2025
Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data
Zhang H, Jiang Z, Zhang S, Tu L, Carlson D. Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data. Pattern Recognition 2025, 168: 111724. DOI: 10.1016/j.patcog.2025.111724.Peer-Reviewed Original ResearchSingle-cell RNA-seq dataHigh-throughput single-cell RNA sequencingGene pathway informationCell type annotationRNA-seq dataSingle-cell datasetsSingle-cell RNA sequencingGene expression vectorScRNA-seqPathway informationDiverse speciesRNA sequencingExpression vectorAnnotation methodGene expressionDropout eventsExpression patternsGenesSpeciesType annotationsAnnotationCellsComprehensive intra-Cell levelSequenceChemPerturb-seq screen identifies a small molecule cocktail enhancing human beta cell survival after subcutaneous transplantation
Vandana J, Zhu J, Giani A, Zhang T, Lacko L, Leng D, Taylor D, Lee B, Han Z, Jiao T, Huang Y, Zhao M, Liu X, Chong A, Xue D, Meng Z, Xiang J, Pan C, Wang W, Naji A, Evans T, Liu J, Collins F, Liu C, Chen S. ChemPerturb-seq screen identifies a small molecule cocktail enhancing human beta cell survival after subcutaneous transplantation. Cell Stem Cell 2025 PMID: 40562034, DOI: 10.1016/j.stem.2025.06.002.Peer-Reviewed Original ResearchProtocol to implement saturation mutagenesis-reinforced functional assays to resolve small-sized variants in disease-related genes
Gauthier L, Wang Z, Ng K, Huang S, Mao Y, Lek M, Ma K. Protocol to implement saturation mutagenesis-reinforced functional assays to resolve small-sized variants in disease-related genes. STAR Protocols 2025, 6: 103909. PMID: 40540392, DOI: 10.1016/j.xpro.2025.103909.Peer-Reviewed Original ResearchDisease-related genesDisease-causing genetic variantsFluorescence-based cell sortingNext-generation sequencingFunctional assaysDisease genesAllelic seriesSaturation mutagenesisGenetic variantsGenesFunctional impactCell sortingHigh-throughputVariantsDisease fieldAssayMutagenesisSequenceCellsNucleofectionSortingEnergetics of Whole Genome Doubling and Genomic Instability
Beck R, Tagal V, Amin S, Bakhoum S, Maley C, Verhaak R, Gomes A, Andor N. Energetics of Whole Genome Doubling and Genomic Instability. Cancer Letters 2025, 217878. PMID: 40517938, DOI: 10.1016/j.canlet.2025.217878.Peer-Reviewed Original ResearchWhole-genome doublingGenome doublingBuffering deleterious mutationsDeleterious mutationsHaploinsufficient genesGenomic instabilityGenomic alterationsEnergetic constraintsTime of diagnosisCancer cellsMutationsPloidyCancer researchTissue sitesCancerAneuploidyTime of detectionGenomeCellsGenesShed lightRole of Chimeric Antigen Receptor–Expressing Cell Therapy in Immune-Mediated Kidney Diseases: A Review
Peng J, Zhang Y, Wang J, Zhang H, Schett G. Role of Chimeric Antigen Receptor–Expressing Cell Therapy in Immune-Mediated Kidney Diseases: A Review. American Journal Of Kidney Diseases 2025 PMID: 40484342, DOI: 10.1053/j.ajkd.2025.04.012.Peer-Reviewed Original ResearchImmune-mediated kidney diseasesB-cell depletionB cellsKidney diseaseCell therapyPlasma cellsTreatment of immune-mediated kidney diseasesB-cell-depleting monoclonal antibodyB-cell targeted therapiesComplete B-cell depletionAutoantibody-producing plasma cellsDeplete plasma cellsMonoclonal antibodiesAntigen-presenting cellsAdaptive immune responsesImmune-mediatedSelf-antigensT cellsImmune cellsImmune responseTherapyInfiltrated tissuesDiseaseAntibodiesCellsMetabolic switches in cell death regulation
Galluzzi L. Metabolic switches in cell death regulation. Cell Metabolism 2025, 37: 1252-1254. PMID: 40466623, DOI: 10.1016/j.cmet.2025.04.017.Peer-Reviewed Original ResearchFrom genes to geometry: Controlling embryo models by programming genomic activation
McNamara H, Sozen B. From genes to geometry: Controlling embryo models by programming genomic activation. Cell Stem Cell 2025, 32: 857-858. PMID: 40480203, DOI: 10.1016/j.stem.2025.04.013.Peer-Reviewed Original ResearchExtracellular Vesicle (EV) Targeted Cells Release Secondary Effector EVs: Indication of How To Account for Histocompatibility and Disease Specificity of EV Treatments
