T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1

Abstract

Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC 'stemness'. Using single-cell RNA-seq analysis, we identify a master regulator, SPI1, the LSC-specific expression of which determines the molecular signature and activity of LSCs in the murine <i>Pten</i>-null T-ALL model. Although initiated by PTEN-controlled β-catenin activation, <i>Spi1</i> expression and LSC 'stemness' are maintained by a β-catenin-SPI1-HAVCR2 regulatory circuit independent of the leukemogenic driver mutation. Perturbing any component of this circuit either genetically or pharmacologically can prevent LSC formation or eliminate existing LSCs. LSCs lose their 'stemness' when <i>Spi1</i> expression is silenced by DNA methylation, but <i>Spi1</i> expression can be reactivated by 5-AZ treatment. Importantly, similar regulatory mechanisms may be also present in human T-ALL.