Abstract
BackgroundA fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. Recent advances in single-cell gene expression profiling have created new possibilities to characterize this heterogeneity and to dissect the potential intra-cancer cellular hierarchy.ResultsHere, we apply single-cell analysis to systematically characterize the heterogeneity within leukemic cells using the MLL-AF9 driven mouse model of acute myeloid leukemia. We start with fluorescence-activated cell sorting analysis with seven surface markers, and extend by using a multiplexing quantitative polymerase chain reaction approach to assay the transcriptional profile of a panel of 175 carefully selected genes in leukemic cells at the single-cell level. By employing a set of computational tools we find striking heterogeneity within leukemic cells. Mapping to the normal hematopoietic cellular hierarchy identifies two distinct subtypes of leukemic cells; one similar to granulocyte/monocyte progenitors and the other to macrophage and dendritic cells. Further functional experiments suggest that these subtypes differ in proliferation rates and clonal phenotypes. Finally, co-expression network analysis reveals similarities as well as organizational differences between leukemia and normal granulocyte/monocyte progenitor networks.ConclusionsOverall, our single-cell analysis pinpoints previously uncharacterized heterogeneity within leukemic cells and provides new insights into the molecular signatures of acute myeloid leukemia.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0525-9) contains supplementary material, which is available to authorized users.
Highlights
A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood
Further studies suggested that leukemia stem cell (LSC) are located almost exclusively downstream of the normal progenitor compartment based on immunophenotype [6] and that they display a phenotype similar to granulocyte/monocyte progenitors (GMPs) [4]
Leukemic cell populations can be distinguished by their green fluorescent protein (GFP) expression, which originates from the MLL-AF9 construct
Summary
A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. Recent advances in single-cell gene expression profiling have created new possibilities to characterize this heterogeneity and to dissect the potential intra-cancer cellular hierarchy. Characterization of cancer heterogeneity is of immense importance with significant clinical implications. To describe this heterogeneity, a model of considerable current interest posits that tumors are hierarchically organized, and initiated by cancer stem cells, which are able to selfrenew as well as to differentiate into all other lineages in the tumor [1]. One of the few cancer-types in which cancer stem cells have been intensively studied is acute myeloid leukemia (AML) [2,3,4]. The critical pathways for LSC functions remain incompletely understood [8,9,10]
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