Askenase P. Extracellular Vesicle (EV) Targeted Cells Release Secondary Effector EVs: Indication of How To Account for Histocompatibility and Disease Specificity of EV Treatments. Journal Of Extracellular Vesicles 2025, 14: e70076. PMID: 40415199, PMCID: PMC12104073, DOI: 10.1002/jev2.70076.Peer-Reviewed Original ResearchConceptsMesenchymal stromal cellsSpinal cord injuryT cellsExtracellular vesiclesEffector T cellsSuppressor T cellsDisease specificityTreating spinal cord injuryImmune toleranceHistocompatibility barriersRecipient macrophagesEV treatmentStromal cellsTarget cellsCord injuryMSC-derivedPathological conditionsDiverse injuriesCellsInjuryDiseasePer treatmentTreatmentHealingHealing effectVDAC2 enforces a mitochondrial checkpoint to cancer immunity
Cosentino K, Verduijn J, Galluzzi L. VDAC2 enforces a mitochondrial checkpoint to cancer immunity. Nature Immunology 2025, 26: 808-809. PMID: 40389564, DOI: 10.1038/s41590-025-02171-1.Peer-Reviewed Original ResearchCoarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci
Mader A, Rodriguez A, Yuan T, Surovtsev I, King M, Mochrie S. Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci. Biophysical Journal 2025, 124: 2120-2132. PMID: 40369871, DOI: 10.1016/j.bpj.2025.05.008.Peer-Reviewed Original ResearchChromatin polymerChromatin configurationLocus identityGenomic positionsLabeled lociLiving cellsLocus configurationsChromatin dynamicsMultiple lociGene locusChromatin researchChromatinLociSingle-particle trackingFluorescent labelingCorrect assignmentDynamic loopTemporal dynamicsCellsGenesModel polymersLabelingIdentityTowards a consensus atlas of human and mouse adipose tissue at single-cell resolution
Loft A, Emont M, Weinstock A, Divoux A, Ghosh A, Wagner A, Hertzel A, Maniyadath B, Deplancke B, Liu B, Scheele C, Lumeng C, Ding C, Ma C, Wolfrum C, Strieder-Barboza C, Li C, Truong D, Bernlohr D, Stener-Victorin E, Kershaw E, Yeger-Lotem E, Shamsi F, Hui H, Camara H, Zhong J, Kalucka J, Ludwig J, Semon J, Jalkanen J, Whytock K, Dumont K, Sparks L, Muir L, Fang L, Massier L, Saraiva L, Beyer M, Jeschke M, Mori M, Boroni M, Walsh M, Patti M, Lynes M, Blüher M, Rydén M, Hamda N, Solimini N, Mejhert N, Gao P, Gupta R, Murphy R, Pirouzpanah S, Corvera S, Tang S, Das S, Schmidt S, Zhang T, Nelson T, O’Sullivan T, Efthymiou V, Wang W, Tong Y, Tseng Y, Mandrup S, Rosen E. Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution. Nature Metabolism 2025, 7: 875-894. PMID: 40360756, DOI: 10.1038/s42255-025-01296-9.Peer-Reviewed Original ResearchConceptsCell annotationSingle-cell dataRegulation of metabolic homeostasisSingle-cell resolutionSingle-cell atlasMouse adipose tissueAdipose tissueMetabolic homeostasisSpecialized cellsPrimary repositoryAnnotationCellsExcess caloriesBionetworkProportion of adipocytesConnective tissueMiceTissueComplex connective tissueAdipocytesHomeostasisCardiac macrophage: Insights from murine models to translational potential for human studies
Liu Y, Wang T, Lu Y, Riaz M, Qyang Y. Cardiac macrophage: Insights from murine models to translational potential for human studies. Journal Of Molecular And Cellular Cardiology 2025, 204: 17-31. PMID: 40354877, PMCID: PMC12162190, DOI: 10.1016/j.yjmcc.2025.05.001.Peer-Reviewed Original ResearchConceptsCardiovascular diseaseMurine studiesCardiac macrophagesImmune cellsDisease progressionCardiac homeostasisHuman studiesFunctional significanceCell typesTherapeutic targetCardiac microenvironmentTranslational potentialProgressive pathologyDevelopmental originsPhysiological maintenanceMacrophagesMicroenvironmentMechanical stimuliDiseaseFunctional responseCellsDynamic roleExperimental toolHuman modelLineagesMolecular basis of cell fate plasticity — insights from the privileged cells
Scalf S, Wu Q, Guo S. Molecular basis of cell fate plasticity — insights from the privileged cells. Current Opinion In Genetics & Development 2025, 93: 102354. PMID: 40327951, DOI: 10.1016/j.gde.2025.102354.Peer-Reviewed Original ResearchThe application of irreversible genomic states to define and trace ancient cell type homologies
