Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer

Abstract

BackgroundA number of clinico-pathological criteria and molecular profiles have been used to stratify patients into high- and low-risk groups. Currently, there are still no effective methods to determine which patients harbor micrometastatic disease after standard breast cancer therapy and who will eventually develop local or distant recurrence. The purpose of our study was to identify circulating DNA methylation changes that can be used for prediction of metastatic breast cancer (MBC).ResultsDifferential methylation analysis revealed ~5.0 × 106 differentially methylated CpG loci in MBC compared with healthy individuals (H) or disease-free survivors (DFS). In contrast, there was a strong degree of similarity between H and DFS. Overall, MBC demonstrated global hypomethylation and focal CpG island (CPGI) hypermethylation. Data analysis identified 21 novel hotspots, within CpG islands, that differed most dramatically in MBC compared with H or DFS.ConclusionsThis unbiased analysis of cell-free (cf) DNA identified 21 DNA hypermethylation hotspots associated with MBC and demonstrated the ability to distinguish tumor-specific changes from normal-derived signals at the whole-genome level. This signature is a potential blood-based biomarker that could be advantageous at the time of surgery and/or after the completion of chemotherapy to indicate patients with micrometastatic disease who are at a high risk of recurrence and who could benefit from additional therapy.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0135-8) contains supplementary material, which is available to authorized users.

The potential for liquid biopsies in the precision medical treatment of breast cancer

“…In patients with PIK3CA mutations identified by ctDNA, median PFS was 7.0 months in patients treated with buparlisib vs. 3.2 months in those treated with placebo. In those with nonmutant PIK3CA by liquid biopsy, there was no difference in PFS 218 .…”

“…In order to attain such a goal, CTCs and ctDNA sequencing data must be integrated into systematic and broad-based trials with clinical endpoints. Several trials discussed in this paper strive toward this goal, with the DETECT 3, BOLERO-2, BELLE 2 trials and others focusing on this very concept by evaluating therapeutic response based on phenotypes of CTCs or ctDNA in patients with breast cancer 124,216,218 . In summary, once further established, the molecular characterization of circulating biomarkers has the potential to provide the ideal mechanism of personalizing treatment in breast cancer for the best clinical results by predicting treatment response, evaluating minimal residual disease and allowing for the rational selection of targeted therapies.…”

“…Furthermore multiple alterations in genes related to the PI3K-mTOR pathway may confer resistance to trastuzumab 218,242 . A recent trial in breast cancer established a CTC PD-L1 assay that can be used for liquid biopsy in future clinical trials for stratification and monitoring of cancer patients undergoing immune checkpoint blockade 243 .…”

Genome-wide epigenomic profiling for biomarker discovery

“…For a range of tumors, including childhood acute lymphoblastic leukemia [86], kidney cancer [87], NSCLC [88], rectal cancer [89], cervical cancer [90, 91], breast cancer [92, 93], and glioblastoma [94], DNA methylome analysis has been shown to be of prognostic value. Most of these studies define changes in DNA methylation at single sites or at small subsets of sites that represent potential disease signatures.…”

Methylation analyses in liquid biopsy

“…WGBS can be performed with ~30 ng of DNA, and in some cases as little as 125 pg, which makes it an applicable method for analysis of cfDNA. Hence, several recent studies have used WGBS to analyze the methylomes of plasma cfDNA (72)(73)(74). Since only a small fraction of the genome is differentially methylated in cancer, enrichment methods can be coupled to bisulfite sequencing to limit the cost associated with WGBS.…”