Related Experiment Video
Updated: Jul 5, 2025
Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP
E Harvey-Jones1, M Raghunandan2, L Robbez-Masson2
1The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK.
Background:
Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance.
Patients And Methods:
Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51.
Results:
BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient.
Conclusions:
These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.
Insights
BRCA1/2 reversion mutations are the most common cause of resistance to homologous recombination deficiency (HRD) targeted therapies in breast cancer. These reversions, detected early in circulating tumor DNA, impact treatment strategies and clinical trial design for HRD-positive breast cancers.
Area of Science:
- Oncology
- Genetics
- Genomics
Background:
- Resistance to homologous recombination deficiency (HRD) targeted therapies is a significant challenge in breast cancer treatment.
- Understanding resistance mechanisms is crucial for improving therapeutic effectiveness.
Purpose of the Study:
- To investigate the prevalence and mechanisms of resistance to HRD-targeted therapy in metastatic breast cancer.
- To analyze longitudinal circulating tumor DNA (ctDNA) and tumor biopsy data to identify resistance drivers.
Main Methods:
- Longitudinal ctDNA mutation and methylation profiling in 47 patients with metastatic BRCA1-, BRCA2-, or PALB2-mutant breast cancer.
- Sequencing of ctDNA using a novel >750-gene targeted panel at multiple time points.
- Whole exome and RNA sequencing of matched tumor biopsies and assessment of nuclear RAD51 status.
Main Results:
- BRCA1/2 reversion mutations were the most prevalent resistance mechanism (60% of patients), often detectable in ctDNA before clinical progression.
- Two novel reversion mechanisms were identified: intragenic deletions and secondary mutations creating new splice sites.
- Non-reversion mechanisms, including TP53BP1, RIF1, or PAXIP1 loss-of-function mutations, were also observed, sometimes coexisting with reversions.
Conclusions:
- BRCA1/2 reversion mutations are the primary drivers of resistance to HRD-targeted therapy in breast cancer.
- Early detection of resistance mechanisms via ctDNA has implications for clinical management and trial design.
- The coexistence of multiple resistance mechanisms highlights the complexity of acquired resistance in HRD breast cancer.
