In vitro advances in predicting resistance to PARP inhibitors for BRCA1/2 mutations

Despite the increasing use of PARP inhibitors in treating several solid tumours including ovarian, prostate and breast cancers, pre-existing innate or intrinsic resistance remains a challenge. Drs Olga Brieieva and Martin Higgs discuss new advances using in vitro genomic models that offer promising insights into predicting clinical resistance to PARP inhibitors and developing strategies to overcome it.

Poly (adenosine diphosphate (ADP)-ribose) polymerase (PARP) inhibitors were first identified as potential targeted treatments for tumours deficient in homologous recombination (HR), a sub-pathway of DNA double-strand break repair. Indeed, four different PARP inhibitors are now approved for the treatment of both early- and late-stage breast¹ and ovarian cancers² that harbour mutations in the HR factors BRCA1 or BRCA2. These are olaparib, rucaparib, talazoparib and niraparib.

PARP inhibitors are also approved for use in prostate^3,4 and pancreatic cancers⁵ encoding mutations in BRCA1/2, and their use is expanding into other genetic deficiencies of DNA repair. This ranges from widespread use as maintenance therapy to a more limited use in metastatic settings after failure of other treatment options.

Resistance to PARP inhibitors

Unfortunately, the clinical utility of PARP inhibitors is hampered by both pre-existing and de novo resistance, which limits their use as long-term maintenance therapies. Although estimates vary between tumour subgroups, approximately 40% of patients with metastatic breast cancer or ovarian cancer fail to benefit from olaparib.^1,6,7 This likely reflects high proportions of both intrinsic and innate resistance and is relevant for thousands of patients across Europe receiving PARP inhibitors.

Extensive studies using in vitro cellular models and/or patient-derived xenografts have revealed multiple mechanisms that drive resistance to PARP inhibitors.^8–10 These can be classified into four categories:

1. Secondary mutations in BRCA1/2 that restore the protein’s partial function
2. Alterations in target enzymes (i.e., PARP1, PARG)
3. Increased efflux of PARP inhibitors from cells
4. Rewiring of the DNA damage response.

In many of these cases, mechanisms that restore HR in BRCA1-deficient cells, including loss of proteins that promote non-homologous end-joining (NHEJ), or secondary mutation of BRCA1/2 that restore HR, drive PARP inhibitor resistance in vitro. Of relevance, loss of pro-NHEJ factors, such as 53BP1, partially restores HR in BRCA1-deficient cells and thus allows repair of PARP inhibitor-induced lesions, thereby driving resistance.^11–16

However, despite these mechanistic advances, predicting resistance in the clinic is less straightforward. Several of these alterations – including secondary alterations in BRCA1/2, increased expression of drug efflux effectors and deregulation of pro-NHEJ factors – are observed in a small subset of patients receiving PARP inhibitors or derived xenografts.^17–23 However, in approximately 50% of patients, the mechanism of resistance remains unclear, likely due to unidentified factors such as epigenetic alterations.²²

Moreover, few, if any, biomarkers for PARP inhibitors have been systematically analysed or tested in the clinic, and the field sorely lacks robust predictors for the onset of PARP inhibitor resistance in patient populations.

SETD1A and PARP inhibitor resistance

The lysine methyltransferase SETD1A has multiple roles in DNA repair, including the response to replication damage and in promoting NHEJ. Our two recent studies have identified an epigenetic mechanism of PARP inhibitor resistance that involves loss of SETD1A.

Mechanistically, PARP inhibitor resistance upon the loss of SETD1A involves two pathways that hinge around the ability of SETD1A to catalyse methylation of lysine 4 of histone H3 (H3K4). We originally demonstrated that PARP inhibitor resistance in BRCA1-deficient cells lacking SETD1A was due to defective H3K4 methylation and subsequent destabilisation of replication-independent factor-1 (RIF1) on damaged chromatin.²⁴ This led to a concomitant loss of NHEJ and restoration of HR, driving PARP inhibitor resistance.

More recent studies from our group suggest that this is not the only mechanism.²⁵ Analyses of BRCA1-deficient cells depleted of SETD1A revealed that SETD1A is required for efficient expression of the structure-specific nuclease EME1 specifically in HR-deficient cells. Moreover, loss of EME1 alone can drive resistance of BRCA1-deficient cells to PARP inhibitors, and at least partially restore HR.²⁵ This is somewhat surprising, as EME1 is not a pro-NHEJ factor; rather, it maintains genome integrity by resolving recombination intermediates.²⁶

Therefore, it seems that loss of either of these pathways can partially restore HR and render BRCA1-deficient cells resistant to olaparib, although it remains to be seen whether these pathways are linked. However, in keeping with multiple previous studies, neither of these pathways has any impact on the sensitivity of BRCA2-deficient cells to PARP inhibitors.

SETD1A and EME1 as biomarkers for PARP inhibitor resistance

Our data from two-dimensional cell models implies that low SETD1A activity would correlate with PARP inhibitor resistance in HR-deficient breast and ovarian tumours. One question arising from these studies is whether SETD1A, H3K4me3 and/or EME1 expression can be used in the clinic as predictive biomarkers for PARP inhibitor resistance.

