The functional effect of ARID1A mutation in human endometrial epithelium

ARID1A, a subunit of Switch/Sucrose Non-Fermentable (SWI/SNF) complex, is mutated at high frequency in specific subtypes of ovarian and endometrial cancers. However, despite the high prevalence of ARID1A mutations, there is no clinical relevance in terms of tumor grade, prognosis and overall survival with loss of ARID1A for the patients. Approximately 97% of ARID1A mutations are nonsense or frameshift, leading to a loss of protein expression. ARID1A mutation is an early event in tumour progression, driving from endometriosis and atypical hyperplasia toward malignancy. We hypothesized that ARID1A deficiency in gynecological cancers results in temporal epigenetic and transcriptomic alterations along the transformation continuum which may provide insights on the biology of these cancers and suggest potential therapeutic options. We developed an isogenic organoid model to investigate molecular changes associated with ARID1A deficiency. Using single cell RNA and ATAC sequencing, we identified differentially expressed genes, including upregulation of S100A4, a known metastasis associated gene. We further validated S100A4 protein upregulation in ARID1A mutant clear cell ovarian and endometrial cancer cell lines and patient derived tumour tissues. Functional studies revealed that S100A4 enhances proliferation and metastasis in both cell lines and animal models. We performed additional studies, including IP-MS and RNA-seq experiments, on multiple S100A4 isogenic lines, including knockout and overexpression models, to further investigate the functional role of S100A4 in the context of ARID1A mutant and WT backgrounds. Our analysis from IP-MS identified potential interaction partners from metabolic and epigenetic pathways. Additionally, RNA-seq analysis revealed cell cycle pathways associated with proliferation and migration to be regulated by S100A4, highlighting the importance of targeting S100A4 in these cancers. Further validation of these pathways and genes regulated in S100A4 isogenic lines could provide deeper insights into the underlying mechanisms and potential therapeutic strategies.