2025
ti-scMR: trajectory-inference-based dynamic single-cell Mendelian randomization identifies causal genes underlying phenotypic differences
Sun J, Dong Q, Wei J, Gao Y, Yu Z, Hu X, Zhang Y. ti-scMR: trajectory-inference-based dynamic single-cell Mendelian randomization identifies causal genes underlying phenotypic differences. NAR Genomics And Bioinformatics 2025, 7: lqaf082. PMID: 40630931, PMCID: PMC12231591, DOI: 10.1093/nargab/lqaf082.Peer-Reviewed Original ResearchConceptsMendelian randomizationCausal genesSingle-cell expressionGenetic instrumental variablesPhenotypic differencesIndividual phenotypesPotential causal genesPresence of confoundersEffects of gene expressionGenotype to phenotypeCausal pathwaysSingle-cell datasetsDifferential expression analysisExpression of genesPopulation genomicsSingle-cell transcriptomicsComplex traitsPopulation geneticsTrait lociImmune cell differentiationTranscriptomic landscapeTrajectory inferenceTranscriptional featuresInstrumental variablesCellular developmentSpatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq
Li H, Bao S, Farzad N, Qin X, Fung A, Zhang D, Bai Z, Tao B, Fan R. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature Protocols 2025, 20: 2383-2417. PMID: 40119005, DOI: 10.1038/s41596-025-01145-9.Peer-Reviewed Original ResearchNear single-cell resolutionControl cell identityTargeting histone modificationsSingle-cell resolutionTn5 transposaseAccessible chromatinEpigenomic landscapeIn situ reverse transcriptionHistone modificationsCell identityTranscriptomic landscapeSequencing protocolSequencing methodsGene transcriptionEpigenomeOligonucleotide barcodesTranscriptomeDiverse biological activitiesIntact tissue sectionsReverse transcriptionTranscriptionBiological activityPrimary antibodyTagmentationTissue pixelsTranscriptomic landscape of cumulus cells from patients <38 years old with a history of poor ovarian response (POR) treated with platelet-rich plasma (PRP)
Roberts L, Herlihy N, Reig A, Titus S, Garcia-Milian R, Knight J, Yildirim R, Margolis C, Cakiroglu Y, Tiras B, Whitehead C, Werner M, Seli E. Transcriptomic landscape of cumulus cells from patients <38 years old with a history of poor ovarian response (POR) treated with platelet-rich plasma (PRP). Aging 2025, 17: 431-447. PMID: 39976580, PMCID: PMC11892918, DOI: 10.18632/aging.206202.Peer-Reviewed Original ResearchConceptsPlatelet-rich plasmaTreated with platelet-rich plasmaCumulus cellsPoor ovarian responseLive birthsGene expressionIntraovarian injection of autologous platelet-rich plasmaPatients treated with platelet-rich plasmaInjection of autologous platelet-rich plasmaHistory of poor ovarian responseAutologous platelet-rich plasmaPlatelet-rich plasma treatmentDiminished ovarian reserveCell-to-cell signalingRNA sequencing librariesCause of infertilityDifferential expression analysisFalse discovery rate thresholdIntraovarian injectionOvarian reserveFailed implantsSequencing librariesOvarian responseTranscriptomic landscapeRNA sequencing
2024
A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma
Pozniak J, Pedri D, Landeloos E, Van Herck Y, Antoranz A, Vanwynsberghe L, Nowosad A, Roda N, Makhzami S, Bervoets G, Maciel L, Pulido-Vicuña C, Pollaris L, Seurinck R, Zhao F, Flem-Karlsen K, Damsky W, Chen L, Karagianni D, Cinque S, Kint S, Vandereyken K, Rombaut B, Voet T, Vernaillen F, Annaert W, Lambrechts D, Boecxstaens V, Saeys Y, van den Oord J, Bosisio F, Karras P, Shain A, Bosenberg M, Leucci E, Paschen A, Rambow F, Bechter O, Marine J. A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma. Cell 2024, 187: 166-183.e25. PMID: 38181739, DOI: 10.1016/j.cell.2023.11.037.Peer-Reviewed Original ResearchConceptsTargeted therapyMesenchymal-likeResistance to immune checkpoint blockadeOn-treatment biopsiesImmune checkpoint blockadeResistance to immunotherapyTranscriptional programsCheckpoint blockadeTumor microenvironmentIncreased immunogenicityNon-respondersMelanoma cellsTargeting TCF4MelanomaTherapySpatial multi-omicsBromodomain inhibitorsMulti-OmicsTCF4Transcriptomic landscapeImmunotherapyBiopsyBlockadeTumorImmunogenicity
2022
Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit.
