2024
Circulating Proteins and IgA Nephropathy
Tang C, Chen P, Xu L, Lv J, Shi S, Zhou X, Liu L, Zhang H. Circulating Proteins and IgA Nephropathy. Journal Of The American Society Of Nephrology 2024, 35: 1045-1057. PMID: 38687828, PMCID: PMC11377805, DOI: 10.1681/asn.0000000000000379.Peer-Reviewed Original ResearchProtein-protein interaction networkProtein-disease pairsColocalization analysisInteraction networkEast Asian ancestryMendelian randomizationPotential drug targetsDrug repurposing opportunitiesVariant annotationAncestry populationsIdentified proteinsNetwork Mendelian randomizationMendelian randomization studiesAsian ancestryDrug targetsProteinAncestryEast AsiansTherapeutic targetColocalizationCirculating proteinsCausal effectsMedicationTargetAnnotationLess-is-more: selecting transcription factor binding regions informative for motif inference
Xu J, Gao J, Ni P, Gerstein M. Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic Acids Research 2024, 52: e20-e20. PMID: 38214231, PMCID: PMC10899791, DOI: 10.1093/nar/gkad1240.Peer-Reviewed Original ResearchConceptsChIP-seq signalsChIP-seqGenomic regionsMotif inferenceTranscription factorsTargeting motifTranscription factor binding regionsChIP-seq datasetsNon-specific interactionsC-scoreDNA motifsBinding regionMotifTranscriptionTF signalingAccurate inferenceStronger signalSignalDNARegionTargetInteraction
2023
TTD: Therapeutic Target Database describing target druggability information
Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F. TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Research 2023, 52: d1465-d1477. PMID: 37713619, PMCID: PMC10767903, DOI: 10.1093/nar/gkad751.Peer-Reviewed Original ResearchInsights in piRNA targeting rules
van Wolfswinkel J. Insights in piRNA targeting rules. Wiley Interdisciplinary Reviews - RNA 2023, 15: e1811. PMID: 37632327, PMCID: PMC10895071, DOI: 10.1002/wrna.1811.Peer-Reviewed Original ResearchPIWI-interacting RNAsTarget transcriptsProtein-RNA interactionsRNA-RNA interactionsPotential target transcriptsPIWI proteinsProtein-RNARNA interactionsSequence complementarityCells of animalsTranscriptionEffective downregulationStructural studiesProteinPiwiTransposonGermlineStem cellsRNATargetCleavageDownregulationDefenseEpigenetic markers and therapeutic targets for metastasis
Kravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEpigenomic alterationsLineage integrityTherapeutic targetEpigenetic markersCancer cellsGenetic aberrationsCurrent knowledgeHuman tumorsMalignant cell cloneTumor progressionDNANumber of discoveriesCell clonesDisseminated diseaseCertain organsPrimary tumorTherapeutic responseMetastatic cancerEpigenomeChromatinHistonesLiquid biopsyAlterationsClonesTargetCarpe DM: The First Global Diabetes Targets
Schwartz J, Ramaiya K, Warren M, Yadav P, Castillo G, George R, McGuire H. Carpe DM: The First Global Diabetes Targets. Global Health Science And Practice 2023, 11: e2200403. PMID: 37116924, PMCID: PMC10141427, DOI: 10.9745/ghsp-d-22-00403.Peer-Reviewed Original Research
2022
Targeting ferroptosis to treat colorectal cancer
Yan H, Talty R, Johnson C. Targeting ferroptosis to treat colorectal cancer. Trends In Cell Biology 2022, 33: 185-188. PMID: 36473802, DOI: 10.1016/j.tcb.2022.11.003.Peer-Reviewed Original ResearchConceptsProtein kinase BArachidonic acidColorectal cancer treatmentProtein kinaseKinase BMammalian targetKey pathwaysGlutathione metabolismFerroptosis inductionEnergy metabolismCRC treatmentColorectal cancerCRC pathogenesisFerroptosisCancer treatmentPromising targetNew conceptual avenuesMetabolismTreatmentHippoKinasePrimary strategyRapamycinTargetConceptual avenuesStructures of a mobile intron retroelement poised to attack its structured DNA target
Chung K, Xu L, Chai P, Peng J, Devarkar S, Pyle A. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science 2022, 378: 627-634. PMID: 36356138, PMCID: PMC10190682, DOI: 10.1126/science.abq2844.Peer-Reviewed Original ResearchConceptsGroup II intronsCryo-electron microscopy structureDNA targetsStem-loop motifMicroscopy structureGenetic diversificationDNA substratesForward splicingRetroelementsAncient elementsDNA targetingIntronsTertiary complexRibozymeRetrotransposonsGenomeRetrotranspositionSplicingComplexesRNPDNAMotifTargetDiversificationTargetingCalcium-Permeable Channels Cooperation for Rheumatoid Arthritis: Therapeutic Opportunities
