Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis

Background: 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. Results: Here, 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. Conclusions: Overall, 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 material The online version of this article (doi:10.1186/s13059-014-0525-9) contains supplementary material, which is available to authorized users

Targeted Disruption of the EZH2/EED Complex Inhibits EZH2-dependent Cancer

Enhancer of zeste homolog2 (EZH2) is the histone lysine N-methyltransferase component of the Polycomb repressive complex 2 (PRC2), which in conjunction with embryonic ectoderm development (EED) and suppressor of zeste 12 homolog (SUZ12), regulates cell lineage determination and homeostasis. Enzymatic hyperactivity has been linked to aberrant repression of tumor suppressor genes in diverse cancers. Here, we report the development of stabilized alpha-helix of EZH2 (SAH-EZH2) peptides that selectively inhibit H3 Lys27 trimethylation by dose-responsively disrupting the EZH2/EED complex and reducing EZH2 protein levels, a mechanism distinct from that reported for small molecule EZH2 inhibitors targeting the enzyme catalytic domain. MLL-AF9 leukemia cells, which are dependent on PRC2, undergo growth arrest and monocyte/macrophage differentiation upon treatment with SAH-EZH2, consistent with observed changes in expression of PRC2-regulated, lineage-specific marker genes. Thus, by dissociating the EZH2/EED complex, we pharmacologically modulate an epigenetic “writer” and suppress PRC2-dependent cancer cell growth

Musings on genome medicine: abuse of genetic tests

The wide general publication of a putative genetic test for athletic supremacy is clearly an abuse of genetics and reveals an undercurrent of hucksterism in biomedical science

Musings on genome medicine: cholesterol and coronary artery disease

Cholesterol levels and not inflammatory markers are the major variables that pose a risk of coronary artery disease. Diabetes greatly increases the risk at any cholesterol level. Coronary artery disease and cancer are linked by a common protein - an apoptotic protein that also functions as a regulator of insulin secretion

Musings on genome medicine: genome wide association studies

http://dx.doi.org/10.1186/gm

Musings on genome medicine: gene therapy

Though the field has moved with glacial speed, gene therapies have been carried out successfully in patients with bone marrow disorders including immune deficiencies. The field may be poised to move forward more rapidly, but many barriers have yet to be surmounted

Musings on genome medicine: enzyme-replacement therapy of the lysosomal storage diseases

The lysosomal storage diseases, such as Gaucher's disease, mucopolysaccharidosis I, II and IV, Fabry's disease, and Pompe's disease, are rare inherited disorders whose symptoms result from enzyme deficiency causing lysosomal accumulation. Until effective gene-replacement therapy is developed, expensive, and at best incomplete, enzyme-replacement therapy is the only hope for sufferers of rare lysosomal storage diseases. Preventive strategies involving carrier detection should be a priority toward the successful management of these conditions

Networking erythropoiesis

Recent findings and technological advances provide insight into how a few transcription factors work together in complex ways to orchestrate red blood cell differentiation

Musings on genome medicine: Crohn's disease

The inflammatory bowel diseases, Crohn's disease and ulcerative colitis, pose a fascinating challenge to specialists in gastroenterology, infectious diseases, immunology and genetics and an often crushing burden to patients and their families