14Human papillomaviruses (HPV) are causative agents in ano-genital and oropharyngeal cancers. 15 The virus must reprogram host gene expression to promote infection, and E6 and E7 contribute 16 to this via targeting of cellular transcription factors including p53 and pRb, respectively. The 17 HPV16 E2 protein regulates host gene expression in U2OS cells and in this study we extend 18 these observations into TERT immortalized oral keratinocytes (NOKs) that are capable of 19 supporting late stages of the HPV16 life cycle. We observed repression of innate immune genes 20 by E2 that are also repressed by the intact HPV16 genome in NOKs. RNA-seq data identified 21 167 up and 395 downregulated genes by E2; there was a highly significant overlap of the E2 22 regulated genes with those regulated by the intact HPV16 genome in the same cell type. siRNA 23 targeting of E2 reversed repression of E2 targeted genes. The ability of E2 to repress innate 24 immune genes was confirmed in an ano-genital immortalized keratinocyte cell line, N/Tert-1. 25 We present analysis of data from The Cancer Genome Atlas (TCGA) for HPV16 positive and 26 negative head and neck cancers (HNC) suggesting that E2 plays a role in regulation of the host 27 genome in cancers. Patients with HPV16 positive HNC with a loss of E2 expression exhibit a 28 worse clinical outcome and we discuss how this could, at least partially, be related to the loss of 29 E2 host gene regulation. 30 31 Importance 32 HPV16 positive tumors that retain expression of E2 have a better clinical outcome than those 33 that have lost E2 expression. It has been suggested that this is due to a loss of E2 repression of 34 E6 and E7 expression but this is not supported by data from tumors where there is not more E6 35 3 and E7 expression in the absence of E2. Here we report that E2 regulates host gene expression 36 and place this regulation in context of the HPV16 life cycle and HPV16 positive head and neck 37 cancers (the majority of which retain E2 expression). We propose that this E2 function may play 38 an important part in the increased response of HPV16 positive cancers to radiation therapy. 39 Therefore, host gene regulation by E2 may be important for promotion of the HPV16 life cycle, 40 and also for the response of HPV16 positive tumors to radiation therapy. 41 42 43 44 High risk human papillomaviruses (HR-HPV) are etiological agents in ano-genital and 45 oropharyngeal cancers (1). HPV16 is causative in around 50% of HPV positive cervical cancers 46 (HPV+CC) and 90% of HPV positive oropharyngeal cancers (HPV+OPC), the latter of which 47 has reached epidemic proportions over the past generation (2-5). 48 Following infection, HPV DNA ultimately reaches the nucleus where cellular factors induce 49 transcription from the viral genome. The viral oncogenes E6 and E7 create an environment that 50 promotes cellular proliferation and one aspect of this manipulation is the alteration of host gene 51 transcription. E7 binds to pocket proteins pRb, p130 and p107 and blo...