Epigenetic screening in organoids identify KMT5A inhibition as a therapeutic strategy via PGK1in endometrial cancer

Endometrial cancer is the most common malignancy of the female reproductive tract, with a continuously rising incidence in recent years. Genomic analyses, including whole-genome and exome sequencing of large tumor cohorts, have revealed widespread epigenetic abnormalities in endometrial cancer. However, the underlying mechanisms driving tumorigenesis remain unclear, highlighting an unmet clinical need for novel therapeutic targets and drugs. Previously, we established genetically defined endometrial cancer organoids with mutations of Trp53, Pten, and amplification of Myc, which recapitulate the tumor heterogeneity and pathology of the disease. In this study, we employed these organoids to perform a high-throughput screen of an epigenetic-targeted compound library. One of the top candidates was UNC0379, an inhibitor of KMT5A. CRISPR/Cas9-mediated genetic inhibiton of KMT5A, encoding the H4K20me1 methyltransferase, consistently suppressed cell viability in both endometrial cancer organoids and cell lines. To further validate the role of KMT5A in vivo, we applied a gene-delivery approach to knock out KMT5A in tumor cells, which significantly inhibited tumor growth in mouse models. Multi-omics analyses were then utilized to investigate the molecular mechanisms underlying KMT5A function. We found that KMT5A deficiency led to significantly reduced ribosome biogenesis, a corresponding decrease in ribosome number, and dysregulated amino acid metabolism. CUT&Tag revealed that KMT5A directly regulated the expression of PGK1 through histone modification. Moreover, inhibition of PGK1 recapitulated both the anti-tumor effects and the abnormal ribosome biogenesis observed upon KMT5A loss.Clinically, high expression of KMT5A was associated with poor prognosis in endometrial cancer patients. Together, this study identifies the KMT5A/PGK1 axis as a key driver of tumor growth in endometrial cancer, revealing a potential therapeutic target for this malignancy.