Ectopic expression of transcription factor ONECUT3 drives complex karyotype in Myelodysplastic Syndromes.

Chromosomal instability is a prominent biological feature of Myelodysplastic Syndromes (MDS), with over 50% of MDS patients harboring chromosomal abnormalities or a complex karyotype. Despite this observation, the mechanisms underlying mitotic and chromosomal defects in MDS remain elusive. In this study, we identified a ectopic expression of transcription factor ONECUT3, associated with complex karyotypes and poorer survival outcomes in MDS. ONECUT3-overexpressing cell models exhibited enrichment of several notable pathways, including signatures of sister chromosome exchange separation and mitotic nuclear division with the upregulation of INCENP and CDCA8 genes. Notably, dysregulation of Chromosome Passenger Complex (CPC) accumulation besides the cell equator and midbody during mitotic phases consequently caused cytokinesis failure and defective chromosome segregation. Mechanistically, the Homeobox (HOX) domain of ONECUT3, serving as the DNA binding domain, occupied the unique genomic regions of INCENP and CDCA8, and transcriptionally activated these two genes. A novel lead compound C5484617, was identified that functionally targeted the HOX domain of ONECUT3 inhibiting its transcriptional activity on downstream genes, and synergistically resensitized MDS cells to hypomethylating agents. This study revealed that ONECUT3 promoted chromosomal instability by transcriptional activation of INCENP and CDCA8, suggesting potential prognosis and therapeutic roles for targeting high-risk MDS patients with complex karyotype.