2024
Multi-omics approaches to decipher the interactions of nanoparticles and biological systems
Wang Y, Xiao Z, Wang Z, Lee D, Ma Y, Wilhelm S, Wang H, Kim B, Jiang W. Multi-omics approaches to decipher the interactions of nanoparticles and biological systems. Nature Reviews Bioengineering 2024, 1-16. DOI: 10.1038/s44222-024-00264-4.Peer-Reviewed Original ResearchMulti-omics approachNano-bio interactionsMulti-omicsMulti-omics pipelineMulti-omics dataSubcellular levelHigh-throughput mannerApplication of transcriptomicsNanoparticles in vivoMetabolomics technologyTreatment strategiesNanoparticle uptakeBiological systemsOptimized nanoparticlesEngineered nanoparticlesBiological informationImplementation of nanoparticlesClinical settingInteraction of nanoparticlesCell typesNano-bio interfaceEpigenomeTranscriptomeMetabolomicsBioinformaticsGut microbiota-derived short-chain fatty acids and depression: deep insight into biological mechanisms and potential applications
Cheng J, Hu H, Ju Y, Liu J, Wang M, Liu B, Zhang Y. Gut microbiota-derived short-chain fatty acids and depression: deep insight into biological mechanisms and potential applications. General Psychiatry 2024, 37: e101374. PMID: 38390241, PMCID: PMC10882305, DOI: 10.1136/gpsych-2023-101374.Peer-Reviewed Original ResearchShort-chain fatty acidsMicrobiota-gut-brain axisGut microbiotaGut microbiota-derived short-chain fatty acidsMicrobiota-derived short-chain fatty acidsFatty acidsHost epigenomeBiological mechanismsMicrobiotaBioactive metabolitesDynamic ecosystemsGutImmune pathwaysPathophysiology of depressionChronic cerebral hypoperfusionCentral nervous systemNeuroendocrine alterationsClinical valueEpigenomeCerebral hypoperfusionNeuropsychiatric disordersMetabolitesDisease statusNervous systemDepression
2023
Ten-Eleven-Translocation Genes in Cancer
Wang Y, Wang X, Lu J. Ten-Eleven-Translocation Genes in Cancer. Cancer Treatment And Research 2023, 190: 363-373. PMID: 38113007, DOI: 10.1007/978-3-031-45654-1_11.Peer-Reviewed Original ResearchConceptsTET mutationsTen-ElevenBiochemical functionsTranslocation (TET) familyTranslocation geneHematopoietic malignanciesHematopoietic expansionGenesHuman cancersMutationsCritical roleImmune responseTET2Clonal hematopoiesisSolid cancersEpigenomeTET1TET3RNABiologyUnanswered questionsDNAHematopoiesisCooperateTETsMore than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome
Minteer C, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Sehgal R, Higgins-Chen A, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine M. More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Science Advances 2023, 9: eadf4163. PMID: 37467337, PMCID: PMC10355820, DOI: 10.1126/sciadv.adf4163.Peer-Reviewed Original ResearchConceptsStem cell divisionImmortalized human cellsTissue-specific cancer riskTumorigenic stateCell divisionDNA methylationEpigenetic changesAge-related accumulationHuman cellsMultiple tissuesSomatic mutationsClinical tissuesTissue differencesEpigenomeCellsTissueNormal tissuesMethylationMutationsReplicationNormal breast tissueSignaturesVitroAccumulationDivisionEpigenetic markers and therapeutic targets for metastasis
Kravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEpigenomic alterationsLineage integrityTherapeutic targetEpigenetic markersCancer cellsGenetic aberrationsCurrent knowledgeHuman tumorsMalignant cell cloneTumor progressionDNANumber of discoveriesCell clonesDisseminated diseaseCertain organsPrimary tumorTherapeutic responseMetastatic cancerEpigenomeChromatinHistonesLiquid biopsyAlterationsClonesTargetThe technological landscape and applications of single-cell multi-omics
Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nature Reviews Molecular Cell Biology 2023, 24: 695-713. PMID: 37280296, PMCID: PMC10242609, DOI: 10.1038/s41580-023-00615-w.Peer-Reviewed Original ResearchConceptsSingle-cell multi-omics technologiesMulti-omics technologiesMolecular cell biology researchCell lineage tracingCell biology researchBioinformatics toolsLineage tracingOmics methodsCell statesBiology researchMathematical modellingCancer geneticsOmics modalitiesComputational methodsEpitranscriptomeEpigenomeTranscriptomeGenomeProteomeOmicsOptimization of throughputGeneticsArt methodsTranslational researchUniquenessSpatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfilingThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky J, Gao J, Borsari B, Yang Y, Galeev T, Gürsoy G, Epstein C, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun M, Wright J, Chang J, Cameron C, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona G, Chee S, Chhetri S, Cortez Martins G, Danyko C, Davis C, Farid D, Farrell N, Gabdank I, Gofin Y, Gorkin D, Gu M, Hecht V, Hitz B, Issner R, Jiang Y, Kirsche M, Kong X, Lam B, Li S, Li B, Li X, Lin K, Luo R, Mackiewicz M, Meng R, Moore J, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt H, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber J, Sedlazeck F, See L, Sherman R, Shi X, Shi M, Sloan C, Strattan J, Tan Z, Tanaka F, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry J, Mendenhall E, Noble W, Weng Z, Levine M, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers R, Snyder M, Choudhary J, Milosavljevic A, Schatz M, Bernstein B, Guigó R, Gingeras T, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023, 186: 1493-1511.e40. PMID: 37001506, PMCID: PMC10074325, DOI: 10.1016/j.cell.2023.02.018.Peer-Reviewed Original ResearchEpigenomic charting and functional annotation of risk loci in renal cell carcinoma
Nassar A, Abou Alaiwi S, Baca S, Adib E, Corona R, Seo J, Fonseca M, Spisak S, El Zarif T, Tisza V, Braun D, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar S, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck J, O’Connor E, Bell C, Nuzzo P, Mary Lee G, Signoretti S, Hirsch M, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri T, Kwiatkowski D, Freedman M. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nature Communications 2023, 14: 346. PMID: 36681680, PMCID: PMC9867739, DOI: 10.1038/s41467-023-35833-5.Peer-Reviewed Original ResearchConceptsMaster transcription factorChIP-seqATAC-seq dataH3K27ac ChIP-seqCcRCC cell linesEpigenomic atlasATAC-seqFunctional annotationTranscriptional landscapePrimary human samplesTranscription factorsRNA-seqRisk lociTranscriptional upregulationSNP arrayRisk SNPsETS-1EpigenomeCell linesFOXI1Renal cell carcinomaEPAS1RCC histologic subtypesHuman samplesBHLHE41
2022
Interferon drives HCV scarring of the epigenome and creates targetable vulnerabilities following viral clearance
Hlady RA, Zhao X, Khoury L, Luna A, Pham K, Wu Q, Lee J, Pyrsopoulos NT, Liu C, Robertson KD. Interferon drives HCV scarring of the epigenome and creates targetable vulnerabilities following viral clearance. Hepatology 2022, 75: 983-996. PMID: 34387871, PMCID: PMC9416882, DOI: 10.1002/hep.32111.Peer-Reviewed Original ResearchConceptsDNA methylationHistone modificationsWide DNA methylationAberrant DNA methylationGene expression analysisDNA methyltransferase inhibitorOpen chromatinEpigenetic mechanismsEpigenetic targetsHuman patient samplesEpigenetic changesEpigenomeMethyltransferase inhibitorTargetable vulnerabilitiesMethylationHCC cell linesImmortalized hepatocytesCell linesFunctional effectsChronic HCV infectionChromatinHCV infectionImmune responsePatient samplesSynergizes
2021
Targeting the T-Cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune-Modulatory Signaling PathwaysTargeting Peripheral T-Cell Lymphoma Epigenome
Scotto L, Kinahan C, Douglass E, Deng C, Safari M, Casadei B, Marchi E, Lue JK, Montanari F, Falchi L, Qiao C, Renu N, Bates SE, Califano A, O'Connor OA. Targeting the T-Cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune-Modulatory Signaling PathwaysTargeting Peripheral T-Cell Lymphoma Epigenome. Molecular Cancer Therapeutics 2021, 20: 1422-1430. PMID: 34108263, PMCID: PMC8941846, DOI: 10.1158/1535-7163.mct-20-0377.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, NeoplasmAntimetabolites, AntineoplasticApoptosisAzacitidineBiomarkers, TumorCell ProliferationDNA (Cytosine-5-)-Methyltransferase 1DNA MethylationEpigenesis, GeneticEpigenomeGene Expression ProfilingGene Expression Regulation, NeoplasticHistone Deacetylase InhibitorsHumansImmunityLymphoma, T-CellMaleTestisTumor Cells, CulturedConceptsEpigenetic geneHistone deacetylaseSuppression of genesHDAC inhibitorsDNA methyltransferase inhibitorTranscriptional inductionDNA methylationMaster regulatorDNMT inhibitorsEpigenetic diseasePeripheral T-cell lymphomaGene expressionMethyltransferase inhibitorMechanistic basisCell deathGenesCancer-testis antigensTestis antigensEpigenomeMutationsCholesterol metabolismInhibitorsInductionMatrisomeTh1-like phenotypeReprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence
Wu Z, Zhou J, Zhang X, Zhang Z, Xie Y, Liu JB, Ho ZV, Panda A, Qiu X, Cejas P, Cañadas I, Akarca FG, McFarland JM, Nagaraja AK, Goss LB, Kesten N, Si L, Lim K, Liu Y, Zhang Y, Baek JY, Liu Y, Patil DT, Katz JP, Hai J, Bao C, Stachler M, Qi J, Ishizuka JJ, Nakagawa H, Rustgi AK, Wong KK, Meyerson M, Barbie DA, Brown M, Long H, Bass AJ. Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nature Genetics 2021, 53: 881-894. PMID: 33972779, PMCID: PMC9124436, DOI: 10.1038/s41588-021-00859-2.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAdenosine DeaminaseAnimalsBase SequenceCarcinogenesisCell Line, TumorCell Transformation, NeoplasticCyclin-Dependent Kinase Inhibitor p16Endogenous RetrovirusesEnhancer Elements, GeneticEpigenomeEsophageal NeoplasmsEsophageal Squamous Cell CarcinomaGene Expression Regulation, NeoplasticGenome, HumanHumansInterferonsIntronsKruppel-Like Transcription FactorsMiceOrganoidsProtein BindingRNA-Binding ProteinsRNA, Double-StrandedSOXB1 Transcription FactorsTumor Suppressor Protein p53ConceptsRNA editing enzyme ADAR1Activity of oncogenesTranscription factor Sox2Chromatin remodelingSox2 bindingSOX2 activityTranscriptional landscapeEnzyme ADAR1Sox2 functionFactor Sox2Esophageal squamous cell carcinomaEsophageal organoidsTargetable vulnerabilitiesEndogenous retrovirusesSOX2Chromosome 3q amplificationSOX2 overexpressionPrecursor cellsP16 inactivationOncogeneEpigenomeCistromeNormal tissuesSquamous esophagusADAR1Annotation of chromatin states in 66 complete mouse epigenomes during development
van der Velde A, Fan K, Tsuji J, Moore J, Purcaro M, Pratt H, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Communications Biology 2021, 4: 239. PMID: 33619351, PMCID: PMC7900196, DOI: 10.1038/s42003-021-01756-4.Peer-Reviewed Original ResearchConceptsChromatin stateMouse epigenomesPolycomb repressive complex proteinsBivalent chromatin stateTranscription start siteRepressive mark H3K27me3Silence target genesCharacteristics of promotersChromHMM algorithmUnique epigenomeGene expression programsENCODE projectTranscribed regionsMulticellular organismsStart siteRepressed regionsActive marksMammalian developmentComplex proteinsEpigenomeTissue specificityTarget genesExpression programsCell typesIntegrated analysisChapter 30 Functional genomics of psychiatric disease risk using genome engineering
Garcia M, Powell S, LaMarca E, Fernando M, Cohen S, Fang G, Akbarian S, Brennand K. Chapter 30 Functional genomics of psychiatric disease risk using genome engineering. 2021, 711-734. DOI: 10.1016/b978-0-12-823577-5.00021-0.ChaptersRisk variantsDisease-relevant cell typesPsychiatric disease riskPluripotent stem cellsFunctional genomicsGenetic risk architectureGenome engineeringComplex geneticsCRISPR engineeringHiPSC modelsCell typesFunctional explorationStem cellsFunctional impactRisk architecturePossible new avenuesGenetic findingsGenetic screeningNew insightsNovel therapeutic approachesFundamental roleNew avenuesDisease pathophysiologyEpigenomeVariants
2020
Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome
Powell SK, O'Shea C, Brennand KJ, Akbarian S. Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome. Biological Psychiatry 2020, 89: 65-75. PMID: 33131715, PMCID: PMC7718420, DOI: 10.1016/j.biopsych.2020.06.033.Peer-Reviewed Original ResearchConceptsGenetic variantsDisease-associated genetic variationProtein-coding lociRisk-associated genetic variantsGene regulatory lociThousands of variantsFunctional impactRare genetic variantsEpigenomic mappingRegulatory lociBrain epigenomeGenetic variationDNA sequencesNoncoding variantsGene expressionIntegrative analysisEpigenomic architectureMolecular pathwaysPsychiatric geneticsFunctional readoutRisk variantsLociVariantsHighlight findingsEpigenomeEpigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Lee MY, Lee J, Hyeon SJ, Cho H, Hwang YJ, Shin J, McKee AC, Kowall NW, Kim J, Stein TD, Hwang D, Ryu H. Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease. Aging Cell 2020, 19: e13153. PMID: 32419307, PMCID: PMC7294781, DOI: 10.1111/acel.13153.Peer-Reviewed Original ResearchConceptsGenome-wide ChIPMRNA sequence dataBiological network analysisHistone H3K9me3Heterochromatin remodelingEpigenetic modificationsAD postmortem brainsEpigenetic signaturesFunction-related genesH3K9me3Cell motilityHeterochromatin condensationEpigenetic alterationsEpigenomeEpigenome signaturesNeuronal differentiationAlzheimer's diseaseExpression levelsHeterochromatinIntegrated analysisPostmortem brainsMRNA expression levelsSporadic Alzheimer's diseaseNetwork analysisPotential role
2019
Biological embedding of experience: A primer on epigenetics
Aristizabal MJ, Anreiter I, Halldorsdottir T, Odgers CL, McDade TW, Goldenberg A, Mostafavi S, Kobor MS, Binder EB, Sokolowski MB, O'Donnell KJ. Biological embedding of experience: A primer on epigenetics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 117: 23261-23269. PMID: 31624126, PMCID: PMC7519272, DOI: 10.1073/pnas.1820838116.BooksConceptsEpigenetic mechanismsSpecific epigenetic mechanismsEpigenetic landscapeEpigenome editingDNA sequencesBiological embeddingGene expressionBiological processesCell typesComparative animalHuman longitudinal studiesMolecular profilingPotential roleCorrelative dataEpigenomeGenomeRecent advancesEpigeneticsEditingProfilingCausal dataPrimersMechanismSequenceExpressionTargeting the epigenome of pancreatic cancer for therapy: challenges and opportunities
Baretti M, Ahuja N, Azad N. Targeting the epigenome of pancreatic cancer for therapy: challenges and opportunities. Annals Of Pancreatic Cancer 2019, 2: 18-18. DOI: 10.21037/apc.2019.10.01.Peer-Reviewed Original ResearchEpigenetic modulatory drugsEpigenetic alterationsGene expressionImmediate translational implicationsProgression of PAADEpigenetic regulationHeritable differencesEpigenetic abnormalitiesPrimary sequenceTumor microenvironmentNucleosomesEssential roleCurrent knowledgeTranslational applicationsComplex seriesDNATranslational implicationsNew therapeutic approachesExpressionPancreatic adenocarcinomaEpigenomeChromatinEpigeneticsSubsequent interactionAlterationsIntegrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma
Hlady RA, Sathyanarayan A, Thompson JJ, Zhou D, Wu Q, Pham K, Lee J, Liu C, Robertson KD. Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma. Hepatology 2019, 69: 639-652. PMID: 30136421, PMCID: PMC6351162, DOI: 10.1002/hep.30211.Peer-Reviewed Original ResearchConceptsHistone modification profilesPromoter/enhancer functionGenome-wide assessmentTranscription of genesEpigenetic marksHistone modificationsEpigenome deregulationEpigenetic regulatorsBioinformatics strategyEpigenetic mechanismsModification profilesEpigenetic underpinningsLiver epigenomeEpigenetic profilesEnhancer functionEpigenetic parametersEpigenomeDecrease cell viabilityDriver lociSignificant deregulationCancer initiationTranscriptionHuman cancersCancer cell linesCell lines
2018
Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency
Hernandez C, Wang Z, Ramazanov B, Tang Y, Mehta S, Dambrot C, Lee YW, Tessema K, Kumar I, Astudillo M, Neubert TA, Guo S, Ivanova NB. Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency. Cell Stem Cell 2018, 23: 396-411.e8. PMID: 30146411, PMCID: PMC6128737, DOI: 10.1016/j.stem.2018.08.001.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsDNA damage response pathwayAcquisition of pluripotencyDamage response pathwayDNA methylation patternsStem cellsEmbryonic stem cellsESC enhancersPluripotent stem cellsMyc factorsPluripotent stateSomatic genesChromatin decompactionMolecular machineryEpigenetic remodelingEfficient reprogrammingResponse pathwaysSomatic cellsMethylation patternsPluripotencyHuman cellsEpigenomeEnhancerCellsKey role
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