Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer

Chromosomal copy number alterations (CNAs) and human papillomavirus (HPV) DNA integration into the host genome are more frequent in invasive cervical cancers compared to precancers. However, the relationship between CNAs and viral integration is not well understood. We analyzed chromosomal CNAs and HPV DNA integration in 17 biopsies from women diagnosed with cervical intraepithelial neoplasia grade 3 (CIN3) and 21 biopsies from women diagnosed with invasive cervical carcinoma. All samples were HPV16-positive. HPV DNA integration was evaluated by sequencing of chimeric transcripts or hybrid capture reads. Chromosomal copy number was measured with the aCGH 1 x 1M (Agilent Technologies, Santa Clara, CA). A genomic instability index (GII) was defined as the fraction of the genome with CNAs. The Wilcoxon rank-sum test was used to compare CIN3 and cancer samples. Unsupervised clustering based on CNAs identified two groups corresponding to CIN3 and cancer. Most differential CNAs were found in chromosomes 3 and 8. HPV DNA was present in episomal form in 15 samples and integrated in 23 samples. The mean GII was 0.12 and 0.21 for CIN3 and cancer, respectively (P = 0.039). The GII was significantly higher in integrated samples (mean GII in episomal samples: 0.12; and integrated samples: 0.20; P = 0.02), but not within CIN3 or cancer. Integration sites were more frequently observed in amplified regions than expected by chance (P = 0.008). Our findings demonstrate that GII increases with HPV integration and at the transition from CIN3 to cancer. However, chromosomal instability can occur in the absence of integration, suggesting that it may facilitate integration.