Targeted inhibition of PRC1 in acute leukemia models induces prominent cell growth and differentiation effects

Background: Polycomb repressive complex 1 (PRC1) is an epigenetic regulatory complex that silences genes important for cellular identity, stemness and differentiation. All PRC1 complexes contain a RING1A or RING1B protein core which elicits E3 ligase activity to monoubiquitinate histone H2A lysine 119 (H2Aub). PRC1 complex binding and H2Aub deposition induces chromatin compaction and repression of target genes. Previous studies have emphasized the role of PRC1 activity in the maintenance of a leukemic stem cell phenotype, and implicated RING1A/B ubiquitination activity as an important driver of leukemogenesis. Indeed, knockdown of RING1A/B in acute myeloid leukemia (AML) stem cells impairs proliferation and induces myeloid differentiation. Therefore, the development of small molecule inhibitors of PRC1 presents a valuable therapeutic strategy for acute leukemia treatment. Results: Here, we report the biological activity and molecular mechanisms of a novel small molecule inhibitor of PRC1, RB-231, in acute myeloid and lymphoblastic leukemia (ALL) models. RB-231 is a lead compound among the first-in-class PRC1 small molecule inhibitors developed in our lab, which bind directly to RING1A/B at the nucleosome interface to prevent PRC1 complex binding and H2Aub deposition. RB-231 has shown potent sub-micromolar activity across panels of both AML and ALL cell lines harboring a variety of chromosomal translocations and mutational drivers. Treatment of acute leukemia cell lines with RB-231 results in significant cell growth inhibition, apoptosis, and differentiation, as demonstrated by increased cell surface and gene expression of lineage-associated maturation markers (CD11b, CD14, CD20 and CD86). Treated cells also exhibit morphological changes resembling mature hematopoietic cells and a reduction of leukemic blast populations. Notably, colony formation assays with RB-231 treated primary AML patient samples display reduced colony number, smaller size, and differentiated morphology, while normal human CD34+ bone marrow cells are unaffected by treatment, suggesting selectivity towards a leukemic stem cell phenotype. RNA-sequencing analyses of RB-231 treated acute leukemia cell lines reveal significant upregulation of PRC1 target gene CDKN1A , encoding for the p21 cell cycle inhibitor. This effect is also observed in p53-mutant AML cell lines. Indeed, CUT&RUN analysis shows significant reduction of H2Aub enrichment at CDKN1A , demonstrating direct de-repression at this locus and RB-231 on-target activity. Conclusions: Overall, our studies have shown that acute leukemia models are sensitive to PRC1 inhibition and demonstrate significant mechanistic and developmental changes upon treatment. Based on these findings, PRC1 inhibition may offer a novel therapeutic approach for leukemia treatment.