Determine differences in gene expression between OPSCC cell lines with different sensitivity to IR

mRNA sequencing was performed on 10 oropharyngeal cancer cell lines (5 HPV-positive and 5 HPV-negative cell lines) for this project. Two cell lines (CU-OP-17 and CU-OP-20) were newly derived from HPV-negative and HPV-positive tonsil cancers, respectively (described in " Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation" by Holzhauser et al. This study was performed with the goal to identify differences in gene expression between irradiated and non-irradiated cell line samples. Additionally, the aim was to identify possible changes in genes, involved in DNA repair or DNA damage response of the HPV-positive and HPV-negative cell lines. The data published showed an increase of HPV integration sites after irradiation. Additionally, all HPV-positive cell lines in this study showed expression of HPV encoded genes. However, no direct correlation of changes or expression of DNA repair genes was identified. Overall design: Identification of differences in gene expression by mRNA sequencing between non-irradiated and irradiated (2Gy) HPV-positive and HPV-negative OPSCC cell lines. Cells were grown under standard cell culture condition, mRNA was extracted and sequencing perfomed with 75bp PE (sequencing readlength)- TruSeq stranded total RNA with ribo-zero GOLD