2025
Predicting response to neoadjuvant chemotherapy in muscle-invasive bladder cancer via interpretable multimodal deep learning
Bai Z, Osman M, Brendel M, Tangen C, Flaig T, Thompson I, Plets M, Scott Lucia M, Theodorescu D, Gustafson D, Daneshmand S, Meeks J, Choi W, Dinney C, Elemento O, Lerner S, McConkey D, Faltas B, Wang F. Predicting response to neoadjuvant chemotherapy in muscle-invasive bladder cancer via interpretable multimodal deep learning. Npj Digital Medicine 2025, 8: 174. PMID: 40121304, PMCID: PMC11929913, DOI: 10.1038/s41746-025-01560-y.Peer-Reviewed Original ResearchMuscle-invasive bladder cancerResponse to neoadjuvant chemotherapyNeoadjuvant chemotherapyBladder cancerPredicting response to neoadjuvant chemotherapyOptimal treatment strategyImprove patient survivalImproving clinical outcomesGene expression profilesBladder preservationPredictive biomarkersPatient survivalUnnecessary treatmentClinical outcomesTreatment responseRNA sequencingTumor heterogeneityTreatment strategiesClinical trialsGene signatureExpression profilesMolecular determinantsCancerChemotherapyBuilding accurate predictive modelsThe human and non-human primate developmental GTEx projects
Bell T, Blanchard T, Hernandez R, Linn R, Taylor D, VonDran M, Ahooyi T, Beitra D, Bernieh A, Delaney M, Faith M, Fattahi E, Footer D, Gilbert M, Guambaña S, Gulino S, Hanson J, Hattrell E, Heinemann C, Kreeb J, Leino D, Mcdevitt L, Palmieri A, Pfeiffer M, Pryhuber G, Rossi C, Rasool I, Roberts R, Salehi A, Savannah E, Stachowicz K, Stokes D, Suplee L, Van Hoose P, Wilkins B, Williams-Taylor S, Zhang S, Ardlie K, Getz G, Lappalainen T, Montgomery S, Aguet F, Anderson L, Bernstein B, Choudhary A, Domenech L, Gaskell E, Johnson M, Liu Q, Marderstein A, Nedzel J, Okonda J, Padhi E, Rosano M, Russell A, Walker B, Sestan N, Gerstein M, Milosavljevic A, Borsari B, Cho H, Clarke D, Deveau A, Galeev T, Gobeske K, Hameed I, Huttner A, Jensen M, Jiang Y, Li J, Liu J, Liu Y, Ma J, Mane S, Meng R, Nadkarni A, Ni P, Park S, Petrosyan V, Pochareddy S, Salamon I, Xia Y, Yates C, Zhang M, Zhao H, Conrad D, Feng G, Brady F, Boucher M, Carbone L, Castro J, del Rosario R, Held M, Hennebold J, Lacey A, Lewis A, Lima A, Mahyari E, Moore S, Okhovat M, Roberts V, de Castro S, Wessel B, Zaniewski H, Zhang Q, Arguello A, Baroch J, Dayal J, Felsenfeld A, Ilekis J, Jose S, Lockhart N, Miller D, Minear M, Parisi M, Price A, Ramos E, Zou S. The human and non-human primate developmental GTEx projects. Nature 2025, 637: 557-564. PMID: 39815096, DOI: 10.1038/s41586-024-08244-9.Peer-Reviewed Original ResearchConceptsChromatin accessibility dataFunctional genomic studiesWhole-genome sequencingEffects of genetic variationSpatial gene expression profilesNon-human primatesGenotype-Tissue ExpressionGene expression profilesGenomic studiesGene regulationGenetic dataGenetic variationGenomic researchDonor diversityCommunity engagementHuman evolutionEarly developmental defectsGene expressionCell statesDevelopmental programmeHuman diseasesExpression profilesAdult tissuesDevelopmental defectsSingle-cell
2024
Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial
Rediti M, Venet D, Joaquin Garcia A, Maetens M, Vincent D, Majjaj S, El-Abed S, Di Cosimo S, Ueno T, Izquierdo M, Piccart M, Pusztai L, Loi S, Salgado R, Viale G, Rothé F, Sotiriou C. Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial. Nature Communications 2024, 15: 10402. PMID: 39613746, PMCID: PMC11607438, DOI: 10.1038/s41467-024-54621-3.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBiomarkers, TumorBreast NeoplasmsClinical Trials, Phase III as TopicFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMiddle AgedNeoplasm Recurrence, LocalPrognosisRandomized Controlled Trials as TopicReceptor, ErbB-2TrastuzumabTumor MicroenvironmentConceptsHER2-positive breast cancerMolecular subtypesBreast cancerRate of pathological complete responseSensitive to HER2-targeted therapiesClinical trialsRisk of distant recurrenceBreast cancer molecular subtypesPathological complete responseHER2-targeted therapyCancer molecular subtypesPotential clinical implicationsNeoALTTO trialDistant recurrenceComplete responseAdjuvant trastuzumabPrognostic/predictive valueHeterogeneous biologySurvival outcomesI-SPY2Clinical outcomesMicroenvironment featuresGene expression profilesExternal cohortTumorArtificial-Intelligence, Data-Driven, Comprehensive Classification of Myeloid Neoplasms Based on Genomic, Morphological and Histological Features
