Leukemia Driven By a NUP98-Phd Domain Fusion Is Highly Sensitive To Disruption Of H3K4me3-Phd Domain Binding By a Small Molecule Inhibitor

NUP98 gene fusions, created by non-random chromosomal translocations, are associated with a wide spectrum of high risk hematologic malignancies, and typically lead to overexpression of abdominal-b HOXA genes, a common theme shared by ∼50% of AML patients. We have generated a transgenic mouse model of the NUP98-PHF23 (NP23) gene fusion, initially identified in patients with AML, which develop AML, erythroleukemia, pre-T lymphoblastic leukemia (pre-T LBL), and a novel pre-B1 B cell acute lymphoblastic leukemia (pre-B1 ALL). A common theme in the leukemias and the premalignant hematopoietic tissues, is the overexpression of a Hoxa/b +Meis1 stem cell-like gene expression signature. GSEA analysis reveals this signature to be enriched in both human AML and ALL malignancies, and in human HSPC profiles. In addition, we found Bahcc1, a gene not previously associated with malignancy, to consistently segregate with the Hoxa/b+Meis1 signature in the NP23 leukemias and the premalignant tissues, independent of hematopoietic cell lineage. Furthermore, data-mining revealed BAHCC1 to be markedly overexpressed in AML patients with HOXA9/MEIS1 overexpression, and in a subset of MLL rearranged pre-B-ALL patients, suggesting BAHCC1 may be a previously unsuspected marker of leukemic transformation.

NUP98-PHF23 belongs to a subset of fusion oncoproteins (including some MLL- and NUP98-fusions) that are potently tumorigenic and act by abrogating the normal reading, writing and erasure of histone methylation. Wild type PHF23 binds H3K4me3 residues via a PHD domain, therefore we used ChIP-seq to characterize global chromatin H3K4me3 and NP23 enrichment in NP23 leukemia derived cell lines. The vast majority (88%) of NP23 binding sites were enriched for H3K4me3 binding. Conversely, the NP23 protein co-localized at only 1.6% of all H3K4me3 enriched sites (including Hoxa, Hoxb and Meis1 loci) identifying these sites as direct targets of the NP23 fusion protein. Given that the NP23 fusion appears to function, at least in part, via binding to H3K4me3 sites at specific loci, we hypothesized that NP23 cells would be sensitive to disruption of the H3K4me4 binding by the NP23 PHD domain. Treatment of leukemic NP23 cells with Tetraethylthiuram disulfide (Disulfiram), a small molecule shown to inhibit PHD domain binding of H3K4me3 marks in vitro, rapidly and selectively killed NP23 myeloblasts but not control myeloblast cell lines (188G3, 189E6 and 32D) at 2 µM. Cell death was rapid, being 100% complete within 24 hours. Cell death was preceded by decreased levels of NP23 protein bound at target loci and decreased expression of these loci (e.g., Hoxa7/9/10, Hoxb5 and Meis1). We conclude that inhibitors of H3K4me3 PHD domain readers are promising therapeutic compounds that can kill leukemic cells driven by proteins that aberrantly read or write the histone code. The NP23 model provides a robust platform on which to identify and improve such compounds.