Pathways Relevant to AML Pathogenesis Targeting the Hematopoietic-Specific Cebpa +37 Kb Enhancer

C/EBPα mediates myeloid differentiation, and its reduced activity is central to myeloid transformation (Friedman Int. J. Hematol. 2015). The murine Cebpa gene contains a 450 bp, +37 kb element that acquires the enhancer-specific H3K4me1 and H3K27Ac histone marks as LT-HSC progress to GMP and directs hCD4 transgene expression to GMP and myeloid CFUs (Guo et al. Blood 2012; Guo et al. J. Leuk. Biol. 2014). Moreover, CRISPR/Cas9 mediated, biallelic replacement of the enhancer with a variant harboring mutations in its seven Ets sites reduces Cebpa RNA >10-fold in 32Dcl3 cells (Cooper et al. PLoS One 2015), and germline or Cre-mediated enhancer deletion leads to marked reduction in Cebpa RNA in marrow LSK, CMP, and GMP, with 3-fold reduction in GMP, CFU-G, and neutrophils and indefinite myeloid colony replating in IL-3, a preleukemic phenotype (Guo et al. PLoS One 2016; Avellino et al. Blood 2016). The enhancer contains four conserved RUNX1 cis elements that bind RUNX1 in gel shift or ChIP assays, Runx1 gene deletion reduces Cebpa RNA 5-fold in Lin^- and 2-fold in GMP marrow cells, Runx1 cis element mutation reduces luciferase reporter activity 6-fold in 32Dcl3 myeloid cells (Guo et al. Blood 2012), and in AMLs with t(8;21) RUNX1-ETO interacts with the human CEBPA locus at the homologous +42 kb enhancer (Ptasinska et al. Leukemia 2012). Mutation of the CEBPA enhancer has not been seen in human AML cases, perhaps reflecting preference for upstream pathway alteration to suppress both alleles and additional genes. As a further example of a leukemic alteration affecting enhancer activity, elevated EVI1 is a high-risk feature in AML, and EVI1 binds and represses the +37 kb Cebpa enhancer (Wilson et al. J. Biol. Chem. 2016). We have characterized additional pathways whose modulation in AML may reduce CEBPA enhancer activity. Deletion of the Pu.1 -14 kb enhancer leads to AML in mice, and PU.1 binds the Cebpa enhancer in ChIP and gel shift; we now find that mutation of the one Cebpa enhancer Ets site that binds PU.1 reduces reporter activity 4-fold in 32Dcl3 cells, providing the first functional evidence that PU.1 regulates the enhancer. ~10% of human AMLs harbor mutant C/EBPα proteins, CEBPα binds the enhancer in ChIP and gel shift, and mutation of the two enhancer C/EBP elements reduces reporter activity; we have now used CRISPR/Cas9 to generate a 32Dcl3 cell line with the two enhancer C/EBPsites mutated in one allele and find 60% reduction in Cebpa RNA expression. FLT3/ITD is a constitutively activated mutant form of the receptor tyrosine kinase found in ~30% of AML cases and confers high risk. While FLT3/ITD predominantly provides proliferative signals, it may also contribute to impaired differentiation, as FLT3/ITD inhibition in AML cases leads to a neutrophilic differentiation syndrome. We previously demonstrated that FLT3/ITD reduces Cebpa RNA in 32Dcl3 cells and patient leukemic blasts and that the first generation FLT3/ITD inhibitor lestaurtinib increases Cebpa; we now find that the effect on Cebpa RNA is also reversed in 32Dcl3 cells by the next generation inhibitor crenolanib, that FLT3/ITD reduces Cebpa enhancer H3K4me1 and H3K27Ac histone marks several-fold, and that both of these activating marks are also restored by crenolanib. FLT3/ITD signaling leads to C/EBPα serine phosphorylation to reduce its activity, which may account in part for the inhibitory effect of FLT3/ITD on Cebpa enhancer activity. Finally, NUP98-HOX fusion proteins contribute to a small percent of AML cases. Vav-NUP98/HOXD13 (NHD13) mice develop MDS and can progress to AML; we now find that Cebpa RNA is reduced 5-fold in Vav-NHD13 CMP and LSK, with 5-fold increased HoxA9 RNA, that Vav-NHD13::Cebpa Enh-hCD4 compound heterozygous mice have reduced hCD4 expression in GMP and CMP, implicating a direct effect on enhancer activity, and that expression of NHD13 in 32Dcl3 subclones prevents G-CSF induction of Cebpa, MPO, and morphologic differentiation. These 32Dcl3 lines retain levels of Gcsfr equal to empty vector-transduced cells in IL-3 and manifest increased HoxA9 in response to G-CSF. Moreover, HoxA9 binds the Cebpa enhancer in ChIP using marrow-derived HoxA9/Meis1 myeloid lines. Potentially, NHD13 induces HoxA9, which then binds the Cebpa enhancer directly or via other factors to repress transcription. Identifying mechanisms that repress CEBPA hematopoietic enhancer activity in AML may identify approaches to induce differentiation.