2025
Interleukin-6 Trans Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis
Sarode G, Hsu M, Haj F, Barace S, Argemi J, Liu M, Pandita P, Cao S, Shah V, Gui D, Bataller R, Rachakonda V. Interleukin-6 Trans Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis. American Journal Of Pathology 2025 PMID: 40562277, DOI: 10.1016/j.ajpath.2025.05.023.Peer-Reviewed Original ResearchSTAT3-dependent gene expressionAlcohol-associated hepatitisSTAT3 activationIL-6 trans signalingRNA-seqTrans signalingIL-6R expressionGene expressionLiver RNA-seqIL-6Hyper-IL-6Neutrophilic inflammationIL-6 receptorIL-6RTGF-b1Intrahepatic neutrophil infiltrationLiver injury responsePathophysiology of AHTranscript enrichmentNegative regulatorChronic liver failureLiver disease patientsMembrane-boundSTAT3Severe AHHost-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells.
D'Mello A, Murphy T, Wade M, Kirkham C, Kong Y, Tettelin H, Pettigrew M. Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells. MSphere 2025, e0024225. PMID: 40492732, DOI: 10.1128/msphere.00242-25.Peer-Reviewed Original ResearchRegulation of quorum sensingTranscriptome profilingBioinformatics analysisCell culture modelBiological pathwaysIron-sulfur metabolismHost-pathogen interactionsHost biological pathwaysHost cell pathwaysIscR regulonChronic obstructive pulmonary diseaseEpithelial cellsQuorum sensingEpithelial cell infectionRNA-seqH292 cell lineHost pathwaysExacerbation of chronic obstructive pulmonary diseaseNontypeable Haemophilus influenzaeRNA sequencingHost cellsDifferential regulationCulture modelBronchial epithelial cellsMono-infectionCo-expression network-based analysis of gene programs contributing to immune checkpoint inhibitor (ICI) resistance in renal cell carcinoma (RCC).
Malik R, Rout R, Kashima S, Saad E, Kane H, Shah V, Hugaboom M, Ye Z, Schindler N, Dighe A, Sun M, Lee G, Xu W, Signoretti S, McGregor B, McKay R, Atkins M, Van Allen E, Choueiri T, Braun D. Co-expression network-based analysis of gene programs contributing to immune checkpoint inhibitor (ICI) resistance in renal cell carcinoma (RCC). Journal Of Clinical Oncology 2025, 43: 4530-4530. DOI: 10.1200/jco.2025.43.16_suppl.4530.Peer-Reviewed Original ResearchImmune checkpoint inhibitorsRenal cell carcinomaImmune cellsImmune infiltrationSignature scoreRCC tumor microenvironmentResistance to immune checkpoint inhibitorsAssociated with worse PFSICI-based therapyScRNA-seq dataGene programCD8+ TPhase II trialICI resistanceImmune-lowCheckpoint inhibitorsRibosomal proteinsCD4+II trialPrognostic roleRenal cell carcinoma tumor sampleRNA-seqCell carcinomaTumor microenvironmentScRNA-seqSteamed panax notoginseng mitigates CA-MRSA USA300-induced necroptosis in human neutrophils
Zhang L, Feng X, An H, Yang W, Xia Y, Wen B, Zheng H, Chen Y, Cheng Y, Jiang C, Lu C, Tan Y. Steamed panax notoginseng mitigates CA-MRSA USA300-induced necroptosis in human neutrophils. Frontiers In Pharmacology 2025, 16: 1546652. PMID: 40520183, PMCID: PMC12163054, DOI: 10.3389/fphar.2025.1546652.Peer-Reviewed Original ResearchCA-MRSAVirulence factorsCommunity-associated methicillin-resistant <i>Staphylococcus aureus</i> (CAQuorum-sensing signaling pathwayPolymorphonuclear neutrophil countMethicillin-resistant <i>Staphylococcus aureus</i> (MRPhagocytic function of polymorphonuclear neutrophilsGenes of MRSAPolymorphonuclear neutrophilsSignaling pathwayCA-MRSA infectionsHost innate immune responseBacterial virulence factorsDrug-resistant bacterial infectionsMCP-1IL-1BIL-8Pro-inflammatory cytokines IL-1bDisrupt innate immunityInnate immune responseRNA-seqFunctions of polymorphonuclear neutrophilsPathogenic microbial infectionsPanax notoginsengCytokines IL-1bDifferential 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 analysisP112 Cytokine driven disease and epigenetic heterogeneity in rheumatoid arthritis
