The Transcriptional Factor ONECUT3 Is a Driver and Therapeutic Target for Complex Karyotype MDS

Myelodysplastic Syndrome (MDS) represents a group of clonal hematopoietic disorders characterized by ineffective hematopoiesis and morphological dysplasia. Chromosomal instability is a prominent biological feature of MDS, with over 50% of patients with MDS harboring chromosomal abnormalities or complex karyotypes (CK). The mechanisms underlying mitotic and chromosomal defects associated with MDS remain elusive. In recent years, most studies have focused on the associations of TP53 mutation or deactivation with CK (Bernard et al, Nat Med 2020). Hitherto, besides TP53, few genes were reported associated with cytogenetic aberration in MDS (Bernard et al, Nat Med 2020).

To fill this knowledge gap, RNA-Seq was conducted to find the CK-associated transcriptional factors and showed that ONECUT3 is significantly upregulated in MDS with CK, independent of TP53 mutation. Intriguingly ONECUT3 predicted poor survival of MDS patients. Our work indicates that ONECUT3 overexpression gave rise to multinucleated variants and complex karyotype in both TP53-KO MEF and TP53-WT MEF.

Mechanistically, overexpressed ONECUT3 transcriptionally activated INCENP and CDCA8 through the direct binding to unique genomic regions, which was performed by RNA-seq and ChIP-seq concurrently. Upregulations of INCENP and CDCA8 induced the assembly of chromosome passenger complex (CPC) that were accumulated in addition to cell equator and midbody during the mitotic phases, consequently causing cytokinesis failure and defective chromosome segregation.

As ONECUT3-OE cells attenuated chemo-sensitivity, we explored whether the compounds targeting the ONECUT3-CPC axis could alleviate chemoresistance. Homeobox domain was identified to function as the DNA binding by domain-deleted mutants and structural modeling (AlphaFold - DeepMind). One novel lead-compound C5484617 was later identified by protein structure-based drug virtual screening, to specifically target ONECUT3 and synergically re-sensitize the hypomethylating reagents in MDS with minimized cytotoxicity.

In summary, the current study demonstrated that CK-associated TF ONECUT3 upregulates the CPC components in MDS, leading to mitotic defects and decreasing chemo-sensitivity. The Aurora B inhibitor (Barasertib) and a lead compound (C5484617) could help increase the sensitivity of MDS cells to HMA. Our findings are mechanistically significant and of great clinical relevance. The present investigation provides the foothold for further studies to identify novel approaches for MDS patients with limited therapeutic options. Moreover, our findings may be implemented for other cancer types, given that CK/genomic instability is a hallmark of cancer.

No relevant conflicts of interest to declare.