Integration of high-risk human papillomavirus (HRHPV) into the host genome is a key event in cervical neoplastic progression. Integration is associated with deregulated expression of the viral oncogenes E6 and E7 and acquisition of a selective growth advantage for cells containing integrants. Overexpression of the viral transcriptional regulator E2 from heterologous promoters has an inhibitory effect on transcription from integrated HRHPV. Therefore, we hypothesized that loss of E2-expressing episomes from cells in which integration had previously occurred would be required for such cells to gain a growth advantage. Using the unique W12 model of cervical squamous carcinogenesis, we show that cells containing integrated HPV16 reproducibly emerged during long-term culture when there had been a rapid fall in episome numbers. During the period of emergence, it is possible to isolate single-cell clones containing an intracellular mixture of the integrant being selected and episomes at reduced load. The lower level of E2 expression seen in such cells is associated with partial inhibition of transcription from the HPV16 integrant. Full deregulation is not observed until complete loss of E2-expressing episomes occurs. Microarray analysis showed that episome loss was closely associated with endogenous activation of antiviral response genes that are also inducible by the type I IFN pathway. Taken together, our results indicate that episome loss, associated with induction of antiviral response genes, is a key event in the spontaneous selection of cervical keratinocytes containing integrated HPV16. We conclude that cervical carcinogenesis requires not only HRHPV integration, but also loss of inhibitory episomes.human papillomavirus Í cervix Í integration Í interferon Í progression I ntegration of high-risk human papillomavirus (HRHPV) into the host genome is an important step in cervical neoplastic progression (1, 2). Integrated viral genomes from which HRHPV early genes are transcribed have been detected in Ï·87.5% of cervical malignancies (3). Integration usually causes deletion or disruption of the viral regulatory E2 gene, while retaining a variable segment including the E6 and E7 oncogenes and the upstream regulatory region (4, 5). Overexpression of E2 from heterologous promoters in cells harboring integrated HRHPV can repress the early promoter of the integrated virus, causing a sharp reduction in E6 and E7 expression (6). Thus, HRHPV integration and disruptionÍdeletion of E2 leads to increased expression of the viral oncogenes (7,8). Cells containing integrated HRHPV acquire a growth advantage over cells harboring episomal HRHPV (the natural viral state in productive infections) and show increased genomic instability (9-11).Cervical keratinocyte cell lines established from precursor low-grade squamous intraepithelial lesions have indicated that episomal HRHPV genomes are maintained at Ï·100 copies per cell in the basal region of an infected epithelium (12, 13). Viral integration is therefore most likely to occur in cel...