Cell-Free RNA from Plasma in Patients with Neuroblastoma: Exploring the Technical and Clinical Potential

SIMPLE SUMMARY: Neuroblastoma mostly affects young children and despite intensive treatment, many children die of progressive disease. It remains challenging to identify those patients at risk. Analyzing blood, as liquid biopsies, is not invasive and can help to identify these patients. We studied whether RNA molecules can be detected in these liquid biopsies. In blood plasma, RNA can be free-floating or packed in small particles, ‘extracellular vesicles’. We present a workflow to analyze this cell-free RNA from small volumes of blood plasma of children with neuroblastoma. We have used neuroblastoma-specific markers and markers involved in cell proliferation. These latter genes can be upregulated in many different tumor types. We demonstrate that both types of markers have a higher expression in patients with metastatic disease, compared to healthy controls and patients with localized disease. These findings are essential for future studies on cell-free RNA, hopefully leading to improved survival for these patients. ABSTRACT: Neuroblastoma affects mostly young children, bearing a high morbidity and mortality. Liquid biopsies, e.g., molecular analysis of circulating tumor-derived nucleic acids in blood, offer a minimally invasive diagnostic modality. Cell-free RNA (cfRNA) is released by all cells, especially cancer. It circulates in blood packed in extracellular vesicles (EV) or attached to proteins. We studied the feasibility of analyzing cfRNA and EV, isolated by size exclusion chromatography (SEC), from platelet-poor plasma from healthy controls (n = 40) and neuroblastoma patients with localized (n = 10) and metastatic disease (n = 30). The mRNA content was determined using several multiplex droplet digital PCR (ddPCR) assays for a neuroblastoma-specific gene panel (PHOX2B, TH, CHRNA3) and a cell cycle regulation panel (E2F1, CDC6, ATAD2, H2AFZ, MCM2, DHFR). We applied corrections for the presence of platelets. We demonstrated that neuroblastoma-specific markers were present in plasma from 14/30 patients with metastatic disease and not in healthy controls and patients with localized disease. Most cell cycle markers had a higher expression in patients. The mRNA markers were mostly present in the EV-enriched SEC fractions. In conclusion, cfRNA can be isolated from plasma and EV and analyzed using multiplex ddPCR. cfRNA is an interesting novel liquid biopsy-based target to explore further.