Hughes S, Costa D, Soria A, Hill D, Figueras A, Scott R, Dimonte S, Monaco F, Jenkins R, Twohig J, Guy C, Cossins B, Andrews R, Szomolay B, Choy E, Vinh N, Lewis M, Jenkins B, Turner S, Tiganis T, Williams N, Yu H, Pitzalis C, Jones G, Jones S. P112 Cytokine driven disease and epigenetic heterogeneity in rheumatoid arthritis. Rheumatology 2025, 64: keaf142.152. DOI: 10.1093/rheumatology/keaf142.152.Peer-Reviewed Original ResearchEctopic lymphoid-like structuresAntigen-induced arthritisRNA-seqTransposase-accessible chromatin (ATAC)-seqRheumatoid arthritisChromatin immunoprecipitation (ChIP)-seqTreatment of immune-mediated inflammatory diseasesClinical response to therapyCytokine signalingSynovial biopsiesImmune-mediated inflammatory diseasesSmall-needle biopsiesLymphoid-like structuresResponse to therapyNature of pathologyWT miceEpigenetic heterogeneityNeedle biopsyTargeting cytokine signallingGenomic signaturesImmune pathologyNGS methodSTAT3 activationTranscription factorsEpigenetic regulationDecreased T helper 1 cell function underlies recurrent sinopulmonary infections in the 17q12 deletion syndrome
Shin J, Shin H, Gutierrez A, Yoo N, Par-Young J, Osmani L, Shin M, Sanchez-Lara P, Bucala R, Soffer G, Kang I. Decreased T helper 1 cell function underlies recurrent sinopulmonary infections in the 17q12 deletion syndrome. EBioMedicine 2025, 112: 105578. PMID: 39891996, PMCID: PMC11840234, DOI: 10.1016/j.ebiom.2025.105578.Peer-Reviewed Original ResearchConceptsCD4<sup>+</sup> T cellsRecurrent sinopulmonary infectionsT cell functionRNA-seq analysisT cellsHealthy controlsSinopulmonary infectionsRNA-seqT-betIFN-gFrequency of CD4<sup>+</sup> T cellsCD4<sup>+</sup> T cell functionTh1 transcription factor T-betDeletion syndromeFlow cytometryCompared to age-matched healthy controlsTranscription factor T-betDecreased T-betUrinary tract abnormalitiesAge-matched healthy controlsMultiplex assayDownstream effector cytokinesEffector cytokinesRecurrent infectionsTh17 cytokinesAge-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
Epigenomics and single cell CRISPR screening to investigate the risk‐modifying role of microglia in Alzheimer’s disease and multiple sclerosis
Gallagher M, Du W, Hazel K, Aydin Z, Cheng Y, Yuan B, Bell G, Young R, Jaenisch R, Corradin O. Epigenomics and single cell CRISPR screening to investigate the risk‐modifying role of microglia in Alzheimer’s disease and multiple sclerosis. Alzheimer's & Dementia 2024, 20: e093591. PMCID: PMC11710746, DOI: 10.1002/alz.093591.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsRisk lociMS risk lociEnhancer landscapeSingle cell screeningCell type-specific enhancersGenome-wide association studiesMicroglia-specific enhancersH3K27ac ChIP-seqNeurodegenerative diseasesCell type-specificEx vivo microgliaSNP enrichmentChIP-seqHi-C.CRISPRi screenEnhancer/promoter interactionNoncoding regionsRNA-seqAssociation studiesCRISPR screensCRISPRiNucleotide polymorphismsSafe harbor locusCell screeningKv1.3 regulation of brain immune function in vitro and in vivo
Bowen C, Nguyen H, Lin Y, Bagchi P, Natu A, Xiao H, Espinosa‐Garcia C, Kumar P, Wulff H, Seyfried N, Rangaraju S. Kv1.3 regulation of brain immune function in vitro and in vivo. Alzheimer's & Dementia 2024, 20: e093042. PMCID: PMC11709668, DOI: 10.1002/alz.093042.Peer-Reviewed Original ResearchProtein processingN-terminusProximity-based proteomicsProtein-protein interactomePDZ-binding motifPDZ-binding domainPlasma membrane proteinsDeletion in vivoJurkat T cellsT cellsKO miceBiotin ligaseCMV-Cre miceRNA-seqTrafficking proteinsBiotinylated proteinsTranscriptome levelC-terminusMembrane proteinsInteractorsMicroglial signatureImmune signalingPlasma membraneLPS stimulationDifferential expressionComparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes
