2025
Profiling Histone Modifications in Differentiating Mouse Spermatogonia with CUT&Tag
Walters B, Yu H, Kataruka S, Lesch B. Profiling Histone Modifications in Differentiating Mouse Spermatogonia with CUT&Tag. Methods In Molecular Biology 2025, 2954: 3-26. PMID: 40601267, DOI: 10.1007/978-1-0716-4698-4_1.Peer-Reviewed Original ResearchConceptsHistone modificationsGenome-wide histone modificationsPostmeiotic stages of spermatogenesisProfiling histone modificationsChIP-seq experimentsGene regulatory informationChIP-seq analysisStages of spermatogenesisMale germ cellsMale germ lineMammalian spermatogenesisChIP-seqFluorescence-activated cell sortingPremeiotic cellsPostmeiotic stagesEpigenetic landscapeChromatin immunoprecipitationGerm lineSeminiferous tubulesGerm cellsMouse spermatogoniaRegulatory informationSpermatogoniaEpigenetic changesCUT&TagPrenatal opioid exposure alters pain perception and increases long-term health risks in infants with neonatal opioid withdrawal syndrome
Radhakrishna U, Radhakrishnan R, Uppala L, Trivedi T, Prajapati J, Rawal R, Muvvala S, Bahado-Singh R, Sadhasivam S. Prenatal opioid exposure alters pain perception and increases long-term health risks in infants with neonatal opioid withdrawal syndrome. Frontiers In Pain Research 2025, 6: 1497801. PMID: 40313396, PMCID: PMC12043715, DOI: 10.3389/fpain.2025.1497801.Peer-Reviewed Original ResearchNeonatal opioid withdrawal syndromeOpioid-exposed infantsOpioid withdrawal syndromePain-related genesOpioid exposureWithdrawal syndromeChronic painEpigenetic changesMaternal opioid exposurePrenatal opioid exposureImprove pain managementIon channel functionIllumina Infinium Methylation EPIC BeadChipInfinium Methylation EPIC BeadChipAnalyzed DNA methylationUnexposed control subjectsLong-term health risksPain reliefPain perceptionPregnant womenGnRH secretionPlacental tissueMorphine addictionHealth of mothersControl subjects
2024
Epigenetic Changes in Cerebrospinal Fluid and Blood of People With Neurosyphilis
Mostaghimi D, Mehta S, Yoon J, Kosana P, Marra C, Corley M, Farhadian S. Epigenetic Changes in Cerebrospinal Fluid and Blood of People With Neurosyphilis. The Journal Of Infectious Diseases 2024, 231: 883-893. PMID: 39356164, PMCID: PMC11998562, DOI: 10.1093/infdis/jiae476.Peer-Reviewed Original ResearchPeripheral blood mononuclear cellsCerebrospinal fluidRNA expression changesEpigenetic changesExpression changesBlood mononuclear cellsDifferentially methylated sitesDNA methylation profilesInsulin-responsive pathwaysAntibiotic treatmentImmune cellsB cellsMononuclear cellsMethylation changesDNA methylationMethylation profilesMatched ControlsBacterial infectionsNon-NENeurosyphilisBlood of peopleInfectionRNANsHuman genetics and epigenetics of alcohol use disorder
Zhou H, Gelernter J. Human genetics and epigenetics of alcohol use disorder. Journal Of Clinical Investigation 2024, 134: e172885. PMID: 39145449, PMCID: PMC11324314, DOI: 10.1172/jci172885.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesEWAS studiesPower of GWASTranscriptome-wide associationGenome-wide scanAlcohol use disorderWhole-genome sequencingDrug-gene interactionsSingle-cell sequencingAssociation studiesDownstream analysisHuman geneticsGenetic variantsEpigenetic risk factorsVariant functionEpigenetic changesSpatial transcriptomicsUse disorderEpigeneticsDisease risk predictionGenetic correlationsDiversity of populationGeneticsComplex etiologyEnvironmental factorsThe association of FKBP5 gene polymorphism with genetic susceptibility to depression and response to antidepressant treatment- a systematic review
Zhang Y, Yue W, Li J. The association of FKBP5 gene polymorphism with genetic susceptibility to depression and response to antidepressant treatment- a systematic review. BMC Psychiatry 2024, 24: 274. PMID: 38609904, PMCID: PMC11010372, DOI: 10.1186/s12888-024-05717-z.Peer-Reviewed Original ResearchConceptsFKBP5 gene polymorphismsAntidepressant treatmentGene polymorphismsResponse to antidepressant treatmentAntidepressant drug treatmentGenetic susceptibilityAffective disordersAssociated with adverse reactionsDepressionTreatment strategiesAdverse reactionsFKBP5Drug treatmentTreatment sensitivityMethodsElectronic databasesGenetic disordersRs1360780Epigenetic changesReplication studySystematic reviewModerate qualityStudy characteristicsTreatmentData extractionDisorders
