Functional diversity of single stem cell clones in patients&#39; acute lymphoblastic leukemia growing in mice: An adverse subclone with distinct DNA-methylation pattern, slow growth<em> in vivo </em>and drug resistance.

Acute lymphoblastic leukemia (ALL) consists of genetically heterogeneous cell subpopulations, but little is known about how genetic differences lead to functional differences between the clones. Of major clinical importance, aggressive, treatment-resistant and putatively relapse-inducing subclones need to be identified and require effective eradication by treatment. The most aggressive subpopulation likely determines prognosis and outcome in each patient. We aimed at characterizing on a functional as well as on a genetic level single stem cell clones derived from patients&#39; samples growing in mice and to combine the results of both levels in order to learn which genetic characteristics are associated with adverse functional behavior. We transplanted primary tumor cells from a 5-year old girl with hyperdiploid ALL involving a trisomic X chromosome at first relapse into severely immune-compromised mice and lentivirally modified them to express the fluorochromes red, blue and green at different amounts and combinations (RGB marking, Weber et al., 2012). Eight single stem cell clones were generated by limiting dilution transplantation and their uniqueness was verified by ligation-mediated (LM) PCR. We functionally compared the single stem cell clones between each other by re-mixing them in a single mouse for in vivo assays; analysis was performed one-by-one for each clone by flow cytometry where they could be distinguished from each other using their unique color codes. Clones showed clear differences in proliferation rate with faster and slower growing clones, independently whether 2 or 5 clones were mixed. When mice harboring clone mixtures were treated with conventional chemotherapy, clonal composition changed markedly and resistant clones overgrew sensitive clones indicating selective clonal responses and clonal advantage. A clone which showed especially slow growth in vivo was most resistant to in vivo treatment with Glucocorticoids. The slowly proliferating, Glucocorticoid-resistant clone had lost the additional X chromosome, which was present in all other clones and the bulk and showed a distinct DNA-methylation pattern analyzed by 450K arrays (illumina). In exome analysis, the clone showed 11 unique alterations including a single nucleotide variant in the oncogene USP6. We are currently performing RNA sequencing analysis to assess the differential gene expression in the clones. Taken together, genetic multicolor marking PDX ALL cells in the individualized xenograft mouse model allowed generating viable single cell clones for genetic functional characterization in vivo. Within the heterogeneous tumor bulk, an subclone existed which showed slow tumor growth and drug resistance which was associated with distinct genetic characteristics. Our studies allow the challenging functional characterization of subclones in vivo in order to develop efficient novel treatment approaches to eliminate aggressive stem cell clones in ALL