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. 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