2025
Transcriptomic landscape of Kaposi sarcoma: Insights into therapeutic targeting of KSHV.
Fei Y, Costa P, Junejo M, Li M, Perry C, Damsky W, Ishizuka J. Transcriptomic landscape of Kaposi sarcoma: Insights into therapeutic targeting of KSHV. Journal Of Clinical Oncology 2025, 43 DOI: 10.1200/jco.2025.43.16_suppl.e23526.Peer-Reviewed Original ResearchKaposi's sarcoma herpesvirusKaposi's sarcomaTranscripts Per MillionKSHV genomeHIV statusPresence of Kaposi’s sarcoma herpesvirusDisease progressionLatency-associated regionExpressed genesHistory of organ transplantationVirus-associated tumorsTherapeutic targetFormalin-fixed paraffin-embedded (FFPEGene expressionParaffin-embedded (FFPEHuman herpesvirus 8Differential gene expression analysisDisseminated diseaseViral eradicationViral gene expressionHIV-positiveBaseline characteristicsHHV-8Gene expression analysisTumor morphologyDifferential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals
Knowles E, Peralta J, Rodrigue A, Mathias S, Mollon J, Leandro A, Curran J, Blangero J, Glahn D. Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals. Schizophrenia Research 2025, 280: 85-94. PMID: 40267851, PMCID: PMC12107465, DOI: 10.1016/j.schres.2025.04.018.Peer-Reviewed Original ResearchConceptsGene expressionGenome-wide associationDifferential gene expression studiesGene co-expression network analysisWeighted gene co-expression network analysisCo-expression network analysisGene expression phenotypesIndividuals of European descentOverrepresentation of biological processesGene expression studiesGene expression analysisAfrican American ancestryGenomic regionsPsychosis-spectrum disordersRNA-seqAfrican American individualsPopulation stratificationAssociated with psychosisEtiology of psychosisSignificant genesCellular functionsExpression phenotypesExpression studiesAmerican ancestryExpression analysisBatch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Millard N, Chen J, Palshikar M, Pelka K, Spurrell M, Price C, He J, Hacohen N, Raychaudhuri S, Korsunsky I. Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. Genome Biology 2025, 26: 36. PMID: 40001084, PMCID: PMC11863647, DOI: 10.1186/s13059-025-03479-9.Peer-Reviewed Original ResearchConceptsBatch effectsVisualization of gene expression patternsSpatial gene patternsGene expression analysis of cellsGene expression patternsGene expression analysisGene expression levelsGene colocalizationAnalysis of cellsGene patternsTranscriptome analysisLigand-receptor interactionsExpression patternsSpatial transcriptomicsSpatial transcriptomic analysisExpression levelsGenesMultiple samplesSpatial patternsTranscriptomeColocalizationAnatomical contextPatternsCount dataAcute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis.
