Genomic characterization of viral integration sites in HPV-related cancers

Abstract

Persistent infection with carcinogenic human papillomaviruses (HPV) causes the majority of anogenital cancers and a subset of head and neck cancers. The HPV genome is frequently found integrated into the host genome of invasive cancers. The mechanisms of how it may promote disease progression are not well understood. Thoroughly characterizing integration events can provide insights into HPV carcinogenesis. Individual studies have reported limited number of integration sites in cell lines and human samples. We performed a systematic review of published integration sites in HPV-related cancers and conducted a pooled analysis to formally test for integration hotspots and genomic features enriched in integration events using data from the Encyclopedia of DNA Elements (ENCODE). Over 1,500 integration sites were reported in the literature, of which 90.8% (N = 1,407) were in human tissues. We found 10 cytobands enriched for integration events, three previously reported ones (3q28, 8q24.21 and 13q22.1) and seven additional ones (2q22.3, 3p14.2, 8q24.22, 14q24.1, 17p11.1, 17q23.1 and 17q23.2). Cervical infections with HPV18 were more likely to have breakpoints in 8q24.21 (p = 7.68 × 10(-4) ) than those with HPV16. Overall, integration sites were more likely to be in gene regions than expected by chance (p = 6.93 × 10(-9) ). They were also significantly closer to CpG regions, fragile sites, transcriptionally active regions and enhancers. Few integration events occurred within 50 Kb of known cervical cancer driver genes. This suggests that HPV integrates in accessible regions of the genome, preferentially genes and enhancers, which may affect the expression of target genes.

Keywords: HPV; integration.

Legend Figure 1.. Characteristics of reported HPV events.

A includes all reported HPV integration events form human specimens and cell lines. B and C include HPV integration events reported in human specimens only.

Figure 2 legend.. Distribution of the location of HPV integration events in the human genome.

Data for this plot was restricted to human specimens and with nucleotide information for the integration event. A. Distribution of the locations of the HPV integration events across the genome. The outer circle represents the locations of the 24 human chromosomes. The green bars in the inner circle depict the frequency of the HPV integration event at each location. Each green bar represents a bin size of 3 Kb. The scale for the frequency is represented by the light grey concentric circles, with each concentric circle representing 2 integration events. B. Position of HPV integration events and genes in 3q28 (only integration events with known position are plotted). Green bars are integration events. C. Position of HPV integration events and genes in 8q24.21 (only integration events with known position are plotted). D. Position of HPV integration events and genes in 13q22.1 (only integration events with known position are plotted).

Figure 3 legend.. Integration sites from human specimens with exact position with respected to RefSeq genes and commonly mutated genes.

Only breakpoints with exact nucleotide position were included (N=639). Breakpoints determined with transcript-based assays that did not map to an exon or UTR were excluded. A. Integration breakpoints in relation to UCSC RefGenes, which include protein coding and non-protein coding genes. P-values are based on a test of proportions (Pearson’s χ² test). B. Distribution of minimum distances from intergenic integration breakpoints to UCSC RefGenes. C. Integration breakpoints in relation to 19 significantly mutated genes (ARID1A, ELF3, NFE2L2, CASP8, TGFBR2, PIK3CA, FBXW7, HLA.A, HLA.B, PTEN, KRAS, ERBB3, CBFB, TP53, MED1, ERBB2, STK11, MAPK1, EP300) from Ojesina et al. (17) and TCGA (19). P-value computed using Fisher’s exact test.