Single-Cell Transcriptomics Reveals FXR1 as an Actionable Target for siRNA Therapy in Ovarian Cancer

Ovarian cancer is one of the leading causes of cancer-related mortality among women and remains exceptionally difficult to manage and treat effectively in the clinic. Fragile X-related protein 1 (FXR1) is significantly amplified and overexpressed in ovarian and various other cancers. We have shown that FXR1 acts as a key regulator of the stability and translation of multiple oncogenic mRNAs, establishing it as an excellent therapeutic target for ovarian cancer. Our Single-cell RNA sequencing (scRNA-seq) analysis demonstrates a complex involvement of FXR1 in cancer progression mainly due to its dual role attributed through its autonomous actions in tumor cells and the modulation of tumor microenvironment (TME). Recent advances in RNA interference (RNAi) therapies have enabled targeting previously undruggable genes. In this study, we developed a locked nucleic acid (LNA)-based small interfering RNA (siRNA) to target FXR1 for ovarian cancer therapy. Compared to native siRNA, siFXR1-LNA demonstrates resistance to RNase degradation, improved tumor tissue uptake, and robust inhibition of its target FXR1. siFXR1-LNA inhibited proteins essential for tumor growth and survival while increasing the levels of pro-apoptotic proteins. Importantly, the polyethylenimine-mediated delivery of siFXR1-LNA effectively reduced tumor growth and peritoneal metastasis in ovarian cancer models, without causing toxicity in both immunocompromised and immunocompetent mice. scRNA-seq further revealed that siFXR1-LNA treatment not only suppressed FXR1 in cancer cells but also disrupted translation mechanisms linked to oncogenesis. In TME, siFXR1-LNA diminished tumor cell proliferation, reduced tumor-promoting M2-like macrophages, increased tumor inhibitory T and NK cells and increased dendritic cells with anti-tumor characteristics. Given the autonomous role of FXR1 in tumor cells and TME for oncogenesis, targeting FXR1 with siFXR1-LNA presents a unique opportunity for treating ovarian cancer and other cancers express high levels of FXR1.