceptors, G-Protein-CoupledSex FactorsXenograft Model Antitumor AssaysConceptsFemale tumor-bearing miceFemale CRC patientsTumor-bearing miceCRC patientsTumor growthInferior survivalAssociated with inferior survivalMetabolic reprogrammingG protein-coupled estrogen receptorTriggering metabolic reprogrammingSustained tumor growthSuppressed tumor growthExpression of asparagine synthetaseCancer cell linesBackgroundSex-related differencesSurvival improvementImpact of sexFemale miceEstrogen receptorCancer growthTranslational relevanceRewiring of metabolic pathwaysCancer burdenMetabolic pathwaysAsparagine synthetaseHeterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling
Ohashi Y, Protack C, Aoyagi Y, Gonzalez L, Thaxton C, Zhang W, Kano M, Bai H, Yatsula B, Alves R, Hoshina K, Schneider E, Long X, Perry R, Dardik A. Heterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling. Scientific Reports 2024, 14: 13287. PMID: 38858395, PMCID: PMC11164895, DOI: 10.1038/s41598-024-64075-8.Peer-Reviewed Original ResearchConceptsGene expression patternsArteriovenous fistula groupArteriovenous fistulaExpression patternsHeterogeneous gene expressionGene expression changesOutcomes of arteriovenous fistulaVenous remodelingArteriovenous fistula maturationPostoperative day 7Reduce patient morbidityRNA sequencingUpregulation of metabolismBioinformatics analysisGene expressionDownregulation of metabolismMetabolic pathwaysExpression changesGenesAVF maturationAVF remodelingFistula creationC57BL/6 miceClinical outcomesPatient morbidityNonlinear dynamics in phosphoinositide metabolism
Fung S, Xǔ X, Wu M. Nonlinear dynamics in phosphoinositide metabolism. Current Opinion In Cell Biology 2024, 88: 102373. PMID: 38797149, PMCID: PMC11186694, DOI: 10.1016/j.ceb.2024.102373.Peer-Reviewed Original ResearchMetabolic networksPhosphoinositide metabolismNegative feedback loopCellular physiologyEnzymatic functionSignaling ComplexSignal transductionMembrane dynamicsNetwork motifsMetabolic pathwaysLipid fluxCellular behaviorMolecular circuitsPhosphoinositideFeedforward loopProducts of metabolismMetabolismFeedback loopExperimental challengeNonlinear dynamicsMotifFramework of nonlinear dynamicsTransductionExcited statesComprehensive understandingProperties and predicted functions of large genes and proteins of apicomplexan parasites
Fang T, Mohseni A, Lonardi S, Mamoun C. Properties and predicted functions of large genes and proteins of apicomplexan parasites. NAR Genomics And Bioinformatics 2024, 6: lqae032. PMID: 38584870, PMCID: PMC10993292, DOI: 10.1093/nargab/lqae032.Peer-Reviewed Original ResearchApicomplexan parasitesCausative agent of toxoplasmosisProtein sizeAgent of toxoplasmosisPathogen-host interactionsToxoplasma gondii</i>Conventional metabolic pathwaysCompact genomeEukaryotic organismsEncode proteinsEvolutionary constraintsNutrient acquisitionApicomplexan pathogensEvolutionary pressureAntigenic variationMetabolic pathwaysExpression patternsLarger proteinsParasitesCausative agentProteinGenesImmune evasionErythrocyte invasionPlasmodium falciparum</i>
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