Fragmenting the unknown: impact of treatments on fragmentation profiles of DIPG cfDNA
Cell free DNA (cfDNA) extracted from plasma provides a minimally invasive approach toward medicinal diagnostics. Literature in the field shows that fragmentation patterns of cfDNA differ between healthy individuals and cancer patients. However, it remains unclear whether the fragmentation patterns change with exposure to cancer treatment. Identifying fragmentation patterns in response to therapy may provide a novel method to assess patient response more quickly than current standards. We aim to fill this research gap, specifically in regards to diffuse intrinsic pontine glioma (DIPG), by analyzing the fragmentation patterns of drug induced apoptosis and spontaneous cell death. In this project, cell line PBT 29 was treated with the IC50 concentration of GB13, Quisinostat, Pevonedistat, Temozolomide, and a vehicle control separately. Supernatant was collected following 72 hours incubation with treatment and cfDNA was extracted via MagMax cfDNA isolation kit. Libraries were prepared using the ThruPLEX DNA-Seq kit for whole genome sequencing via iSeq. Results showed the proportion of fragments above or below 150 base pairs (bp) within the range between 50-200 bp. Quisinostat-treated supernatant exhibited a higher number of fragments below 150 bp while Temozolomide-treated supernatant exhibited a higher number of fragments above 150 bp when compared to the control. Although statistical significance could not be determined due to the low sequencing depth and sample size, these results suggest that there may be an underlying mechanism driving this change. With further research examining fragment identity and prevalence, fragmentation profiles may prove useful as a minimally invasive way to track cancer treatment response.