Lanino L, D'Amico S, Maggioni G, Al Ali N, Wang Y, Gurnari C, Gagelmann N, Bewersdorf J, Ball S, Guglielmelli P, Meggendorfer M, Hunter A, Kubasch A, Travaglino E, Campagna A, Ubezio M, Russo A, Todisco G, Tentori C, Buizza A, Sauta E, Zampini M, Riva E, Asti G, Delleani M, Ficara F, Santoro A, Sala C, Dall'Olio D, Dall'Olio L, Kewan T, Casetti I, Awada H, Xicoy B, Vucinic V, Hou H, Chou W, Yao C, Lin C, Tien H, Consagra A, Sallman D, Kern W, Bernardi M, Chiusolo P, Borin L, Voso M, Pleyer L, Palomo L, Quintela D, Jerez A, Cornejo E, Martin P, Díaz-Beyá M, Pita A, Roldan V, Suarez D, Velasco E, Calabuig M, Garcia-Manero G, Loghavi S, Platzbecker U, Sole F, Diez-Campelo M, Maciejewski J, Kröger N, Fenaux P, Fontenay M, Santini V, Haferlach T, Germing U, Padron E, Robin M, Passamonti F, Solary E, Vannucchi A, Castellani G, Zeidan A, Komrokji R, Della Porta M. Artificial-Intelligence, Data-Driven, Comprehensive Classification of Myeloid Neoplasms Based on Genomic, Morphological and Histological Features. Blood 2024, 144: 1005. DOI: 10.1182/blood-2024-204826.Peer-Reviewed Original ResearchGenomic featuresSplicing mutationBiallelic inactivationAnalysis of genomic profilesBiallelic inactivation of TP53Clinical phenotypeGene expression profilesCNV analysisMorphological featuresInactivation of TP53Myeloid neoplasmsGenomic characterizationRNAseq dataMorphological dataMutation screeningExpression profilesMutationsJAK/STATGenomic profilingGenomeHierarchical importanceHeterogeneous phenotypesIntegrated analysisPhenotypeHematological phenotypeExpression and prognostic value of cell‐cycle‐associated genes in lung squamous cell carcinoma
Xu X, Jin K, Xu X, Yang Y, Zhou B. Expression and prognostic value of cell‐cycle‐associated genes in lung squamous cell carcinoma. The Journal Of Gene Medicine 2024, 26: e3735. PMID: 39171952, DOI: 10.1002/jgm.3735.Peer-Reviewed Original ResearchConceptsCell cycle-associated genesLung squamous carcinomaCell cycleMRNA expression dataGene expression profilesAssociated with positive prognosisCause of cancer-related deathExpression dataCancer Genome AtlasExpressed genesSquamous cell carcinomaLung squamous cell carcinomaTargeted therapy trialsGroup of patientsCancer-related deathsExpression of CDK4GenesExpression trendsExpression profilesMolecular studiesGenome AtlasSquamous carcinomaCell carcinomaPathological stagePrognostic valueHepatotoxicity assessment of innovative nutritional supplements based on olive-oil formulations enriched with natural antioxidants
Prodromou S, Chatzopoulou F, Saiti A, Giannopoulos-Dimitriou A, Koudoura L, Pantazaki A, Chatzidimitriou D, Vasiliou V, Vizirianakis I. Hepatotoxicity assessment of innovative nutritional supplements based on olive-oil formulations enriched with natural antioxidants. Frontiers In Nutrition 2024, 11: 1388492. PMID: 38812942, PMCID: PMC11133736, DOI: 10.3389/fnut.2024.1388492.Peer-Reviewed Original ResearchNutritional supplementsLong-term effects of oxidative stressOxidative stressCell culturesReal-time PCRNatural antioxidantsEvaluate cell viabilityGene expression profilesPotential nutritional supplementEffects of oxidative stressHepG2 cell culturesMolecular pathophysiologyTherapeutic strategiesQuantitative real-time PCRInflammatory signalingAlleviate symptomsAlzheimer's diseaseLong-term effectsLong-term consequencesProliferation capacityMolecular pathwaysCell toxicityDelivery modeCellular toxicityOlive-oilSurveillance with dual noninvasive testing for acute cellular rejection after heart transplantation: Outcomes from the Surveillance HeartCare Outcomes Registry
