2025
Senescence Cell Induction Methods Display Diverse Metabolic Reprogramming and Reveal an Underpinning Serine/Taurine Reductive Metabolic Phenotype
Berardi D, Farrell G, AlSultan A, McCulloch A, Hall N, Sousa R, Jimenez M, Selman C, Bellantuono I, Johnson C, Rattray Z, Rattray N. Senescence Cell Induction Methods Display Diverse Metabolic Reprogramming and Reveal an Underpinning Serine/Taurine Reductive Metabolic Phenotype. Aging Cell 2025, e70127. PMID: 40530891, DOI: 10.1111/acel.70127.Peer-Reviewed Original ResearchSenescence inductionLabel-free proteomicsDNA damage markersRedox circuitsCell inductionImpaired proteostasisP21 levelsTherapeutic strategiesCellular phenotypesMetabolic phenotypeMetabolic reprogrammingProteomic heterogeneityMetabolic shiftSenescence markersProteomic profilingMetabolic processesSenescence biomarkersDamage markersProtein levelsSenescenceSubphenotypesSenescence modelInfluence cellsPhenotypeInductionIntegration of Metabolomic and Brain Imaging Data Highlights Pleiotropy Among Posttraumatic Stress Disorder, Glycoprotein Acetyls, and Pallidum Structure
Løkhammer S, Tesfaye M, Cabrera-Mendoza B, Sandås K, Pathak G, Friligkou E, Le Hellard S, Polimanti R. Integration of Metabolomic and Brain Imaging Data Highlights Pleiotropy Among Posttraumatic Stress Disorder, Glycoprotein Acetyls, and Pallidum Structure. Biological Psychiatry Global Open Science 2025, 5: 100482. PMID: 40270839, PMCID: PMC12013147, DOI: 10.1016/j.bpsgos.2025.100482.Peer-Reviewed Original ResearchPosttraumatic stress disorderLocal genetic correlationImaging-derived phenotypesBrain imaging-derived phenotypesStress disorderAssociated with posttraumatic stress disorderDevelopment of posttraumatic stress disorderExposure to severe traumatic eventsGenetic correlationsGenome-wide dataSevere traumatic eventsBrain frontal cortexBrain imaging markersFrontal cortexLeft pallidumMap genesGenetic regionsGlycoprotein acetylsTraumatic eventsMetabolic biomarkersGenetic relationshipsTranscriptome regulationGenetic overlapStress responseMetabolic processes
2024
Neuroinflammatory Stress Exerts Distinct Proteomic Effects on Soma, Synapses and Mitochondria in Excitatory Neurons
Espinosa‐Garcia C, Srivastava U, Kumar P, Tobin B, Xiao H, Cheng L, Bagchi P, Duong D, Seyfried N, Faundez V, Wood L, Rangaraju S. Neuroinflammatory Stress Exerts Distinct Proteomic Effects on Soma, Synapses and Mitochondria in Excitatory Neurons. Alzheimer's & Dementia 2024, 20: e090723. PMCID: PMC11710382, DOI: 10.1002/alz.090723.Peer-Reviewed Original ResearchProteomic effectsLabel-free quantitative mass spectrometryCytoskeleton-related proteinsAlzheimer's disease pathogenesisProteome in vivoIncreased aerobic respirationCellular signaling pathwaysQuantitative mass spectrometryDisease pathogenesisCytoskeleton organizationSubcellular compartmentsOxidoreductase activitySynaptic vesiclesProteomic approachAerobic respirationBiological pathwaysNeuroinflammatory stressSignaling pathwaySynapse-related proteinsMAPK signalingMetabolic processesDifferential centrifugationMitochondriaSomatodendritic compartmentRegulating activityMachine learning on unbiased proteomics of cerebrospinal fluid uncovers differential molecular signatures of Alzheimer’s disease and Normal Pressure Hydrocephalus
