Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma

Abstract

β-Human papillomavirus (β-HPV) DNA is present in some cutaneous squamous cell carcinomas (cuSCCs), but no mechanism of carcinogenesis has been determined. We used ultra-high-throughput sequencing of the cancer transcriptome to assess whether papillomavirus transcripts are present in these cancers. In all, 67 cuSCC samples were assayed for β-HPV DNA by PCR, and viral loads were measured with type-specific quantitative PCR. A total of 31 SCCs were selected for whole transcriptome sequencing. Transcriptome libraries were prepared in parallel from the HPV18-positive HeLa cervical cancer cell line and HPV16-positive primary cervical and periungual SCCs. Of the tumors, 30% (20/67) were positive for β-HPV DNA, but there was no difference in β-HPV viral load between tumor and normal tissue (P=0.310). Immunosuppression and age were significantly associated with higher viral load (P=0.016 for immunosuppression; P=0.0004 for age). Transcriptome sequencing failed to identify papillomavirus expression in any of the skin tumors. In contrast, HPV16 and HPV18 mRNA transcripts were readily identified in primary cervical and periungual cancers and HeLa cells. These data demonstrate that papillomavirus mRNA expression is not a factor in the maintenance of cuSCCs.

Figure 1. Comparison of HPV DNA viral load and abundance of HPV-derived transcripts for established HPV-driven cancers versus normal skin and cuSCCs

(A) HPV DNA viral loads determined by type-specific qPCR. For each sample with multiple type infection, the sum of the type-specific viral loads is shown (for details, see Table 2.) (B) Abundance of HPV-derived transcripts determined by mRNA-seq. Reads were filtered to remove host-derived and low-complexity sequence prior to viral mapping (see methods), and HPV counts are each presented as a percentage of their total dataset. The most frequently matched HPV type for the HeLa, periungual SCC, and cervical SCC samples is indicated. Cervical cancer is presented as the union of 2 technical replicate datasets. (C) Congruence between HPV genomic load (blue; presented as in panel A) and abundance of HPV-derived transcripts (red; presented as in panel B) among those control samples from which both types of data were collected.