2024
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in TH17 cells
Thakore P, Schnell A, Huang L, Zhao M, Hou Y, Christian E, Zaghouani S, Wang C, Singh V, Singaraju A, Krishnan R, Kozoriz D, Ma S, Sankar V, Notarbartolo S, Buenrostro J, Sallusto F, Patsopoulos N, Rozenblatt-Rosen O, Kuchroo V, Regev A. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in TH17 cells. Nature Immunology 2024, 25: 1395-1410. PMID: 39009838, DOI: 10.1038/s41590-024-01901-1.Peer-Reviewed Original ResearchConceptsTransposase-accessible chromatin sequencingSingle-cell RNA sequencingTh17 heterogeneitySingle-cell assaysScATAC-seqChromatin landscapeChromatin stateChromatin sequencingRegulatory networksScRNA-seqTh17 cell pathogenicityHuman geneticsIn vivoRNA sequencingChromatin configurationRegulatory pathwaysTissue homeostasisCell statesCells in vitroBach2ChromatinSequenceCellsType 1 helper T (Th1) cellsCD4+ T cell subsetsSpatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols 2024, 19: 3389-3425. PMID: 38943021, DOI: 10.1038/s41596-024-01013-y.Peer-Reviewed Original ResearchTn5 transpositionDeterministic barcodingGenome-wide profiling of histone modificationsProfiling of histone modificationsTransposase-accessible chromatin sequencingEpigenomic profiling methodsGenome-wide profilingSingle-base resolutionGene regulation programsGenomic DNA locusNext-generation sequencingDNA lociBioinformatics skillsLibrary preparationDNA barcodingChromatin accessibilityChromatin sequencingHistone modificationsEpigenome sequencingEpigenetic landscapeEpigenetic mapsCellular functionsEpigenetic markersCustom pipelineBarcodingDetecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling
Zarif T, Meador C, Qiu X, Seo J, Davidsohn M, Savignano H, Lakshminarayanan G, McClure H, Canniff J, Fortunato B, Li R, Banwait M, Semaan K, Eid M, Long H, Hung Y, Mahadevan N, Barbie D, Oser M, Piotrowska Z, Choueiri T, Baca S, Hata A, Freedman M, Berchuck J. Detecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling. Clinical Cancer Research 2024, 30: 3798-3811. PMID: 38912901, PMCID: PMC11369616, DOI: 10.1158/1078-0432.ccr-24-0466.Peer-Reviewed Original ResearchConceptsEGFR mutant lung adenocarcinomaSmall cell lung cancerSmall cell transformationLung cancer patient-derived xenograftPatient-derived xenograftsLung adenocarcinomaEGFR mutantsChIP-seqEpigenomic featuresMeDIP-seqImmunoprecipitation sequencingCell transformationHistological transformation to small cell lung cancerTransformation to small cell lung cancerMethylated DNA immunoprecipitation sequencingTransposase-accessible chromatin sequencingH3K27ac ChIP-seqMechanisms of treatment resistanceChromatin immunoprecipitation sequencingHistone modification H3K27acMutant lung adenocarcinomaCell lung cancerChromatin accessibilityChromatin sequencingEpigenomic landscape
2023
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
Chen X, Wang Y, Cappuccio A, Cheng W, Zamojski F, Nair V, Miller C, Rubenstein A, Nudelman G, Tadych A, Theesfeld C, Vornholt A, George M, Ruffin F, Dagher M, Chawla D, Soares-Schanoski A, Spurbeck R, Ndhlovu L, Sebra R, Kleinstein S, Letizia A, Ramos I, Fowler V, Woods C, Zaslavsky E, Troyanskaya O, Sealfon S. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nature Computational Science 2023, 3: 644-657. PMID: 37974651, PMCID: PMC10653299, DOI: 10.1038/s43588-023-00476-5.Peer-Reviewed Original ResearchCell-type resolutionRegulatory circuitsMethicillin resistanceTransposase-accessible chromatin sequencingDisease-associated transcription factorsOmics data typesSingle-cell dataSingle-cell RNA sequencingGene expression changesChromatin sitesMethicillin-susceptible S. aureus infectionsChromatin sequencingTranscription factorsRNA sequencingStaphylococcus aureus sepsisMultiomics dataExpression analysisExpression changesBloodstream infectionsBacterial sepsisCD14 monocytesSequencePredictive valueHierarchical Bayesian approachUninfected controls
2022
Acly Deficiency Enhances Myelopoiesis through Acetyl Coenzyme A and Metabolic–Epigenetic Cross-Talk
Greenwood D, Ramsey H, Nguyen P, Patterson A, Voss K, Bader J, Sugiura A, Bacigalupa Z, Schaefer S, Ye X, Dahunsi D, Madden M, Wellen K, Savona M, Ferrell P, Rathmell J. Acly Deficiency Enhances Myelopoiesis through Acetyl Coenzyme A and Metabolic–Epigenetic Cross-Talk. ImmunoHorizons 2022, 6: 837-850. PMID: 36547387, PMCID: PMC9935084, DOI: 10.4049/immunohorizons.2200086.Peer-Reviewed Original ResearchConceptsChromatin accessibilityMyeloid differentiationTransposase-accessible chromatin sequencingEpigenetic cross talkHematopoietic stemSingle-cell RNA sequencingFamily transcription factorsProgenitor cellsSmall molecule inhibitionSingle-cell assaysATP-citrate lyaseEpigenetic marksAcetyl coenzyme AGene expression signaturesEpigenetic modificationsTranscription factorsRNA sequencingACLY inhibitionMitochondrial metabolismReactive oxygen speciesMitochondrial polarizationMurine hematopoiesisCell metabolismMus musculusEssential substrate
2021
Landmarks of human embryonic development inscribed in somatic mutations
Bizzotto S, Dou Y, Ganz J, Doan R, Kwon M, Bohrson C, Kim S, Bae T, Abyzov A, Network† N, Park P, Walsh C. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021, 371: 1249-1253. PMID: 33737485, PMCID: PMC8170505, DOI: 10.1126/science.abe1544.Peer-Reviewed Original ResearchConceptsSomatic single nucleotide variantsHuman embryonic developmentEmbryonic developmentEarly embryonic cell divisionsTransposase-accessible chromatin sequencingSingle cellsSingle-nucleus assayHigh-depth whole-genome sequencingSingle-nucleus RNA sequencingEmbryonic cell divisionCell lineage informationDistinct germ layersOnset of gastrulationSingle nucleotide variantsOrganismal developmentWhole-genome sequencingExtraembryonic tissuesCell divisionRNA sequencingProgenitor poolLineage informationGerm layersEarly progenitorsMultiple tissuesSequencing
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