Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer ModelsRocco Sciarrillo 1,2,3, Anna Wojtuszkiewicz 1, Irsan E. Kooi 4, Valentina E. Gómez 3, Ugo Boggi 5, Gerrit Jansen 6, Gert-Jan Kaspers 1,7, Jacqueline Cloos *1, Elisa Giovannetti *3,8,9
1Department of Pediatric Oncology/Hematology, VU University Medical Center, 2Department of Hematology, VU University Medical Center, 3Department of Medical Oncology, VU University Medical Center, 4Department of Clinical Genetics, VU University Medical Center, 5Division of General and Transplant Surgery, Azienda Ospedaliera Universitaria Pisana, Universita’ di Pisa, 6Amsterdam Immunology and Rheumatology Center, VU University Medical Center, 7Princess Máxima Center for Pediatric Oncology, 8Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, 9Institute of Nanoscience and Nanotechnology, CNR-Nano
Here we describe a protocol aimed at investigating the impact of aberrant splicing on drug resistance in solid tumors and hematological malignancies. To this goal, we analyzed the transcriptomic profiles of parental and resistant in vitro models through RNA-seq and established a qRT-PCR based method to validate candidate genes.
