2024
Structural basis for transcription activation by the nitrate-responsive regulator NarL
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Research 2024, 52: 1471-1482. PMID: 38197271, PMCID: PMC10853779, DOI: 10.1093/nar/gkad1231.Peer-Reviewed Original ResearchTranscription activation complexC-terminal domainTranscription activationAlpha C-terminal domainStructural basisGlobal transcription factorCryo-EM structureDetailed mechanistic understandingPromoter DNATranscription initiationBinds DNATranscription assaysTranscription factorsActivation complexÅ resolutionNarLDimer bindsMolecular mechanismsNovel mechanismActivation mechanismMechanistic understandingDNAStress factorsPromoterActivationInterferon-stimulated neutrophils as a predictor of immunotherapy response
Benguigui M, Cooper T, Kalkar P, Schif-Zuck S, Halaban R, Bacchiocchi A, Kamer I, Deo A, Manobla B, Menachem R, Haj-Shomaly J, Vorontsova A, Raviv Z, Buxbaum C, Christopoulos P, Bar J, Lotem M, Sznol M, Ariel A, Shen-Orr S, Shaked Y. Interferon-stimulated neutrophils as a predictor of immunotherapy response. Cancer Cell 2024, 42: 253-265.e12. PMID: 38181798, PMCID: PMC10864002, DOI: 10.1016/j.ccell.2023.12.005.Peer-Reviewed Original ResearchImmunotherapy responseNon-small cell lung cancerAnti-PD1 responseAnti-PD1 therapyCohort of patientsNon-responsive tumorsCell lung cancerAnti-cancer immunotherapyPre-clinical findingsBlood-borne biomarkersCytotoxic TLung cancerPredictive biomarkersCurrent biomarkersTreatment responseNeutrophilsLY6EBiomarkersActive biomarkersPatientsMiceFurther mechanistic understandingActivationResponseImmunotherapy
2023
Reframing macrophage diversity with network motifs
Pizzurro G, Miller-Jensen K. Reframing macrophage diversity with network motifs. Trends In Immunology 2023, 44: 965-970. PMID: 37949786, PMCID: PMC11057955, DOI: 10.1016/j.it.2023.10.009.Commentaries, Editorials and LettersConceptsNetwork motifsDistinct biological functionsSystems biology conceptsMacrophage stateMacrophage responseBiological functionsMacrophage diversityExtracellular networkMacrophage activationDisease contextsMotifLocal molecular interactionsMolecular interactionsFunctional modulesBiology conceptsDiversityActivationTissueIntracellularResponseStructure and molecular mechanism of bacterial transcription activation
Kompaniiets D, Wang D, Yang Y, Hu Y, Liu B. Structure and molecular mechanism of bacterial transcription activation. Trends In Microbiology 2023, 32: 379-397. PMID: 37903670, DOI: 10.1016/j.tim.2023.10.001.Peer-Reviewed Original ResearchTranscription activation mechanismTranscription activation complexTranscription activationGene expressionActivation mechanismRecent structural studiesSignal transduction processesTranscription activatorExtracellular signalsTAC componentsActivation complexMechanistic diversityMolecular mechanismsTransduction processesDifferent intracellularImportant checkpointStructural studiesStructural featuresActivationExpressionMechanismCheckpointDiversitySystematic classificationActivatorLeishmania major-derived lipophosphoglycan influences the host’s early immune response by inducing platelet activation and DKK1 production via TLR1/2
Ihedioha O, Sivakoses A, Beverley S, McMahon-Pratt D, Bothwell A. Leishmania major-derived lipophosphoglycan influences the host’s early immune response by inducing platelet activation and DKK1 production via TLR1/2. Frontiers In Immunology 2023, 14: 1257046. PMID: 37885890, PMCID: PMC10598878, DOI: 10.3389/fimmu.2023.1257046.Peer-Reviewed Original ResearchConceptsLeukocyte-platelet aggregatesEarly immune responseImmune responsePlatelet activationHost's early immune responseCell-mediated immune responsesTh2 cell polarizationAdaptive immune responsesPro-inflammatory responsePattern recognition receptorsKey virulence factorsRecognition receptorsInfectious diseasesPathogenic moleculesEndothelial cellsWnt antagonistsInfection siteVirulence factorsTLR1/2PlateletsDickkopf1Cell typesLipophosphoglycanActivationResponseMitochondrial leak metabolism induces the Spemann-Mangold Organizer via Hif-1α in Xenopus