Hu X, He Y, Li S, Jiang Y, Yu R, Wu Y, Fu X, Song Y, Lin C, Shi J, Li H, Gao Y. Acute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis. Development 2025, 152 PMID: 39817838, DOI: 10.1242/dev.204226.Peer-Reviewed Original ResearchFetal hematopoiesisMegakaryocyte-erythroid progenitorsAcute inflammationInterferon-stimulated genesDouble-stranded RNAMegakaryocyte maturationPlatelet productionImpaired platelet productionFormation of double-stranded RNADownstream interferon-stimulated genesCell fate determinationRNA m6A modificationPhosphorylation of STAT1Hematopoietic progenitorsMegakaryocyte progenitorsHematopoietic cellsM6A methyltransferase METTL3Hematopoietic developmentGene expression analysisImmune responseMegakaryopoiesisHematopoiesisInflammationFate determinationIGF1 expressionInterneuron loss and microglia activation by transcriptome analyses in the basal ganglia of Tourette disorder
Wang Y, Fasching L, Wu F, Suvakov M, Huttner A, Berretta S, Roberts R, Leckman J, Fernandez T, Abyzov A, Vaccarino F. Interneuron loss and microglia activation by transcriptome analyses in the basal ganglia of Tourette disorder. Biological Psychiatry 2025 PMID: 39892689, DOI: 10.1016/j.biopsych.2024.12.022.Peer-Reviewed Original ResearchActivity of cis-regulatory elementsCis-regulatory elementsMedium spiny neuronsDifferential gene expression analysisChromatin accessibility analysesCell typesDifferential gene expressionGene expression changesMitochondrial oxidative metabolismGene expression analysisSnATAC-seqOpen chromatin datasetsPutative enhancersSynaptic adhesionChromatin datasetsOxidative metabolismEpigenomic regulationTranscriptome analysisActivation of immune responsesIdentified cell typesExpression analysisSynaptic dysfunctionGene expressionExpression changesTranscriptome
2024
A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS
Boddu P, Roy R, Baumgartner F, Hutter S, Haferlach T, Pillai M. A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS. Blood 2024, 144: 2732-2732. DOI: 10.1182/blood-2024-211458.Peer-Reviewed Original ResearchRNA-binding proteinsIntron retentionAlternative splicing patternsPost-transcriptional mechanismsIR eventsSF mutationsSR proteinsSF3B1 mutantsAnalyzed RNA-seq datasetsMyelodysplastic syndromeCo-transcriptional splicingCo-transcriptional mechanismsRNA-seq datasetsPost-transcriptional splicingWild-typeSub-compartmentsNuclear sub-compartmentsHEK293T cellsGene expression analysisWild-type K562 cellsRNA processingMutant cellsPhospho-proteomicsExon featuresAS eventsPhysalia gonodendra are not yet sexually mature when released
Oguchi K, Yamamoto G, Kohtsuka H, Dunn C. Physalia gonodendra are not yet sexually mature when released. Scientific Reports 2024, 14: 23011. PMID: 39362967, PMCID: PMC11450099, DOI: 10.1038/s41598-024-73611-5.Peer-Reviewed Original ResearchConceptsGerm cell maturationGene expression analysisGerm cell markersReproductive ecologySexual reproductionHaploid cellsGerm cellsReproductive biologyGonophoresExpression analysisRelated genesLife cycleGenesCell maturationGermConsistent with other studiesFlow cytometryPhysalia utriculusExpressionCnidariaCell markersCellsPhysaliaSpermHydrozoaO-077 EXPOSOME CHARACTERIZATION OF DIESEL ENGINE EXHAUST EXPOSURE
Lan Q, Vermeulen R, Rahman M, Dai Y, Hu W, Irving B, Lin X, Blechter B, Chaoyang D, Duan H, Wong J, Niu Y, Xu J, Chaoyang W, Meliefste K, Hosgood D, Ye M, Jia X, Meng T, Bin P, Silverman D, Zheng Y, Rothman N, Walker D. O-077 EXPOSOME CHARACTERIZATION OF DIESEL ENGINE EXHAUST EXPOSURE. Occupational Medicine 2024, 74: 0-0. DOI: 10.1093/occmed/kqae023.0598.Peer-Reviewed Original ResearchMetabolome-wide association studyAssociated with increased lung cancer riskHigh-resolution mass spectrometryAssociated with tumor developmentLung cancer riskMetabolic pathway enrichmentMolecular mechanismsTumor developmentCancer riskUrine mutagenicityEndothelial pathwaysUrinary mutagenicityLC-HRMSPlasma samplesMetabolic featuresGene expression analysisPlasma proteomePotential molecular mechanismsUntargeted analysisBiological alterationsMolecular featuresOxidative stressGenome-wide gene expressionBiological response profilesResponse profilesCorrelation of hormone receptor positive HER2-negative/MammaPrint high-2 breast cancer with triple negative breast cancer: Results from gene expression data from the ISPY2 trial.