There is some correlation between levels of SETD1A/EME1 mRNA and overall survival of BRCA1-deficient patients from the Cancer Genomic Atlas,²⁵ which is seen neither in BRCA2-deficient nor BRCA wild-type tumours. However, these data predate the use of PARP inhibitors in the clinic. Moreover, they are unlikely to provide information on SETD1A enzymatic activity as mRNA levels only partly correlates with protein expression in these samples.^27,28

Therefore, further work needs to be done to profile the protein expression and levels of these targets and to investigate how they might be used as a combinatorial biomarker to predict pre-existing or acquired resistance.

Conclusion

Increasing knowledge of in vitro mechanisms of PARP inhibitor resistance has led to the discovery and characterisation of important potential biomarkers. However, there is a lack of a systematic approach to including these in the clinical study of PARP inhibitors, for current approvals and novel indications.

We recommend that future studies involving PARP inhibitors assess the expression and mutation status of biomarkers such as SETD1A, RIF1 and 53BP1 and their downstream targets alongside clinical response and resistance. This will also likely shed light on novel combinations of PARP inhibitors with epigenetic drugs, such as those targeting lysine methyltransferases and/or lysine demethylases, to overcome such resistance.

Authors

Olga Brieieva BSc MSc PhD
Visiting research fellow and Cara fellow, Department of Cancer and Genomic Sciences, School of Medical Sciences, University of Birmingham, UK

Martin Higgs BSc PhD
Associate professor and head of research, School of Medical Sciences and deputy director of the Centre for Rare Disease Studies, University of Birmingham, UK

References

1. Robson M et al.Olaparib for Metastatic Breast Cancer in Patients with a Germline BRCA Mutation. N Engl J Med 2017;377(6):523–33.
2. Moore K et al. Maintenance Olaparib in Patients with Newly Diagnosed Advanced Ovarian Cancer. N Engl J Med 2018;379(26):2495–505.
3. 3 Abida W et al. Rucaparib in Men With Metastatic Castration-Resistant Prostate Cancer Harboring a BRCA1 or BRCA2 Gene Alteration. J Clin Oncol 2020;38(32):3763–72.
4. de Bono J et al. Olaparib for Metastatic Castration-Resistant Prostate Cancer. N Engl J Med 2020;382(22):2091–102.
5. Golan T et al. Maintenance Olaparib for Germline BRCA-Mutated Metastatic Pancreatic Cancer. N Engl J Med 2019;381(4):317–27.
6. Audeh MW et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial. Lancet 2010;376(9737):245–51.
7. Fong PC et al. Poly(ADP)-ribose polymerase inhibition: frequent durable responses in BRCA carrier ovarian cancer correlating with platinum-free interval. J Clin Oncol 2010;28(15):2512–9.
8. Kyo S et al. Clinical Landscape of PARP Inhibitors in Ovarian Cancer: Molecular Mechanisms and Clues to Overcome Resistance. Cancers (Basel) 2022;14(10).
9. Noordermeer SM, van Attikum H. PARP Inhibitor Resistance: A Tug-of-War in BRCA-Mutated Cells. Trends Cell Biol 2019;29(10):820–34.
10. Dias MP et al. Understanding and overcoming resistance to PARP inhibitors in cancer therapy. Nat Rev Clin Oncol 2021;18(12):773–91.
11. Chapman JR et al. RIF1 is essential for 53BP1-dependent nonhomologous end joining and suppression of DNA double-strand break resection. Mol Cell 2013;49(5):858–71.
12. Dev H et al. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Nat Cell Biol 2018;20(8):954–65.
13. Escribano-Diaz C et al. A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice. Mol Cell 2013;49(5):872–83.
14. Noordermeer SM et al. The shieldin complex mediates 53BP1-dependent DNA repair. Nature 2018;560(7716):117–21.
15. Setiaputra D et al. RIF1 acts in DNA repair through phosphopeptide recognition of 53BP1. Mol Cell 2022;82(7):1359–71 e9.
16. Zimmermann M et al. 53BP1 regulates DSB repair using Rif1 to control 5′ end resection. Science 2013;339(6120):700–4.
17. Jaspers JE et al. Loss of 53BP1 causes PARP inhibitor resistance in Brca1-mutated mouse mammary tumors. Cancer Discov 2013;3(1):68–81.
18. Castroviejo-Bermejo M et al. A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation. EMBO Mol Med 2018;10(12).
19. Guillemette S et al. Resistance to therapy in BRCA2 mutant cells due to loss of the nucleosome remodeling factor CHD4. Genes Dev 2015;29(5):489–94.
20. Bouwman P et al. 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol 2010;17(6):688–95.
21. Waks AG et al. Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer. Ann Oncol 2020;31(5):590–8.
22. Harvey-Jones E et al. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer. Ann Oncol 2024;35(4):364–80.
23. Li H et al. PARP inhibitor resistance: the underlying mechanisms and clinical implications. Mol Cancer 2020;19(1):107.
24. Bayley R et al. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ. Mol Cell 2022;82(10):1924–39 e10.
25. Sweatman E et al. SETD1A-dependent EME1 transcription drives PARPi sensitivity in HR deficient tumour cells. Br J Cancer 2025;132:690–702.
26. Wyatt HD, West SC. Holliday junction resolvases. Cold Spring Harb Perspect Biol 2014;6(9):a023192.
27. Mertins P et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 2016;534(7605):55–62.
28. National Cancer Institute. Proteomic Data Commons. 2024. [Accessed June 2025].