A Small Molecular Agonist of Histone Demethylase KDM3B Selectively Represses MLL-Rearranged Acute Leukemia

Background: Acute leukemia (AL) originates from both genetic and epigenetic changes that can be targeted to cure AL. Dysregulated DNA methylation has been shown to be associated with AL and demethylating agents 5-azacytidine and decitabine show favored improvement in secondary leukemia. Deficient histone acetylation has also been reported in AL and can be corrected to relieve leukemia. Histone methylation harbors more structural complexities compared to DNA methylation and histone acetylation and is broadly involved in AL. In particular, histone H3 lysine 9 (H3K9) methylation has been associated with AL. Di-methylation of H3K9 is reportedly involved in human hematopoietic stem cell lineage commitment. Moreover, tri-methylation of H3K9 predicts AML survival. H3K9 demethylation is catalyzed by exclusive KDM3 family members (KDM3A, KDM3B, and JMJD1C) that catalyze mono- and di-demethylation of H3K9, non-exclusive KDM4 family members (KDM4A, KDM4B, KDM4C, and KDM4D) that catalyze both H3K9 and H3K36 di- and tri-demethylation, KDM1A (LSD1) that catalyzes H3K4 and H3K9 mono- and di-demethylation, and PHF8 that catalyzes H3K9 mono- and di-demethylation and H4K20 demethylation. Among these, KDM3B, JMJD1C, KDM4C, LSD1, and PHF8 have been reported to be associated with AL in an enzymatic activity-dependent way. Furthermore, small molecular inhibitors of KDM4C and LSD1 have been developed for treatment of AML. H3K9 demethylase KDM3B is located at chromosome 5 band 31, a region frequently deleted or lost in acute myeloid leukemias (AML) and myelodysplasias (MDS). Different from other H3K9 demethylases that are usually responsible for leukemia maintenance, KDM3B harbors potential tumor-suppressive activities in acute myeloid leukemia and myelodysplastic syndromes. However, small molecular antagonists and agonists are lacking for KDM3B.

Results: We aim to identify small molecular modulators of KDM3B. We focused on crystal structure of KDM3B Jumonji domain that catalyzes histone demethylation for virtual screening. From approximately 200,000 natural products and Chinese medicine components, we identified a potential KDM3B modulator, namely compound #7. Surface plasmon resonance technology showed that compound #7 binds to KDM3B with favorable affinity. In vitro and in vivo demethylation assay showed that compound #7 is able to increase H3K9 demethylating activity of KDM3B. We thus named compound #7 as KA-7 (KDM3B agonist #7). Interestingly, the identified KDM3B agonist KA-7 is able to selectively repress MLL-rearranged AL in cell proliferation and colony formation assays. Considering that KA-7 targets KDM3B that is located at chromosome 5q, a frequently deleted region in AML and MDS, we explored if KA-7 collaborates with Lenalidomide, an FDA approved drug for treating MDS with deletion at 5q where KDM3B is located. KA-7 was found to be able to synergistically increase the selective killing of AL cells by Lenalidomide.

Conclusion: To sum up, physiologic H3K9 demethylase activity of KDM3B can be enhanced by a small molecular modulator KA-7 and causes selective killing against MLL-arranged AL cells.

Disclosures. No relevant conflicts of interest to declare.