Poster Presentation 46th Lorne Genome Conference 2025

CRISPR screens identify RNASEH2B-AS1 as a novel therapeutic target to enhance PARP inhibitor sensitivity in breast cancer (#120)

Francesco Casciello 1 2 , Maina Bitar 1 , Haran Sivakumaran 1 , Sneha Nair 1 , Lu Wang 1 , Xue Lu 1 , Yaowu He 3 , Sebastien Jacquelin 4 , John Hooper 3 , Juliet D French 1 5 6 , Stacey L Edwards 1 5 6
  1. Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
  2. Division of Genome Sciences and Cancer, Australian National University, Canberra, ACT, Australia
  3. Cancer Biology, Mater Research, Brisbane, QLD, Australia
  4. Macrophage Biology Laboratory, Mater Research, Brisbane, QLD, Australia
  5. Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
  6. Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia

Triple-negative breast cancer (TNBC) is highly metastatic subtype, characterized by a lack of hormone receptors, which limits the effectiveness of standard therapies. Despite the significant heterogeneity of TNBC tumours, many have defects in double-strand break repair by homologous recombination (HR), making them particularly sensitive to DNA repair-targeting agents such as poly(ADP-ribose) polymerase inhibitors (PARPi). While PARPi have shown promise in the management of HR-deficient TNBC, resistance develops in ~50% of patients, highlighting the need for novel therapeutic strategies to enhance treatment response. In this study, we performed pooled CRISPR interference (CRISPRi) screens to identify long noncoding RNAs (lncRNAs) that could increase PARPi efficacy in TNBC. We discovered that RNASEH2B-AS1, an annotated but uncharacterized lncRNA localised primarily in the cytoplasm, could sensitise TNBC cells to PARPi. In breast tumours, RNASEH2B-AS1 expression is significantly enriched in HR-proficient TNBC, where it correlates with a PARPi-resistant phenotype. Targeting this lncRNA significantly enhances the efficacy of various PARPis in both HR-deficient and HR-proficient TNBC cell lines. Transcriptomic analysis revealed that PARPi treatment activates the KRAS signaling pathway in TNBC, leading to NF-κB activation – a pathway previously implicated in PARPi resistance. Targeting RNASEH2B-AS1 with specific antisense oligonucleotides (ASOs) suppressed KRAS induction, ultimately blocking NF-kB activation. Mechanistic studies, including RNA IP followed by mass spectrometry, revealed that RNASEH2B-AS1 primarily interacts with RALB, a Ras-like GTPase that is a downstream effector of KRAS. Inhibiting RNASEH2B-AS1 disrupted RALB activity and its associated signaling, further enhancing PARPi efficacy. These findings reveal a novel mechanism of acquired resistance to PARPi and establish RNASEH2B-AS1 as a promising therapeutic target to overcome PARPi resistance in TNBC.