Rios-Hoyo A, Xiong K, Marczyk M, García-Millán R, Wolf D, Huppert L, Nanda R, Yau C, Hirst G, van 't Veer L, Esserman L, Pusztai L. Correlation of hormone receptor positive HER2-negative/MammaPrint high-2 breast cancer with triple negative breast cancer: Results from gene expression data from the ISPY2 trial. Journal Of Clinical Oncology 2024, 42: 573-573. DOI: 10.1200/jco.2024.42.16_suppl.573.Peer-Reviewed Original ResearchGene expression dataGene expression analysisExpression dataExpressed genesExpression analysisTriple-negativeDistance analysisPathway analysisDifferential gene expression analysisCell cycle pathwayGene Set Enrichment AnalysisBreast cancerIngenuity Pathway AnalysisRate of pathological complete responseHigh-risk stage IIGlucocorticoid receptor signalingTriple negative breast cancerCycle pathwayPathological complete responseDNA repairEnrichment analysisOptimal treatment strategyNegative breast cancerI-SPY2 trialGenesGene-edited Mtsoc1 triple mutant Medicago plants do not flower
Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel J, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. Frontiers In Plant Science 2024, 15: 1357924. PMID: 38469328, PMCID: PMC10926907, DOI: 10.3389/fpls.2024.1357924.Peer-Reviewed Original ResearchTriple mutant linesSingle mutantsFlowering timeMutant linesMultiple gene duplication eventsGene duplication eventsSOC1-like genesModel Arabidopsis thalianaMADS transcription factorsWild-type backgroundRegulation of floweringOptimal flowering timeNon-flowering plantsShort-day photoperiodCRISPR-Cas9 gene editingGene expression analysisDuplication eventsArabidopsis thalianaSOC1 genesDelayed floweringFloral promotersCrop productionFlower developmentFlowering pathwayMedicago truncatula
2023
Endothelial nitric oxide synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation
Nguyen T, Rahman N, Sessa W, Lee M. Endothelial nitric oxide synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation. Frontiers In Cardiovascular Medicine 2023, 10: 1279868. PMID: 38034389, PMCID: PMC10683645, DOI: 10.3389/fcvm.2023.1279868.Peer-Reviewed Original ResearchAtherosclerotic plaque formationPlaque formationAkt1 null miceSingle amino acid substitutionMutant miceLesion formationImportance of AktUnique expression patternGene expression analysisIndex of atherosclerosisFavorable lipid profileVascular protective roleAtherosclerotic lesion formationAthero-protective effectsEndothelial NO generationAmino acid substitutionsDouble knockout miceDeletion backgroundPhosphorylation sitesAspartate substitutionPhosphorylation statusExpression analysisEnzyme functionExpression patternsENOS deletionT65. GENES IN POSTMORTEM BRAIN TISSUE DIFFERENTIALLY EXPRESSED IN CHRONIC PAIN
Collier L, Seah C, Kozik E, Group T, Girgenti M, Huckins L, Johnston K. T65. GENES IN POSTMORTEM BRAIN TISSUE DIFFERENTIALLY EXPRESSED IN CHRONIC PAIN. European Neuropsychopharmacology 2023, 75: s196-s197. DOI: 10.1016/j.euroneuro.2023.08.350.Peer-Reviewed Original ResearchChronic painBackground Chronic painBone cancer painPain-related conditionsVEGF BFalse discovery rate correctionCancer painEndometrial cancerRheumatoid arthritisBrain gene expression datasetsGene expressionPainPsychiatric conditionsLinear regression modelsMultiple testingSpecific cell typesGene expression analysisCell typesRate correctionRegression modelsSurrogate variablesDifferential gene expression analysisDACCMeasured variablesExpressionPharmacological Modulation of Energy and Metabolic Pathways Protects Hearing in the Fus1/Tusc2 Knockout Model of Mitochondrial Dysfunction and Oxidative Stress
