Oncogenic ZEB2 Activation Drives Sensitivity Towards LSD1 Inhibition in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemias (T-ALLs) are rare aggressive hematologic tumors resulting from the malignant transformation of T-cell progenitors. The prognosis of T-ALL has gradually improved with the introduction of intensified chemotherapy. However, the outcome of T-ALL patients with primary resistant or relapsed leukemia remains extremely poor. Therefore, current research efforts are focused on the development of more effective and less toxic anti-leukemic drugs, which will likely require an improved understanding of the molecular biology of chemotherapy resistant residual tumor cells that eventually drive disease recurrence.

Using a conditional gain-of-function mouse model, we recently demonstrated that ZEB2 is an oncogenic driver of an immature subtype of T-ALL with increased leukemia-initiating properties. ZEB2 is a large multidomain homeobox transcription factor that recognizes bipartite E-box motifs through its amino- and carboxyterminal Zinc finger domains. The domains outside the Zn-finger clusters have been shown to be essential for the recruitment of various tissue-specific co-activators/repressors. Identification and targeting of these interaction partners that are essential for the oncogenic properties of ZEB2 could be a feasible option for the development of novel therapeutics to treat this aggressive leukemia.

In this study, we performed ZEB2 protein pull down experiments and subsequent mass spectrometry to explore the ZEB2 interactome in the context of T-ALL. We identified the Lysine-specific demethylase KDM1A/LSD1 as a novel interaction partner of ZEB2. The ZEB2-LSD1 interaction was confirmed via bi-directional co-immunoprecipitation experiments in both mouse and human T-ALL cell lines. KDM1A/LSD1 is a flavin-containing amino oxidase that specifically catalyzes the demethylation of mono- and di-methylated lysines on histone 3. LSD1 has been reported to regulate the balance between self-renewal and differentiation of pluripotent stem cells and its expression is upregulated in various cancers. Pharmacological inhibition of LSD1 has been proposed as a novel promising therapy to treat and kill cancer stem cells and novel potent inhibitors are being tested in clinical trials. We demonstrated that mouse and human T-ALLs with increased ZEB2 levels critically depend on LSD1 activity for their leukemic survival. In addition, doxycycline induced ZEB2 overexpression significantly increased sensitivity to LSD1 inhibition in the MLL-AFX positive T-ALL cell line KARPAS-45.

We conclude that targeting the ZEB2 protein complex through direct disruption of the ZEB2-LSD1 interaction or pharmacological inhibition of the LSD1 demethylase activity itself, could serve as a novel therapeutic strategy for this aggressive subtype of T-ALL, and possibly other ZEB2-driven malignancies.