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
2023
Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes
Yankee T, Oh S, Winchester E, Wilderman A, Robinson K, Gordon T, Rosenfeld J, VanOudenhove J, Scott D, Leslie E, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nature Communications 2023, 14: 4623. PMID: 37532691, PMCID: PMC10397224, DOI: 10.1038/s41467-023-40363-1.Peer-Reviewed Original ResearchConceptsGene co-expression analysisSingle-cell RNA-seqCraniofacial disordersSet of genesCo-expression analysisTranscriptome dynamicsDevelopmental enhancersRegulatory hubEpigenomic dataCraniofacial developmentRNA-seqDe novo mutationsDisease genesGene expressionIntegrative analysisCraniofacial tissuesGenesNovo mutationsHuman tissuesMutationsDevelopment identifiesCommon congenital defectsWeeks post conceptionPost conceptionCraniofacial region
2017
Precocious Phenotypic Transcription‐Factor Expression During Early Development
VanOudenhove J, Medina R, Ghule P, Lian J, Stein J, Zaidi S, Stein G. Precocious Phenotypic Transcription‐Factor Expression During Early Development. Journal Of Cellular Biochemistry 2017, 118: 953-958. PMID: 27591551, PMCID: PMC5336526, DOI: 10.1002/jcb.25723.Peer-Reviewed Original ResearchConceptsPhenotypic transcription factorsTranscription factorsPrecocious expressionRUNX1 transcription factorTranscriptional controlLineage identityGene expressionNovel roleBiological importanceMesenchymal transitionEarly differentiationMesenchymal differentiationTransient upregulationDetailed mechanistic studiesExpressionDifferentiationMechanistic studiesRUNX1RoleUpregulationFurther studies