2025
Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes
Wang Y, Wang F, Meng G, Lopez-Giraldez F, Dong C, Wang Z, Townsend J. Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes. Molecular Biology And Evolution 2025, 42: msaf131. PMID: 40452442, PMCID: PMC12203517, DOI: 10.1093/molbev/msaf131.Peer-Reviewed Original ResearchConceptsRate of gene expression evolutionGene expression evolutionExpression evolutionGene expressionPhenotypic evolutionHeterogeneous rates of evolutionNonsynonymous to synonymous substitution ratesRates of phenotypic evolutionDevelopmental stagesSingle-copy orthologsGene sequence evolutionSynonymous substitution ratesRate of evolutionExpression of genesFunctional pathway analysisCarbon metabolismEvolutionary forcesConsequent phenotypesSexual reproductionSequence evolutionConserved pathwaysMeiosis pathwaysSubstitution ratesCell cyclePathway analysisCutaneous lupus features specialized stromal niches and altered retroelement expression
Gehlhausen J, Kong Y, Baker E, Ramachandran S, Koumpouras F, Ko C, Vesely M, Little A, Damsky W, King B, Iwasaki A. Cutaneous lupus features specialized stromal niches and altered retroelement expression. Journal Of Investigative Dermatology 2025 PMID: 40409678, DOI: 10.1016/j.jid.2025.04.033.Peer-Reviewed Original ResearchRetroelement expressionCGAS-STING pathwayRIG-IType I interferonCutaneous lupusCGAS-STINGElevated expression of genesPathway enrichment analysisI interferonExpression of genesResponse to type I interferonsLupus skinRetroelement familiesInterferon-stimulated genesNucleic acid signalsApoptotic signalingSingle-cell RNAMultiple cell typesAcid signalingEnrichment analysisInflammatory cell recruitmentType II interferonInflammatory skin diseaseTumor necrosis factorCell types
2024
Sphingosine‐1‐Phosphate Signalling Inhibition Suppresses Th1‐Like Treg Generation by Reversing Mitochondrial Uncoupling
Coulombeau R, Selck C, Giang N, Al‐Mohammad A, Ng N, Maher A, Argüello R, Scalfari A, Varley J, Nicholas R, Dominguez‐Villar M. Sphingosine‐1‐Phosphate Signalling Inhibition Suppresses Th1‐Like Treg Generation by Reversing Mitochondrial Uncoupling. Immunology 2024, 174: 153-166. PMID: 39444366, PMCID: PMC11652410, DOI: 10.1111/imm.13870.Peer-Reviewed Original ResearchTh1-like TregsSphingosine-1-PhosphateSuppressive functionMitochondrial uncouplingSignaling inhibitionIncreased suppressive functionMultiple sclerosisTreg plasticityTreg reprogrammingTreg frequencyTreg generationTregsAutoimmune conditionsExpression of genesInflammatory environmentMS patientsS1P inhibitionFTY720Defective functionS1PMTORC1 signalingInhibitionReprogrammingTranscriptional regulation of postnatal aortic development
Weiss D, Yeung N, Ramachandra A, Humphrey J. Transcriptional regulation of postnatal aortic development. Cells And Development 2024, 180: 203971. PMID: 39426523, PMCID: PMC11634634, DOI: 10.1016/j.cdev.2024.203971.Peer-Reviewed Original ResearchA genome-wide investigation into the underlying genetic architecture of personality traits and overlap with psychopathology
Gupta P, Galimberti M, Liu Y, Beck S, Wingo A, Wingo T, Adhikari K, Kranzler H, Stein M, Gelernter J, Levey D. A genome-wide investigation into the underlying genetic architecture of personality traits and overlap with psychopathology. Nature Human Behaviour 2024, 8: 2235-2249. PMID: 39134740, PMCID: PMC11576509, DOI: 10.1038/s41562-024-01951-3.Peer-Reviewed Original ResearchPersonality traitsPsychiatric traitsBidirectional effectsGenetic architectureHuman personality traitsGenetic correlation analysisGene-based association testsGenome-wide significant lociNeuroticismAgreeablenessGenome-wide association studiesGenome-wide association study meta-analysisMental illnessGenome-wide investigationAssociation TestComplex human traitsProteome-wide analysisAnxietyDepressionExtraversionConscientiousnessExpression of genesNovel lociSignificant lociTranscriptome-wideReducing brain Aβ burden ameliorates high-fat diet-induced fatty liver disease in APP/PS1 mice