Khush K, Hall S, Kao A, Raval N, Dhingra R, Shah P, Bellumkonda L, Ravichandran A, Van Bakel A, Uriel N, Patel S, Pinney S, DePasquale E, Baran D, Pinney K, Oreschak K, Kobulnik J, Shen L, Teuteberg J. Surveillance with dual noninvasive testing for acute cellular rejection after heart transplantation: Outcomes from the Surveillance HeartCare Outcomes Registry. The Journal Of Heart And Lung Transplantation 2024, 43: 1409-1421. PMID: 38759766, DOI: 10.1016/j.healun.2024.05.003.Peer-Reviewed Original ResearchAcute cellular rejectionIncidence of acute cellular rejectionBiopsy rateGene expression profilesNon-invasive testsMolecular testingDd-cfDNACellular rejectionGraft dysfunctionHeart transplantationFollow-up testing ratesIncidence of graft dysfunctionLow biopsy rateFollow-up biopsiesPositive likelihood ratioNon-invasive surveillanceBiopsy dataClinical decision-makingExcellent survivalOutcomes RegistryFollow-upLow incidenceBiopsyPositive groupDual testingRevisiting the Potency of Tbx2 Expression in Transforming Outer Hair Cells into Inner Hair Cells at Multiple Ages In Vivo
Bi Z, Ren M, Zhang Y, He S, Song L, Li X, Liu Z. Revisiting the Potency of Tbx2 Expression in Transforming Outer Hair Cells into Inner Hair Cells at Multiple Ages In Vivo. Journal Of Neuroscience 2024, 44: e1751232024. PMID: 38688721, PMCID: PMC11154855, DOI: 10.1523/jneurosci.1751-23.2024.Peer-Reviewed Original ResearchSpatiotemporal patterns of locus coeruleus integrity predict cortical tau and cognition
Bueichekú E, Diez I, Kim C, Becker J, Koops E, Kwong K, Papp K, Salat D, Bennett D, Rentz D, Sperling R, Johnson K, Sepulcre J, Jacobs H. Spatiotemporal patterns of locus coeruleus integrity predict cortical tau and cognition. Nature Aging 2024, 4: 625-637. PMID: 38664576, PMCID: PMC11108787, DOI: 10.1038/s43587-024-00626-y.Peer-Reviewed Original ResearchConceptsTau spreadingDisease pathologyGene expression profilesTau positron emission tomography imagingTranscriptomic informationLocus coeruleusHyperphosphorylated tauAlzheimer's disease pathologyTau accumulationBiological functionsExpression profilesTau depositionGenetic featuresCortical tauAlzheimer's diseaseLocus coeruleus integrityTauAssociated with lower cognitive performanceLower cognitive performanceTransport regulationLC integrityCognitive performanceAlzheimerAllocortical regionsSpatiotemporal patternsDedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease
Chandran R, Adams T, Kabir I, Gallardo-Vara E, Kaminski N, Gomperts B, Greif D. Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease. Frontiers In Cell And Developmental Biology 2024, 12: 1335061. PMID: 38572485, PMCID: PMC10987733, DOI: 10.3389/fcell.2024.1335061.Peer-Reviewed Original ResearchRNA sequencing analysisSMA+ myofibroblastsGene expression profilesLung myofibroblastsAdult lungSequence analysisResponse to lung injurySingle cell RNA sequencing analysisTissue remodeling genesSmooth muscle cell markersLung to hypoxiaExpression profilesRemodeling genesMuscle cell markersResponse to injuryCell typesSMA cellsLineage tracingLung injuryCell markersLineagesGenesAdult diseaseDrug bleomycinLung surface areaHomotopic functional connectivity disruptions in schizophrenia and their associated gene expression
Cai M, Ji Y, Zhao Q, Xue H, Sun Z, Wang H, Zhang Y, Chen Y, Zhao Y, Zhang Y, Lei M, Wang C, Zhuo C, Liu N, Liu H, Liu F. Homotopic functional connectivity disruptions in schizophrenia and their associated gene expression. NeuroImage 2024, 289: 120551. PMID: 38382862, DOI: 10.1016/j.neuroimage.2024.120551.Peer-Reviewed Original ResearchConceptsVoxel-mirrored homotopic connectivityAbnormal VMHCAllen Human Brain AtlasFunctional connectivity disruptionsHuman Brain AtlasExtensive cortical regionsBrain gene expression profilesIllness durationHomotopic connectivitySchizophreniaDecoding analysesCortical regionsConnectivity disruptionsDevelopmental time windowCell communicationChanges compared to controlsExpression of identified genesGene expression dataBrain atlasesRegulation of cell communicationMeta-regression analysisGene expression profilesNervous system developmentExpression dataNeurosynth
2023
Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress
Melnick A, Mullin C, Lin K, McCarter A, Liang S, Liu Y, Wang Q, Jerome N, Choe E, Kunnath N, Bodanapu G, Akter F, Magnuson B, Kumar S, Lombard D, Muntean A, Ljungman M, Sekiguchi J, Ryan R, Chiang M. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. Blood 2023, 142: 2159-2174. PMID: 37616559, PMCID: PMC10733839, DOI: 10.1182/blood.2023020144.Peer-Reviewed Original ResearchConceptsT-cell acute lymphoblastic leukemiaNotch signalingActivate transcription of genesExpression programsDNA damageTranscription of genesT-ALL oncogenesTranscription factor ETS1Elevated Notch signalingT-cell leukemia cellsImpaired mitochondrial functionGene expression profilesGene expression programsT cell developmentTranscription machineryActivate transcriptionActivate Notch signalingMitochondrial stressOncogenic NotchTargeting Notch signalingOxidative phosphorylationActivate expressionDNA repairMitochondrial functionNotch complexThrombocyte-derived Dickkopf1 promotes macrophage polarization in the Bleomycin-induced lung injury model
Sung E, Park M, Song S, Alanya H, Henegariu O, Liu J, Erson-Omay E, Sime P, Chae W. Thrombocyte-derived Dickkopf1 promotes macrophage polarization in the Bleomycin-induced lung injury model. Frontiers In Immunology 2023, 14: 1247330. PMID: 38162655, PMCID: PMC10757334, DOI: 10.3389/fimmu.2023.1247330.Peer-Reviewed Original ResearchConceptsLung injury modelMacrophage polarizationTissue repair processInjury modelMonocyte-derived alveolar macrophagesInjury-induced inflammationTissue repairRepair processRole of WntGene expression profilesImmunomodulatory roleIL-13Tissue injuryImmune responseInflammationCollagen depositionAlveolar macrophagesMacrophagesTissue homeostasisProtein expressionGene expressionRegulatory ligandsExpression profilesWnt antagonist Dickkopf1Dickkopf1Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts
Dighe A, Maziarz J, Ibrahim-Hashim A, Gatenby R, Kshitiz, Levchenko A, Wagner G. Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts. IScience 2023, 27: 108593. PMID: 38174318, PMCID: PMC10762354, DOI: 10.1016/j.isci.2023.108593.Peer-Reviewed Original ResearchGene expression changesGene expression evolutionEndometrial stromal fibroblastsExpression evolutionExpression changesCell typesGene expressionSimilar gene expression changesSubstantial gene expression changesGene expression profilesSkin fibroblastsMultiple cell typesEvolutionary correlationPhylogenetic evidenceEvolutionary changeDermal skin fibroblastsMammalian speciesExpression profilesPlacental invasivenessComparative datasetCancer growthCultured skin fibroblastsStromal fibroblastsFibroblastsMouse strainsMYC to BCL6 State-Transitions Determine Cell Size and Metabolic Fluctuations and Define a Novel Biorhythm in B-Cell Malignancies
Cheng Z, Kume K, Müschen M. MYC to BCL6 State-Transitions Determine Cell Size and Metabolic Fluctuations and Define a Novel Biorhythm in B-Cell Malignancies. Blood 2023, 142: 2769. DOI: 10.1182/blood-2023-190972.Peer-Reviewed Original ResearchGerminal center-derived B-cell lymphomaB cell developmentCell size fluctuationsCell cycleImmunoglobulin light chain gene recombinationDNA damage-induced apoptosisDistinct cellular statesNormal B cell developmentDamage-induced apoptosisExit cell cycleCell sizeB cell transitionGene expression profilesQuiescent phenotypeOncogenic tyrosine kinasesCell cycle arrestActivation of autophagySingle-cell sortingCellular statesCell divisionHigher glycolysis activityMYC transcriptionB cell cycleSuppression of glycolysisExpression profilesFinal 36-Month Outcomes from the Multicenter DynamX Study Evaluating a Novel Thin-Strut Novolimus-Eluting Coronary Bioadaptor System and Supporting Preclinical Data
