Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors
Jinhyuk Bhin, Mariana Paes Dias, Ewa Gogola, Frank Rolfs, Sander R. Piersma, Roebi de Bruijn, Julian R. de Ruiter, Bram van den Broek, Alexandra A. Duarte, Wendy Sol, Ingrid van der Heijden, Christina Andronikou, Taina Susanna Kaiponen, Lara Bakker, Cor Lieftink, Ben Morris, Roderick L. Beijersbergen, Marieke van de Ven, Connie R. Jiménez, Lodewyk F.A. Wessels, Sven Rottenberg, Jos Jonkers
Abstract
BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis), but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combine molecular profiling with functional analysis of HR of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent reactivation of BRCA1/2. We observe restoration of HR in 62% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we find that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by PARG loss. Furthermore, combined multi-omics analysis identifies additional genes and pathways potentially involved in modulating PARPi response.