2025
Spermidine is a key polyamine required by intracellular parasites for survival within host erythrocytes
Singh P, Choi J, Cornillot E, Mamoun C. Spermidine is a key polyamine required by intracellular parasites for survival within host erythrocytes. Science Advances 2025, 11: eadv2397. PMID: 40531988, PMCID: PMC12175890, DOI: 10.1126/sciadv.adv2397.Peer-Reviewed Original ResearchConceptsSpermidine biosynthesisIntracellular parasitesRegulate protein translationOxidative stress defenseDe novo synthesisProduction of reactive oxygen speciesTranslational regulationIncreased production of reactive oxygen speciesMolecular functionsProtein translationStress defensePlasmodium falciparum</i>Evolutionary adaptationReactive oxygen speciesAgent of human babesiosisIntraerythrocytic developmentBiosynthesisOxygen speciesHost erythrocytesTherapeutic targetAge-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39888841, PMCID: PMC11810059, DOI: 10.18632/aging.206195.Peer-Reviewed Original ResearchRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathwayAge-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39873648, PMCID: PMC11810070, DOI: 10.18632/aging.206192.Peer-Reviewed Original ResearchConceptsRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathway
2024
3046 – FUNCTIONAL CHARACTERIZATION OF RBM15-MKL1 FUSION PROTEIN IN AMKL TUMORIGENESIS
Chen M, Mayday M, Espinosa A, Zhang M, Zhang P, Wang L, Rahman N, Krause D. 3046 – FUNCTIONAL CHARACTERIZATION OF RBM15-MKL1 FUSION PROTEIN IN AMKL TUMORIGENESIS. Experimental Hematology 2024, 137: 104368. DOI: 10.1016/j.exphem.2024.104368.Peer-Reviewed Original ResearchChromatin associationRBM15-MKL1TPA-induced megakaryocytic differentiationHuman erythroleukemiaAcute megakaryoblastic leukemiaAssociated with chromatinTranscriptional regulatory functionRNA-binding proteinsTranscriptional co-activatorM6A RNA modificationShRNA-mediated knock-downHuman erythroleukemia cellsChromatin regionsRNA modificationsTranscriptional regulationMolecular functionsAberrant transcriptsFusion proteinGO analysisMKL1Knock-downBinding proteinRegulatory functionsFusion geneDifferentiation blockIn the Eyes of the Beholder—New Mertk Knockout Mouse and Re-Evaluation of Phagocytosis versus Anti-Inflammatory Functions of MERTK
Ghosh S, Finnemann S, Vollrath D, Rothlin C. In the Eyes of the Beholder—New Mertk Knockout Mouse and Re-Evaluation of Phagocytosis versus Anti-Inflammatory Functions of MERTK. International Journal Of Molecular Sciences 2024, 25: 5299. PMID: 38791338, PMCID: PMC11121519, DOI: 10.3390/ijms25105299.Peer-Reviewed Original ResearchReceptor tyrosine kinasesFamily of receptor tyrosine kinasesTAM family of receptor tyrosine kinasesEarly-onset photoreceptor degenerationKnockout mouse modelMolecular functionsNegative regulator of inflammationKnockout phenotypesNegative regulatorMouse geneticsRegulation of inflammationMolecular approachesEmbryonic stem cellsAnti-inflammatory functionsRetinal degenerationTyrosine kinasePhotoreceptor degenerationKnockout miceKnockout modelsMouse modelRodent modelsTAM familyMerTK functionStem cellsAllelesTranscriptome-Connectome association from fetal stage to adulthood
Ouyang M, Poddar T, Santpere G, Andrijevic D, Ma S, Pattabiraman K, Gobeske K, Sestan N, Huang H. Transcriptome-Connectome association from fetal stage to adulthood. Proceedings Of The International Society For Magnetic Resonance In Medicine ... Scientific Meeting And Exhibition. 2024 DOI: 10.58530/2024/2389.Peer-Reviewed Original ResearchEvolution of the functionality of microbial communities in patients with metastatic renal cell carcinoma (mRCC) receiving cabozantinib (cabo)/nivolumab (nivo) with or without CBM588: A randomized clinical trial.
