UBE2E3 Supports Survival of Leukemia Stem Cells By Regulation of Polycomb Repression Complex (PRC) 1.1

AML cells are arranged in a hierarchy with leukemia stem cells giving rise to a more differentiated bulk leukemia cells. The determinants that support stemness are still not completely understood.

Recently, we identified importin 11 (IPO11), a nuclear transport receptor, as a regulator of stemness in AML. To identify cargo protein imported into the nucleus by IPO11, we conducted a BioID-mass spectrometry screen. Through this screen, we discovered that IPO11 interacts with the E2 ligase, UBE2E3 to regulate its nuclear localization. The importance of UBE2E3 in AML and its role in leukemia stemness is currently unknown. Therefore, we focused our investigation on UBE2E3.

To understand the role of UBE2E3 in AML and leukemia stem cells, we knocked down UBE2E3 in AML cell lines. Silencing of UBE2E3 shifted the transcriptomic signature away from leukemia stem cells and hematopoietic stem cell progenitors toward a more differentiated and mature signature: LSC+ vs. LSC- (FDR ≤0.01, GSE76008) and progenitor/stem vs. myeloid cluster (FDR ≤ 0.01, TCGA-AML). Moreover, knockdown of UBE2E3 in OCI-AML2, NB4 and K562 AML cells reduced growth and viability of by 60-70%, as well as reduced clonogenic growth, consistent with an effect on leukemia initiating cells.

To investigate how UBE2E3 regulates leukemic stemness, we performed a BioID mass spectrometry screen for proteins that interact with UBE2E3. Through this screen, we discovered that UBE2E3 interacted with poly-comb repression complex (PRC) proteins, including four core components of a variant of PRC-1, designated PRC1.1, KDM2B, BCOR, RING1 and PCGF1. The PRC mediates epigenetic transcriptional repression, governing key cellular processes, including proliferation and differentiation. Previous work has shown that PRC1.1 control specific genes required for leukemic cell viability. Knockdown of UBE2E3 decreased expression of known PRC 1.1 target genes specific for AML (FDR ≤0.01, GSE54580), such as PKM, MAP3K6 and ERCC1, demonstrating that UBE2E3 positively regulates PRC1.1 activity.

In summary, we identified UBE2E3 as a novel regulator of non-canonical PRC 1.1 complex in AML and through that mechanism a positive regulator of leukemia stemness. Thus, we identified UBE2E3 as a possible novel target in AML.

Gatt:Hadassah Medical Center Jerusalem: Current Employment. Schimmer:Medivir AB: Research Funding; Novartis: Consultancy; Jazz: Consultancy; Otsuka Pharmaceuticals: Consultancy; UHN: Patents & Royalties: DNT cells; BMS: Research Funding; Takeda: Consultancy, Research Funding. Nachmias:Stemline: Consultancy; Medison: Consultancy; Abbvie: Consultancy.