Liang H, Yin H, Li S, Chen Y, Zhao Y, Hu W, Zhou R. Calcium-Permeable Channels Cooperation for Rheumatoid Arthritis: Therapeutic Opportunities. Biomolecules 2022, 12: 1383. PMID: 36291594, PMCID: PMC9599458, DOI: 10.3390/biom12101383.Peer-Reviewed Original ResearchConceptsPathogenesis of RARheumatoid arthritisCalcium-permeable channelsIntra-articular inflammationCommon autoimmune diseaseTreatment of RAEntry of CaDrug targetsSynovial invasionPatients' qualityAutoimmune diseasesNovel drug targetsCartilage damageArthritisTherapeutic opportunitiesPathological processesCalcium signalingInflammationPathogenesisSpecific roleRAHuman cellsTargetCell membraneDiseaseA translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility
Voloudakis G, Vicari J, Venkatesh S, Hoffman G, Dobrindt K, Zhang W, Beckmann N, Higgins C, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee K, Bian J, Lee J, Iyengar S, Luoh S, Akbarian S, Striker R, Assimes T, Schadt E, Lynch J, Merad M, tenOever B, Charney A, Brennand K, Fullard J, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. Npj Genomic Medicine 2022, 7: 52. PMID: 36064543, PMCID: PMC9441828, DOI: 10.1038/s41525-022-00324-x.Peer-Reviewed Original ResearchCandidate gene targetsGene targetsTranslational genomics approachesHost susceptibilityGenomic approachesGenetic susceptibility variantsGenetic lociDruggable genesGene expressionMolecular pathwaysSusceptibility variantsCOVID-19 susceptibilityGenetic findingsApproach identifiesExpressionCOVID-19 patient bloodCritical next stepGenesLociOverexpressionTargetPathwaySusceptibilityIL10RBRecent effortsMetabolic signatures of regulation by phosphorylation and acetylation
Smith K, Shen F, Lee H, Chandrasekaran S. Metabolic signatures of regulation by phosphorylation and acetylation. IScience 2022, 25: 103730. PMID: 35072016, PMCID: PMC8762462, DOI: 10.1016/j.isci.2021.103730.Peer-Reviewed Original ResearchPosttranslational modificationsTarget of phosphorylationGenome-scale metabolic networksRational rewiringRegulatory circuitsMammalian cellsCellular metabolismMetabolic networksPhosphorylated enzymeMetabolic regulationPhosphoproteome datasetEnzyme propertiesPhosphorylationAcetylationMetabolic signaturesRegulationAcetylomeTranscriptomeDiverse conditionsProteomePhosphoproteomicsTargetCondition-specific factorsEssentialityOrganisms
2021
Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi
Liu T, Pyle AM. Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi. Nucleic Acids Research 2021, 49: 12422-12432. PMID: 34850132, PMCID: PMC8643640, DOI: 10.1093/nar/gkab1077.Peer-Reviewed Original ResearchConceptsGroup II intronsSelf-splicing group II intronsPathogenic fungiDrug targetsAntifungal drug targetsSelf-splicing intronsHuman pathogenic fungiMitochondrial genomeNear-physiological conditionsPromising drug targetProtein cofactorsStriking diversitySequence dataIntronsFungal pathogensInformatics searchBioinformatics workflowsFungiDimorphic fungusStructural signaturesPathogensGenomeCofactorDiversityTargetNoncoding RNAs: biology and applications—a Keystone Symposia report
Cable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications—a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsKeystone Symposia reportPotential drug targetsRNA biologyHuman transcriptomeEpigenetic modificationsKeystone eSymposiumNoncoding RNAsCell signalingBasic biologyDrug targetsRNABiologyDisease mechanismsNucleotidesSpeciesTranscriptomeImportant roleRNAsTranscriptionSymposium reportSignalingTranslationRoleTargetPTEN mutations in autism spectrum disorder and congenital hydrocephalus: developmental pleiotropy and therapeutic targets
DeSpenza T, Carlson M, Panchagnula S, Robert S, Duy PQ, Mermin-Bunnell N, Reeves BC, Kundishora A, Elsamadicy AA, Smith H, Ocken J, Alper SL, Jin SC, Hoffman EJ, Kahle KT. PTEN mutations in autism spectrum disorder and congenital hydrocephalus: developmental pleiotropy and therapeutic targets. Trends In Neurosciences 2021, 44: 961-976. PMID: 34625286, PMCID: PMC8692171, DOI: 10.1016/j.tins.2021.08.007.Peer-Reviewed Original ResearchConceptsDevelopmental pleiotropyPTEN-PI3KMTOR pathwayMolecular pathophysiologyPTEN mutationsMolecular similarityTherapeutic targetCommon underlying mechanismNeurodevelopmental disordersUnderlying mechanismTherapeutic promisePleiotropyBiologyPhenotypicMutationsLimited understandingPathwayCommon neurodevelopmental disorderAutism spectrum disorderSimilarityTarget
2020
Metric Selection, Metric Targets, and Risk Adjustment Should be Considered in the Design of Gainsharing Models for Bundled Payment Programs in Total Joint Arthroplasty
