2025
Effect of endometriosis-linked microRNAs on hepatic gene expression
Mamillapalli R, Slutzky R, Mangla A, Gawde N, Taylor H. Effect of endometriosis-linked microRNAs on hepatic gene expression. F&S Science 2025 PMID: 39971156, DOI: 10.1016/j.xfss.2025.02.001.Peer-Reviewed Original ResearchMiR-3613-5pMiR-let-7bMiR-125b-5pMiR-150MiR-150-5pCirculating microRNAsMicroRNAsReactionExpression of IGFBP1Quantitative polymerase chain reactionSuppress target genesExpression of MRC1Polymerase chain reactionBinding sitesReal-time quantitative polymerase chain reactionHepatic gene expressionExpression of CYP2R1Bioinformatics analysisEffect of endometriosisSerum of womenCirculation of womenGene expressionChain reactionMiRsHepatic cellsMultifaceted analysis of noncoding and coding de novo variants implicates NOTCH signaling pathway in tetralogy of Fallot in Chinese population
Lin Q, Zhang D, Gruber P, Tam P, Lui V, Wu Z, Hong H, Chien K, Sham P, Tang C. Multifaceted analysis of noncoding and coding de novo variants implicates NOTCH signaling pathway in tetralogy of Fallot in Chinese population. Human Genetics And Genomics Advances 2025, 6: 100414. PMID: 39921258, PMCID: PMC11910093, DOI: 10.1016/j.xhgg.2025.100414.Peer-Reviewed Original ResearchPediatric Cardiac Genomics ConsortiumProtein-protein interactionsNoncoding variantsCoding de novo variantsNotch signalingPopulation genetic heterogeneityEvidence of genetic contributionEtiology of TOFDysregulated gene expressionNotch signaling pathwayNotch signaling genesDysregulation of Notch signalingChinese populationTetralogy of FallotCyanotic heart defectsCandidate genesOutflow tract morphogenesisGenetic heterogeneitySignaling genesGenomics ConsortiumBioinformatics analysisGene expressionCo-expressionGenetic contributionSignaling pathway
2024
Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis
Bigdeli A, Ghaderi-Zefrehei M, Lesch B, Behmanesh M, Arab S. Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis. PLOS ONE 2024, 19: e0308817. PMID: 39775333, PMCID: PMC11684644, DOI: 10.1371/journal.pone.0308817.Peer-Reviewed Original ResearchConceptsBile salt hydrolaseMyelin oligodendrocyte glycoproteinBioinformatics approachProtein structureMyelin basic proteinIn silico bioinformatics approachesAmino acidsIdentical amino acidsAmino acid sequenceCapsid protein structureCentral nervous systemAspergillus speciesAcid sequenceBacterial proteinsMultiple sclerosisMyelin sheath componentsBiological insightsGut flora metabolitesBioinformatics analysisMOG proteinPathogenesis of multiple sclerosisCNS diseaseWzyBacteriaProteinRare genetic variation in fibronectin 1 (FN1) protects against APOE ɛ4 in Alzheimer’s Disease
Bhattarai P, Gunasekaran T, Uzrek B, Reyes‐Dumeyer D, Jülich D, Lee A, Yilmaz E, Tayran H, Lantigua R, Medrano M, Mejia D, Recio P, Flaherty D, Dalgard C, Nuriel T, Ertekin‐Taner N, Dickson D, Teich A, Holley S, Mayeux R, Kizil C, Vardarajan B. Rare genetic variation in fibronectin 1 (FN1) protects against APOE ɛ4 in Alzheimer’s Disease. Alzheimer's & Dementia 2024, 20: e089111. PMCID: PMC11710415, DOI: 10.1002/alz.089111.Peer-Reviewed Original ResearchWhole-genome sequencingLoss-of-functionIn vivo functional studiesFibronectin 1Genetic variationAlzheimer's diseaseFunctional studiesWhole-genome sequence analysisTarget genesRare genetic variationLoss-of-function mutationsPotential gene variantsZebrafish modelGenome sequenceProtective variantsAPOE variantsGenetic variantsECM proteinsZebrafish AD modelBioinformatics analysisAD pathologyPotential therapeutic interventional targetsPathway analysisPostmortem human brain tissueRare variantsA substitution at the cytoplasmic tail of the spike protein enhances SARS-CoV-2 infectivity and immunogenicity