Tsay H, Gan Y, Su Y, Sun Y, Yao H, Chen H, Hsu Y, Hsu J, Wang H, Shie F. Reducing brain Aβ burden ameliorates high-fat diet-induced fatty liver disease in APP/PS1 mice. Biomedicine & Pharmacotherapy 2024, 173: 116404. PMID: 38471275, DOI: 10.1016/j.biopha.2024.116404.Peer-Reviewed Original ResearchAPP/PS1 miceAmeliorate fatty liver diseaseAlzheimer's diseaseAD-like pathologyHFD-induced hyperglycemiaAD-related pathologyExpression of genesFatty liver diseaseFatty acid oxidationHFD-induced fatty liverAD therapyLipid accumulationHigh-fat diet-induced fatty liver diseaseAPP/PS1HFD feedingCharacteristics of microgliaExposure to HFDHepatic lipogenesisLiver diseaseDiet-induced fatty liver diseaseAcid oxidationHepatic lipidsPlants distinguish different photoperiods to independently control seasonal flowering and growth
Wang Q, Liu W, Leung C, Tarté D, Gendron J. Plants distinguish different photoperiods to independently control seasonal flowering and growth. Science 2024, 383: eadg9196. PMID: 38330117, PMCID: PMC11134419, DOI: 10.1126/science.adg9196.Peer-Reviewed Original ResearchConceptsPhotoperiodic growthSeasonal floweringControl expression of genesDuration of photosynthetic activityGrowth-regulating pathwaysExpression of genesPhotosynthetic periodMeasure photoperiodPhotoperiodic floweringPhotosynthetic activityControl expressionFlowering mechanismRegulation pathwaysSeasonal growthFlowersLong daysDifferent photoperiodsPhotoperiodLight intensityPlantsGrowthMutantsGenesPathway
2023
FRI032 Cellular Insights Into Metabolically Healthy And Unhealthy Obesity
Petersen M, Smith G, Yu J, Barve R, Yoshino J, Shulman G, Klein S. FRI032 Cellular Insights Into Metabolically Healthy And Unhealthy Obesity. Journal Of The Endocrine Society 2023, 7: bvad114.043. PMCID: PMC10555440, DOI: 10.1210/jendso/bvad114.043.Peer-Reviewed Original ResearchAbdominal subcutaneous adipose tissueWhole-body insulin sensitivityInsulin sensitivityMUO groupMuscle ceramide contentCeramide contentAdipose tissueGreater whole-body insulin sensitivityPlasma C-peptide concentrationC-peptide concentrationsAdverse metabolic effectsSubcutaneous adipose tissueExpression of genesSkeletal muscle expressionMitochondrial content/functionHealthy obesityMitochondrial structure/functionSkeletal muscle diacylglycerolUnhealthy obesityExtracellular matrix remodelingExcess adiposityMHL groupMetabolic effectsMuscle diacylglycerolInsulin actionTransendothelial Migration of Human B Cells: Chemokine versus Antigen.
Wang V, Pober J, Manes T. Transendothelial Migration of Human B Cells: Chemokine versus Antigen. The Journal Of Immunology 2023, 211: 923-931. PMID: 37530585, PMCID: PMC10529164, DOI: 10.4049/jimmunol.2200887.Peer-Reviewed Original ResearchConceptsB cellsLeukocyte cell adhesion moleculeTransendothelial migrationEndothelial cellsCell adhesion moleculeAdhesion moleculesPeripheral blood CD19B cell subsetsMemory B cellsInnate immune propertiesSites of inflammationMicrovascular endothelial cellsHuman microvascular endothelial cellsHuman B cellsBlood CD19Peripheral bloodCell subsetsVenular flowT cellsICAM-1VCAM-1Immune propertiesSyk activationChemokinesExpression of genesActivity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders
Ma Y, Bendl J, Hartley B, Fullard J, Abdelaal R, Ho S, Kosoy R, Gochman P, Rapoport J, Hoffman G, Brennand K, Roussos P. Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders. Biological Psychiatry 2023, 95: 187-198. PMID: 37454787, PMCID: PMC10787819, DOI: 10.1016/j.biopsych.2023.07.003.Peer-Reviewed Original ResearchConceptsTranscriptional programsBrain-related disordersGlutamatergic neuronsGene coexpression network analysisSignificant heritability enrichmentsEnhancer-promoter interactionsCoexpression network analysisDisease-associated genesExpression of genesLarge-scale geneticMultiomics data integrationChromatin accessibilityEpigenomic changesHeritability enrichmentGenetic regulationRegulatory elementsMultiple genesSequence variationGene expressionAxon guidanceGenetic riskPotassium chloride-induced depolarizationActivity-dependent changesDepolarization-induced changesGenesDOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement
Malla A, Rainsford S, Smith Z, Lesch B. DOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement. Development 2023, 150 PMID: 37082969, PMCID: PMC10259660, DOI: 10.1242/dev.201497.Peer-Reviewed Original ResearchConceptsHistone replacementMale sterilityProtamine exchangeSpermatid differentiationHistone H3 lysine 79Chromatin remodeling factorsRNA polymerase IIH3 lysine 79Expression of genesMature sperm headSperm headPostmeiotic germ cellsHistone methyltransferase DOT1LPolymerase IILysine 79Embryonic lethalityRemodeling factorsProtamine transitionProtamine replacementTranscriptional dysregulationMethyltransferase DOT1LIndispensable regulatorDOT1LHistonesGerm cellsConnexin 43-mediated neurovascular interactions regulate neurogenesis in the adult brain subventricular zone
Genet N, Genet G, Chavkin N, Paila U, Fang J, Vasavada H, Goldberg J, Acharya B, Bhatt N, Baker K, McDonnell S, Huba M, Sankaranarayanan D, Ma G, Eichmann A, Thomas J, Ffrench-Constant C, Hirschi K. Connexin 43-mediated neurovascular interactions regulate neurogenesis in the adult brain subventricular zone. Cell Reports 2023, 42: 112371. PMID: 37043357, PMCID: PMC10564973, DOI: 10.1016/j.celrep.2023.112371.Peer-Reviewed Original ResearchConceptsSubventricular zoneEndothelial cellsNSC proliferationNSC quiescenceAdult brain subventricular zoneBlood-brain barrierBrain subventricular zoneStem cell therapyNeural stem cell nicheNeurovascular interactionsNeuroblast generationAdult brainSingle-cell RNA sequencingNeurodegenerative disordersChannel-independent mannerCell therapySVZ-NSCsConnexin 43Expression of genesERK activationNSC regulationNSC behaviorRNA sequencingCx43ProliferationTh1 bias of liver mucosal‐associated invariant T cells promotes hepatic gluconeogenesis in type 2 diabetes mellitus
Tang W, Ge K, Shen L, Wang H, Feng W, Sun X, Chu X, Zhu D, Yin H, Bi Y. Th1 bias of liver mucosal‐associated invariant T cells promotes hepatic gluconeogenesis in type 2 diabetes mellitus. Diabetes/Metabolism Research And Reviews 2023, 39: e3620. PMID: 36738300, DOI: 10.1002/dmrr.3620.Peer-Reviewed Original ResearchConceptsHepatic MAIT cellsMAIT cellsMAIT cell subsetsType 2 diabetes mellitusInnate-like T cell subsetMucosal-associated invariant T (MAIT) cellsHepatic gluconeogenesisMucosal-Associated Invariant T CellsExpression of pyruvate carboxylaseGene expression of pyruvate carboxylaseCell subsetsExpression of genesT2DM subjectsInvariant T cellsIFN-gMAIT cell frequencyPyruvate carboxylaseProduction of interleukin-17HepG2 cells co-culturedT cell subsetsTumor necrosis factor-aDevelopment of type 2 diabetes mellitusGene expressionDiagnosed T2DM subjectsMetabolic homoeostasisAssessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing
Marczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Pusztai L, Hatzis C, Symmans W. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathology 2023, 131: 289-299. PMID: 36650408, PMCID: PMC10614161, DOI: 10.1002/cncy.22679.Peer-Reviewed Original ResearchConceptsCytology smearsBreast cancerConcordance correlation coefficientTumor tissue samplesParaffin-embedded sectionsClinical diagnostic proceduresSurgical resectionRNA sequencingTumor stromaCytologic specimensDiagnostic proceduresLin's concordance correlation coefficientPapanicolaou stainCancerTissue samplesDNA mutation testingSmearsSimilar concordanceTranscriptome RNA-SeqDiagnostic cytologyAllele fractionExpression levelsRNA-seqExpression of genesGene expression levels
2022
Na+ riboswitches regulate genes for diverse physiological processes in bacteria
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na+ riboswitches regulate genes for diverse physiological processes in bacteria. Nature Chemical Biology 2022, 18: 878-885. PMID: 35879547, PMCID: PMC9337991, DOI: 10.1038/s41589-022-01086-4.Peer-Reviewed Original ResearchConceptsOsmotic stressGene expressionDiverse physiological processesMetal ion transportersGene expression changesExpression of genesRiboswitch classesBacterial proteinsIon transportersExpression changesPhysiological processesATP productionLow mM rangeGenesProteinExpressionBacteriaTranscriptionDissociation constantsOrganismsBiologyMM rangeTransportersMotifStressExpression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids
Cakir B, Tanaka Y, Kiral FR, Xiang Y, Dagliyan O, Wang J, Lee M, Greaney AM, Yang WS, duBoulay C, Kural MH, Patterson B, Zhong M, Kim J, Bai Y, Min W, Niklason LE, Patra P, Park IH. Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids. Nature Communications 2022, 13: 430. PMID: 35058453, PMCID: PMC8776770, DOI: 10.1038/s41467-022-28043-y.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsHuman cortical organoidsTranscription factor PUSingle-cell RNA sequencingMicroglia-like cellsSingle-cell transcriptomicsEmbryonic stem cellsDisease stage IIIRole of microgliaAD-associated genesExpression of genesCortical organoidsNeurodegenerative disordersRNA sequencingMolecular damageIntact complementStem cellsDysfunction of microgliaFunctional microgliaReduced expressionGenesCell clustersExpressionChemokine systemHuman microglia
2021
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, Capellini TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Molecular Biology And Evolution 2021, 39: msab304. PMID: 34662402, PMCID: PMC8760939, DOI: 10.1093/molbev/msab304.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsGene expressionPutative cis-regulatory elementsParallel reporter assaysImmune transcription factorsReporter gene expressionExpression of genesGenic targetsSelective sweepsMPRA dataInnate immune pathwaysPositive selectionTranscription factorsEndogenous sequencesReporter assaysAntiviral defenseDriver variantsGenetic variantsFunctional significanceImmune pathwaysWhite blood cell countGenesModern humansPotential immune responseBlood cell countEvaluation of high salinity tolerance in Pongamia pinnata (L.) Pierre by a systematic analysis of hormone‐metabolic network
Marriboina S, Sharma K, Sengupta D, Yadavalli AD, Sharma RP, Attipalli R. Evaluation of high salinity tolerance in Pongamia pinnata (L.) Pierre by a systematic analysis of hormone‐metabolic network. Physiologia Plantarum 2021, 173: 1514-1534. PMID: 34165187, DOI: 10.1111/ppl.13486.Peer-Reviewed Original ResearchConceptsSalt-treated plantsCarbon exchange rateSalt stressSalinity toleranceJasmonic acid levelsSalt stress conditionsRelative water contentHigh salinity toleranceExpression of genesGene expression analysisPongamia pinnata (L.) PierreBiofuel treeSalinity stressPlant productivitySodium sequestrationExpression analysisZeatin contentProton exchangersDismutase geneStress conditionsMolecular levelSaline environmentsMetabolic adaptationLeavesGenesUnveiling the neuroimaging-genetic intersections in the human brain
Diez I, Sepulcre J. Unveiling the neuroimaging-genetic intersections in the human brain. Current Opinion In Neurology 2021, 34: 480-487. PMID: 34227572, PMCID: PMC8265485, DOI: 10.1097/wco.0000000000000952.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic dataExpression of genesFunctional annotationGenetic networksGenetic dataTranscriptome dataTranscriptomic datasetsBrain genesGenesBrain phenotypesBrain expressionBiological mechanismsNeuroimaging workNeuroimaging mapsBrain-wideNeuroimaging findingsLife spanExpressionTranscriptomeHuman brainNeuroimaging
2020
Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits
Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB. Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. Nature Communications 2020, 11: 5562. PMID: 33144568, PMCID: PMC7642344, DOI: 10.1038/s41467-020-19265-z.Peer-Reviewed Original ResearchConceptsGenome-wide significant lociGenome-wide association studiesNearby gene expressionExpression of genesSmoking traitsGenetic architectureSignificant lociGenetic variationMultiple traitsGene expressionAssociation studiesLociTraitsGenetic knowledgeComposite phenotypeUK BiobankExpressionTENM2GNAI1GenesGeneticsVariantsPhenotype
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