Keswani AH, Snyder DJ, Ahn A, Austin DC, Jayakumar P, Grauer JN, Poeran J, Bozic KJ, Moschetti WE, Jevsevar DS, Galatz LM, Bronson MJ, Chen DD, Moucha CS. Metric Selection, Metric Targets, and Risk Adjustment Should be Considered in the Design of Gainsharing Models for Bundled Payment Programs in Total Joint Arthroplasty. The Journal Of Arthroplasty 2020, 36: 801-809. PMID: 33199096, DOI: 10.1016/j.arth.2020.10.007.Peer-Reviewed Original ResearchConceptsPatient-reported outcomesTotal joint arthroplastyRisk adjustmentJoint arthroplastyLength of stayUrban health systemSurgeon performanceBundled payment programsBundled payment modelReadmission ratesPRO collectionInclusion criteriaPatientsLevel IIIHealth systemArthroplastyPayment modelsAcceptable targetsPayment programsImportant mechanismAdjustmentTargettRFtarget: 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 roleRNAhybridTargetIntaRNA
2019
Association of Personalized Blood Pressure Targets With Hemorrhagic Transformation and Functional Outcome After Endovascular Stroke Therapy
Petersen NH, Silverman A, Wang A, Strander S, Kodali S, Matouk C, Sheth KN. Association of Personalized Blood Pressure Targets With Hemorrhagic Transformation and Functional Outcome After Endovascular Stroke Therapy. JAMA Neurology 2019, 76: 1256-1258. PMID: 31355872, PMCID: PMC6664391, DOI: 10.1001/jamaneurol.2019.2120.Peer-Reviewed Original ResearchDifferential regulation of OCT4 targets facilitates reacquisition of pluripotency
Thakurela S, Sindhu C, Yurkovsky E, Riemenschneider C, Smith ZD, Nachman I, Meissner A. Differential regulation of OCT4 targets facilitates reacquisition of pluripotency. Nature Communications 2019, 10: 4444. PMID: 31570708, PMCID: PMC6768871, DOI: 10.1038/s41467-019-11741-5.Peer-Reviewed Original ResearchConceptsEctopic transcription factorsReacquisition of pluripotencySomatic cell reprogrammingCis-regulatory elementsTranscription factor expressionExact molecular mechanismsOCT4 targetsPluripotent stem cellsPluripotency inductionCell reprogrammingTranscription factorsSomatic cellsMolecular mechanismsDifferential regulationPluripotencyStem cellsVivo differentiationPrimary targetCellsFactor expressionFinal stepExperimental systemReprogrammingTargetDifferentiationO-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth
Singh JP, Qian K, Lee JS, Zhou J, Han X, Zhang B, Ong Q, Ni W, Jiang M, Ruan HB, Li MD, Zhang K, Ding Z, Lee P, Singh K, Wu J, Herzog RI, Kaech S, Wendel HG, Yates JR, Han W, Sherwin RS, Nie Y, Yang X. O-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth. Oncogene 2019, 39: 560-573. PMID: 31501520, PMCID: PMC7107572, DOI: 10.1038/s41388-019-0975-3.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationAcetylglucosamineAnimalsAntigens, NeoplasmCarrier ProteinsCell Line, TumorDatasets as TopicDisease ProgressionFemaleGene Expression ProfilingGlycolysisHEK293 CellsHistone AcetyltransferasesHumansHyaluronoglucosaminidaseMaleMembrane ProteinsMiceN-AcetylglucosaminyltransferasesNeoplasm GradingNeoplasm StagingNeoplasmsProtein Processing, Post-TranslationalThyroid HormonesTissue Array AnalysisUp-RegulationXenograft Model Antitumor AssaysConceptsPyruvate kinase M2O-GlcNAcaseAerobic glycolysisO-GlcNAcylationKinase M2Lysine acetyltransferase activityTumor growthMetabolic rheostatAcetyltransferase activityGlcNAc transferaseMolecular basisMetabolic shiftHuman cancersGlycolysisCancer cellsHigh glucose conditionsGlucose availabilityTumor progressionGlucose conditionsExquisite controlGrowthRheostatCausative roleTargetEnzymeZebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation
McCarroll MN, Gendelev L, Kinser R, Taylor J, Bruni G, Myers-Turnbull D, Helsell C, Carbajal A, Rinaldi C, Kang HJ, Gong JH, Sello JK, Tomita S, Peterson RT, Keiser MJ, Kokel D. Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation. Nature Communications 2019, 10: 4078. PMID: 31501447, PMCID: PMC6733874, DOI: 10.1038/s41467-019-11936-w.Peer-Reviewed Original ResearchConceptsParadoxical excitationGABAA receptorsCentral nervous system depressantsSerotonin 6 receptorMost anesthetic drugsDifferent neuronal targetsHuman GABAA receptorsNeuronal targetsNeuronal activityAnesthetic drugsMotor activitySerotonin receptor ligandsSedationReceptor ligandsReceptorsCaudal hindbrainAnestheticsPrimary targetPrevious studiesGABATargetNeuronsActivityBrain
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