Acute Myeloid Leukemia iPSCs reveal a role for RUNX1 in the maintenance of human Leukemia Stem Cells

Leukemia stem cells (LSCs) in acute myeloid leukemia (AML) are believed to possess distinct biological properties than the bulk AML cells, but their rarity and the unavailability of universal immunophenotypic markers for their prospective isolation hampers their study. We report that hematopoietic cells from genetically clonal AML patient-derived induced pluripotent stem cells (iPSCs) contain two morphologically and immunophenotypically distinct subpopulations: a cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth which we termed induced leukemai stem cells (iLSCs) and a non-adherent fraction of more differentiated cells, which we termed induced blasts (iBlasts). Through fate-tracking experiments, xenotransplantation and single cell transcriptomics, we show that iLSCs cells reside on the apex of a phenotypic and functional hierarchy and fulfill the hallmark features of leukemia stem cells. Through integrative genomics studies of their transcriptome and chromatin landscape, we derive an LSC 16-gene set that predicts patient survival and identify RUNX1 as a new dependency of AML LSCs. Hematopoietic cells obtained from the AML-4.10 iPSC line were plated in 6 wells of a 6-well tissue culture-treated plate on day 14 of hematopoietic differentiation. After 2 days the iBlasts cells were removed from all 6 wells by washing. The iLSCs cells from 2 wells were collected independently with accutase as the day 16 duplicates. The total cells from two of the remaining wells were independently harvested after 1 and after 2 weeks as day 23 and day 30 duplicates, respectively. All samples were sorted for live (DAPI-) CD45+ cells on a BD FACS Aria II and single cell RNA sequencing was performed using Chromium 10X v2.