Tan W, Santos-Sacchi J, Tonello J, Shanker A, Ivanova A. Pharmacological Modulation of Energy and Metabolic Pathways Protects Hearing in the Fus1/Tusc2 Knockout Model of Mitochondrial Dysfunction and Oxidative Stress. Antioxidants 2023, 12: 1225. PMID: 37371955, PMCID: PMC10294946, DOI: 10.3390/antiox12061225.Peer-Reviewed Original ResearchPharmacological modulationKO miceMitochondrial metabolismComparative gene expression analysisMetabolic pathwaysOxidative stressCritical biological processesHearing-related genesDrug-specific responsesPremature hearing lossGene expression analysisAdrenal axisHearing lossImmune responseMitochondrial morphologyMotor proteinsExpression analysisVoltage-gated channelsBiological processesMTOR pathwayNormal hearingPronounced upregulationMolecular pathwaysMitochondrial activityEnergy sensingArtemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia
Ogana H, Hurwitz S, Hsieh C, Geng H, Müschen M, Bhojwani D, Wolf M, Larocque J, Lieber M, Kim Y. Artemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia. Frontiers In Cell And Developmental Biology 2023, 11: 1134121. PMID: 37082620, PMCID: PMC10111164, DOI: 10.3389/fcell.2023.1134121.Peer-Reviewed Original ResearchMature B cell lineB-cell acute lymphoblastic leukemiaB cell linesDNA double-strand break repairChromosome breaksDouble-strand break repairDNA-PKcs complexDNA-PK inhibitorGene expression analysisCell linesAcute lymphoblastic leukemiaKey endonucleaseDNA-PKcsBreak repairNonhomologous endExpression analysisLymphoblastic leukemiaTherapeutic strategiesRefractory B-cell acute lymphoblastic leukemiaHigh-risk prePharmacological inhibitionNovel therapeutic strategiesIndirect suppressionDirect inhibitionProliferation
2022
Mildly dysplastic oral lesions with optically-detectable abnormalities share genetic similarities with severely dysplastic lesions
Brenes D, Nipper A, Tan M, Gleber-Netto F, Schwarz R, Pickering C, Williams M, Vigneswaran N, Gillenwater A, Sikora A, Richards-Kortum R. Mildly dysplastic oral lesions with optically-detectable abnormalities share genetic similarities with severely dysplastic lesions. Oral Oncology 2022, 135: 106232. PMID: 36335817, PMCID: PMC9881670, DOI: 10.1016/j.oraloncology.2022.106232.Peer-Reviewed Original ResearchConceptsOral premalignant lesionsMild dysplasiaSevere dysplasiaOral lesionsPremalignant lesionsDysplastic oral lesionsHigh-grade pathologySubset of lesionsLoss of autofluorescenceDysplastic lesionsOptical imaging studiesOral surgeryDysplasiaDetectable abnormalitiesPatient careLesionsImaging studiesEpithelial cell nucleiPatientsGene expressionGene expression profilesMarkersGene expression analysisSimilar gene expressionExpression profilesInternode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids
Yanagui K, Camargo ELO, Abreu LGF, Nagamatsu ST, Fiamenghi MB, Silva NV, Carazzolle MF, Nascimento LC, Franco SF, Bressiani JA, Mieczkowski PA, Grassi MCB, Pereira GAG. Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids. Gene 2022, 828: 146476. PMID: 35413393, DOI: 10.1016/j.gene.2022.146476.Peer-Reviewed Original ResearchConceptsInternode elongationSaccharum hybridsSecondary cell wall formationDetailed transcriptome analysisCell wall formationDevelopment of plantsMolecular regulatory mechanismsEnergy caneRNA-seq analysisGrowth-related genesDifferent biological processesGene expression analysisCell wall characterizationDivision zoneTranscriptional regulationUnique genesCellulose synthesisTranscriptome analysisHigh biomass productionKey genesCell divisionWall formationBreeding programsBiomass biosynthesisExpression analysisInterferon drives HCV scarring of the epigenome and creates targetable vulnerabilities following viral clearance
