2025
Perturb-tracing enables high-content screening of multi-scale 3D genome regulators
Cheng Y, Hu M, Yang B, Jensen T, Zhang Y, Yang T, Yu R, Ma Z, Radda J, Jin S, Zang C, Wang S. Perturb-tracing enables high-content screening of multi-scale 3D genome regulators. Nature Methods 2025, 22: 950-961. PMID: 40211002, PMCID: PMC12074983, DOI: 10.1038/s41592-025-02652-z.Peer-Reviewed Original ResearchConceptsLoss-of-function screensPooled CRISPR screensIdentified new regulatorsGenome organizationChromatin domainsGenome regulationChromatin organizationChromosome territoriesChromatin tracingChromatin foldingChromatin topologyCRISPR screensHigh-content screeningChromatin compactionNuclear architectureLoop extrusionChromatinGenomic mechanismsHigh-content screening platformHuman cellsCompartmentalization mechanismFunctional linkTopological regulationGenomic effectsScreening platform
2022
Nanoparticle‐mediated genome editing in single‐cell embryos via peptide nucleic acids
Putman R, Ricciardi A, Carufe K, Quijano E, Bahal R, Glazer P, Saltzman W. Nanoparticle‐mediated genome editing in single‐cell embryos via peptide nucleic acids. Bioengineering & Translational Medicine 2022, 8: e10458. PMID: 37206203, PMCID: PMC10189434, DOI: 10.1002/btm2.10458.Peer-Reviewed Original ResearchSingle-cell embryosPeptide nucleic acidGene editingNucleic acidsNanoparticlesGross developmental abnormalitiesGenome editingNormal physiological developmentOff-target effectsDonor DNAGenetic diseasesConcept workEmbryosGenomic effectsDevelopmental abnormalitiesNormal growthEmbryogenesisPhysiological developmentEditingUnderlying mutationPreimplantation genetic diagnosisDisease pathogenesisGenetic diagnosisNormal morphologyAcid
2020
Convergent network effects along the axis of gene expression during prostate cancer progression
Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint N, Fritz C, Yuan C, Chen H, Rupp N, Christiansen A, Rutishauser D, Rüschoff J, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore A, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martínez M, Manica M, Haffner M, Aebersold R, Wild P, Beyer A. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biology 2020, 21: 302. PMID: 33317623, PMCID: PMC7737297, DOI: 10.1186/s13059-020-02188-9.Peer-Reviewed Original ResearchConceptsHigh-throughput genomic measurementsProstate cancer progressionGene expressionMolecular networksCopy number alterationsCancer progressionComplex genomic alterationsTumor phenotypePrediction of recurrence-free survivalGenomic measurementsRecurrence-free survivalProstate cancer patientsProteomic alterationsGenomic aberrationsAggressive tumor phenotypeGenomic alterationsDownstream proteinsGenomic effectsNetwork-based approachProstate samplesTumor siteBiochemical stateMalignant tumorsProtein levelsTumor tissues
2014
Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers
Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Alves M, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers. Clinical Cancer Research 2014, 20: 3842-3848. PMID: 24874835, PMCID: PMC4102633, DOI: 10.1158/1078-0432.ccr-14-0565.Peer-Reviewed Original ResearchConceptsSquamous cell carcinomaOlder patientsOral tongueYounger patientsCell carcinomaWhole-exome sequencingOlder smokersSimilar patientsTongue tumorsNon smokersIncreasing incidenceEpidemiologic studiesIndependent cohortPatientsSCCOTSmokingTumorsCohortAlteration frequencyGenomic effectsTCGA dataCopy number analysisGene-specific mutationsOlder cohortTypes of mutations
2005
Rapid, Estrogen Receptor–Mediated Signaling: Why Is the Endothelium So Special?
Kim KH, Bender JR. Rapid, Estrogen Receptor–Mediated Signaling: Why Is the Endothelium So Special? Science Signaling 2005, 2005: pe28. PMID: 15956360, DOI: 10.1126/stke.2882005pe28.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAnimalsCaveolaeCoronary DiseaseEndothelium, VascularEnzyme ActivationEstrogen Replacement TherapyFemaleHumansMaleMiddle AgedNitric OxideNitric Oxide Synthase Type IIIPostmenopausePremenopauseProtein IsoformsProto-Oncogene Proteins pp60(c-src)Randomized Controlled Trials as TopicReceptors, EstrogenSex DistributionSignal TransductionConceptsEstrogen receptorEndothelial NO synthaseNitric oxideEndothelial cellsHormone replacement therapyMembrane estrogen receptorsEndothelial activationVascular healthReplacement therapyCardiovascular diseaseVascular pathologyNO synthasePotent stimulusEstrogen responseFunctional alterationsENOS activationNongenomic responsesNO releaseRegulatory tissuesGenomic effectsCommon formProtective substancesMajor targetEndotheliumReceptors
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