MacColl Garfinkel A, Mnatsakanyan N, Patel J, Wills A, Shteyman A, Smith P, Alavian K, Jonas E, Khokha M. Mitochondrial leak metabolism induces the Spemann-Mangold Organizer via Hif-1α in Xenopus. Developmental Cell 2023, 58: 2597-2613.e4. PMID: 37673063, PMCID: PMC10840693, DOI: 10.1016/j.devcel.2023.08.015.Peer-Reviewed Original ResearchConceptsSpemann-Mangold organizerATP productionMitochondrial respirationC subunit ringHIF-1αMitochondrial oxidative metabolismEmbryonic patterningCell fateATP synthaseC subunitVentral mesodermHIF-1α activationInstructive roleHypoxia-inducible factor-1αΒ-cateninGeneral mechanismXenopusFactor-1αRespirationMembrane leakOxidative metabolismMetabolismMesodermActivationOxygen consumptionPeriodicity, mixed-mode oscillations, and multiple timescales in a phosphoinositide-Rho GTPase network
San Tong C, Xǔ X, Wu M. Periodicity, mixed-mode oscillations, and multiple timescales in a phosphoinositide-Rho GTPase network. Cell Reports 2023, 42: 112857. PMID: 37494180, DOI: 10.1016/j.celrep.2023.112857.Peer-Reviewed Original ResearchNeurovascular coupling is optimized to compensate for the increase in proton production from nonoxidative glycolysis and glycogenolysis during brain activation and maintain homeostasis of pH, pCO2, and pO2
DiNuzzo M, Dienel G, Behar K, Petroff O, Benveniste H, Hyder F, Giove F, Michaeli S, Mangia S, Herculano‐Houzel S, Rothman D. Neurovascular coupling is optimized to compensate for the increase in proton production from nonoxidative glycolysis and glycogenolysis during brain activation and maintain homeostasis of pH, pCO2, and pO2. Journal Of Neurochemistry 2023, 168: 632-662. PMID: 37150946, PMCID: PMC10628336, DOI: 10.1111/jnc.15839.Peer-Reviewed Original ResearchHigher cerebral blood flowCerebral blood flowOxygen extraction fractionNeurovascular couplingBlood flowLower oxygen extraction fractionNonoxidative glycolysisCerebral metabolic rateBrain pHCapillary densityNeurovascular diseasesNonoxidative metabolismTissue oxygenationHuman cortexBrain functionExtraction fractionBrain activationMitochondrial ATP productionPET measurementsCMROOxygen consumptionHomeostasisGlycogenolysisFMRI contrastActivationAcetate controls endothelial-to-mesenchymal transition
Zhu X, Wang Y, Soaita I, Lee H, Bae H, Boutagy N, Bostwick A, Zhang R, Bowman C, Xu Y, Trefely S, Chen Y, Qin L, Sessa W, Tellides G, Jang C, Snyder N, Yu L, Arany Z, Simons M. Acetate controls endothelial-to-mesenchymal transition. Cell Metabolism 2023, 35: 1163-1178.e10. PMID: 37327791, PMCID: PMC10529701, DOI: 10.1016/j.cmet.2023.05.010.Peer-Reviewed Original ResearchConceptsTGF-β signalingChronic vascular diseaseTGF-β receptor ALK5Mesenchymal transitionInduction of EndMTVascular diseaseMolecular basisPositive feedback loopReceptor ALK5Cellular levelSMADs 2Novel targetEndMT inductionMetabolic modulationMetabolic basisFibrotic stateSignalingPotential treatmentEndMTTGFDiseaseActivationInductionACSS2PDK4Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport
Ton W, Wang Y, Chai P, Beauchamp-Perez C, Flint N, Lammers L, Xiong H, Zhang K, Markus S. Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nature Structural & Molecular Biology 2023, 30: 1365-1379. PMID: 37322240, PMCID: PMC10590275, DOI: 10.1038/s41594-023-01010-x.Peer-Reviewed Original ResearchConceptsCryo-EM structureCargo transportProtein Lis1Human dyneinDynein mutantsCytoplasmic dyneinStructural insightsDynein activityIntracellular localizationCritical regulatorDynein activationLIS1Conformational changesDyneinMotor domainMutantsBindingHigh affinityAffinityYeastMicrotubulesRegulatorRegulationTransportActivationSGLT2 inhibitors and diuretics in heart failure: clicking reset on the renal volume setpoint?
