Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

Arrested bone marrow (BM) lymphoid cell differentiation underlies the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). Recurrent genetic lesions often directly involve transcription factors (TFs), such as ETV6 and RUNX1 found in the most common ALL translocation. Here, we studied differential gene expression in ETV6-RUNX1 primary ALL samples and the REH cell line using single cell RNA-seq (scRNA-seq). Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns. The raw data can be accessed at https://www.ebi.ac.uk/ega/studies/EGAS00001004374 Primary patient samples from diagnosis (N=6 BM samples, subtype ETV6-RUNX1, 4000-8000 cells per donor) with day 15 post-treatment sample collected from two cases. Cell line experiment in REH comparing two drugs targeting ETS-factors (TK216 ERG/FLI1 and XRP44X ELK3) at 72 h (N=1, 900-2500 cells per treatment).