The increased incidence of non-melanoma skin cancer (NMSC) among immunosuppressed patients has suggested that infectious agent(s) may be involved. In previous studies, sequencing of skin lesions identified >400 different HPVs, including over 200 putatively novel types. Cervical cancer is known to be caused by HPV; however, some tumors appear to be HPV-negative by primer-based detection systems. As all established oncogenic infectious agents persist transcriptionally active in their host, we wanted to analyze tumors by RNA-sequencing to investigate if there is transcriptionally active HPV present.
NMSC biopsies from 2 patients, cervical cancer biopsies from 6 patients (including 4 apparently “HPV-negative” by primer-based detection) together with an HPV-positive cervical cancer cell line control (CaSki cell-line, known to contain around 600 copies of integrated HPV 16 DNA) were analyzed by RNA-sequencing.
RNA from HPV type 110 was detected in the 2 NMSC tumors (106 and 10 reads respectively). RNA from one or more HPV types (HPV types 119, 128, 129, 144, 147 and 16) were detected in 5 of 6 cervical cancer samples (including 3 “HPV-negative” cancers). HPV type 16 was also detected in the HPV-positive cell line control (18386 reads). The results implicate that the HPV genomes in the NMSC are actively transcribed. The transcribed HPV genes detected in the NMSC tumor with 106 reads were E6, E7, E1, E2/E4 and L2, whereas L1 was not detected. Only E7-transcription was detected in the NMSC tumor with 10 reads. Highly transcribed HPV genes in the CaSki cell line were E6, E7, L1 and L2, whereas E2, E4 and E5 showed very little transcription and E1 was not represented with a single read.
RNA metagenomic sequencing can be used to detect transcriptionally active HPV infection in NMSC and cervical cancer that have been “HPV-negative” by primer-based HPV-detection.