E-Poster Presentation 33rd Lorne Cancer Conference 2021

Acquired PARP inhibitor resistance via RAD51C promoter methylation loss in high grade serous ovarian carcinoma (#107)

Ksenija Nesic 1 2 , Olga Kondrashova 3 , Rachel M Hurley 4 , Cordelia McGehee 4 , Cassandra J Vandenberg 1 2 , Gwo-Yaw Ho 1 2 5 , Elizabeth Lieschke 1 2 , Genevieve Dall 1 2 , Nirashaa Bound 1 2 , Kristy Shield-Artin 1 2 , Marc Radke 6 , Ashan Musafer 7 , Zi Qing Chai 7 8 , Maria I Harrell 6 , Damien Kee 1 9 10 , Inger Olesen 11 , Orla McNally 9 12 , Nadia Traficante 9 , Australian Ovarian Cancer Study 9 13 , Anna deFazio 13 14 15 , David D Bowtell 9 , Elizabeth M Swisher 6 , S. John Weroha 4 , Katia Nones 3 , Nic Waddell 3 , Scott H Kaufmann 4 , Alexander Dobrovic 7 8 , Matthew J Wakefield 1 2 , Clare L Scott 1 2 9 12
  1. Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
  2. University of Melbourne, Parkville, VIC, Australia
  3. QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
  4. Mayo Clinic, Rochester, MN, United States of America
  5. Monash University, Clayton, VIC, Australia
  6. University of Washington, Seattle, WA, United States of America
  7. Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
  8. University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
  9. Peter MacCallum Cancer Center, Melbourne, VIC, Australia
  10. Department of Medical Oncology, Austin Health, Heidelberg, Victoria, Australia
  11. The Andrew Love Cancer Centre, Barwon Health, Geelong, Victoria, Australia
  12. Royal Women’s Hospital, Melbourne, VIC, Australia
  13. Westmead Institute for Medical Research, Sydney, NSW, Australia
  14. Westmead Hospital, Sydney, NSW, Australia
  15. The University of Sydney, Sydney, NSW, Australia

High Grade Serous Ovarian Carcinoma (HGSOC) is characterized by loss of homologous recombination (HR) DNA repair, with platinum agents and PARP inhibitors (PARPi) suggested to cure a proportion of the ~20% of women with BRCA1/2 mutant HGSOC [1], and impressive efficacy in other “HR defective” (HRD) HGSOC. Beyond this, limited therapeutic options result in poor prognosis for most women.

 

HR genes BRCA1 and RAD51C are epigenetically silenced via promoter methylation in ~13% of HGSOC. Loss of  BRCA1  promoter methylation following treatment restores HR and causes PARP inhibitor (PARPi) resistance in HGSOC, with a single unmethylated gene copy shown to be sufficient [2]. We now show the same principles apply to RAD51C methylation (meRAD51C) in two rare Patient Derived Xenograft (PDX) models and 11 HGSOC cases.

 

Cyclical PARPi retreatment drove complete meRAD51C loss, RAD51C re-expression and PARPi resistance in PDXPH039. PDX#183, however, was less susceptible to meRAD51C loss under treatment pressure. Targeted bisulfite sequencing revealed no pre-existing unmethylated epialleles, suggesting an acquired mode of resistance. This was confirmed using SNP analysis of two PDXPH039 lineages with distinct genomic profiles, where meRAD51C loss and PARPi resistance developed independently. This PARPi resistance mechanism was observed in one of three pre-treated patients, where 1/3 RAD51C copies had lost methylation following neoadjuvant chemotherapy. “Heterogeneous” patterns of meRAD51C (representing a mixture of variably methylated epialleles) were also seen in untreated PH039 and 5/11 patient samples, causing HRD in vivo and not associated with reduced platinum sensitivity in patient samples.

 

We show that meRAD51C, including the novel heterogeneous pattern, is a true HR defect associated with PARPi response, while loss of methylation of even a single gene copy is sufficient to restore HR and drive PARPi resistance. Early scheduling of PARPi and avoidance of epigenetic treatments that may exacerbate methylation loss should be prioritised when making clinical decisions with these patients. Hence, patients with BRCA1 or RAD51C methylation need to be identified soon after diagnosis.

  1. [1] Banerjee, S., Moore, K. N., Colombo, N., Scambia, G., Kim, B. G., Oaknin, A., ... & Sonke, G. S. (2020). 811MO Maintenance olaparib for patients (pts) with newly diagnosed, advanced ovarian cancer (OC) and a BRCA mutation (BRCAm): 5-year (y) follow-up (f/u) from SOLO1. Annals of Oncology, 31, S613.
  2. [2] Kondrashova, O., Topp, M., Nesic, K., Lieschke, E., Ho, G. Y., Harrell, M. I., ... & Heong, V. (2018). Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nature communications, 9(1), 1-16.