Next Generation Sequencing of whole SAS and FaDu spheroids transcriptomes treated with Hyperthermia (HT) and Radiation therapy (RT)

By employing a global gene expression profiling, we performed the differential gene expression analysis and the analysis of the molecular pathways which are deregulated in Hyperthermia (HT) and Radiation therapy (RT) treated SAS and FaDu spheroids from the head-and-neck cancer cell lines. The RNA-Seq analysis was done on FaDu and SAS spheroids treated with clinically relevant HT dose of 42.5°C for 60 minutes alone or in combination of single dose irradiation of 7 and 10 Gy for FaDu and SAS, respectively. The main pathways and networks modulated by the treatments (0.5 h after treatment) were identified using Gene Ontology (GO) enrichment analysis. Direct comparisons of the total genome of Control, RT, HT and HT+RT treated FaDu and SAS spheroids were performed using the Illumina NovaSeq™ 6000 System. Differential gene expression and pathways analysis were done in the format Control versus each Treatment groups (HT, RT and HR+RT) for defined spheroids and also for SAS Control vs. FaDu Control samples. Each of 8 samples has been prepared in 3 replicates.