Sura G, Tran K, Trevarton A, Marczyk M, Fu C, Du L, Qu J, Lau R, Tasto A, Gould R, Tinnirello A, Sinn B, Pusztai L, Hatzis C, Symmans W. Comparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes. Journal Of The American Society Of Cytopathology 2024, 14: 91-101. PMID: 39668068, DOI: 10.1016/j.jasc.2024.11.001.Peer-Reviewed Original ResearchRNA integrity numberRNA qualityRNA-seqMeasurement of gene expressionRNA-seq analysisMetastatic breast cancerFicoll-Hypaque methodDensity gradient enrichmentSequence dataRead-basedVariant detectionMalignant effusionsCytospin slidesFresh frozen samplesRNA fragmentsTranscript abundanceSequencing outcomesSequencing methodsBreast cancerRNA sequencingFicoll-HypaqueUMI-basedGene expressionRNAMalignant effusion specimensUnraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies
Biancon G, Busarello E, Cheng M, Sidoli S, VanOudenhove J, Bucciarelli G, Tebaldi T, Halene S. Unraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies. Blood 2024, 144: 4117. DOI: 10.1182/blood-2024-211265.Peer-Reviewed Original ResearchRNA-binding proteinsStress granulesRNA-seqArsenite stressSF mutationsAcute myeloid leukemiaSplicing factorsSG proteinsStress responseClonal advantageSG coresMulti-omicsDeregulated genesMyelodysplastic syndromeEnhances SG formationU2AF1 S34F mutationSingle-cell RNA-seqWT cellsMegakaryocyte-erythroid progenitorsRegulation of translationTranslation initiation factorsImprove cell fitnessRNA-seq analysisPost-translational modificationsU2AF1 mutationsCytoplasmic Intron Retention As a Regulatory Mechanism of Mitochondrial Homeostasis in Erythroid Cells
Roy R, Boddu P, Pillai M. Cytoplasmic Intron Retention As a Regulatory Mechanism of Mitochondrial Homeostasis in Erythroid Cells. Blood 2024, 144: 1075-1075. DOI: 10.1182/blood-2024-211280.Peer-Reviewed Original ResearchNonsense-mediated decayIntron retentionRetained intronsCry transcriptsSplicing factorsRI transcriptionFunctional genomics dataLong-read sequencingAbsence of intronsErythroid cellsENCODE consortiumPolyadenylated RNAGenomic dataRNA-seqHUDEP-2 cellsMRNA processingNuclear exportCRISPR deletionMitochondrial homeostasisProtein isoformsRNA abundanceUnspliced RNAIntronStages of erythropoiesisPeptide translationEnhancing Personalized Prognostic Assessment of Myelodysplastic Syndromes through a Multimodal and Explainable Deep Data Fusion Approach (MAGAERA)
Sauta E, Sartori F, Lanino L, Asti G, D'Amico S, Delleani M, Riva E, Zampini M, Zazzetti E, Bicchieri M, Maggioni G, Campagna A, Todisco G, Tentori C, Ubezio M, Russo A, Buizza A, Ficara F, Crisafulli L, Brindisi M, Ventura D, Pinocchio N, Rahal D, Lancellotti C, Bonometti A, Di Tommaso L, Savevski V, Santoro A, Derus N, Dall'Olio D, Santini V, Sole F, Platzbecker U, Fenaux P, Diez-Campelo M, Komrokji R, Garcia-Manero G, Haferlach T, Kordasti S, Zeidan A, Castellani G, Sanavia T, Fariselli P, Della Porta M. Enhancing Personalized Prognostic Assessment of Myelodysplastic Syndromes through a Multimodal and Explainable Deep Data Fusion Approach (MAGAERA). Blood 2024, 144: 105-105. DOI: 10.1182/blood-2024-205413.Peer-Reviewed Original ResearchPersonalized medicine programsMyelodysplastic syndrome patientsMyelodysplastic syndromeOverall survivalConcordance indexClinical outcomesMay-Grunwald-GiemsaHypomethylating agentsBone marrowAnalysis of hematological malignanciesSomatic mutation screeningEvaluation of T lymphocytesResponse to hypomethylating agentsCD34+ bone marrowStudies of myelodysplastic syndromesGenomic featuresMDS populationRNA-seqPrediction of patient outcomeGenomic characterizationHarrell's concordance indexPredicting clinical outcomesHematoxylin and eosin (H&EMorphological dataMulti-omicsThe Immune-Related 27-Gene Signature DetermaIO Predicts Response to Neoadjuvant Atezolizumab plus Chemotherapy in Triple-Negative Breast Cancer
