Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer - RT-qPCR biomarker validation raw data

Raw RT-qPCR data for the following paper: Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer Abstract Background: Anaplastic thyroid cancer (ATC) is an aggressive and rare disease. Rapid metastasis and limited treatments call for additional therapeutic options, including drug repurposing. The early spreading of ATC highlights the importance of rapid therapy success assessment, which could be achieved by measurement of extracellular vesicle (EV)-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. Objective: Here, we present an in vitro study addressing holistic transcriptional and proteomic changes induced in the ATC cell line Cal62 by three doses of vandetanib and quantified by high-throughput methods. Methods: 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. Results: Out of these, we report a final signature of eight transcriptional biomarkers, validated in cellular and cell-free RNA by RT-qPCR and verified for biological significance and discriminatory power by pathway over-representation analysis and partial least-squares regression. This transcriptional biomarker signature can distinguish vandetanib treatment from control in cell-free RNA isolated from Cal62 EVs and can be measured reliably, easily, and quickly using RT-qPCR. Conclusions: Our findings may serve as a basis for future clinical trials with liquid biopsy samples from ATC patients undergoing off-label vandetanib treatment. Authors: Christian Grätz1*, Prashant Changoer2, Dapi Menglin Chiang1, Johannes Kersting3, Martin Jaeger2, Romana Netea-Maier2, Christina Ludwig4, Markus List3,5, Benedikt Kirchner1,6, Marlene Reithmair7, Michael W. Pfaffl1 Affiliations: 1Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany. 2Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. 3Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, Munich, Germany.4Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Freising, Germany. 5Munich Data Science Institute, Technical University of Munich, Germany 6Division of Pediatric Neuro-oncology, German Cancer Research Center, Heidelberg, Germany. 7Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany. *corresponding author: [e-mail]