Mutations in the gene encoding the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) occur in 10–15% of acute myeloid leukemia (AML). Frameshifts in the CEBPA N-terminus resulting in exclusive expression of a truncated p30 isoform represent the most prevalent type of CEBPA mutations in AML. C/EBPα p30 interacts with the epigenetic machinery, but it is incompletely understood how p30-induced changes cause leukemogenesis. We hypothesized that critical effector genes in CEBPA-mutated AML are dependent on p30-mediated dysregulation of the epigenome. We mapped p30-associated regulatory elements (REs) by ATAC-seq and ChIP-seq in a myeloid progenitor cell model for p30-driven AML that enables inducible RNAi-mediated knockdown of p30. Concomitant p30-dependent changes in gene expression were measured by RNA-seq. Integrative analysis identified 117 p30-dependent REs associated with 33 strongly down-regulated genes upon p30-knockdown. CRISPR/Cas9-mediated mutational disruption of these genes revealed the RNA-binding protein MSI2 as a critical p30-target. MSI2 knockout in p30-driven murine AML cells and in the CEBPA-mutated human AML cell line KO-52 caused proliferation arrest and terminal myeloid differentiation, and delayed leukemia onset in vivo. In summary, this work presents a comprehensive dataset of p30-dependent effects on epigenetic regulation and gene expression and identifies MSI2 as an effector of the C/EBPα p30 oncoprotein.
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We thank the members of the Grebien laboratory for stimulating discussions and T. Weiss, E. Rzepa, and M. Piontek for technical help. We thank D. Berger and G. Stefanzl for skillful technical assistance and P. Valent for providing access to human samples. Next Generation Sequencing was performed at the VBCF NGS Unit (www.viennabiocenter.org/facilities) and at the BSF (https://cemm.at/research/facilities/). This project has received funding from the European Union’s Horizon 2020 research and innovation program (European Research Council grant agreement No 636855 and Marie Sklodowska-Curie grant agreement No 813091). LS is a recipient of the DOC Fellowship of the Austrian Academy of Sciences at the Ludwig Boltzmann Institute for Cancer Research.
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Heyes, E., Schmidt, L., Manhart, G. et al. Identification of gene targets of mutant C/EBPα reveals a critical role for MSI2 in CEBPA-mutated AML. Leukemia (2021). https://doi.org/10.1038/s41375-021-01169-6