Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in-vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer

Anaplastic thyroid cancer (ATC) is a very aggressive and rare disease. Rapid metastasis and limited promising treatments call for additional therapeutical options, including drug repurposing. The rapid spreading of ATC highlights the importance of rapid therapy success assessment, which could be achieved by measurement of extracellular vesicle-associated cell-free RNA in liquid biopsy samples. Recent studies have discovered the potential of the receptor tyrosine kinase inhibitor vandetanib for ATC treatment in vitro and in vivo. Given the rarity of ATC patients receiving off-label vandetanib treatment, acquiring patient samples for clinical studies is a prolonged process, and pre-clinical investigations are needed to elucidate the effects of vandetanib on ATC cells. Here, we present an in vitro study addressing the transcriptional and proteomic changes induced in the ATC cell line Cal62 by three doses of vandetanib. By comparing the transcriptional and proteomic data sets and applying dimensional reduction models such as sparse partial least-squares discriminant analysis, we refined a set of 21 biomarker candidates. We report a signature of eight transcriptional biomarkers, validated in the cellular and cell-free RNA by RT-qPCR and verified for its biological significance and discriminatory power by pathway over-representation analysis and partial least-squares regression. This biomarker signature can distinguish vandetanib treatment from the control in the cell-free RNA isolated from Cal62 extracellular vesicles and can be measured reliably, easily, and quickly using RT-qPCR. Our findings may serve as a basis for future clinical trials with liquid biopsy samples from ATC patients undergoing off-label vandetanib treatment.