Simakov O, Wagner G. The application of irreversible genomic states to define and trace ancient cell type homologies. EvoDevo 2025, 16: 5. PMID: 40319312, PMCID: PMC12049793, DOI: 10.1186/s13227-025-00242-w.Peer-Reviewed Original ResearchImpact gene expressionGenomic stateCell typesGene expressionGene regulatory networksHomologous cell typesBranching animalsGenomic charactersRegulatory elementsRegulatory networksRegulatory signaturesMorphological traitsHomologyPhenotypic levelMolecular signaturesOntogenetic originGenesMorphological featuresNon-functionalCellsHypothesis articleGenomeExpressionTraitsTypeA molecular systems perspective on calcium oscillations beyond ion fluxes
Xiong D, Tong C, Wu M. A molecular systems perspective on calcium oscillations beyond ion fluxes. Current Opinion In Cell Biology 2025, 94: 102523. PMID: 40311263, PMCID: PMC12113571, DOI: 10.1016/j.ceb.2025.102523.Peer-Reviewed Original ResearchGlial cells diverge in fly brain evolution
Jiao Y, Sorrells T. Glial cells diverge in fly brain evolution. PLOS Biology 2025, 23: e3003136. PMID: 40305742, PMCID: PMC12043326, DOI: 10.1371/journal.pbio.3003136.Peer-Reviewed Original ResearchMitochondria‐Catalyzed Activation of Anticancer Prodrugs
Raucheisen M, Attia D, Körber M, Crevillén A, Hidalgo A, Beierlein F, Imhof P, Mokhir A. Mitochondria‐Catalyzed Activation of Anticancer Prodrugs. ChemCatChem 2025, 17 DOI: 10.1002/cctc.202500054.Peer-Reviewed Original ResearchCancer cellsElectron transport chainBone marrow cellsProof-of-concept studyMitochondria of cancer cellsOvarian cancer A2780Toxicity in vivoMarrow cellsHuman ovarian cancer A2780Anticancer efficacyCancerTHP1 cellsHealthy cellsProdrugCellsEfficacyATP synthaseTransport chainDrug camptothecinCamptothecinActivation efficacyEvaluation of nonspecific reactivity rates across three immunohematology testing platforms with assessment of subsequent specific alloantibody development
Yurtsever N, Carmichael G, Malonis R, Madden M, Isik N, Ahmed M, Bizzario L, Shah B, Tormey C, Lee E. Evaluation of nonspecific reactivity rates across three immunohematology testing platforms with assessment of subsequent specific alloantibody development. Transfusion 2025, 65: 978-984. PMID: 40251842, PMCID: PMC12092180, DOI: 10.1111/trf.18256.Peer-Reviewed Original ResearchNonspecific reactivityAntibody screeningStrength of reactivityRate of positivityReagent red cellsAlloantibody developmentKruskal-Wallis testAntibody historyChart reviewPretransfusion testingAntibody identificationIRB approvalIdentification panelKruskal-WallisPositive screenAntibody detectionRed cellsAntibodiesAlloantibodiesStudy periodReactivation rateTube testNonspecific reactionsScreeningCellsCasz1 is required for both inner hair cell fate stabilization and outer hair cell survival
Sun Y, Ren M, Zhang Y, Li S, Luo Z, Sun S, He S, Wang G, Zhang D, Mansour S, Song L, Liu Z. Casz1 is required for both inner hair cell fate stabilization and outer hair cell survival. Science 2025, 388: eado4930. PMID: 39883789, DOI: 10.1126/science.ado4930.Peer-Reviewed Original ResearchCell fate stabilityLoss of Casz1Transcription factor CASZ1Outer hair cell survivalCochlear inner hair cellsTranscription factor GATA3Transcription factorsCASZ1Mouse developmentCell survivalHair cell survivalInner hair cellsOuter hair cell numberTranscriptionDown-regulationHair cellsOverexpressing GATA3Mutant miceOuter hair cellsCellsOHC survivalGATA3MiceA Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function
Jiménez-Jiménez V, Sánchez-Cabo F, Schwartz M, Sánchez-Álvarez M, del Pozo M. A Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function. International Journal Of Molecular Sciences 2025, 26: 3789. PMID: 40332409, PMCID: PMC12027754, DOI: 10.3390/ijms26083789.Peer-Reviewed Original ResearchConceptsGenotype-Tissue ExpressionTranscript levelsProtein-coding genesRNA-seq datasetsUpstream regulatory networkCell type proportionsInter-species comparisonsTissue-specific correlationsChromatin modifiersRegulatory networksPRC2 complexTissue-specific influencesCav1Complexity of human tissuesPhysiological regulationHuman tissuesPhysiological conditionsRegulationMetabolic stimuliCAV1 levelsDisease statesTissue dataInfiltration of immune cellsCellsChromatin
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