Poster Presentation 35th Lorne Cancer Conference 2023

Understanding BRCA1-methylation stability to improve PARP inhibitor responses in high-grade serous ovarian carcinomas (#151)

Franziska Geissler 1 2 , Ksenija Nesic 1 2 , Cassandra J. Vandenberg 1 2 , Olga Kondrashova 3 , Fan Zhang 4 , Alexander Dobrovic 4 , Marc Radke 5 , Elizabeth Swisher 5 , Joep Vissers 6 , Jocelyn Penington 1 2 , Sean Grimmond 6 , Tony Papenfuss 1 , Clare L. Scott 1 2 7 , Matthew J. Wakefield 1 2 7
  1. Walter and Eliza Hall Institute of Medicine, Parkville, VICTORIA, Australia
  2. Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
  3. QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
  4. University of Melbourne, Department of Surgery, Austin Health, Heidelberg, VIC, Australia
  5. University of Washington, Seattle, WA, United States
  6. University of Melbourne Centre for Cancer Research (UMCCR), Parkville, VIC, Australia
  7. Department of Obstetrics and Gynaecology,, University of Melbourne, Parkville, VIC, Australia

Poly-ADP ribose polymerase inhibitors (PARPi) provide impressive therapeutic responses in carcinomas with deficiencies in the homologous recombination (HR) DNA repair pathway. After BRCA1/2 mutations, epigenetic silencing of BRCA1 is the next most common HR defect in high grade serous ovarian carcinomas (HGSOC), present in 7-17% of cases. BRCA1 promoter hypermethylation (meBRCA1), when homozygous, silences gene expression and correlates with clinical response to PARPi (1). Loss of meBRCA1 after chemotherapy and PARPi treatment is a reported mechanism of acquired PARPi resistance (1). However, long term responders to PARPi with stable meBRCA1 in the HGSOC have been observed. The identification of mechanisms promoting stable meBRCA1, may allow us to exploit these, enabling patients to achieve durable PARPi responses in the clinic.

In addition to four previously described patient derived xenograft (PDX) models of HGSOC with varying degrees of meBRCA1 stability after chemotherapy (1), we have three PDX characterized from patients post-PARPi: PDX#1305 (complete meBRCA1 loss), PDX#1428 (heterozygous meBRCA1) and PDX#1334 (homozygous meBRCA1, 5-year long-term responder). PARPi-responsive HGSOC cell line WEHI-CS62, shows stable homozygous meBRCA1, given it has retained homozygous meBRCA1 in cell culture (1). We are now selecting for methylation loss under PARPi pressure. Treatment with demethylating agents, decitabine and GSK-3484862, resulted in a heterogenous methylation pattern of meBRCA1, which was associated with BRCA1 re-expression. To identify genes involved in the development of PARPi resistance, and potentially in methylation stability, we are performing a genome-wide pooled PARPi-resistance CRISPR screen in this unique cell line. To our knowledge this will be the first CRISPR screen carried out in a homozygously methylated BRCA1 model of HGSOC. Hits identified will be validated in our cohort of unique meBRCA1 pre-clinical models (cell lines and PDX), both in vitro and in vivo.

This study is designed to reveal novel targetable pathways capable of overcoming PARPi resistance in meBRCA1 cancers.  Improved understanding of mechanisms impacting epigenetic silencing and methylation stability of BRCA1 may inform future combination therapies and guide trials of epigenetic modulating therapies in HGSOC.

  1. Kondrashova O, Topp M et al. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nat Commun. 2018 Sep 28;9(1):3970. doi:10.1038/s41467-018-05564-z. PMID: 30266954; PMCID: PMC6162272.