de Geus M, Wu C, Dodge H, Leslie S, Wang W, Lam T, Nairn A, Kivisäkk P, Arnold S, Carlyle B. Machine learning on unbiased proteomics of cerebrospinal fluid uncovers differential molecular signatures of Alzheimer’s disease and Normal Pressure Hydrocephalus. Alzheimer's & Dementia 2024, 20: e091783. PMCID: PMC11714358, DOI: 10.1002/alz.091783.Peer-Reviewed Original ResearchGene Set Enrichment AnalysisAlzheimer's diseaseSignatures of Alzheimer's diseasePathology of ADMolecular signaturesPathways related to glycolysisNormal pressure hydrocephalusImmune response pathwaysGene setsResponse pathwaysData-independent acquisition mass spectrometryMolecular-level investigationsEnrichment analysisProteomic investigationsCerebrospinal fluidMetabolic processesProteome quantificationProteinNogo-B inhibition facilitates cholesterol metabolism to reduce hypercholesterolemia
Xue C, Zeng P, Gong K, Li Q, Feng Z, Wang M, Chen S, Yang Y, Li J, Zhang S, Yin Z, Liang Y, Yan T, Yu M, Feng K, Zhao D, Yang X, Zhang X, Ma L, Iwakiri Y, Chen L, Tang X, Chen Y, Chen H, Duan Y. Nogo-B inhibition facilitates cholesterol metabolism to reduce hypercholesterolemia. Cell Reports 2024, 43: 114691. PMID: 39235944, DOI: 10.1016/j.celrep.2024.114691.Peer-Reviewed Original ResearchLow-density lipoprotein receptorNogo-BCholesterol levelsCellular cholesterol levelsCholesterol excretionDecreased cellular cholesterol levelsATP-binding cassette transportersLiver x receptor-aHepatic uptakeLow-density lipoprotein receptor expressionCholesterol metabolic processHepatic cholesterol uptakeNogo-B expressionLowering cholesterol levelsMetabolic processesCassette transportersLipoprotein receptorApolipoprotein ELower cholesterol levelsCholesterol metabolismCholesterol uptakeDecreased cholesterol levelsReduce hypercholesterolemiaMolecular targetsExcretionPO-05-168 CARDIOMYOCYTE STIM1 EXPRESSION REGULATES POST-ISCHEMIC CARDIAC FUNCTION BY CONTROLLING METABOLIC PROCESSES AND MITOCHONDRIAL ULTRASTRUCTURE
Cacheux M, Wu X, Akar F. PO-05-168 CARDIOMYOCYTE STIM1 EXPRESSION REGULATES POST-ISCHEMIC CARDIAC FUNCTION BY CONTROLLING METABOLIC PROCESSES AND MITOCHONDRIAL ULTRASTRUCTURE. Heart Rhythm 2024, 21: s570-s571. DOI: 10.1016/j.hrthm.2024.03.1439.Peer-Reviewed Original ResearchImmunometabolism of CD8+ T cell differentiation in cancer
Shi H, Chen S, Chi H. Immunometabolism of CD8+ T cell differentiation in cancer. Trends In Cancer 2024, 10: 610-626. PMID: 38693002, PMCID: PMC11342304, DOI: 10.1016/j.trecan.2024.03.010.Peer-Reviewed Original ResearchCD8<sup>+</sup> cytotoxic T lymphocytesT cell receptorImmune signalingCD8+ T cell differentiationMediators of tumor immunityTumor antigen recognitionCytotoxic T lymphocytesT cell differentiationTumor-immune interactionsTumor immunityNovel immunotherapiesT lymphocytesIntracellular metabolic pathwaysCo-StimulationAntigen recognitionMetabolic programmingDesign novel immunotherapiesImmunotherapyCentral mediatorsMetabolic landscapePost-transcriptional mechanismsTumorBidirectional regulationSignaling eventsMetabolic processes
2023
Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo
Akingbesote N, Leitner B, Jovin D, Desrouleaux R, Owusu D, Zhu W, Li Z, Pollak M, Perry R. Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo. ELife 2023, 12: e78335. PMID: 37219930, PMCID: PMC10205083, DOI: 10.7554/elife.78335.Peer-Reviewed Original ResearchConceptsMetabolic scalingMetabolic fluxMetabolic processesBody sizeMitochondrial metabolic processesMultiple cellular compartmentsVivo metabolic fluxesLevel of genesKey metabolic pathwaysProtein expressionMetabolic flux analysisAspects of metabolismCellular compartmentsGene expressionDifferential expressionMetabolic pathwaysGenesFlux analysisOxidative damageEnzyme activitySubstrate supplyFold rangeSpeciesExpressionMetabolic rateUridine-derived ribose fuels glucose-restricted pancreatic cancer