2023
Transcription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape
Boddu P, Gupta A, Roy R, Herrero A, Verma A, Neugebauer K, Pillai M. Transcription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape. Blood 2023, 142: 709. DOI: 10.1182/blood-2023-188083.Peer-Reviewed Original ResearchChromatin organizationSuch epigenetic changesGenome editing approachesRNA splicing factorsChromatin landscapeSingle mutant alleleEpigenetic landscapeGenomic integrityTranscription defectTranscription kineticsSplicing factorsChIP-seqEpigenetic regulatorsEpigenetic changesEpigenetic therapyMutant allelesEditing approachesFactor mutationsK562 cell lineDownstream effectsCell linesMyeloid disordersClonal myeloid disordersHDAC pathwayMutationsThe Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms
Ladel L, Tan W, Jeyakanthan T, Sailo B, Sharma A, Ahuja N. The Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms. Cells 2023, 12: 1962. PMID: 37566041, PMCID: PMC10417136, DOI: 10.3390/cells12151962.Peer-Reviewed Original ResearchMore 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 tissueSignaturesVitroAccumulationDivisionPilot study suggests DNA methylation of the glucocorticoid receptor gene (NR3C1) is associated with MDMA-assisted therapy treatment response for severe PTSD
Lewis C, Tafur J, Spencer S, Green J, Harrison C, Kelmendi B, Rabin D, Yehuda R, Yazar-Klosinski B, Cahn B. Pilot study suggests DNA methylation of the glucocorticoid receptor gene (NR3C1) is associated with MDMA-assisted therapy treatment response for severe PTSD. Frontiers In Psychiatry 2023, 14: 959590. PMID: 36815187, PMCID: PMC9939628, DOI: 10.3389/fpsyt.2023.959590.Peer-Reviewed Original ResearchPost-traumatic stress disorderSevere post-traumatic stress disorderTreatment responseClinical trialsRecent phase 3 clinical trialsPhase 3 clinical trialsClinician-Administered PTSD ScaleParent clinical trialKey HPA axis genesHPA axis genesPTSD symptom improvementGlucocorticoid receptor geneFalse discovery rate correctionAdrenal genesPlacebo groupSymptom improvementLarge cohortMethylation changesEpigenetic changesSymptom reductionPTSD ScaleTherapyHPA genesStress disorderPilot study
2022
Pathogenesis of chronic chikungunya arthritis: Resemblances and links with rheumatoid arthritis
Amaral J, Bingham C, Taylor P, Vilá L, Weinblatt M, Schoen R. Pathogenesis of chronic chikungunya arthritis: Resemblances and links with rheumatoid arthritis. Travel Medicine And Infectious Disease 2022, 52: 102534. PMID: 36549417, DOI: 10.1016/j.tmaid.2022.102534.Peer-Reviewed Original ResearchConceptsChronic chikungunya arthritisMesenchymal stem cellsJoint painChikungunya virusReactivation of dormant virusesMorphologically similar to fibroblastsChikungunya feverEpigenetic changesChronic joint painAcute febrile illnessChikungunya virus infectionSimilar to fibroblastsMaculopapular rashChikungunya arthritisDormant virusesFebrile illnessLatent infectionMultipotent cellsStem cellsHeterogeneous groupRheumatoid arthritisPathogenic hypothesisGroup of multipotent cellsPainPatientsInterferon 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 samplesSynergizesEpigenetics of alcohol-related liver diseases
Habash N, Sehrawat T, Shah V, Cao S. Epigenetics of alcohol-related liver diseases. JHEP Reports 2022, 4: 100466. PMID: 35462859, PMCID: PMC9018389, DOI: 10.1016/j.jhepr.2022.100466.Peer-Reviewed Original ResearchAlcohol-related liver diseaseLiver diseaseMajor public health problemChronic liver diseasePublic health problemProinflammatory roleSignificant morbidityMultiple disease statesHealth problemsDisease statesDiseaseClinical applicationNon-coding RNADiagnosisEpigenetic alterationsPrimary causeCurrent knowledgeEpigenetic changesReview articleStudy of epigeneticsHepatologistsMorbidityComplicationsChemokinesPathophysiology
2021
The Embryological Landscape of Mayer-Rokitansky-Kuster-Hauser Syndrome: Genetics and Environmental Factors.