Borlaug B, Testani J. SGLT2 inhibitors and diuretics in heart failure: clicking reset on the renal volume setpoint? European Heart Journal 2023, 44: 2944-2946. PMID: 37220086, DOI: 10.1093/eurheartj/ehad345.Commentaries, Editorials and LettersMolecular mechanism of hyperactivation conferred by a truncation of TRPA1
Bali A, Schaefer S, Trier I, Zhang A, Kabeche L, Paulsen C. Molecular mechanism of hyperactivation conferred by a truncation of TRPA1. Nature Communications 2023, 14: 2867. PMID: 37208332, PMCID: PMC10199097, DOI: 10.1038/s41467-023-38542-1.Peer-Reviewed Original ResearchConceptsChannel sensitizationPlasma membraneHeterologous cellsGenetic analysisMolecular mechanismsBiochemical assaysHeteromeric channelsNonsense mutationPhysiological impactMutantsAgonist sensitivityCalcium permeabilityEnergetic barrierSubunitsTRPA1MutationsTractable mechanismMechanismHyperactivationMembraneCellsActivationAssaysGatingTruncationCroquemort elicits activation of the immune deficiency pathway in ticks
O’Neal A, Singh N, Rolandelli A, Laukaitis H, Wang X, Shaw D, Young B, Narasimhan S, Dutta S, Snyder G, Samaddar S, Marnin L, Butler L, Mendes M, Paz F, Valencia L, Sundberg E, Fikrig E, Pal U, Weber D, Pedra J. Croquemort elicits activation of the immune deficiency pathway in ticks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2208673120. PMID: 37155900, PMCID: PMC10193931, DOI: 10.1073/pnas.2208673120.Peer-Reviewed Original ResearchConceptsImmune deficiency (IMD) pathwayIMD pathwayNon-insect arthropodsPeptidoglycan recognition proteinsJun N-terminal kinaseN-terminal kinaseArthropod immunityMembrane localizationRecognition proteinsLyme disease spirocheteEcdysteroid synthesisMicrobial moietiesDistinct mechanismsProteinArthropodsPathwayHost defenseElicit activationCroquemortPancrustaceaHomologInsectsActivationCrustaceansKinaseApoptotic cell death in disease—Current understanding of the NCCD 2023
Vitale I, Pietrocola F, Guilbaud E, Aaronson S, Abrams J, Adam D, Agostini M, Agostinis P, Alnemri E, Altucci L, Amelio I, Andrews D, Aqeilan R, Arama E, Baehrecke E, Balachandran S, Bano D, Barlev N, Bartek J, Bazan N, Becker C, Bernassola F, Bertrand M, Bianchi M, Blagosklonny M, Blander J, Blandino G, Blomgren K, Borner C, Bortner C, Bove P, Boya P, Brenner C, Broz P, Brunner T, Damgaard R, Calin G, Campanella M, Candi E, Carbone M, Carmona-Gutierrez D, Cecconi F, Chan F, Chen G, Chen Q, Chen Y, Cheng E, Chipuk J, Cidlowski J, Ciechanover A, Ciliberto G, Conrad M, Cubillos-Ruiz J, Czabotar P, D’Angiolella V, Daugaard M, Dawson T, Dawson V, De Maria R, De Strooper B, Debatin K, Deberardinis R, Degterev A, Del Sal G, Deshmukh M, Di Virgilio F, Diederich M, Dixon S, Dynlacht B, El-Deiry W, Elrod J, Engeland K, Fimia G, Galassi C, Ganini C, Garcia-Saez A, Garg A, Garrido C, Gavathiotis E, Gerlic M, Ghosh S, Green D, Greene L, Gronemeyer H, Häcker G, Hajnóczky G, Hardwick J, Haupt Y, He S, Heery D, Hengartner M, Hetz C, Hildeman D, Ichijo H, Inoue