Li Y, Zhang X, Tai W, Zhuang X, Shi H, Liao S, Yu X, Mei R, Chen X, Huang Y, Liu Y, Liu J, Liu Y, Zhu Y, Wang P, Tian M, Yu G, Li L, Cheng G. A substitution at the cytoplasmic tail of the spike protein enhances SARS-CoV-2 infectivity and immunogenicity. EBioMedicine 2024, 110: 105437. PMID: 39531918, PMCID: PMC11603013, DOI: 10.1016/j.ebiom.2024.105437.Peer-Reviewed Original ResearchS proteinCytoplasmic tailFERM-binding motifTrans-complementation systemSpike proteinAmino acid substitutionsProline-to-leucine substitutionSystematic bioinformatics analysisHigh-frequency mutationsSARS-CoV-2 virionsBinding motifAcid substitutionsSARS-CoV-2Natural selectionBioinformatics analysisEzrin/radixin/moesin proteinsMolecular mechanismsMutationsOmicron variantProteinVaccine developmentMRNA vaccinesGlobal disseminationSARS-CoV-2 Omicron sublineagesSublineagesPRMT6 facilitates EZH2 protein stability by inhibiting TRAF6-mediated ubiquitination degradation to promote glioblastoma cell invasion and migration
Wang J, Shen S, You J, Wang Z, Li Y, Chen Y, Tuo Y, Chen D, Yu H, Zhang J, Wang F, Pang X, Xiao Z, Lan Q, Wang Y. PRMT6 facilitates EZH2 protein stability by inhibiting TRAF6-mediated ubiquitination degradation to promote glioblastoma cell invasion and migration. Cell Death & Disease 2024, 15: 524. PMID: 39043634, PMCID: PMC11266590, DOI: 10.1038/s41419-024-06920-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrain NeoplasmsCell Line, TumorCell MovementEnhancer of Zeste Homolog 2 ProteinFemaleGene Expression Regulation, NeoplasticGlioblastomaHumansMaleMiceMice, Inbred BALB CMice, NudeNeoplasm InvasivenessNuclear ProteinsProtein StabilityProtein-Arginine N-MethyltransferasesProteolysisTNF Receptor-Associated Factor 6UbiquitinationConceptsProtein arginine methyltransferase 6Glioblastoma cell invasionStability of EZH2Protein stabilityCell invasionOverexpression of PRMT6Inhibited glioblastoma cell invasionGlioblastoma cellsEZH2 protein stabilityHistone methylation marksMigration of glioblastoma cellsHallmarks of cancerProliferation of glioblastoma cellsMethylation marksTumor cell invasionEpigenetic regulationGlioblastoma cells in vivoBioinformatics analysisMigration in vitroRegulatory relationshipsEZH2 proteinUbiquitination degradationProteinCells in vivoTRAF6Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation
Trogdon M, Abbott K, Arang N, Lande K, Kaur N, Tong M, Bakhoum M, Gutkind J, Stites E. Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation. Npj Systems Biology And Applications 2024, 10: 75. PMID: 39013872, PMCID: PMC11252164, DOI: 10.1038/s41540-024-00400-1.Peer-Reviewed Original ResearchConceptsSignaling networksMathematical models of biochemical reaction networksModels of biochemical reaction networksG-proteinCell signaling networksDisease-causing mutationsComputational systems biologyBiochemical reaction networksDownstream pathway activationSignaling phenotypeSystems biologyBioinformatics analysisGPCR signalingMutationsCo-occurring mutationsOncogenic mutationsPathway activationDiscovery toolPathwayReaction networkSignalCYSLTR2 mutationsDiscoveryPhenotypeMutually-exclusiveHeterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling
Ohashi Y, Protack C, Aoyagi Y, Gonzalez L, Thaxton C, Zhang W, Kano M, Bai H, Yatsula B, Alves R, Hoshina K, Schneider E, Long X, Perry R, Dardik A. Heterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling. Scientific Reports 2024, 14: 13287. PMID: 38858395, PMCID: PMC11164895, DOI: 10.1038/s41598-024-64075-8.Peer-Reviewed Original ResearchConceptsGene expression patternsArteriovenous fistula groupArteriovenous fistulaExpression patternsHeterogeneous gene expressionGene expression changesOutcomes of arteriovenous fistulaVenous remodelingArteriovenous fistula maturationPostoperative day 7Reduce patient morbidityRNA sequencingUpregulation of metabolismBioinformatics analysisGene expressionDownregulation of metabolismMetabolic pathwaysExpression changesGenesAVF maturationAVF remodelingFistula creationC57BL/6 miceClinical outcomesPatient morbidityGenetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation
Soares L, King C, Fernando C, Roth A, Breaker R. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2318008121. PMID: 38306478, PMCID: PMC10861870, DOI: 10.1073/pnas.2318008121.Peer-Reviewed Original ResearchConceptsMotif RNAsGenetic disruptionSecondary structure modelKnock-out strainTrans-acting factorsNoncoding RNAsCell differentiation processAbundant RNATransfer RNANcRNA classesRibosomal RNASpore formationMotif genesCellular processesBacterial speciesCellular functionsBioinformatics analysisExpression analysisMotifRNAGenesBiochemical mechanismsNcRNAsDifferentiation processStructural probesSUMOylation Fine-Tunes Endothelial HEY1 in the Regulation of Angiogenesis
Ren R, Ding S, Ma K, Jiang Y, Wang Y, Chen J, Wang Y, Kou Y, Fan X, Zhu X, Qin L, Qiu C, Simons M, Wei X, Yu L. SUMOylation Fine-Tunes Endothelial HEY1 in the Regulation of Angiogenesis. Circulation Research 2024, 134: 203-222. PMID: 38166414, PMCID: PMC10872267, DOI: 10.1161/circresaha.123.323398.Peer-Reviewed Original ResearchDNA-binding capabilityElectrophoretic mobility shift assaysEndothelial cell-specific expressionMobility shift assaysHairy/EnhancerCell-specific expressionPrimary human endothelial cellsNotch pathway componentsE-box promoter elementsEndothelial cellsRegulation of angiogenesisHelix familyPostnatal vascular growthHey1 functionsTranscriptional complexChromatin immunoprecipitationE3 ligaseRTK signalingEmbryonic developmentMatrigel plug assayPromoter elementsBioinformatics analysisShift assaysSUMOylationDNA binding
2023
Novel hippocampal genes involved in enhanced susceptibility to chronic pain-induced behavioral emotionality
Garman A, Ash A, Kokkinos E, Nerland D, Winter L, Langreck C, Forgette M, Girgenti M, Banasr M, Duric V. Novel hippocampal genes involved in enhanced susceptibility to chronic pain-induced behavioral emotionality. European Journal Of Pharmacology 2023, 964: 176273. PMID: 38135263, DOI: 10.1016/j.ejphar.2023.176273.Peer-Reviewed Original ResearchBlood-brain barrier integrityChronic pain statesBehavioral emotionalityHippocampal genesPain statesGenome-wide RNA-seq analysisStress responseBarrier integrityCommon stress responseRNA-seq analysisAurora kinase BChronic inflammatory painDepressive-like behaviorChronic pain conditionsRodent stress modelsLimbic brain regionsTight junction proteinsBioinformatics analysisInflammatory painAstrocyte activationPain groupPain conditionsTranscriptomic profilesAltered moodKinase BLow expression of m6A reader YTHDC1 promotes progression of ovarian cancer via PIK3R1/STAT3/GANAB axis