Ebrahimi H, Meza L, Lee K, Malhotra J, Alcantara M, Zengin Z, Dizman N, Hsu J, Llamas-Quitiquit M, Castro D, Mercier B, Barragan-Carrillo R, Chawla N, Li X, Liu S, Chehrazi-Raffle A, Dorff T, Frankel P, Tripathi A, Pal S. Evolution of the functionality of microbial communities in patients with metastatic renal cell carcinoma (mRCC) receiving cabozantinib (cabo)/nivolumab (nivo) with or without CBM588: A randomized clinical trial. Journal Of Clinical Oncology 2024, 42: 460-460. DOI: 10.1200/jco.2024.42.4_suppl.460.Peer-Reviewed Original ResearchMetastatic renal cell carcinomaMetabolic pathwaysClinical outcomesAnnotated open reading framesFunction of microbial communitiesMetatranscriptomic sequencing dataWhole metagenome sequencingOpen reading frameGut microbial functionsGut microbiome functionsResponse rate to sorafenibExperimental armElectron transfer chainCancer cell typesAssociated with clinical outcomesRenal cell carcinomaReading frameSequence dataTaxonomic profilesBiosynthesis pathwayMetagenomic sequencingMicrobiome functionMicrobial functionsMolecular functionsRandomized clinical trials
2023
Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning
Martínez M, Barberis M, Niarakis A. Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning. ImmunoInformatics 2023, 12: 100029. DOI: 10.1016/j.immuno.2023.100029.Peer-Reviewed Original ResearchHigh-throughput experimental technologiesComputational biologyDevelopment of high-throughput experimental technologiesImmune systemHigh-throughput data analysisImmunological mechanismsMolecular functionsSystems biologyImmune-related diseasesOptimal immunotherapyTherapeutic optionsAutoimmune diseasesComplex disorderInterpretable machine learningMachine learning modelsCellular interactionsGeneration of computational modelsBiologyComputer scienceMachine learningMachine-learning modelsDiverse domainsLearning modelsExperimental technologyInterpretable machineSynaptophysin chaperones the assembly of 12 SNAREpins under each ready-release vesicle
Bera M, Radhakrishnan A, Coleman J, Sundaram R, Ramakrishnan S, Pincet F, Rothman J. Synaptophysin chaperones the assembly of 12 SNAREpins under each ready-release vesicle. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2311484120. PMID: 37903271, PMCID: PMC10636311, DOI: 10.1073/pnas.2311484120.Peer-Reviewed Original ResearchConceptsSpecific molecular functionsSynaptic vesicle protein synaptophysinTarget membrane bilayerSensor synaptotagminSNARE proteinsMolecular functionsMembrane proteinsSNAREpinsReceptor vesiclesSingle-molecule measurementsGene knockoutMembrane bilayerLipid bilayersProtein synaptophysinVesiclesDetergent extractsHexamer structureSYPMechanism of actionProteinAssemblyChaperonesSynaptotagminExocytosisBilayers
2022
Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways
Kasher M, Williams F, Freidin M, Malkin I, Cherny S, Benjamin E, Chasman D, Dehghan A, Ahluwalia T, Meigs J, Tracy R, Alizadeh B, Ligthart S, Bis J, Eiriksdottir G, Pankratz N, Gross M, Rainer A, Snieder H, Wilson J, Psaty B, Dupuis J, Prins B, Vaso U, Stathopoulou M, Franke L, Lehtimaki T, Koenig W, Jamshidi Y, Siest S, Abbasi A, Uitterlinden A, Abdollahi M, Schnabel R, Schick U, Nolte I, Kraja A, Hsu Y, Tylee D, Zwicker A, Uher R, Davey-Smith G, Morrison A, Hicks A, van Duijn C, Ward-Caviness C, Boerwinkle E, Rotter J, Rice K, Lange L, Perola M, de Geus E, Morris A, Makela K, Stacey D, Eriksson J, Frayling T, Slagboom E, Livshits G. Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways. Human Molecular Genetics 2022, 31: 2623-2632. PMID: 35349660, PMCID: PMC9402243, DOI: 10.1093/hmg/ddac061.Peer-Reviewed Original ResearchConceptsCausal single nucleotide polymorphismsSingle nucleotide polymorphismsGenetic architectureColocalization analysisSame molecular functionAnalysis of pleiotropyComplex genetic architectureGenome-wide association study summary statisticsOp phenotypeMolecular functionsGenomic regionsPleiotropyOsteoporosis ConsortiumGenetic relationshipsGenetic backgroundGenetic variantsNucleotide polymorphismsMendelian randomizationGenesTraitsPhenotypeGenetic factorsProtein bindingUK BiobankHorizontal pleiotropyBioactive lipids and metabolic syndrome—a symposium report
