Aim: Explore the relationship between circulating tumour DNA (ctDNA) and exosomal DNA (exoDNA) to determine how each component reflects tumour heterogeneity and their significance to disease monitoring in breast cancer.
Background: It has been reported that a large proportion of ctDNA is contained within exosomes, small extracellular vesicles which are actively secreted by tumour cells into the bloodstream. However, we have shown previously that the mutational landscape of exoDNA differs from that of ctDNA, suggesting they may be distinct entities which can give different information regarding tumour biology. We believe that these disparities can be exploited to provide a greater understanding of tumour clonality in the context of treatment monitoring.
Methods: Exosomes were isolated from the blood of metastatic breast cancer patients using ultracentrifugation and treated with DNase to remove any external DNA prior to extraction. Blood collected at the same timepoint was also used for ctDNA extraction. Targeted sequencing was performed on DNA with the Ion Torrent platform, using patient-matched genomic DNA as internal controls.
Results: DNase treatment of exosomes significantly decreased DNA concentration prior to extraction, suggesting that ctDNA associates with exosomes in solution. However, upon sequencing, it was found that variants detected in patient samples were unique to either exoDNA or ctDNA, indicating that they have discrete genomic profiles reflective of their different biological origins.
Conclusions: Complementary assessment of both exoDNA and ctDNA may allow greater insight into tumour heterogeneity and response to therapy in breast cancer patients.