Tahmid Anwar

Helios Scholar

Diffuse intrinsic pontine glioma (DIPG) is an aggressive and often lethal pediatric brain tumor with limited therapeutic options and poor prognosis. Circulating tumor DNA (ctDNA) analysis offers a non-invasive method to monitor tumor dynamics and therapeutic response, providing critical insights into the molecular landscape of DIPG. Our research aimed to analyze how ctDNA fragmentation patterns are affected by drug induced tumor cell death. To accomplish this objective, DIPG cell line PBT29 was treated with four chemotherapeutic drugs: GB13, quisinostat, pevonedistat, and temozolomide (TMZ). ctDNA was extracted from cell culture supernatants and sequenced using low-pass whole genome sequencing. Fragmentation analysis revealed distinct fragment size distributions for each treatment group. Compared to the control cultures, cells treated with TMZ exhibited a higher proportion of larger ctDNA fragments (>150 bp), while cells treated with quisinostat exhibited a higher proportion of shorter ctDNA fragments (<150 bp). These preliminary results indicated that the fragmentation patterns are consistent with drug mechanics. TMZ being a crosslinking agent, is expected to have a more compact chromatin structure, leading to inhibition of nuclease activity and thus longer ctDNA fragments. Inhibition of histone deacetylase by quisinostat should produce more open chromatin and thus result in shorter fragmentation patterns due to increased nuclease activity. Our hope is that the distinct fragmentation profiles observed can better help in understanding drug mechanisms and potentially guide the development of personalized therapeutic strategies for DIPG patients in future studies.