Nwosu Z, Ward M, Sajjakulnukit P, Poudel P, Ragulan C, Kasperek S, Radyk M, Sutton D, Menjivar R, Andren A, Apiz-Saab J, Tolstyka Z, Brown K, Lee H, Dzierozynski L, He X, PS H, Ugras J, Nyamundanda G, Zhang L, Halbrook C, Carpenter E, Shi J, Shriver L, Patti G, Muir A, Pasca di Magliano M, Sadanandam A, Lyssiotis C. Uridine-derived ribose fuels glucose-restricted pancreatic cancer. Nature 2023, 618: 151-158. PMID: 37198494, PMCID: PMC10232363, DOI: 10.1038/s41586-023-06073-w.Peer-Reviewed Original ResearchConceptsUridine phosphorylase 1Pancreatic ductal adenocarcinomaExpression of uridine phosphorylase 1Central carbon metabolismPDA cellsGlucose-deprived conditionsBlunted tumor growthUridine utilizationImmunocompetent mouse modelPDAC therapyCohort of patientsCarbon metabolismNutrient restrictionPancreatic ductal adenocarcinoma cellsPancreatic cell linesNon-tumor tissuesTumor microenvironmentMetabolic axisMetabolic processesDuctal adenocarcinomaTumor progressionPoor survivalRedox balanceTumor growthSpectrum of metabolitesLeveraging GWAS data derived from a large cooperative group trial to assess the risk of taxane-induced peripheral neuropathy (TIPN) in patients being treated for breast cancer: Part 2—functional implications of a SNP cluster associated with TIPN risk in patients being treated for breast cancer
Lustberg M, Wu X, Fernández-Martínez J, de Andrés-Galiana E, Philips S, Leibowitz J, Schneider B, Sonis S. Leveraging GWAS data derived from a large cooperative group trial to assess the risk of taxane-induced peripheral neuropathy (TIPN) in patients being treated for breast cancer: Part 2—functional implications of a SNP cluster associated with TIPN risk in patients being treated for breast cancer. Supportive Care In Cancer 2023, 31: 178. PMID: 36809570, PMCID: PMC11344472, DOI: 10.1007/s00520-023-07617-6.Peer-Reviewed Original ResearchConceptsGWAS dataSNP clustersFunctional analysisGO termsNon-protein coding genesGene Ontology termsGene Set Enrichment AnalysisCluster of SNPsNervous system developmentCoding genesRetinoic acid bindingOntology termsProtein kinase C bindingEnrichment analysisMetabolic processesGenesAcid bindingGlycosyltransferase activitySNPsPathological implicationsGWASC bindingGene signaturePhenotypeTransferase activity
2022
Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut
Runyen-Janecky L, Scheutzow J, Farsin R, Cabo L, Wall K, Kuhn K, Amador R, D’Souza S, Vigneron A, Weiss B. Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut. PLOS Neglected Tropical Diseases 2022, 16: e0010833. PMID: 36441823, PMCID: PMC9731421, DOI: 10.1371/journal.pntd.0010833.Peer-Reviewed Original ResearchConceptsTsetse midgutHeme environmentDNA-binding proteinsGene Ontology termsBlood mealTsetse fly midgutVertebrate bloodBacterial genesHost midgutOntology termsDisease-causing pathogensBiological functionsGene expressionMutant strainFucose transporterInsertion mutationsMetabolic processesHost competencyEnvironmental stressorsFly midgutMidgutGenesSodalisTsetse fliesHemeProteotype coevolution and quantitative diversity across 11 mammalian species
Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.Peer-Reviewed Original ResearchConceptsMammalian speciesRNA metabolic processesCommon mammalian speciesUbiquitin-proteasome systemEvolutionary profilingMammalian lineagesProteomic methodsProtein degradationProtein abundanceGene expressionProtein expression levelsHigh interspeciesMetabolic processesCovariation analysisFunctional roleNucleotide levelExpression levelsQuantitative diversityCoevolutionMammalsSpeciesRemarkable variationExpressionTranscriptomeBiological variabilityRedesigning therapies for pantothenate kinase–associated neurodegeneration
Munshi MI, Yao SJ, Mamoun C. Redesigning therapies for pantothenate kinase–associated neurodegeneration. Journal Of Biological Chemistry 2022, 298: 101577. PMID: 35041826, PMCID: PMC8861153, DOI: 10.1016/j.jbc.2022.101577.Peer-Reviewed Original ResearchConceptsPantothenate kinase-associated neurodegenerationCellular metabolic processesMore common diseasesMetabolic processesPhysiological importancePANK2 genePantothenate kinaseCoenzyme ACoenzyme A.Rare genetic disorderCommon neurodegenerative diseaseNeurodegenerative diseasesGenetic disordersNeurodegenerationNew avenuesBiosynthesisKinaseGenesNew lightFuture investigationsCofactorMutationsCommon diseaseEnzymeAlzheimer's disease
2021
Jazf1 acts as a regulator of insulin‐producing β‐cell differentiation in induced pluripotent stem cells and glucose homeostasis in mice
Park S, Kwon W, Park S, Jeong J, Kim D, Jang S, Kim S, Sung Y, Kim M, Choi S, Ryoo Z. Jazf1 acts as a regulator of insulin‐producing β‐cell differentiation in induced pluripotent stem cells and glucose homeostasis in mice. The FEBS Journal 2021, 288: 4412-4427. PMID: 33555104, DOI: 10.1111/febs.15751.Peer-Reviewed Original ResearchIndividuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study
Rodríguez-López ML, Martínez-Magaña JJ, Ruiz-Ramos D, García AR, Gonzalez L, Tovilla-Zarate CA, Sarmiento E, Juárez-Rojop IE, Nicolini H, Gonzalez-Castro TB, Genis-Mendoza AD. Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study. Nutrients 2021, 13: 1413. PMID: 33922358, PMCID: PMC8145109, DOI: 10.3390/nu13051413.Peer-Reviewed Original ResearchConceptsGenome-wide DNA methylation differencesSubunits of AMPKInfinium Methylation EPIC arrayGenome-wide significanceDNA methylation differencesMethylation EPIC arrayDNA methylationMethylation differencesGene expressionMetabolic processesEPIC arrayGenesEnvironmental changesMetabolic systemsImportant insightsEpigeneticsAMPKMethylationSubunitsPRKAG2DNAPresent studySitesExpressionActivation
2020
FGF23 contains two distinct high-affinity binding sites enabling bivalent interactions with α-Klotho
Suzuki Y, Kuzina E, An SJ, Tome F, Mohanty J, Li W, Lee S, Liu Y, Lax I, Schlessinger J. FGF23 contains two distinct high-affinity binding sites enabling bivalent interactions with α-Klotho. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 31800-31807. PMID: 33257569, PMCID: PMC7749347, DOI: 10.1073/pnas.2018554117.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCalcinosisCell MembraneFibroblast Growth Factor-23Fibroblast Growth FactorsGlucuronidaseHEK293 CellsHumansHyperostosis, Cortical, CongenitalHyperphosphatemiaImmunoglobulin Fc FragmentsKlotho ProteinsMutationOsteomalaciaProtein BindingProtein DomainsProtein MultimerizationRecombinant Fusion ProteinsRickets, HypophosphatemicConceptsFGF receptorsTotal internal reflection fluorescence microscopyChimeric receptor moleculesReflection fluorescence microscopyBinding sitesDisulfide bridge formationCritical metabolic processesMAPK responseCytoplasmic domainGrowth factor familyTerminal tailFactor familyKinase activationSimilar binding affinitiesExtracellular domainFGFR1 activationTandem repeatsMetabolic processesDisulfide bridgesCell surfaceDistinct ligandsCell membraneFluorescence microscopyDistinct high-affinity binding sitesPhosphate homeostasisOncogenic Mechanisms and Therapeutic Targeting of Metabolism in Leukemia and Lymphoma