Hlady RA, Zhao X, Khoury L, Luna A, Pham K, Wu Q, Lee J, Pyrsopoulos NT, Liu C, Robertson KD. Interferon drives HCV scarring of the epigenome and creates targetable vulnerabilities following viral clearance. Hepatology 2022, 75: 983-996. PMID: 34387871, PMCID: PMC9416882, DOI: 10.1002/hep.32111.Peer-Reviewed Original ResearchConceptsDNA methylationHistone modificationsWide DNA methylationAberrant DNA methylationGene expression analysisDNA methyltransferase inhibitorOpen chromatinEpigenetic mechanismsEpigenetic targetsHuman patient samplesEpigenetic changesEpigenomeMethyltransferase inhibitorTargetable vulnerabilitiesMethylationHCC cell linesImmortalized hepatocytesCell linesFunctional effectsChronic HCV infectionChromatinHCV infectionImmune responsePatient samplesSynergizesGlobal DNA methylation of WTC prostate cancer tissues show signature differences compared to non-exposed cases
Yu H, Tuminello S, Alpert N, van Gerwen M, Yoo S, Mulholland D, Aaronson S, Donovan M, Oh W, Gong Y, Wang L, Zhu J, Taioli E. Global DNA methylation of WTC prostate cancer tissues show signature differences compared to non-exposed cases. Carcinogenesis 2022, 43: 528-537. PMID: 35239955, PMCID: PMC9234756, DOI: 10.1093/carcin/bgac025.Peer-Reviewed Original ResearchConceptsPathway enrichment analysisGlobal DNA methylationEpithelial mesenchymal transitionDNA methylationProstate cancerEnrichment analysisGene expressionIncreased incidence of prostate cancerIncidence of prostate cancerDNA methylation findingsMYC-target pathwaysBlood of healthy individualsBisulfite-treated DNATGF-beta signaling pathwayTumor tissue blocksBeta signaling pathwayNon-exposed casesGene expression analysisProstate cancer tissuesStatistically significant differenceRNA gene expressionMethylation dataGleason scoreMitotic spindleTumor blocksResponse of Human Toll–Like Receptor 2 During the Infection of Leptospirosis
Kappagoda C, Senavirathna I, Warnasekara J, Srimantha S, De Silva N, Agampodi S. Response of Human Toll–Like Receptor 2 During the Infection of Leptospirosis. International Journal Of Infectious Diseases 2022, 116: s71. DOI: 10.1016/j.ijid.2021.12.167.Peer-Reviewed Original ResearchToll-like receptor2Human TLR2 geneTLR2 geneMouse modelToll-like receptor 2Human Toll-like receptor 2Results 64 patientsInnate immune responsePathogenic Leptospira sppGene expression analysisImmune responseStudy populationReceptor 2Receptor responsesTLR2 regulationPatientsLeptospirosisLeptospira sppNew therapeuticsWhole bloodGene expression studiesGene amplificationReverse transcriptaseInfectionTotal RNASOX2 mediates metabolic reprogramming of prostate cancer cells
de Wet L, Williams A, Gillard M, Kregel S, Lamperis S, Gutgesell L, Vellky J, Brown R, Conger K, Paner G, Wang H, Platz E, De Marzo A, Mu P, Coloff J, Szmulewitz R, Vander Griend D. SOX2 mediates metabolic reprogramming of prostate cancer cells. Oncogene 2022, 41: 1190-1202. PMID: 35067686, PMCID: PMC8858874, DOI: 10.1038/s41388-021-02157-x.Peer-Reviewed Original ResearchConceptsProstate cancer cellsSOX2 expressionCancer cellsTherapy resistanceMetastatic progressionMetabolic reprogrammingAssociated with multiple oncogenic pathwaysAndrogen-sensitive prostate cancer cellsGene targetingCastration-resistant prostate cancer cellsIncreased spare respiratory capacityChIP-seq analysisRNA-seq datasetsStem cell transcription factor Sox2Prostate cancer cell linesAnnotated tumor specimensSOX2 binding sitesPentose phosphate pathwayCRISPR-mediated deletionDecreased patient survivalSpare respiratory capacityQuantity of mitochondriaDeletion of Sox2Case-control cohortGene expression analysis
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