Kyei-Barffour I, Margetts M, Vash-Margita A, Pelosi E. The Embryological Landscape of Mayer-Rokitansky-Kuster-Hauser Syndrome: Genetics and Environmental Factors. The Yale Journal Of Biology And Medicine 2021, 94: 657-672. PMID: 34970104, PMCID: PMC8686787.Peer-Reviewed Original ResearchConceptsMRKH syndromeClinical presentationMayer-RokitanskyEmbryonic developmentEnvironmental factorsEpigenetic changesFunctional validationCandidate genesGenetic analysisMolecular mechanismsDevelopmental pathwaysKüster-Hauser syndromeEarly organogenesisKuster-Hauser syndromeKey pathwaysGenetic componentInheritance patternEnvironmental compoundsIncomplete penetranceClinical managementDiscordant phenotypesEarly diagnosisAnimal modelsGeneticsTranslational studiesImmune Therapy: What Can We Learn From Acquired Resistance?
Grant M, Politi K, Gettinger S. Immune Therapy: What Can We Learn From Acquired Resistance? Current Cancer Research 2021, 75-114. DOI: 10.1007/978-3-030-74028-3_5.ChaptersNon-small cell lung cancerAdvanced non-small cell lung cancerDeath-1 pathway inhibitorsPD-1 axis inhibitorsInitial tumor regressionCell lung cancerImmune checkpoint pathwaysIFN-γ signalingMediators of resistanceDisease stabilitySystemic progressionMost patientsLocal therapyClinical criteriaLung cancerTumor regressionTumor typesDisease sitesPathway inhibitorAcquired ResistancePresentation defectPatientsTranslational workProgressionEpigenetic changesGenome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer
Liu Q, Liu G, Martin DT, Xing YT, Weiss RM, Qi J, Kang J. Genome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer. Asian Journal Of Andrology 2021, 23: 472-478. PMID: 33762478, PMCID: PMC8451484, DOI: 10.4103/aja.aja_20_21.Peer-Reviewed Original ResearchConceptsDNA methylationRisk lociGene expressionGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisMethylation-regulated genesEpigenetic association studiesSingle nucleotide polymorphism analysisNucleotide polymorphism analysisTranscript regulationGenomic regionsCancer Genome AtlasEpigenetic changesEpigenetic alterationsLocus analysisAssociation studiesAssociation analysisProgression of tumorsCpG sitesGenesLociMethylationGenome AtlasImportant locusThe genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis
Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nature Communications 2021, 12: 821. PMID: 33547282, PMCID: PMC7865055, DOI: 10.1038/s41467-021-21064-z.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCore Binding Factor Alpha 2 SubunitCpG IslandsDNA MethylationDown SyndromeEpigenesis, GeneticFemaleFetusGATA1 Transcription FactorGenome-Wide Association StudyGenome, HumanHematopoiesisHematopoietic Stem CellsHumansInfant, NewbornLiverMalePromoter Regions, GeneticProto-Oncogene Protein c-fli-1ConceptsDNA methylationGenome-wide impactGenome-wide effectsGenome-wide perturbationsPromoter/enhancer regionEpigenome-wide association studiesAssociation study resultsGene expression changesHematopoietic stem/progenitor cellsCell-type heterogeneityStem/progenitor cellsEpigenome-wide significant CpGsHematopoietic developmentDifferential methylationEpigenetic changesGene expressionPromoter regionEnhancer regionExpression changesAssociation studiesSignificant CpGsImportant regulatorSignificant hypermethylationHematopoietic cellsMethylation
2020
Advances in Molecular Classification and Therapeutic Opportunities in Meningiomas