DeVito LM, Dennis EA, Kahn BB, Shulman GI, Witztum JL, Sadhu S, Nickels J, Spite M, Smyth S, Spiegel S. Bioactive lipids and metabolic syndrome—a symposium report. Annals Of The New York Academy Of Sciences 2022, 1511: 87-106. PMID: 35218041, PMCID: PMC9219555, DOI: 10.1111/nyas.14752.Peer-Reviewed Original ResearchConceptsBioactive lipidsMetabolic syndromeCardiometabolic conditionsCardiovascular diseaseAnimal modelsDietary lipidsLipid metabolismMetabolic homeostasisMultitude of functionsLipidomic approachLipid pathwaysContinued investigationSyndromeMolecular functionsSymposium reportGenetic studiesLipidsPathwayInflammationGreater understandingDiseaseLiverMacrophagesLipogenesisModeling uniquely human gene regulatory function via targeted humanization of the mouse genome
Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. Nature Communications 2022, 13: 304. PMID: 35027568, PMCID: PMC8758698, DOI: 10.1038/s41467-021-27899-w.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell DifferentiationChondrocytesChondrogenesisEmbryo, MammalianEnhancer Elements, GeneticEpigenesis, GeneticExtremitiesGene Expression ProfilingGene Expression RegulationGene Knock-In TechniquesGenomeHomeodomain ProteinsHomozygoteHumansMesodermMice, Inbred C57BLModels, GeneticPan troglodytesPromoter Regions, GeneticTime FactorsConceptsHuman Accelerated RegionsGene expressionHuman-specific sequence changesDevelopmental gene regulationSingle-cell RNA sequencingGene regulatory functionsHuman evolutionEndogenous gene expressionAlters gene expressionSkeletal patterningMolecular functionsGene regulationChondrogenic mesenchymeMouse genomeRegulatory modificationHomozygous embryosLimb developmentTranscriptional enhancersTranscription factorsRNA sequencingEnhancer activityMouse embryosRegulatory functionsAccelerated regionSequence changes
2021
TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling
Liu D, Nguyen T, Gao H, Huang H, Kim D, Sharp B, Ye Z, Lee J, Coombes B, Ordog T, Wang L, Biernacka J, Frye M, Weinshilboum R. TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling. Molecular Psychiatry 2021, 26: 7454-7464. PMID: 34535768, PMCID: PMC8872993, DOI: 10.1038/s41380-021-01274-z.Peer-Reviewed Original ResearchConceptsSignificant single-nucleotide polymorphismsGenome-wide association studiesFunction of TCF7L2Expression quantitative trait lociGenome-wide significant single-nucleotide polymorphismsChromatin immunoprecipitation sequencingQuantitative trait lociNon-coding transcriptsBD risk genesRNA sequencing dataSingle-nucleotide polymorphismsGlucocorticoid-dependent repressionChIP-seqSequence dataTrait lociAssociation studiesParental genesMolecular functionsNon-coding RNAsTranscription factor 7Transcript variantsRisk genesInsulin signalingTCF7L2 knockdownLong non-coding RNAsEmerging roles of PLCγ1 in endothelial biology
Chen D, Simons M. Emerging roles of PLCγ1 in endothelial biology. Science Signaling 2021, 14 PMID: 34344833, PMCID: PMC8507396, DOI: 10.1126/scisignal.abc6612.Peer-Reviewed Original ResearchConceptsUnique protein structurePhospholipase C-γ1Receptor tyrosine kinasesRole of PLCγ1Major physiological roleMolecular functionsDistinct vascular phenotypePLC familyC-γ1Signal transducerProtein structureDirect effectorTyrosine kinaseMembrane lipidsSecond messengerFunction mutationsPhysiological rolePLCγ1Endothelial biologyEndothelial cancerCritical roleVascular phenotypeEndothelial cellsKinaseFuture investigations
2020
Genetic determinants of ammonia-induced acute lung injury in mice
Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Genetic determinants of ammonia-induced acute lung injury in mice. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2020, 320: l41-l62. PMID: 33050709, PMCID: PMC7847062, DOI: 10.1152/ajplung.00276.2020.Peer-Reviewed Original ResearchConceptsSNP associationsWide association mappingGenetic determinantsSignificant SNP associationsAcute lung injuryIntegrative functional approachAssociation mappingMolecular functionsTranscriptomic analysisCandidate genesFunctional domainsNonsynonymous SNPsPromoter regionLung injuryDiverse panelGenesSNPsMouse strainsPathophysiological roleAATFInjuryProteinLAMA3ExpressionAssemblytRFtarget: a database for transfer RNA-derived fragment targets
