2025
A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer
Shen C, Salazar-Morales A, Jung W, Erwin J, Gu Y, Coelho A, Gupta K, Yalcin S, Samatey F, Malvankar N. A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer. Cell Chemical Biology 2025, 32: 239-254.e7. PMID: 39818215, PMCID: PMC11845295, DOI: 10.1016/j.chembiol.2024.12.013.Peer-Reviewed Original ResearchConceptsExtracellular electron transferPhylogenetically diverse speciesATP-dependent mannerMicrobial extracellular electron transferBacterial machineryDiverse prokaryotesDiverse speciesBiotechnological applicationsGeobacter sulfurreducensCell growthSurface-displayedMorphology maintenanceBiophysical methodsMulti-heme cytochromesCytochromeElectron transferOsCHSProkaryotesPhylogeneticallySulfurreducensGeobacterOverexpressionSpeciesMachinery
2024
Cell Growth Trajectories of B-Cell Lymphomas Are Defined By Oscillations between MYC- and BCL6-Dependent States
Cheng Z, Kume K, Shanmugam V, Müschen M. Cell Growth Trajectories of B-Cell Lymphomas Are Defined By Oscillations between MYC- and BCL6-Dependent States. Blood 2024, 144: 45-45. DOI: 10.1182/blood-2024-206563.Peer-Reviewed Original ResearchActivation of MYCCell divisionCell growthDNA damage-induced apoptosisTurnover of damaged organellesB-cell lymphomaTranscriptional activity of MYCChIP-seq dataDamage-induced apoptosisOscillatory expression patternsCell shrinkageDegradation of MYCPhenotype to cellsTranscription of MYCInduce transcriptional activationAmino acid depletionTime-lapse confocal imagingLive-cell imagingStall cell growthB cell developmentChIP-seqB cellsDegron systemRepress transcriptionCell sizeLysosomal TBK1 responds to amino acid availability to relieve Rab7-dependent mTORC1 inhibition
Talaia G, Bentley-DeSousa A, Ferguson S. Lysosomal TBK1 responds to amino acid availability to relieve Rab7-dependent mTORC1 inhibition. The EMBO Journal 2024, 43: 3948-3967. PMID: 39103493, PMCID: PMC11405869, DOI: 10.1038/s44318-024-00180-8.Peer-Reviewed Original ResearchTANK-binding kinase 1MTORC1 activityAmino acid-dependent mTORC1 activationOrganelle quality controlRegulate cell growthElevated amino acid levelsAmino acid levelsAssociated with amyotrophic lateral sclerosisIncreased mTORC1 activityCellular demandSerine 72Amino acid availabilityLysosomal homeostasisSignaling proteinsMacromolecule degradationSites of amino acidsCell growthLysosomal poolMTORC1 inhibitionKinase 1Lysosomal functionAmino acidsInnate immunityLysosomesAmyotrophic lateral sclerosisThe cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis
McCool M, Bryant C, Abriola L, Surovtseva Y, Baserga S. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLOS Biology 2024, 22: e3002718. PMID: 38976757, PMCID: PMC11257408, DOI: 10.1371/journal.pbio.3002718.Peer-Reviewed Original ResearchRibosome biogenesis factorsRibosome biogenesisBiogenesis factorsCell growthNucleolar functionRegulation of nucleolar functionHuman ribosome biogenesisProtein synthesisProduction of ribosomesFamily of proteinsSource of mutagenesisLevel of protein synthesisCytidine deaminase familyIncreased cell growthPromote cell growthPre-rRNAPotential direct rolePre-mRNATransient overexpressionRibosomeGenomic mutationsBiogenesisMCF10A cellsMaturation stepsAPOBEC3AMechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis
Kural M, Djakbarova U, Cakir B, Tanaka Y, Chan E, Arteaga Muniz V, Madraki Y, Qian H, Park J, Sewanan L, Park I, Niklason L, Kural C. Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis. Cell Death & Disease 2024, 15: 440. PMID: 38909035, PMCID: PMC11193792, DOI: 10.1038/s41419-024-06822-3.Peer-Reviewed Original ResearchConceptsFas-induced apoptosisCell surface Fas expressionDeath receptor FasInhibition of endocytosisSurface Fas expressionPlasma membrane tensionCancer cell apoptosisEndocytosis dynamicsApoptotic signalingReceptor FasGlioblastoma cell growthFas expressionPlasma membraneCell growthEndocytosisXenograft mouse modelSoluble FasLCell apoptosisFasApoptosisRho-kinase inhibitorCancer cellsMembrane tensionNonmalignant cellsInduce tumor regressionIs Lipid Metabolism of Value in Cancer Research and Treatment? Part I- Lipid Metabolism in Cancer