Verheye S, Vrolix M, Montorfano M, Giannini F, Bedogni F, Dubois C, De Bruyne B, Costa R, Chamié D, Costa J, Abizaid A, Colombo A. Final 36-Month Outcomes from the Multicenter DynamX Study Evaluating a Novel Thin-Strut Novolimus-Eluting Coronary Bioadaptor System and Supporting Preclinical Data. Reviews In Cardiovascular Medicine 2023, 24: 221. PMID: 39076703, PMCID: PMC11266769, DOI: 10.31083/j.rcm2408221.Peer-Reviewed Original ResearchDrug-eluting stentsOptical coherence tomographyTarget lesion revascularizationExpression of contractile genesPreclinical studiesLesion revascularizationGene expression profilesClinically-driven target lesion revascularizationIntention-to-treat populationContractile genesCoronary arteryIncreased expressionLong-term adverse outcomesClinical follow-upLate lumen enlargementCell gene expression profilesRestoring vessel functionTarget vessel revascularizationTarget lesion failureReal-time polymerase chain reactionPreclinical dataExpression profilesClinical outcomesLumen enlargementCardiac deathProfiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex
Rompala G, Nagamatsu S, Martínez-Magaña J, Nuñez-Ríos D, Wang J, Girgenti M, Krystal J, Gelernter J, Hurd Y, Montalvo-Ortiz J. Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex. Nature Communications 2023, 14: 4544. PMID: 37507366, PMCID: PMC10382503, DOI: 10.1038/s41467-023-40285-y.Peer-Reviewed Original ResearchConceptsOpioid use disorderMulti-omics findingsGene expression patternsCo-methylation analysisGene expression profilesMulti-omics profilingGene networksDNA methylationNeuronal methylomesDNA hydroxymethylationMethylomic analysisExpression patternsExpression profilesEpigenetic disturbancesUse disordersPsychiatric traitsOrbitofrontal cortexOpioid-related drugsPostmortem orbitofrontal cortexEnvironmental factorsDrug interaction analysisOUD treatmentHuman orbitofrontal cortexOpioid signalingInteraction analysisAssessing transcriptomic reidentification risks using discriminative sequence models
Sadhuka S, Fridman D, Berger B, Cho H. Assessing transcriptomic reidentification risks using discriminative sequence models. Genome Research 2023, 33: 1101-1112. PMID: 37541758, PMCID: PMC10538488, DOI: 10.1101/gr.277699.123.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociGene expression dataExpression dataQuantitative trait lociOmics data setsGene expression profilesTrait lociGenomic regionsGenetic variationGene expressionExpression profilesMolecular insightsLinkage disequilibriumFunctional impactGenotypesTranscriptomicsLociSame individualDisequilibriumSequenceExpressionPrevious studiesFull extentData setsThe C. elegans anchor cell transcriptome: ribosome biogenesis drives cell invasion through basement membrane
Costa D, Kenny-Ganzert I, Chi Q, Park K, Kelley L, Garde A, Matus D, Park J, Yogev S, Goldstein B, Gibney T, Pani A, Sherwood D. The C. elegans anchor cell transcriptome: ribosome biogenesis drives cell invasion through basement membrane. Development 2023, 150 PMID: 37039075, PMCID: PMC10259517, DOI: 10.1242/dev.201570.Peer-Reviewed Original ResearchConceptsRibosome biogenesisCell invasionAnchor cell invasionTranslation of proteinsFocused RNAi screenGene expression profilesAC invasionRibosome productionRNAi screenEndomembrane systemBM transmigrationRibosomal proteinsSec61 transloconCell transcriptomeBasement membrane barriersGene enrichmentExpression profilesTumor proteinTranscriptomeER stressCancer progressionInvasion regulatorsMembrane barrierProteinBiogenesisThe evolving role of liver sinusoidal endothelial cells in liver health and disease
McConnell M, Kostallari E, Ibrahim S, Iwakiri Y. The evolving role of liver sinusoidal endothelial cells in liver health and disease. Hepatology 2023, 78: 649-669. PMID: 36626620, PMCID: PMC10315420, DOI: 10.1097/hep.0000000000000207.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsLiver diseaseAlcohol-associated liver diseaseEndothelial cellsLiver transplant rejectionIschemia-reperfusion injuryLiver sinusoidal endothelial cellsSinusoidal endothelial cellsPortal hypertensionLiver inflammationMicrovascular thrombosisViral hepatitisReperfusion injuryTransplant rejectionLiver healthLiver pathologyLiver homeostasisLiver regenerationQuiescent phenotypePathological processesUnique populationDiseaseLSECLiver biologyGene expression profilesInflammation
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