Wang X, Chen Q, Bing Z, Zhou S, Xu Z, Hou Y, Zhao Y, Zhao S, Wang T. Low expression of m6A reader YTHDC1 promotes progression of ovarian cancer via PIK3R1/STAT3/GANAB axis. International Journal Of Biological Sciences 2023, 19: 4672-4688. PMID: 37781028, PMCID: PMC10535707, DOI: 10.7150/ijbs.81595.Peer-Reviewed Original ResearchConceptsReversible epigenetic modificationAbundant internal modificationPhosphoinositide-3-kinase regulatory subunit 1Glucosidase II alpha subunitRNA immunoprecipitation sequencingM6A reader proteinM6A-dependent mannerRegulatory subunit 1Reader proteinsYTH domainOvarian cancer progressionReader YTHDC1Chromatin immunoprecipitationImmunoprecipitation sequencingWestern blotEpigenetic modificationsGlycan biosynthesisBioinformatics analysisRNA sequencingRNA immunoprecipitationSignal transducerBiological roleGene expressionRegulatory mechanismsTranscription 3Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels
Wong M, Wei Y, Ho Y. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Current Opinion In HIV And AIDS 2023, 18: 246-256. PMID: 37535039, PMCID: PMC10442869, DOI: 10.1097/coh.0000000000000809.Peer-Reviewed Original ResearchConceptsSurface protein expressionMultiomics approachATAC-seqProtein expressionTranscription factor activityProtein levelsRNA mappingRNA-seqBioinformatics analysisHIV-1-infected cellsFalse positive discoveriesBiological insightsBulk transcriptomeFactor activityDNA amplificationExpressionCellsTranscriptomeTherapeutic strategiesEpigeneticsDiscoveryDNA PCRRNADNAHIV-1Transcriptional signatures of heroin intake and relapse throughout the brain reward circuitry in male mice
Browne C, Futamura R, Minier-Toribio A, Hicks E, Ramakrishnan A, Martínez-Rivera F, Estill M, Godino A, Parise E, Torres-Berrío A, Cunningham A, Hamilton P, Walker D, Huckins L, Hurd Y, Shen L, Nestler E. Transcriptional signatures of heroin intake and relapse throughout the brain reward circuitry in male mice. Science Advances 2023, 9: eadg8558. PMID: 37294757, PMCID: PMC10256172, DOI: 10.1126/sciadv.adg8558.Peer-Reviewed Original ResearchConceptsOpioid use disorderHeroin intakeContext-induced drug-seekingBrain reward circuitryHeroin self-administrationRNA-seqDrug seekingReward circuitryGenome-wide association study dataSelf-administrationHeroin exposureDrug-takingIntegration of RNA-seq dataUse disorderPatterns of transcriptional regulationRNA-seq dataBehavioral outcomesMale miceMolecular changesTranscriptional regulationRegion-specificGene candidatesRNA sequencingHeroinBioinformatics analysisIdentification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans
Elankumuran P, Browning G, Marenda M, Kidsley A, Osman M, Haenni M, Johnson J, Trott D, Reid C, Djordjevic S. Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans. Microbial Genomics 2023, 9: mgen000930. PMID: 36752777, PMCID: PMC9997745, DOI: 10.1099/mgen.0.000930.Peer-Reviewed Original ResearchConceptsPopulation structureIdentification of genesWhole genome sequencesPropanediol utilization (pdu) operonGenomic traitsAccessory genomeCanine sourcesBioinformatics analysisUtilization operonPhylogenetic clustersGlobal collectionDistinct populationsVirulence genesOperonGenesDominant hostSequence typesSequenceExtraintestinal infectionsPhylogenyCladeGenomeLineagesHumansTraitsCore Constituents of Caragana sinica Root for Rheumatoid Arthritis Treatment and the Potential Mechanism
Qu B, Wang S, Zhu H, Yin T, Zhou R, Hu W, Lu C. Core Constituents of Caragana sinica Root for Rheumatoid Arthritis Treatment and the Potential Mechanism. ACS Omega 2023, 8: 2586-2595. PMID: 36687056, PMCID: PMC9851025, DOI: 10.1021/acsomega.2c07094.Peer-Reviewed Original ResearchRheumatoid arthritis treatmentAnti-inflammatory effectsRA treatmentEthyl acetate extractArthritis treatmentHerbal constituentsPotential mechanismsNuclear factor kappa B (NF-κB) signal pathwayGood anti-inflammatory effectAnti-arthritis effectsUltra-performance liquid chromatographyNF-κB p65Herb productsB signal pathwayNF-κB pathwayArthritis ratsBioinformatics analysisBetter efficacyTherapeutic efficacyPharmacological roleOral bioavailabilityDrug-like propertiesFolk medicineSignal pathwayTreatmentA basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology
Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.Peer-Reviewed Original ResearchPost-translational modificationsData-independent acquisitionSystems biologySite-specific phosphorylation eventsImportant post-translational modificationMost human proteinsCritical protein functionsPhosphorylation eventsProtein functionPhosphoproteomic studiesPhosphoproteomic analysisBioinformatics AdvancesHuman proteinsMass spectrometry technologyBioinformatics analysisLarge-scale quantificationExperimental workflowHigh-resolution mass spectrometry technologySpectrometry technologyPhosphoproteomicsPhosphorylationBiologyProteinSystems medicineSingle experiment
2022
Diversification of aminoacyl-tRNA synthetase activities via genomic duplication
Krahn N, Söll D, Vargas-Rodriguez O. Diversification of aminoacyl-tRNA synthetase activities via genomic duplication. Frontiers In Physiology 2022, 13: 983245. PMID: 36060688, PMCID: PMC9437257, DOI: 10.3389/fphys.2022.983245.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenomic duplicationSynthetase familyRecent bioinformatic analysisAminoacyl-tRNA synthetase familySynthetic biology applicationsDomains of lifeNew drug targetsAminoacyl-tRNA synthetase activityGene duplicationPhylogenetic diversityEvolutionary eventsGenetic codeBioinformatics analysisImportant bioactive moleculesAdaptive advantageBiological functionsBiological processesBiology applicationsDrug targetsDuplicationAaRSsCatalytic siteSynthetase activityProteinBioactive moleculesThe driver role of JAK‐STAT signalling in cancer stemness capabilities leading to new therapeutic strategies for therapy‐ and castration‐resistant prostate cancer
Lo U, Chen Y, Cen J, Deng S, Luo J, Zhau H, Ho L, Lai C, Mu P, Chung L, Hsieh J. The driver role of JAK‐STAT signalling in cancer stemness capabilities leading to new therapeutic strategies for therapy‐ and castration‐resistant prostate cancer. Clinical And Translational Medicine 2022, 12: e978. PMID: 35908276, PMCID: PMC9339240, DOI: 10.1002/ctm2.978.Peer-Reviewed Original ResearchConceptsCastration-resistant prostate cancerProstate cancerCancer stem cellsActivation of JAKJAK-STAT signalingGene set enrichment analysisJAK-STAT1 pathwaySTAT1 inhibitorAcquisition of stemness propertiesProstate cancer cell linesProstate cancer stemnessAssociated with cancer stem cellsIn vivo anti-tumor activityMetastatic prostate cancerTumor-initiating capabilityJAK-STATProstasphere assayDownstream effectorsIngenuity PathwayGenetic manipulationCSC genesBioinformatics analysisEnrichment analysisJAK-STAT1Signaling pathwayHigh-content CRISPR screening
Bock C, Datlinger P, Chardon F, Coelho M, Dong M, Lawson K, Lu T, Maroc L, Norman T, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi L, Shapiro R, Shendure J, Weissman J, Zhuang X. High-content CRISPR screening. Nature Reviews Methods Primers 2022, 2: 8. DOI: 10.1038/s43586-021-00093-4.Peer-Reviewed Original ResearchCRISPR screeningCRISPR screensBiological discoverySingle-cell RNA sequencingPooled CRISPR screensList of genesHigh-content methodBiological challengesGene functionCell competitionUnbiased interrogationGuide RNARNA sequencingBioinformatics analysisDetailed biological insightsTarget genesBasic biologyPool of cellsBiological insightsCRISPR technologyMolecular mechanismsSuch screensGenesMedical GeneticsBroad utility
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