2024
Clonal Dissection of MDS and Secondary AML Resolves Shared Splicing Neoantigens and Mechanistic Underpinnings of Hypomethylating Agent Therapeutic Response
Zhang X, Li G, Oliverio A, VanOudenhove J, DeZern A, Ghiaur G, Halene S, Grimes H, Salomonis N. Clonal Dissection of MDS and Secondary AML Resolves Shared Splicing Neoantigens and Mechanistic Underpinnings of Hypomethylating Agent Therapeutic Response. Blood 2024, 144: 1810-1810. DOI: 10.1182/blood-2024-211099.Peer-Reviewed Original ResearchHematopoietic stem cellsHypomethylating agent therapyHypomethylating agentsMyelodysplastic syndromeSecondary AMLBone marrow hematopoietic stem cellsHigh-risk myelodysplastic syndromeQuiescent hematopoietic stem cellsMarrow hematopoietic stem cellsSplicing alterationsPrimary myelodysplastic syndromesMyelodysplastic syndrome patientsGene programHeterogeneous hematological disorderMDS therapyAged bone marrowAssociated with down-regulationHuman hematopoietic progenitorsSingle-cell populationsAssociated with mutationsSurface protein expressionGene expressionCell statesIllumina short readsPrimitive HSCs
2022
Spatial profiling of chromatin accessibility in mouse and human tissues
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022, 609: 375-383. PMID: 35978191, PMCID: PMC9452302, DOI: 10.1038/s41586-022-05094-1.Peer-Reviewed Original ResearchConceptsChromatin accessibilityATAC-seqSpecific epigenetic landscapesChromatin accessibility profilingCell fate decisionsEpigenetic informationEpigenetic landscapeGenome scaleFate decisionsAccessible genomeCell identityEpigenetic underpinningsNext-generation sequencingGene regulatorsCell statesMouse embryosSpatial biologySpatial transcriptomicsCell typesCellular levelImmune cell typesDistinct organizationHuman tissuesProfilingSpatial profiling