This study aimed at analyzing the DNA methylation pattern and TP53 mutation status of intrinsic breast cancer (BC) subtypes for improved characterization and survival prediction. DNA methylation of 17 genes was tested by methylation-specific PCR in 116 non-familial BRCA mutation-negative BC and 29 control noncancerous cases. At least one gene methylation was detected in all BC specimens and a 10-gene panel statistically significantly separated tumors from noncancerous breast tissues. Methylation of FILIP1L and MT1E was predominant in triple-negative (TN) BC, while other BC subtypes were characterized by RASSF1, PRKCB, MT1G, APC, and RUNX3 hypermethylation. TP53 mutation (TP53-mut) was found in 38% of sequenced samples and mainly affected TN BC cases (87%). Cox analysis revealed that TN status, age at diagnosis, and RUNX3 methylation are independent prognostic factors for overall survival (OS) in BC. The combinations of methylated biomarkers, RUNX3 with MT1E or FILIP1L, were also predictive for shorter OS, whereas methylated FILIP1L was predictive of a poor outcome in the TP53-mut subgroup. Therefore, DNA methylation patterns of specific genes significantly separate BC from noncancerous breast tissues and distinguishes TN cases from non-TN BC, whereas the combination of two-to-three epigenetic biomarkers can be an informative tool for BC outcome predictions.

Approximately 10% of all breast cancer (BC) cases are familial and caused by inheritance of mutant BRCA1, BRCA2, or some other genes from the same DNA reparation pathway. Genetic counseling in families with cancer history is a powerful means for early cancer detection and active risk reduction through preventive interventions. This is the first report of the rare inherited BRCA2 frameshift-deletion mutation c.3847_3848delGT in one Lithuanian pedigree with the intense familial history of BC. Three BRCA2-positive blood relatives with BC of different biological types were identified in this pedigree with the same type mutation. All three cases were diagnosed with advanced stage ductal carcinoma. Markedly, polymorphic cells and numerous mitoses were identified in BC from the cases. Two patients from the family were diagnosed with the triple negative tumors, while one case had early onset of the hormone positive BC. Despite the variation in clinical and biological presentation of BC, all cases showed a good response to conventional treatment. In conclusion, the strong influence of BRCA2 mutation on the onset of BC of various biological types reveals the complexity of genetic counselling in families with BC history.

Background: Current breast cancer (BC) diagnostics include detailed pathological and genetic analysis for biological subtype identification; however, throughout the course of the disease, new alterations determining the progression of the disease or resistance to treatment appear. The tests based on liquid biopsy allow minimally invasive real-time monitoring of tumour-specific alteration during the entire disease treatment. Tumour-specific genetic material fragments occur in bodily fluids, and cell-free nucleic acids are a convenient tool for analysing genetic and epigenetic changes in tumours. Evidence for the diagnostic and prognostic value of epigenetic biomarkers is gradually increasing. Although, up to date, there is limited access to in vitro diagnostic (IVD) epigenetic liquid biopsy-based tests for BC management, the data on the clinical potential of such tests and biomarkers are accumulating rapidly. Methods: In this review, we focused on research involving cell-free DNA methylation biomarkers in blood serum or plasma samples from BC patients. Results: Our review systematises data from genome-wide and targeted studies of DNA methylation changes in liquid biopsies from BC patients, aiming to highlight the most critical biomarkers suitable for early BC diagnosis, treatment personalisation and prognosis. Conclusion: In summary, cell-free DNA methylation biomarkers show strong potential to enhance breast cancer diagnosis, prognosis, and personalised treatment through integrated clinical profiling.