Dugo M, Huang C, Egle D, Bermejo B, Zamagni C, Seitz R, Nielsen T, Thill M, Antón-Torres A, Russo S, Ciruelos E, Schweitzer B, Ross D, Galbardi B, Greil R, Semiglazov V, Gyorffy B, Colleoni M, Kelly C, Mariani G, Del Mastro L, Blasi O, Callari M, Pusztai L, Valagussa P, Viale G, Gianni L, Bianchini G. The Immune-Related 27-Gene Signature DetermaIO Predicts Response to Neoadjuvant Atezolizumab plus Chemotherapy in Triple-Negative Breast Cancer. Clinical Cancer Research 2024, 30: of1-of10. PMID: 39308141, PMCID: PMC11528202, DOI: 10.1158/1078-0432.ccr-24-0149.Peer-Reviewed Original ResearchPathologic complete response ratePathological complete responseTriple-negative breast cancerRNA-seqI-SPY2Immuno-oncologyBreast cancerPatients treated with pembrolizumabTumor-infiltrating lymphocyte countsPublicly available microarray dataPretreatment core biopsiesImmune checkpoint therapyRNA-seq dataPer-protocol populationAvailable microarray dataI-SPY2 trialPDL1 protein expressionNeoadjuvant atezolizumabNeoadjuvant immunotherapyPlus chemotherapyCheckpoint therapyComplete responseTriple-negativeCore biopsyRT-qPCR dataSingle-nuclei RNA-seq reveals aberrant cell populations in restrictive allograft syndrome after lung transplantation
Leiber L, Christian L, Neubert L, Yilmaz H, Kamp J, Plucinski E, Welte T, Falk C, Kaminski N, Jonigk* D, Gottlieb* J, Schupp* J. Single-nuclei RNA-seq reveals aberrant cell populations in restrictive allograft syndrome after lung transplantation. 2024, oa985. DOI: 10.1183/13993003.congress-2024.oa985.Peer-Reviewed Original ResearchMitochondrial reprogramming by activating OXPHOS via glutamine metabolism in African American patients with bladder cancer
Reddy K, Piyarathna D, Park J, Putluri V, Amara C, Kamal A, Xu J, Kraushaar D, Huang S, Jung S, Eberlin L, Johnson J, Kittles R, Ballester L, Parsawar K, Siddiqui M, Gao J, Gramer A, Bollag R, Terris M, Lotan Y, Creighton C, Lerner S, Sreekumar A, Kaipparettu B, Putluri N. Mitochondrial reprogramming by activating OXPHOS via glutamine metabolism in African American patients with bladder cancer. JCI Insight 2024, 9: e172336. PMID: 39253977, PMCID: PMC11385078, DOI: 10.1172/jci.insight.172336.Peer-Reviewed Original ResearchConceptsBladder cancerOxidative phosphorylationComponents of complex IComplex IElevated mitochondrial oxidative phosphorylationComprehensive RNA-seqReduced basal respirationActive oxidative phosphorylationMitochondrial oxidative phosphorylationDecreased tumor growthTumor growth potentialIncreased disease progressionMitochondrial respiration rateAfrican American patientsRNA-seqRace-specific differencesMitochondrial reprogrammingEuropean AmericansMetabolic rewiringOXPHOS activityBasal respirationGlutamine metabolismGLS1 expressionPreclinical studiesATP productionCharacterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq
Guo L, Grinko A, Olson S, Leipold A, Graveley B, Saliba A, Pyle A. Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq. RNA 2024, 30: rna.080032.124. PMID: 39174298, PMCID: PMC11482623, DOI: 10.1261/rna.080032.124.Peer-Reviewed Original ResearchNontemplated additionRNA-seqRNA sequencingGroup II self-splicing intronsTemplate-switching oligonucleotidesLong-read sequencingRNA-seq technologySelf-splicing intronsTemplate-switching reactionsLong RNA transcriptsRNA sequencing methodsWell-characterized enzymesPoly(A)-enriched RNART enzymeRNA identityNucleotide specificityEnzymatic specificityRNA librariesRNA transcriptsLong RNAsHuman RNARNA moleculesRNA referenceAccurate sequencingBinding specificityCRISPR-based dissection of microRNA-23a ~ 27a ~ 24-2 cluster functionality in hepatocellular carcinoma
Cui M, Liu Z, Wang S, Bae S, Guo H, Zhou J, Liu R, Wang L. CRISPR-based dissection of microRNA-23a ~ 27a ~ 24-2 cluster functionality in hepatocellular carcinoma. Oncogene 2024, 43: 2708-2721. PMID: 39112518, PMCID: PMC11364504, DOI: 10.1038/s41388-024-03115-z.Peer-Reviewed Original ResearchConceptsMiR-23aMiR-27aCRISPR interferenceCRISPR activationHigh-throughput RNA-seqCell migrationCDK1/cyclin B activityReduced cell growth in vitroMiRNA target predictionCell cycle arrestMiRNA clusterHepatocellular carcinoma cellsCell growth in vitroRNA-seqGene networksTarget predictionCRISPR knockoutOncogenic roleGrowth in vitroCycle arrestMature miRNAsMiRNAsG2/M phaseSignaling pathwayOncogenic function
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