Barroso-Sousa R, Forman J, Collier K, Weber ZT, Jammihal TR, Kao KZ, Richardson ET, Keenan T, Cohen O, Manos MP, Brennick RC, Ott PA, Hodi FS, Dillon DA, Attaya V, O'Meara T, Lin NU, Van Allen EM, Rodig S, Winer EP, Mittendorf EA, Wu CJ, Wagle N, Stover DG, Shukla SA, Tolaney SM. Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit. JCO Precision Oncology 2022, 6: e2100413. PMID: 35797509, PMCID: PMC9848556, DOI: 10.1200/po.21.00413.Peer-Reviewed Original ResearchConceptsGene expression pathwaysMetastatic triple-negative breast cancerExpression pathwaysWhole-exome sequencingFollicular helper T cellsDNA damage repair pathwaysTriple-negative breast cancerProgression-free survivalMemory T cellsDamage repair pathwaysHelper T cellsTumor mutational burdenT cellsClonal evolutionOverall survivalDNA whole-exome sequencingTranscriptomic landscapeHomologous recombinationRepair pathwaysRNA sequencingM1 macrophagesBreast cancerDefective repairMutational burdenDNA damageSingle cell transcriptomic landscape of diabetic foot ulcers
Theocharidis G, Thomas BE, Sarkar D, Mumme HL, Pilcher WJR, Dwivedi B, Sandoval-Schaefer T, Sîrbulescu RF, Kafanas A, Mezghani I, Wang P, Lobao A, Vlachos IS, Dash B, Hsia HC, Horsley V, Bhasin SS, Veves A, Bhasin M. Single cell transcriptomic landscape of diabetic foot ulcers. Nature Communications 2022, 13: 181. PMID: 35013299, PMCID: PMC8748704, DOI: 10.1038/s41467-021-27801-8.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersCell Adhesion MoleculesChitinase-3-Like Protein 1Diabetes MellitusDiabetic FootEndothelial CellsExome SequencingFibroblastsGene Expression RegulationHigh-Throughput Nucleotide SequencingHumansHypoxia-Inducible Factor 1, alpha SubunitKeratinocytesLeukocytesMacrophagesMatrix Metalloproteinase 1Matrix Metalloproteinase 11Matrix Metalloproteinase 3Single-Cell AnalysisSkinTranscriptomeWound HealingConceptsDiabetic foot ulcerationSpatial transcriptomicsSingle-cell transcriptomic landscapeSingle-cell RNA sequencingPeripheral blood mononuclear cellsBlood mononuclear cellsDiabetic foot ulcersM1 macrophage polarizationNovel therapeutic approachesTranscriptomic landscapeWound healing microenvironmentRNA sequencingDFU patientsDevastating complicationFoot ulcerationDFU healingFoot ulcersDFU treatmentMononuclear cellsM1 macrophagesM2 macrophagesMacrophage polarizationTherapeutic approachesSame patientHigh abundance
2020
Transcriptomic organization of the human brain in post-traumatic stress disorder
Girgenti MJ, Wang J, Ji D, Cruz DA, Stein M, Gelernter J, Young K, Huber B, Williamson D, Friedman M, Krystal J, Zhao H, Duman R. Transcriptomic organization of the human brain in post-traumatic stress disorder. Nature Neuroscience 2020, 24: 24-33. PMID: 33349712, DOI: 10.1038/s41593-020-00748-7.Peer-Reviewed Original ResearchMeSH KeywordsAdultAutopsyBrain ChemistryCohort StudiesDepressive Disorder, MajorFemaleGene Expression RegulationGene Regulatory NetworksGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansInterneuronsMaleMiddle AgedNerve Tissue ProteinsSex CharacteristicsStress Disorders, Post-TraumaticTranscriptomeYoung AdultConceptsGenome-wide association studiesSignificant gene networksDifferential gene expressionSystems-level evidenceSignificant genetic liabilityMajor depressive disorder cohortGene networksTranscriptomic organizationTranscriptomic landscapeDownregulated setsGenomic networksGene expressionAssociation studiesMolecular determinantsExtensive remodelingGenotype dataSexual dimorphismSignificant divergenceMolecular profileNetwork analysisELFN1TranscriptsDimorphismPostmortem tissueDivergence
2019
Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
Hie B, Cho H, DeMeo B, Bryson B, Berger B. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. Cell Systems 2019, 8: 483-493.e7. PMID: 31176620, PMCID: PMC6597305, DOI: 10.1016/j.cels.2019.05.003.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic landscapeSingle-cell RNA sequencing studiesSingle-cell omicsCell typesSeq data integrationSingle-cell data analysisRare cell typesRNA sequencing studiesScRNA-seq dataTranscriptional diversityTranscriptomic landscapeBiological cell typesTranscriptomic heterogeneitySequencing studiesRare subpopulationAnalysis pipelineCellsUmbilical cord bloodEssential stepInflammatory macrophagesOmicsComprehensive visualizationDiversityGeometric sketchHundreds of thousands
2017
Genome and transcriptome profiling of fibrolamellar hepatocellular carcinoma demonstrates p53 and IGF2BP1 dysregulation
Sorenson E, Khanin R, Bamboat Z, Cavnar M, Kim T, Sadot E, Zeng S, Greer J, Seifert A, Cohen N, Crawley M, Green B, Klimstra D, DeMatteo R. Genome and transcriptome profiling of fibrolamellar hepatocellular carcinoma demonstrates p53 and IGF2BP1 dysregulation. PLOS ONE 2017, 12: e0176562. PMID: 28486549, PMCID: PMC5423588, DOI: 10.1371/journal.pone.0176562.Peer-Reviewed Original ResearchConceptsRNA-seqFrequencies of genomic amplificationFibrolamellar hepatocellular carcinomaFL-HCCTumor specimensP53 tumor suppressor pathwayRNA-seq analysisTumor suppressor pathwayDysregulated gene expressionHepatocellular carcinomaAbsence of preclinical modelsInsulin-like growth factor 2 mRNA-binding protein 1Transcriptome sequencingGenome amplificationGrowth factor 2 mRNA-binding protein 1Transcriptomic landscapeSuppressor pathwayTranscriptome analysisVariant of HCCGenomic instabilityChromosomal alterationsTranscriptome profilingRB1 pathwayGene expressionRare variants
2013
Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.Peer-Reviewed Original ResearchConceptsPerithecial developmentNeurospora crassaGene expressionSexual developmentBody developmentFruiting-body developmentMost upregulated genesReverse genetics approachGlobal gene expressionSimilar expression patternsSame developmental stageMulticellular organismsSexual crossingMat AUnclassified proteinsDevelopmental traitsN. crassaKnockout analysisTranscriptomic landscapeType genesUpregulated genesGenetic basisDiverse functionsExpression patternsStage specificity
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