Stahl M, Epstein-Peterson Z, Intlekofer A. Oncogenic Mechanisms and Therapeutic Targeting of Metabolism in Leukemia and Lymphoma. Cold Spring Harbor Perspectives In Medicine 2020, 11: a035477. PMID: 32816875, PMCID: PMC8247556, DOI: 10.1101/cshperspect.a035477.Peer-Reviewed Original ResearchConceptsIncreased acquisition of nutrientsRegulate cell fateAcquisition of nutrientsMetabolically active cancer cellsBuffer oxidative stressActive cancer cellsUnrestrained cell growthAccelerated metabolic processesRapid cell divisionBiosynthetic reactionsPromote terminal differentiationCell fateCell biomassCell divisionReducing equivalentsCell growthMalignant cellsLymphoma cellsMetabolic processesTherapeutic vulnerabilitiesBiomass accumulationTerminal differentiationIntermediary metabolismLymphomaRedox balanceThe evolution of the human brain and disease susceptibility
Pattabiraman K, Muchnik SK, Sestan N. The evolution of the human brain and disease susceptibility. Current Opinion In Genetics & Development 2020, 65: 91-97. PMID: 32629339, DOI: 10.1016/j.gde.2020.05.004.Peer-Reviewed Original ResearchConceptsGene expression patternsField of evolutionDisease risk genesNervous system developmentExtant speciesGene regulationEvolutionary changeExtinct ancestorsExpression patternsGenetic studiesMetabolic processesHuman-specific aspectsRisk genesCell typesHuman biologyEvolutionary perspectiveDisease susceptibilityNeurodegenerative disease riskNeurodegenerative diseasesDifficult hypothesisComplex processGenomicsAncestorEvolutionGenes
2019
A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle
Shen H, Qu Z, Harata-Lee Y, Cui J, Aung TN, Wang W, Kortschak RD, Adelson DL. A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle. Scientific Reports 2019, 9: 15889. PMID: 31685921, PMCID: PMC6828681, DOI: 10.1038/s41598-019-52375-3.Peer-Reviewed Original ResearchConceptsTranscriptome analysisCompound Kushen InjectionCo-expression analysisPotential targetPotential molecular mechanismsTranscriptome dataImportant genesMDA-MB-231 cellsProof of principlePhenotype resultsMolecular mechanismsCytotoxic effectsMetabolic processesMajor regulatorA431 cellsAntagonistic cytotoxic effectsKushen InjectionDNA synthesisCancer cellsInhibition of MyD88GenesComplex herbal mixturesMyD88 geneChemotherapy drugsCancer chemotherapy drugsCharacterization of Circular RNA and microRNA Profiles in Septic Myocardial Depression: a Lipopolysaccharide-Induced Rat Septic Shock Model
Zhang TN, Yang N, Goodwin JE, Mahrer K, Li D, Xia J, Wen R, Zhou H, Zhang T, Song WL, Liu CF. Characterization of Circular RNA and microRNA Profiles in Septic Myocardial Depression: a Lipopolysaccharide-Induced Rat Septic Shock Model. Inflammation 2019, 42: 1990-2002. PMID: 31332662, DOI: 10.1007/s10753-019-01060-8.Peer-Reviewed Original ResearchConceptsCircular RNAsDifferential expressionGene Ontology term enrichmentFeatures of circRNAsMiRNA-mRNA networkMicroRNA profilesBasic molecular mechanismsNovel miRNAsCellular functionsRegulatory networksTerm enrichmentRNA sequencingBioinformatics analysisComprehensive circRNARegulator networkRegulatory relationshipsMolecular mechanismsCircRNAsMetabolic processesMiRNAsHeart tissueBiological mechanismsMiRNARNAPathological processes
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