Nassar A, Nie X, Zhang T, Yeung J, Norris P, He J, Ogura H, Babar M, Muldoon A, Libreros S, Chen L. Is Lipid Metabolism of Value in Cancer Research and Treatment? Part I- Lipid Metabolism in Cancer. Metabolites 2024, 14: 312. PMID: 38921447, PMCID: PMC11205345, DOI: 10.3390/metabo14060312.Peer-Reviewed Original ResearchMass spectrometryLipid metabolismTherapeutic efficacy of treatmentLipidomic studiesEfficacy of treatmentStudy of lipidsEmergence of lipidomicsLipid categoriesSpectrometryEnergy storageTumor microenvironmentPharmaceutical candidatesTherapeutic efficacyLipidomicsCancer patientsLipid profileCancer samplesCancerLarge-scale studiesCancer researchTargeted approachAlterationsDisease developmentCell growthMetabolism
2023
Identification of a New Integration Site and Study on Site-Specific Integration in CHO-K1 Cells
Liu H, Zhang W, Xie L, Hu Y. Identification of a New Integration Site and Study on Site-Specific Integration in CHO-K1 Cells. Pharmaceuticals 2023, 17: 8. PMID: 38275994, PMCID: PMC10819697, DOI: 10.3390/ph17010008.Peer-Reviewed Original ResearchPairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis
Alfaro-Murillo J, Townsend J. Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis. Mathematical Biosciences 2023, 366: 109091. PMID: 37996064, PMCID: PMC10847963, DOI: 10.1016/j.mbs.2023.109091.Peer-Reviewed Original ResearchStrength of selectionEpistatic effectsSelection coefficientsMutation rateHigher-order epistatic effectsLarge mutation ratesLarge selection coefficientsSomatic cancer mutationsUncontrolled cell growthSomatic evolutionMultiple somatic mutationsDriver genesCancer mutationsCancer research communityGenesSomatic genotypeCell growthOncogenesisMutationsSomatic mutationsEvolutionary modelsConsequent trajectoriesCancer genotypesPersonalized cancer therapyMutual exclusivityEvidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria
Breaker R, Harris K, Lyon S, Wencker F, Fernando C. Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology 2023, 120: 324-340. PMID: 37469248, DOI: 10.1111/mmi.15129.Peer-Reviewed Original ResearchConceptsOLE RNAPrecise biochemical functionFundamental cellular processesCell growthTOR complexesProtein partnersRibonucleoprotein complexesCellular processesRNP complexesBiochemical functionsGram-positive bacteriaNoncoding RNAsRibonucleoprotein particleExtremophilic bacteriaBacterial speciesGenetic disruptionStress conditionsDiverse pathwaysRNAMetabolic adaptationCell membraneExtreme environmentsCarbon sourceBacteriaComplexesMutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity
Hollander M, Malaker S, Riley N, Perez I, Abney N, Gray M, Maxson J, Cochran J, Bertozzi C. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. Journal Of Biological Chemistry 2023, 299: 104755. PMID: 37116708, PMCID: PMC10245049, DOI: 10.1016/j.jbc.2023.104755.Peer-Reviewed Original ResearchConceptsProtein domain mappingSingle amino acid mutationLigand-independent activityChronic neutrophilic leukemiaCell surface receptorsAmino acid mutationsColony-stimulating factor 3 receptorSerine residuesPresence of GalNAcHotspot residuesNeutrophilic leukemiaHuman diseasesAcid mutationsReceptor signalingAmino acidsCell growthSurface receptorsReceptor alpha chainMutationsAbundant typeDomain mappingDisease mechanismsUncontrolled activityAlpha chainWhite blood cellsCell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin beta receptor signaling
Feng X, Sun R, Lee M, Chen X, Guo S, Geng H, Müschen M, Choi J, Pereira J. Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin beta receptor signaling. ELife 2023, 12: e83533. PMID: 36912771, PMCID: PMC10042536, DOI: 10.7554/elife.83533.Peer-Reviewed Original ResearchConceptsMesenchymal stem cellsLymphotoxin beta receptorLeukemic cellsBeta receptorsLeukemic cell growthBone marrow microenvironmentStem cellsTransplant recipientsAML cellsMyeloblastic leukemiaMouse modelBone marrowLeukemia growthLymphotoxin α1β2Marrow microenvironmentPharmacological disruptionLymphopoiesisReceptorsHematopoietic outputMolecular mechanismsErythropoiesisDNA damage response pathwayCell growthCellsPhysiological mechanismsAn intrinsic purine metabolite AICAR blocks lung tumour growth by targeting oncoprotein mucin 1
Aftab F, Rodriguez-Fuguet A, Silva L, Kobayashi I, Sun J, Politi K, Levantini E, Zhang W, Kobayashi S, Zhang W. An intrinsic purine metabolite AICAR blocks lung tumour growth by targeting oncoprotein mucin 1. British Journal Of Cancer 2023, 128: 1647-1664. PMID: 36810913, PMCID: PMC10133251, DOI: 10.1038/s41416-023-02196-z.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProximity ligation assayWhole transcriptomic profileEGFR inhibitorsMUC1-CTThermal stability assaysRNA sequencingTransgenic micePurine biosynthesisTranscriptomic profilesAICARTumor cell growthLigation assayMucin 1DNA damageCell growthMethodsCell viabilityLung tumor tissuesTumor formationCancer cellsEGFR-mutant lung cancerStability assaysJAKJAK1Dual immunofluorescence staining
2022
Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activity
Han W, Peng B, Wang C, Townsend G, Barry N, Peske F, Goodman A, Liu J, Rodnina M, Groisman E. Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activity. The EMBO Journal 2022, 42: embj2022112372. PMID: 36472247, PMCID: PMC9841332, DOI: 10.15252/embj.2022112372.Peer-Reviewed Original ResearchConceptsEF-G1Protein synthesisGTPase activityGuanosine triphosphateElongation factor GCarbon starvationCellular processesStarvation conditionsBacteroides thetaiotaomicronFactor GSingular abilityAmino acidsCell growthParalogsMurine cecumTranslocationGut colonizationColonizationCellsRibosomesProteinStarvationThetaiotaomicronBacteriaFitnessHuman WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation
Cai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. ELife 2022, 11: e78163. PMID: 36043466, PMCID: PMC9584608, DOI: 10.7554/elife.78163.Peer-Reviewed Original ResearchConceptsBreast cancer cellsMetastatic breast cancerBreast cancerRibosomal gene expressionCancer cellsKnockdown of WDR5Vivo genetic screenReversible epigenetic mechanismsGenetic screenTranslation regulationTriple-negative breast cancerEpigenetic regulatorsEpigenetic mechanismsBreast cancer growthCancer-related deathTranslation efficiencyWDR5Novel therapeutic strategiesTranslation rateGene expressionCell growthAdvanced diseaseEffective therapyMetastatic capabilityPotent suppressionAPOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma
Cannataro VL, Kudalkar S, Dasari K, Gaffney SG, Lazowski HM, Jackson LK, Yildiz I, Das RK, Rothberg BE, Anderson KS, Townsend JP. APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma. Lung Cancer 2022, 171: 34-41. PMID: 35872531, PMCID: PMC10126952, DOI: 10.1016/j.lungcan.2022.07.004.Peer-Reviewed Original ResearchConceptsCytidine deaminationMutagenic processesDefective homologous recombinationGenomic sequencesHomologous recombinationAttractive potential targetAPOBEC mutagenesisLung squamous cell carcinomaDeamination activityCancer cell growthAPOBEC proteinsAPOBEC activityCell growthCellular proliferationNFE2L2MutationsMolecular investigationsCancer effectsPotential targetMolecular variantsAPOBECSurvival of cancerSquamous cell carcinomaDeaminationVariantsCollective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments
Mattingly H, Emonet T. Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2117377119. PMID: 35727978, PMCID: PMC9245662, DOI: 10.1073/pnas.2117377119.Peer-Reviewed Original ResearchConceptsNongenetic inheritanceCollective migrationPhenotype compositionIsogenic populationsDifferential lossSwimming phenotypeCell divisionBacterial populationsCell growthMultiple environmentsPhenotypePhenotypic compositionDifferent phenotypesInheritanceChemotactic bacteriaModel systemHigh inheritanceMigration speedDifferent environmentsNew environmentCollective behaviorMigrationPopulationGrowthDiversityDevelopment of patient derived organoids for cancer drug screening applications
Baskar G, Palaniyandi T, Viswanathan S, Rajendran B, Ravi M, Sivaji A. Development of patient derived organoids for cancer drug screening applications. Acta Histochemica 2022, 124: 151895. PMID: 35486967, DOI: 10.1016/j.acthis.2022.151895.Peer-Reviewed Original ResearchConceptsPre-clinical modelsEx vivo tissue cultureDevelopment of patientsCancer researchStem cellsVivo tissue culturePatient responseAbnormal cell growthProgenitor cellsHigh-throughput drug screeningVivo propertiesOrganoidsHuman organoidsPluripotent stem cellsCell growthDrug screening applicationsDrug screeningThroughput drug screeningEmbryonic stem cellsTissueCellsTissue cultureEffective recapitulationPatientsClinicTousled-like kinase 2 targets ASF1 histone chaperones through client mimicry
Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nature Communications 2022, 13: 749. PMID: 35136069, PMCID: PMC8826447, DOI: 10.1038/s41467-022-28427-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceCatalytic DomainCell Cycle ProteinsConserved SequenceCrystallography, X-RayHistonesHumansMolecular ChaperonesMolecular Docking SimulationMolecular MimicryMutagenesisPeptide LibraryPhosphorylationProtein KinasesRecombinant ProteinsSubstrate SpecificityConceptsTousled-like kinaseDNA replication-coupled nucleosome assemblyNuclear serine-threonine kinaseReplication-coupled nucleosome assemblyHistone chaperone proteinsGlobular N-terminal domainProper cell divisionPhosphorylation site motifsSerine-threonine kinaseShort sequence motifsAsf1 histone chaperonesC-terminal tailN-terminal domainHistone chaperonesGenome maintenanceNucleosome assemblySequence motifsChaperone proteinsNon-catalytic interactionsCatalytic domainCell divisionSite motifN-terminusStringent selectivityCell growth
2021
Knocking down claudin receptors leads to a decrease in prostate cancer cell migration, cell growth, cell viability and clonogenic cell survival
Liu Q, Shen H, Naguib A, Weiss RM, Martin DT. Knocking down claudin receptors leads to a decrease in prostate cancer cell migration, cell growth, cell viability and clonogenic cell survival. Molecular Biomedicine 2021, 2: 31. PMID: 35006480, PMCID: PMC8607359, DOI: 10.1186/s43556-021-00053-0.Peer-Reviewed Original ResearchProstate cancer cell growthCancer cell growthProstate cancer cellsProstate cancerLNCaP cellsCommon solid organ malignancyHuman prostate cancer specimensProstate cancer cell migrationSolid organ malignanciesAdvanced prostate cancerCancer cellsHuman prostate cancer cellsNormal human prostate cellsMetastatic human prostate cancer cellsProstate cancer specimensHuman prostate cellsCell growthNew molecular targetsCell viabilityCell migrationCancer cell migrationClaudin receptorsOrgan malignanciesProstate cancer PC3Clonogenic cell survivalCoupling lipid synthesis with nuclear envelope remodeling
Barger SR, Penfield L, Bahmanyar S. Coupling lipid synthesis with nuclear envelope remodeling. Trends In Biochemical Sciences 2021, 47: 52-65. PMID: 34556392, PMCID: PMC9943564, DOI: 10.1016/j.tibs.2021.08.009.Peer-Reviewed Original ResearchConceptsNuclear envelopeEndoplasmic reticulumNuclear membraneNuclear envelope remodelingLipid-protein interactionsBiosynthesis of lipidsNE remodelingGenome protectionDynamic remodeling processesNE dynamicsLipid speciesCell growthBilayer lipidsLipid synthesisNew roleMembraneLipidsRecent evidenceRemodeling processGenomeRemodelingBiosynthesisProtective barrierSpeciesProtein
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