H1‐0 is a specific mediator of the repressive ETV6::RUNX1 transcriptional landscape in preleukemia and B cell acute lymphoblastic leukemia

<i>ETV6::RUNX1</i>, the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL), induces a clinically silent preleukemic state that can persist in carriers for over a decade and may progress to overt leukemia upon acquisition of secondary lesions. The mechanisms contributing to quiescence of <i>ETV6::RUNX1</i>+ preleukemic cells still remain elusive. In this study, we identify linker histone H1-0 as a critical mediator of the <i>ETV6::RUNX1</i>+ preleukemic state by employing human -induced pluripotent stem cell (hiPSC) models engineered by using CRISPR/Cas9 gene editing. Global gene expression analysis revealed upregulation of <i>H1-0</i> in <i>ETV6::RUNX1</i>+ hiPSCs that was preserved upon hematopoietic differentiation. Moreover, whole transcriptome data of 1,727 leukemia patient samples showed significantly elevated <i>H1-0</i> levels in <i>ETV6::RUNX1</i>+ BCP-ALL compared to other leukemia entities. Using dual-luciferase promoter assays, we show that ETV6::RUNX1 induces <i>H1-0</i> promoter activity. We further demonstrate that depletion of H1-0 specifically inhibits ETV6::RUNX1 signature genes, including <i>RAG1</i> and <i>EPOR</i>. Single-cell sequencing showed that <i>H1-0</i> is highly expressed in quiescent hematopoietic cells. Importantly, H1-0 protein levels correspond to susceptibility of BCP-ALL cells towards histone deacetylase inhibitors (HDACis) and combinatorial treatment using the H1-0-inducing HDACi Quisinostat showed promising synergism with established chemotherapeutic drugs. Taken together, our data identify H1-0 as a key regulator of the <i>ETV6::RUNX1</i>+ transcriptome and indicate that the addition of Quisinostat may be beneficial to target non-responsive or relapsing <i>ETV6::RUNX1</i>+ BCP-ALL.