2024
VCAM-1 mediates proximal tubule-immune cell cross talk in failed tubule recovery during AKI-to-CKD transition
Melchinger I, Guo K, Li X, Guo J, Cantley L, Xu L. VCAM-1 mediates proximal tubule-immune cell cross talk in failed tubule recovery during AKI-to-CKD transition. American Journal Of Physiology. Renal Physiology 2024, 327: f610-f622. PMID: 39116349, PMCID: PMC11483080, DOI: 10.1152/ajprenal.00076.2024.Peer-Reviewed Original ResearchAcute kidney injuryChronic kidney diseaseVCAM-1 expressionProximal tubule cellsVCAM-1Tubule cellsKidney Precision Medicine ProjectProinflammatory cytokinesAcute kidney injury to chronic kidney diseaseModel of chronic kidney diseaseExpression of vascular cell adhesion protein 1Cell adhesion pathwaysInflammatory response to injuryInjured proximal tubule cellsVascular cell adhesion protein 1Mouse model of chronic kidney diseaseRisk of progressionChronic kidney disease transitionIncreased immune cell adhesionVCAM-1-positive cellsOverexpression of VCAM-1Inhibition of NF-kB signalingActivation of NF-kBImmune cell adhesionSingle-cell transcriptome analysisTRIM71 mutations cause a neurodevelopmental syndrome featuring ventriculomegaly and hydrocephalus
Duy P, Jux B, Zhao S, Mekbib K, Dennis E, Dong W, Nelson-Williams C, Mehta N, Shohfi J, Juusola J, Allington G, Smith H, Marlin S, Belhous K, Monteleone B, Schaefer G, Pisarska M, Vásquez J, Estrada-Veras J, Keren B, Mignot C, Flore L, Palafoll I, Alper S, Lifton R, Haider S, Moreno-De-Luca A, Jin S, Kolanus W, Kahle K. TRIM71 mutations cause a neurodevelopmental syndrome featuring ventriculomegaly and hydrocephalus. Brain 2024, 147: 4292-4305. PMID: 38833623, PMCID: PMC11629693, DOI: 10.1093/brain/awae175.Peer-Reviewed Original ResearchCongenital hydrocephalusCerebral ventriculomegalyStructural brain defectsCohort of patientsAnalysis of human embryosNeurodevelopmental syndromeCorpus callosum dysgenesisWhite matter hypoplasiaSingle-cell transcriptome analysisNeural stem cellsDysmorphic featuresTransmitted variantsPatient cohortVentriculomegalyNHL domainCross-sectional analysisLin-41Subcellular localizationBrain defectsDevelopmental delayHuman embryosProcessing bodiesHomologous positionsPatientsStem cellsSingle-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE)
Hanin A, Zhang L, Huttner A, Plu I, Mathon B, Bielle F, Navarro V, Hirsch L, Hafler D. Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE). Neurology Neuroimmunology & Neuroinflammation 2024, 11: e200259. PMID: 38810181, PMCID: PMC11139018, DOI: 10.1212/nxi.0000000000200259.Peer-Reviewed Original ResearchConceptsNew-onset refractory status epilepticusTemporal lobe epilepsyGABAergic neuronsExcitatory neuronsInfiltrating MacrophagesProportion of GABAergic neuronsChronic temporal lobe epilepsyRefractory status epilepticusInhibitory GABAergic neuronsSingle-cell transcriptome analysisDecreased expression of genesDegree of demyelinationImmune disturbancesNeuronal excitabilityImmune dysregulationNew-onsetStatus epilepticusPoor outcomeRefractory epilepsyHealthy childrenMicroglial reactivitySingle-nucleus RNA sequencingNLRP3 inflammasome activationInflammatory responseLobe epilepsyInvestigation of T cell phenotypes associated with response or resistance to immune checkpoint inhibitors (ICI) through single-cell analysis of renal cell carcinoma (RCC).
