HOXA9 Nucleates a Repressive Chromatin Complex with Nuclear Matrix-Associated Protein- Safb to Maintain Acute Myeloid Leukemia

HOXA9 is an exemplar of the clustered homeobox domain proteins critical for the axial body plan and other developmental processes. However in leukemia, HOXA9 has long been known to be a critical driver of Acute Myeloid Leukaemia (AML) and is a downstream mediator of multiple recurrent mutations that drive AML. However, its detailed mechanisms of action and targets remain poorly studied, partly due to a lack of available tools, although its role as an activator of leukemic transcriptional programmes is well accepted.

In this work we report the first protein interactome for endogenous human HOXA9, and via an interdisciplinary combination of proteomics, genomics and functional analyses in vitro and in vivo, identify a novel interaction partner at chromatin, scaffold attachment factor B (SAFB). We then demonstrate that SAFB nucleates a repressive chromatin complex with HOXA9 and that, functionally, this complex is required for the maintenance of the leukaemia state via active repression of myeloid differentiation allowing sustained proliferation and increased cell survival.

Mechanistically, the downstream gene repression programme mediated via the HOXA9-SAFB (H9SB) complex is independent from the activating HOX programme. Furthermore, via chromatin proteomics, genome-wide chromatin mapping and genetic and pharmacological perturbation, we demonstrate that its repressive function requires the recruitment and catalytic function of the NURD complex and the heterochromatin regulator CBX3/HP1γ.

This work therefore not only describes an entirely novel function for HOXA9, but also provides granular molecular detail of the mechanisms downstream of the complex that mediates this repressive function. Moreover, conceptually it also demonstrates the importance of the active maintenance of differentiation block, rather than the passive failure of the induction of differentiation in leukaemia biology. These findings not only have profound implications for the understanding of leukemias, but also have implications for other tumours and for the function of clustered homeobox genes in other contexts, such as development. In addition, although it is likely that inhibition of all aspects of HOXA9 function would be accompanied with unacceptable toxicity, we propose that directly interfering with the HOXA9-SAFB interface and/or the activity of its downstream catalytic mediators may have significant therapeutic potential

Sasca:Abbvie: Honoraria; Astra-Zeneca: Honoraria; Bristol-Myers-Squibb: Honoraria; Biontech: Other: Current Employment (Spouse).