Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer

Abstract

Purpose Resistance to platinum-based chemotherapy or PARP inhibition in germline BRCA1 or BRCA2 mutation carriers may occur through somatic reversion mutations or intragenic deletions that restore BRCA1 or BRCA2 function. We assessed whether BRCA1/2 reversion mutations could be identified in circulating cell-free DNA (cfDNA) of ovarian or breast cancer patients previously treated with platinum and/or PARP inhibitors. Experimental Design cfDNA from 24 prospectively accrued BRCA1- or BRCA2-germline mutant patients, including 19 platinum-resistant/refractory ovarian cancer and five platinum and/or PARP inhibitor pre-treated metastatic breast cancer patients, was subjected to massively parallel sequencing targeting all exons of 141 genes and all exons and introns of BRCA1 and BRCA2. Functional studies were performed to assess the impact of the putative BRCA1/2 reversion mutations on BRCA1/2 function. Results Diverse and often polyclonal putative BRCA1 or BRCA2 reversion mutations were identified in cfDNA from four ovarian cancer patients (21%) and from two breast cancer patients (40%). BRCA2 reversion mutations were detected in cfDNA prior to PARP inhibitor treatment in a breast cancer patient who did not respond to treatment, and were enriched in plasma samples after PARP inhibitor therapy. Foci formation and immunoprecipitation assays suggest that a subset of the putative reversion mutations restored BRCA1/2 function. Conclusions Putative BRCA1/2 reversion mutations can be detected by cfDNA sequencing analysis in ovarian and breast cancer patients. Our findings warrant further investigation of cfDNA sequencing to identify putative BRCA1/2 reversion mutations and to aid the selection of patients for PARP inhibition therapy.

Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP‐seq

“…Detection of mutations with target or genome scale sequencing was the widest application of cfDNA in both NIPT and liquid biopsy. 38,39 For this application, we firstly analyzed mutations in each cfDNA sample (Supporting Information Table S8). We then compared the mutations of different types of cfDNA.…”

The value of cell‐free DNA for molecular pathology

“…cfDNA can be used to monitor acquisition of resistance, through screening for known resistance mutations [86][87][88][89][90][91][92][93][94], or searching for novel mechanisms of resistance [95][96][97]. Serial sampling can be performed to identify resistant clones prior to the onset of clinical progression [88,89].…”

PARP‐1 regulates DNA repair factor availability

“…However, while most responders (14/16) in this trial were categorized as biomarker positive for HR deficiency, the biomarker suite included single copy loss of DNA repair factors, as well as alterations to HDAC2, which is involved in transcriptional repression (Rountree et al, 2000). While these studies that not all PARPi responders with PCa harbor HR-defective tumors, and not all PCa tumors that exhibit aberrant DNA repair are PARPi responsive, there is clinical evidence that PARPi resistance is associated with restored HR function in multiple tumor types (Edwards et al, 2008;Barber et al, 2013;Christie et al, 2017;Kondrashova et al, 2017;Pishvaian et al, 2017;Weigelt et al, 2017), including PCa (Goodall et al, 2017;Quigley et al, 2017). Additionally, PARPi resistance has been associated with differential DNA damage response (DDR) network functioning (Jaspers et al, 2013;Johnson et al, 2013;Gogola et al, 2018).…”