Kashima S, Ye Z, Meliki A, Hugaboom M, Schindler N, Graham J, Moritz V, El Ahmar N, Nabil Laimon Y, Canniff J, Saliby R, Lee G, Machaalani M, Sun M, Xu W, Signoretti S, McGregor B, McKay R, CHOUEIRI T, Braun D. Investigation of T cell phenotypes associated with response or resistance to immune checkpoint inhibitors (ICI) through single-cell analysis of renal cell carcinoma (RCC). Journal Of Clinical Oncology 2024, 42: 4515-4515. DOI: 10.1200/jco.2024.42.16_suppl.4515.Peer-Reviewed Original ResearchImmune checkpoint inhibitorsRenal cell carcinomaCD8+ T cell infiltrationT cell infiltrationNon-respondersTumor microenvironmentT cellsRCC tumor microenvironmentResistance to immune checkpoint inhibitorsICI responseImmune checkpoint inhibitor treatmentImmune checkpoint inhibitor efficacyCD8+ T cellsExpressed PD-1ICI-treated patientsGene programGene signature scoresTumor mutation loadCellular compositionGene expression signaturesSingle-cell transcriptome analysisCheckpoint inhibitorsPD-1Partial responseSystemic therapySLAMF7+ CD8+ T cells exhibit decreased anti-tumor responses in renal cell carcinoma
Wirth L, Hugaboom M, Street K, Ruthen N, Jegede O, Schindler N, McDermott D, Plimack E, Sosman J, Haas N, Hurwitz M, Hammers H, Signoretti S, Atkins M, Wu C, Braun D. SLAMF7+ CD8+ T cells exhibit decreased anti-tumor responses in renal cell carcinoma. The Journal Of Immunology 2024, 212: 1491_5876-1491_5876. DOI: 10.4049/jimmunol.212.supp.1491.5876.Peer-Reviewed Original ResearchCD8+ T cellsImmune-checkpoint inhibitorsRenal cell carcinomaCD8+ T-cell effector functionT cell effector functionT cellsCell carcinomaResistance to immune-checkpoint inhibitorsEffector functionsPopulation of CD8+ T cellsCD3+ T cellsTreatment of renal cell carcinomaHealthy human PBMCTumor-infiltrating lymphocytesAnti-tumor responsesPatient T cellsReduction of pro-inflammatory cytokinesAnti-tumor functionPro-inflammatory cytokinesSingle-cell transcriptome analysisNivolumab monotherapySLAMF7 expressionClinical benefitGranzyme BIFN-gRevisiting 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 ResearchSingle-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma
Obacz J, Valer J, Nibhani R, Adams T, Schupp J, Veale N, Lewis-Wade A, Flint J, Hogan J, Aresu G, Coonar A, Peryt A, Biffi G, Kaminski N, Francies H, Rassl D, Garnett M, Rintoul R, Marciniak S. Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma. European Respiratory Journal 2024, 63: 2300143. PMID: 38212075, PMCID: PMC10809128, DOI: 10.1183/13993003.00143-2023.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptome atlasSingle-cell levelSingle-cell transcriptome analysisTranscriptome dataTranscriptomic atlasTranscriptomic characterisationMesothelial cellsCell atlasDevelopment of targeted therapiesMalignant mesothelial cellsModel of mesotheliomaUniversal fibroblastsIn vitro model
2020
Single-cell transcriptional landscapes reveal HIV-1–driven aberrant host gene transcription as a potential therapeutic target
Liu R, Yeh YJ, Varabyou A, Collora JA, Sherrill-Mix S, Talbot CC, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, Ambinder RF, Hoh R, Deeks SG, Chiarella J, Spudich S, Douek DC, Bushman FD, Pertea M, Ho YC. Single-cell transcriptional landscapes reveal HIV-1–driven aberrant host gene transcription as a potential therapeutic target. Science Translational Medicine 2020, 12 PMID: 32404504, PMCID: PMC7453882, DOI: 10.1126/scitranslmed.aaz0802.Peer-Reviewed Original ResearchConceptsHost gene transcriptionGene transcriptionLong terminal repeatHIV-1 reactivationCellular factorsIntegration sitesNonsense-mediated RNA decaySingle-cell transcriptional landscapePotential therapeutic targetSingle-cell transcriptome analysisHIV-1-host interactionsHIV-1HIV-1 promoterTherapeutic targetHIV-1 5' long terminal repeatRNA decayTranscriptional landscapeHIV-1-infected individualsHIV-1-infected cellsTranscriptome analysisAberrant transcriptionRNA transcriptionHost RNACellular survivalTranscription pathway
