Inhibition of RNA Polymerase I Transcription Activates Targeted DNA Damage Response and Enhances the Efficacy of PARP Inhibitors in High-Grade Serous Ovarian Cancer

Abstract

High-grade serous ovarian cancer (HGSOC) accounts for the majority of ovarian cancer and has a dismal prognosis. PARP inhibitors (PARPi) have revolutionized disease management of patients with homologous recombination (HR) DNA repair-deficient HGSOC. However, acquired resistance to PARPi by complex mechanisms including HR restoration and stabilisation of replication forks is a major challenge in the clinic. Here, we demonstrate CX-5461, an inhibitor of RNA polymerase I transcription of ribosomal RNA genes (rDNA), induces replication stress at rDNA leading to activation of DNA damage response and DNA damage involving MRE11-dependent degradation of replication forks. CX-5461 cooperates with PARPi in exacerbating DNA damage and enhances synthetic lethal interactions of PARPi with HR deficiency in HGSOC-patient-derived xenograft (PDX) in vivo. We demonstrate CX-5461 has a different sensitivity spectrum to PARPi and destabilises replication forks irrespective of HR pathway status, overcoming two well-known mechanisms of resistance to PARPi. Importantly, CX-5461 exhibits single agent efficacy in PARPi-resistant HGSOC-PDX. Further, we identify CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC. Therefore, CX-5461 is a promising therapy alone and in combination therapy with PARPi in HR-deficient HGSOC. CX-5461 is also an exciting treatment option for patients with relapsed HGSOC tumors that have poor clinical outcome.

Targeting RNA Polymerase I transcription synergises with TOP1 inhibition in potentiating the DNA damage response in high-grade serous ovarian cancer

“…The combination was also effective using low-dose topotecan in HGSC xenografts, thus providing a strategy to facilitate dose reduction to minimise the potential for toxicity while retaining efficacy to treat HGSC. In addition to confirming the importance of HR deficiency conferring sensitivity to CX-5461 in HGSC as we and others have shown 12,20 , we found TOP1 inhibition can cooperate with CX-5461 in the HR-proficient context, thereby potentially expanding the application of CX-5461 to a larger HGSC cohort, including patients previously harbouring HR-deficient tumours that have acquired chemotherapeutic resistance due to restored HR.…”

“…STRING network analysis of these genes demonstrated significance in homologous recombination (HR) (Fig. 1C), consistent with a previous study in breast cancer 20 and our findings that CX-5461 is synthetic lethal with HR deficiency and a HR deficiency gene expression signature predicts HGSC sensitivity to CX-5461 12 .…”

“…TOP1 also colocalised with the upstream binding factor (UBF) to the nucleolar periphery ( Fig. S1B) where rDNA is repaired, agreeing with our previous finding that CX-5461 induces nucleolar-specific defects in rDNA chromatin 10,12 .…”

rDNA Chromatin Activity Status as a Biomarker of Sensitivity to the RNA Polymerase I Transcription Inhibitor CX-5461

“…Pol I transcription is a therapeutic target for small anticancer drugs (Bywater et al, 2012;Hein et al, 2013;Peltonen et al, 2014). The first-in-class Pol I transcription inhibitor, CX-5461 is a promising cancer therapy as a single agent and in combination therapy in pre-clinical models of lymphoma, acute myeloid leukemia, prostate and ovarian cancer (Bywater et al, 2012;Devlin et al, 2016;Rebello et al, 2016;Hein et al, 2017;Yan et al, 2019;Sanij et al, 2020). Recently, the sensitivity profile of CX-5461 was shown to closely resemble a topoisomerase II (TOP2) poison (Olivieri et al, 2019;Bruno et al, 2020).…”

“…(B) A summary of the rDNA activity parameters assessed in this study. (C) Basal rDNA transcription rates of OVCA cell lines was reported in Sanij et al (2020). We have re-used the data under the Creative Commons Attribution 4.0 International License [http://creativecommons.org/licenses/by/4.0/].…”