Li N, Shan N, Lu L, Wang Z. tRFtarget: a database for transfer RNA-derived fragment targets. Nucleic Acids Research 2020, 49: d254-d260. PMID: 33035346, PMCID: PMC7779015, DOI: 10.1093/nar/gkaa831.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase PairingBase SequenceCaenorhabditis elegansDatabases, Nucleic AcidDrosophila melanogasterGene OntologyHumansMiceMolecular Sequence AnnotationNucleic Acid ConformationNucleic Acid HybridizationRhodobacter sphaeroidesRNA, MessengerRNA, Small UntranslatedRNA, TransferSchizosaccharomycesThermodynamicsXenopusZebrafishConceptsTarget genesTransfer RNASmall non-coding RNAsGene Ontology annotationsNon-coding RNAsFunctional pathway analysisAccessible web-based databaseMolecular functionsOntology annotationsBiological functionsPathway analysisMolecular mechanismsPhysiological processesTarget predictionHuman diseasesGenesMRNA transcriptsRNAWeb-based databaseConvenient linkTRFImportant roleRNAhybridTargetIntaRNARegulation and Function of RNA Pseudouridylation in Human Cells
Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annual Review Of Genetics 2020, 54: 1-28. PMID: 32870730, PMCID: PMC8007080, DOI: 10.1146/annurev-genet-112618-043830.Peer-Reviewed Original ResearchConceptsRNA pseudouridylationHuman cellsRNA-binding proteinDistinct RNA sequencesMRNA pseudouridylationPseudouridine synthasesMolecular functionsRNA metabolismPseudouridylationGene expressionRNA conformationRNA targetsProtein productionRNA sequencesMessenger RNADiverse classRNATherapeutic mRNAWidespread effectsDestabilizing interactionsCellsRecent advancesSplicingSynthasesPotential effectsEpigenetic regulator function through mouse gastrulation
Grosswendt S, Kretzmer H, Smith ZD, Kumar AS, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S, Meissner A. Epigenetic regulator function through mouse gastrulation. Nature 2020, 584: 102-108. PMID: 32728215, PMCID: PMC7415732, DOI: 10.1038/s41586-020-2552-x.Peer-Reviewed Original ResearchConceptsMutant phenotypePolycomb Repressive Complex 1Single-cell RNA sequencingComplex mutant phenotypesSingle totipotent cellRepressive Complex 1Mutant mouse embryosSpecific transcription factorsMouse gastrulationTranscriptional informationEpigenetic machineryHistone residuesMolecular functionsCellular diversityTotipotent cellsTranscriptional changesTranscription factorsEssential regulatorRNA sequencingDevelopmental roleMouse embryosGenetic templatesRegulator functionSubstantial cooperativityGastrulationSeizure protein 6 controls glycosylation and trafficking of kainate receptor subunits GluK2 and GluK3
Pigoni M, Hsia H, Hartmann J, Rudan Njavro J, Shmueli MD, Müller SA, Güner G, Tüshaus J, Kuhn P, Kumar R, Gao P, Tran ML, Ramazanov B, Blank B, Hipgrave Ederveen A, Von Blume J, Mulle C, Gunnersen JM, Wuhrer M, Rammes G, Busche MA, Koeglsperger T, Lichtenthaler SF. Seizure protein 6 controls glycosylation and trafficking of kainate receptor subunits GluK2 and GluK3. The EMBO Journal 2020, 39: embj2019103457. PMID: 32567721, PMCID: PMC7396870, DOI: 10.15252/embj.2019103457.Peer-Reviewed Original ResearchConceptsPrimary neuronsCell surface localizationMolecular functionsKainate receptor subunit GluK2Trafficking factorsSecretory pathwayNovel functionHeterologous cellsMajor substrateSurface localizationProtein 6Alzheimer's diseaseCA1 pyramidal neuronsAcute hippocampal slicesProtease BACE1Kainate-evoked currentsGlycosylationGluK2/3Pyramidal neuronsGluK2Hippocampal slicesKainate receptorsPsychiatric disordersNervous systemPsychiatric diseasesRole of VPS13, a protein with similarity to ATG2, in physiology and disease
Ugur B, Hancock-Cerutti W, Leonzino M, De Camilli P. Role of VPS13, a protein with similarity to ATG2, in physiology and disease. Current Opinion In Genetics & Development 2020, 65: 61-68. PMID: 32563856, PMCID: PMC7746581, DOI: 10.1016/j.gde.2020.05.027.Peer-Reviewed Original ResearchConceptsAutophagy protein ATG2N-terminal halfVPS13 proteinsMolecular functionsCellular processesFamily proteinsVps13Contact sitesAtg2Intracellular organellesFunctional studiesNovel mechanismProteinSimilar roleHydrophobic channelStructural studiesNeurodegenerative disordersPhysiologyDirect transferOrganellesSimilarityMutationsRoleLipidsBilayers
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