Evaluation of ctDNA as a prognostic biomarker in patients with localized Ewing sarcoma
Ewing sarcoma is the second most common primary bone malignancy in children and young adults. Approximately 70-75% of patients with localized Ewing sarcoma are expected to survive their disease with multi-agent chemotherapy regimens and local control of the primary tumor. Identification of the 25-30% of patients with localized disease who are likely to relapse after conventional therapy remains challenging.
While a range of prognostic factors (e.g. tumor site, age) have been evaluated in this disease, the presence of metastatic disease at initial diagnosis has consistently been the strongest adverse prognostic factor for patients with Ewing sarcoma and has led to attempts to intensify treatment for this group. Development of biomarkers that might reflect micrometastatic disease in patients with localized disease is a high priority. Prior groups have evaluated RT-PCR to detect characteristic Ewing sarcoma fusion mRNA transcripts (most commonly EWSR1/FLI1) in the peripheral blood for this purpose with equivocal results. With the advent of next generation sequencing approaches, we have an opportunity to evaluate circulating tumor DNA (ctDNA) for this purpose.
Given our desire to detect ctDNA, we developed a novel hybrid-capture assay called TranSS-Seq. As proof of concept, we evaluated our assay in a large retrospective cohort of 57 patients with localized Ewing sarcoma and an available plasma sample from initial diagnosis. TranSS-Seq detected a Ewing sarcoma fusion in the peripheral blood of 44% of patients, with a median allele frequency of 7% (range 0-58). Patients with detectable ctDNA at diagnosis were found to have inferior EFS. We also used ctDNA allele frequency as a continuous predictor and demonstrated that increasing levels of ctDNA, among patients with detectable ctDNA, increased the hazard for event.
In the current proposal, we aim to prospectively evaluate a novel circulating tumor DNA (ctDNA) assay, TranSS-Seq, designed to detect characteristic Ewing sarcoma translocations as a means of characterizing the micrometastatic disease burden at diagnosis. If validated, this approach holds potential for risk-stratification of patients with localized disease, allowing for intensification of therapy for patients likely to relapse and potentially de-intensification of therapy for those likely to respond well to therapy.