Cordova C, Kurz S. Advances in Molecular Classification and Therapeutic Opportunities in Meningiomas. Current Oncology Reports 2020, 22: 84. PMID: 32617743, DOI: 10.1007/s11912-020-00937-4.Peer-Reviewed Original ResearchConceptsWHO classification of CNS tumorsClassification of CNS tumorsWHO classificationCNS tumorsWHO grade IDNA methylation patternsBiology of meningiomasClinical trial designPrognostic implicationsTERT promoterTumor biologyGrade IMethylation patternsHistopathological featuresGenetic alterationsEffective therapyLoss of functionMeningiomasMolecular classificationReviewOur understandingDMD geneEpigenetic alterationsTumorEpigenetic changesTherapeutic opportunitiesRegulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases
Ohkura N, Yasumizu Y, Kitagawa Y, Tanaka A, Nakamura Y, Motooka D, Nakamura S, Okada Y, Sakaguchi S. Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases. Immunity 2020, 52: 1119-1132.e4. PMID: 32362325, DOI: 10.1016/j.immuni.2020.04.006.Peer-Reviewed Original ResearchMeSH KeywordsAutoimmune DiseasesBiomarkersCell DifferentiationComputational BiologyCpG IslandsDNA MethylationEpigenesis, GeneticEpigenomicsGene Expression ProfilingGenetic Predisposition to DiseaseGenetic VariationHumansImmunophenotypingPolymorphism, Single NucleotideT-Lymphocyte SubsetsT-Lymphocytes, RegulatoryTranscriptomeConceptsCommon autoimmune diseasesSingle-nucleotide polymorphismsSusceptibility to common autoimmune diseasesCell-specific gene transcriptionGenome-wide epigenetic profilingAssociated with common autoimmune diseasesAssociated with transcriptionPolygenic autoimmune diseasesTreg cellsDemethylated regionCpG hypomethylationSuper-enhancersAutoimmune diseasesDeterminants of susceptibilityEpigenetic modificationsEpigenetic profilesGene transcriptionEpigenetic changesTreg-cell-specific demethylated regionNaive Treg cellsNatural Treg cellsRegional variantsTranscriptionActive stateCellsResponse to Epigenetic Disruption in Tumor Suppressor of Hepatocellular Carcinoma (HCC)
Luna A, Wu Q, Hlady R, Sathyanarayan A, Rustgi V, Guarrera J, Robertson K, Liu C. Response to Epigenetic Disruption in Tumor Suppressor of Hepatocellular Carcinoma (HCC). The FASEB Journal 2020, 34: 1-1. DOI: 10.1096/fasebj.2020.34.s1.08693.Peer-Reviewed Original ResearchHepatocellular carcinomaCancer risk detectionInhibitor 5-aza-2'-deoxycytidineHepatocellular carcinoma detectionHepatocellular carcinoma patientsEpigenetic changesHepatocellular carcinoma tumorsHuh7.5 cellsImproved treatment optionsHCC cell linesGene promoter sitesStressed cellsTreatment optionsTumor formationEpigenetic disruptionEffective treatmentGenetic mutationsLiver cancerEpigenetic dysregulationTumorMethylation inhibitorSuppressor of hepatocellular carcinomaTumor pathwaysWestern blot showEpigenetic eventsApplying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy
Lek A, Zhang Y, Woodman KG, Huang S, DeSimone AM, Cohen J, Ho V, Conner J, Mead L, Kodani A, Pakula A, Sanjana N, King OD, Jones PL, Wagner KR, Lek M, Kunkel LM. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Science Translational Medicine 2020, 12 PMID: 32213627, PMCID: PMC7304480, DOI: 10.1126/scitranslmed.aay0271.Peer-Reviewed Original ResearchConceptsGenome-wide CRISPRCellular hypoxia responseFacioscapulohumeral muscular dystrophyHypoxia responseCell deathTherapeutic discoveryGenome-wide perturbationsComplex genetic diseasesEmergence of CRISPRUnbiased genetic screeningSelection assaysGene-editing technologyDUX4 proteinCausal genesDUX4 expressionZebrafish modelEpigenetic changesProtein turnoverMuscular dystrophyCRISPRMyogenic lineDUX4Genetic diseasesGenesMechanistic understanding
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply