RESUMEN
Single-cell genomics technology has transformed our understanding of complex cellular systems. However, excessive cost and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high-content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all main hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables the functional capacities of precisely mapped cell states to be measured at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.
Asunto(s)
Células Sanguíneas/metabolismo , Células de la Médula Ósea/metabolismo , Separación Celular , Citometría de Flujo , Perfilación de la Expresión Génica , Proteoma , Proteómica , Análisis de la Célula Individual , Transcriptoma , Factores de Edad , Células Sanguíneas/inmunología , Células Sanguíneas/patología , Células de la Médula Ósea/inmunología , Células de la Médula Ósea/patología , Células Cultivadas , Bases de Datos Genéticas , Envejecimiento Saludable/genética , Envejecimiento Saludable/inmunología , Envejecimiento Saludable/metabolismo , Humanos , Leucemia/genética , Leucemia/inmunología , Leucemia/metabolismo , Leucemia/patología , RNA-Seq , Biología de SistemasRESUMEN
Inter-patient variability and the similarity of healthy and leukemic stem cells (LSCs) have impeded the characterization of LSCs in acute myeloid leukemia (AML) and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. Although residual healthy and preleukemic cells dominated the dormant stem cell compartment, active LSCs resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors constituted a highly aberrant, disease-defining compartment: their gene expression and differentiation state affected both the chemotherapy response and leukemia's ability to differentiate into transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers misregulated specifically in leukemic cells. Taken together, CloneTracer reveals a differentiation landscape that mimics its healthy counterpart and may determine biology and therapy response in AML.