S, Jäättelä M, Janic A, Joseph B, Jost P, Kanneganti T, Karin M, Kashkar H, Kaufmann T, Kelly G, Kepp O, Kimchi A, Kitsis R, Klionsky D, Kluck R, Krysko D, Kulms D, Kumar S, Lavandero S, Lavrik I, Lemasters J, Liccardi G, Linkermann A, Lipton S, Lockshin R, López-Otín C, Luedde T, MacFarlane M, Madeo F, Malorni W, Manic G, Mantovani R, Marchi S, Marine J, Martin S, Martinou J, Mastroberardino P, Medema J, Mehlen P, Meier P, Melino G, Melino S, Miao E, Moll U, Muñoz-Pinedo C, Murphy D, Niklison-Chirou M, Novelli F, Núñez G, Oberst A, Ofengeim D, Opferman J, Oren M, Pagano M, Panaretakis T, Pasparakis M, Penninger J, Pentimalli F, Pereira D, Pervaiz S, Peter M, Pinton P, Porta G, Prehn J, Puthalakath H, Rabinovich G, Rajalingam K, Ravichandran K, Rehm M, Ricci J, Rizzuto R, Robinson N, Rodrigues C, Rotblat B, Rothlin C, Rubinsztein D, Rudel T, Rufini A, Ryan K, Sarosiek K, Sawa A, Sayan E, Schroder K, Scorrano L, Sesti F, Shao F, Shi Y, Sica G, Silke J, Simon H, Sistigu A, Stephanou A, Stockwell B, Strapazzon F, Strasser A, Sun L, Sun E, Sun Q, Szabadkai G, Tait S, Tang D, Tavernarakis N, Troy C, Turk B, Urbano N, Vandenabeele P, Vanden Berghe T, Vander Heiden M, Vanderluit J, Verkhratsky A, Villunger A, von Karstedt S, Voss A, Vousden K, Vucic D, Vuri D, Wagner E, Walczak H, Wallach D, Wang R, Wang Y, Weber A, Wood W, Yamazaki T, Yang H, Zakeri Z, Zawacka-Pankau J, Zhang L, Zhang H, Zhivotovsky B, Zhou W, Piacentini M, Kroemer G, Galluzzi L. Apoptotic cell death in disease—Current understanding of the NCCD 2023. Cell Death & Differentiation 2023, 30: 1097-1154. PMID: 37100955, PMCID: PMC10130819, DOI: 10.1038/s41418-023-01153-w.Peer-Reviewed Original ResearchConceptsRegulated cell deathCell deathAdult tissue homeostasisMultiple human disordersApoptotic cell deathOrganismal developmentOrganismal homeostasisMolecular machineryContext of diseaseApoptotic apparatusMammalian systemsCaspase familyTissue homeostasisGenetic strategiesHuman disordersNomenclature CommitteeApoptosisHomeostasisMachineryOncogenesisProteaseCell lossActivationFamilyDeathTurning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Maschietto F, Morzan U, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro G, Nekrasov P, Brooks B, Loria J, Rivalta I, Batista V. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications 2023, 14: 2239. PMID: 37076500, PMCID: PMC10115891, DOI: 10.1038/s41467-023-37956-1.Peer-Reviewed Original ResearchConceptsEffector bindingImidazole Glycerol Phosphate SynthaseLocal amino acidsAmino acid dynamicsImidazole glycerolAllosteric drugsAllosteric activationAllosteric responsePhosphate synthaseAllosteric mechanismMode of activationEnzyme functionAmino acidsAllosteryDrug discoverySynthaseNuclear magnetic resonance spectroscopyBindingMolecular dynamics simulationsActivationAllostericCascadeDynamics simulationsMapping N- to C-terminal allosteric coupling through disruption of a putative CD74 activation site in D-dopachrome tautomerase
Chen E, Widjaja V, Kyro G, Allen B, Das P, Prahaladan V, Bhandari V, Lolis E, Batista V, Lisi G. Mapping N- to C-terminal allosteric coupling through disruption of a putative CD74 activation site in D-dopachrome tautomerase. Journal Of Biological Chemistry 2023, 299: 104729. PMID: 37080391, PMCID: PMC10208890, DOI: 10.1016/j.jbc.2023.104729.Peer-Reviewed Original ResearchLithium ameliorates Niemann-Pick C1 disease phenotypes by impeding STING/SREBP2 activation
Han S, Wang Q, Song Y, Pang M, Ren C, Wang J, Guan D, Xu W, Li F, Wang F, Zhou X, Fernández-Hernando C, Zhang H, Wu D, Ye Z. Lithium ameliorates Niemann-Pick C1 disease phenotypes by impeding STING/SREBP2 activation. IScience 2023, 26: 106613. PMID: 37128603, PMCID: PMC10148154, DOI: 10.1016/j.isci.2023.106613.Peer-Reviewed Original ResearchTherapeutic optionsSTING activationPotential therapeutic optionProgressive neurodegenerative phenotypeNiemann-Pick disease type CGenetic lysosomal disorderNP-C patientsCytosolic calcium concentrationDisease type CEffects of lithiumCerebellar inflammationLithium treatmentMouse modelLithium effectsLysosomal disordersNeurodegenerative phenotypeCalcium concentrationSREBP2 activationDisease phenotypeType CMiceSREBP2 pathwayActivationDeficient fibroblastsPhenotypeThe histamine H3 receptor modulates dopamine D2 receptor–dependent signaling pathways and mouse behaviors
Xu J, Pittenger C. The histamine H3 receptor modulates dopamine D2 receptor–dependent signaling pathways and mouse behaviors. Journal Of Biological Chemistry 2023, 299: 104583. PMID: 36871761, PMCID: PMC10139999, DOI: 10.1016/j.jbc.2023.104583.Peer-Reviewed Original ResearchConceptsStress-activated protein kinase 1Receptor-dependent signaling pathwaysSerine/threonineGlycogen synthase kinase 3 betaSynthase kinase 3 betaProtein kinase 1Phosphorylation of mitogenBiochemical approachesMolecular mechanismsKinase 1Signaling pathwaysProximity ligationBeta signalingBiochemical levelPhosphorylation levelsReceptorsActivationHistamine H3 receptorsPhosphorylationSignalingThreonineAktSpiny projection neuronsD2R functionBetter understandingWCN23-0470 BAC-transgenic mice show a novel T-cell intrinsic role for FSGS-associated APOL1 risk-variants in T-cell activation
Pell J, Reghuvaran A, Nagata S, Banu K, He J, Craft J, Shi H, Chernova I, Ishibe S, Menon M. WCN23-0470 BAC-transgenic mice show a novel T-cell intrinsic role for FSGS-associated APOL1 risk-variants in T-cell activation. Kidney International Reports 2023, 8: s392-s393. DOI: 10.1016/j.ekir.2023.02.882.Peer-Reviewed Original ResearchActivation of brain arousal networks coincident with eye blinks during resting state.
Demiral Ş, Kure Liu C, Benveniste H, Tomasi D, Volkow N. Activation of brain arousal networks coincident with eye blinks during resting state. Cerebral Cortex 2023, 33: 6792-6802. PMID: 36653022, PMCID: PMC10233245, DOI: 10.1093/cercor/bhad001.Peer-Reviewed Original Research
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