2019
Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming
Zhou Y, Liu Z, Welch J, Gao X, Wang L, Garbutt T, Keepers B, Ma H, Prins J, Shen W, Liu J, Qian L. Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming. Cell Stem Cell 2019, 25: 149-164.e9. PMID: 31230860, PMCID: PMC6684137, DOI: 10.1016/j.stem.2019.05.020.Peer-Reviewed Original ResearchConceptsCell fate transitionsCell fate determinationSingle-cell transcriptomic studiesCell fate conversionFate transitionsSingle-cell transcriptome analysisReprogramming progressionFate determinationDNA methylationFunctional screeningFate conversionCellular reprogrammingDownstream targetsAnalysis pipelineAnalytical pipelineFibroblast stateReprogrammingCell plasticityReprogramming factorsMolecular featuresCellsHuman cardiacTrajectory prediction algorithmPrediction algorithmFibroblastsEarly alterations in stem-like/resident T cells, innate and myeloid cells in the bone marrow in preneoplastic gammopathy
Bailur JK, McCachren SS, Doxie DB, Shrestha M, Pendleton K, Nooka AK, Neparidze N, Parker TL, Bar N, Kaufman JL, Hofmeister CC, Boise LH, Lonial S, Kemp ML, Dhodapkar KM, Dhodapkar MV. Early alterations in stem-like/resident T cells, innate and myeloid cells in the bone marrow in preneoplastic gammopathy. JCI Insight 2019, 5 PMID: 31013254, PMCID: PMC6629164, DOI: 10.1172/jci.insight.127807.Peer-Reviewed Original ResearchMeSH KeywordsBone MarrowCell Transformation, NeoplasticFemaleGene Expression Regulation, NeoplasticHepatocyte Nuclear Factor 1-alphaHumansImmunity, InnateImmunologic MemoryImmunologic SurveillanceIntercellular Signaling Peptides and ProteinsMaleMiddle AgedMonoclonal Gammopathy of Undetermined SignificanceMultiple MyelomaMyeloid CellsPrecancerous ConditionsRNA-SeqSingle-Cell AnalysisStem CellsT-LymphocytesTumor MicroenvironmentConceptsMemory T cellsSingle-cell transcriptome analysisT cellsMyeloid cellsMyeloma patientsTerminal effector differentiationImmune cellsHealthy donorsProlonged dormancyTranscriptome analysisBone marrowBone marrow immune cellsStem-like cellsStem-like T cellsAge-matched healthy donorsDistinct genomic profilesResident T cellsSingle immune cellsT cell compartmentBone marrow plasmaCell compartmentGenomic profilesCancer cellsPreneoplastic gammopathyImmune microenvironment
2017
Single-Cell Transcriptome Analyses Reveal Taxol Resistant Subpopulations in Esophageal Squamous Cancer Cells
Wu H, Yu J, Chen S, Zhang X, Yang L, Zhang H, Li Y, Hou Q, Hua Y, Jiang M, Wang C, Wu S. Single-Cell Transcriptome Analyses Reveal Taxol Resistant Subpopulations in Esophageal Squamous Cancer Cells. International Journal Of Radiation Oncology • Biology • Physics 2017, 99: e627-e628. DOI: 10.1016/j.ijrobp.2017.06.2115.Peer-Reviewed Original ResearchSingle-cell transcriptome analysisEsophageal squamous cancer cellsTranscriptome analysisSquamous cancer cellsCancer cellsResistant subpopulationsCellsSingle-Cell Transcriptome Analyses Reveal Signals to Radio-Resistance in Esophageal Squamous Cell Carcinoma
Wu H, Yang L, Zhang X, Zhang H, Li Y, Hou Q, Jiang Z, Hua Y, Jiang M, Brunicardi C, Yu J, Wu S. Single-Cell Transcriptome Analyses Reveal Signals to Radio-Resistance in Esophageal Squamous Cell Carcinoma. International Journal Of Radiation Oncology • Biology • Physics 2017, 99: e627. DOI: 10.1016/j.ijrobp.2017.06.2114.Peer-Reviewed Original ResearchSingle-cell transcriptome analysisTranscriptome analysisRadio resistanceEsophageal squamous cell carcinoma
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