Methylation patterns in serum DNA for early identification of disseminated breast cancer

Abstract

BackgroundMonitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We hypothesized that cell-free DNAme markers could indicate disseminated breast cancer, even in the presence of substantial quantities of background DNA.MethodsWe used reduced representation bisulfite sequencing (RRBS) of 31 tissues and established serum assays based on ultra-high coverage bisulfite sequencing in two independent prospective serum sets (n = 110). The clinical use of one specific region, EFC#93, was validated in 419 patients (in both pre- and post-adjuvant chemotherapy samples) from SUCCESS (Simultaneous Study of Gemcitabine-Docetaxel Combination adjuvant treatment, as well as Extended Bisphosphonate and Surveillance-Trial) and 925 women (pre-diagnosis) from the UKCTOCS (UK Collaborative Trial of Ovarian Cancer Screening) population cohort, with overall survival and occurrence of incident breast cancer (which will or will not lead to death), respectively, as primary endpoints.ResultsA total of 18 BC specific DNAme patterns were discovered in tissue, of which the top six were further tested in serum. The best candidate, EFC#93, was validated for clinical use. EFC#93 was an independent poor prognostic marker in pre-chemotherapy samples (hazard ratio [HR] for death = 7.689) and superior to circulating tumor cells (CTCs) (HR for death = 5.681). More than 70% of patients with both CTCs and EFC#93 serum DNAme positivity in their pre-chemotherapy samples relapsed within five years. EFC#93-positive disseminated disease in post-chemotherapy samples seems to respond to anti-hormonal treatment. The presence of EFC#93 serum DNAme identified 42.9% and 25% of women who were diagnosed with a fatal BC within 3–6 and 6–12 months of sample donation, respectively, with a specificity of 88%. The sensitivity with respect to detecting fatal BC was ~ 4-fold higher compared to non-fatal BC.ConclusionsDetection of EFC#93 serum DNAme patterns offers a new tool for early diagnosis and management of disseminated breast cancers. Clinical trials are required to assess whether EFC#93-positive women in the absence of radiological detectable breast cancers will benefit from anti-hormonal treatment before the breast lesions become clinically apparent.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-017-0499-9) contains supplementary material, which is available to authorized users.

ADAM12 is A Potential Therapeutic Target Regulated by Hypomethylation in Triple-Negative Breast Cancer

“…Furthermore, cfDNA from cancer patients is known to carry tumour-specific changes in DNA methylation that are not present in the cfDNA of healthy donors [48,49]. Based on this, panels of tumour-specific methylated genes of potential value for early detection of BC have been described in cfDNA [50,51], including the RASSF1A, PITX2 [52,53] and EFC [54] genes, whose hypermethylation has been associated with poor prognosis of BC. Despite these promising findings, epigenetic alterations in cfDNA have not so far been explored in TNBC.…”

Perspectives of the Application of Liquid Biopsy in Colorectal Cancer

“…Clinical data indicate that circulating SEPT9 DNA as a methylation marker is as sensitive as 87% in detecting stage I CRC, 84% in detecting stage II CRC, and 90% in overall CRC [68]. Two recent studies have shown that tumor-specific methylation changes can be detected in plasma two years before tumor diagnosis [69,70]. Further research by Guo et al showed that ctDNA methylation changes in plasma could not only be applied in the screening of tumors but also reveal the tissue source of tumors [71].…”

The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

“…These techniques have impacted every field of molecular research, escalating previously used sequencing technologies [ 11 ], and opening the way to the -omic sciences foundation [ 1 , 2 ]. Indeed, NGS methods allow the sequencing of entire genomes [ 12 , 13 , 14 , 15 ], of exomes [ 16 , 17 , 18 ], of panels of genes related to a disease of interest [ 19 , 20 , 21 ], or of a single gene [ 22 , 23 , 24 , 25 , 26 ], but can also be used to explore the entire transcriptome [ 27 , 28 , 29 ], small RNAs [ 30 , 31 , 32 ], the epigenome [ 33 , 34 ], and the microbiome [ 35 , 36 , 37 , 38 ].…”

“…In addition to the study of sequence variations at the DNA level, NGS methods can be used to study genetic variability, and the mechanisms underlying the onset of specific diseases at epigenetic, transcriptomic and metagenomic levels [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Indeed, several factors, other than individual genetic predisposition, such as diet, environmental factors and lifestyle, can influence the epigenome, the transcriptome and the microbiome [ 2 , 50 ].…”

“…Similarly, NGS has prompted the study of the epigenome and of the microbiome. By using the preparation protocols of specific libraries, it is possible to analyze the methylation status of DNA at a genome-wide level or by focusing on a custom set of genomic regions of interest [ 33 , 34 ]. Moreover, chromatin immunoprecipitation sequencing (ChIP-Seq) approaches have shown their efficacy in the study of the regulatory networks of gene expression at the genome-wide level, by allowing the identification of the targets of specific transcription factors [ 53 ].…”