Enrichment Tools to Better Understand the Different Types of Circulating Nucleosomes and Their Associated Genome Patterns in the Plasma of Dogs with Lymphoma
Introduction
Nucleosomes contain DNA wrapped around a core histone octamer. Following cell death nucleosomes are released into circulation and, thus, diseases with high cellular turnover rates (e.g., cancer) can have increased nucleosomes in plasma. Interestingly, cancer-derived nucleosomes have shorter DNA (147 bp) than nucleosomes derived from non-cancerous cellular turnover, thus, enabling isolation and specific analysis of cancer-derived nucleosomes.
The aim of this study was to isolate and sequence cancer-derived nucleosomes from dogs diagnosed with lymphoma thereby reducing the complexity of liquid biopsy and enabling the identification of biomarkers of clinical significance.
Methods
Plasma samples from healthy dogs and dogs with lymphoma were collected with owner consent and a proprietary enrichment method (Nu.Q Capture) was used to separate short (cancer-derived) from long (noncancer-derived) nucleosomes. The resulting DNA was sequenced and aligned to the CanFam4 genome. Fragment length and copy number estimates were calculated.
Results
Following enrichment, we found that, as expected, the unbound supernatant contained exclusively mononucleosomes whereas the captured fraction contained mono, di, and tri nucleosomes. Furthermore, we found evidence of increased proportion of shorter nucleosomes (147bp DNA) in dogs with lymphoma, consistent with findings in humans.
Conclusion
Circulating nucleosomes can be enriched from canine lymphoma patients based on DNA size, enabling a less complex substrate for identifying cancer associated genetic aberrations. Further studies are ongoing to determine the scope of DNA alterations that can be identified and what role these differences play in treatment response, minimal residual disease status, progression free survival, and prognosis.
Funding Information
Funding provided by Volition Veterinary Diagnostics.