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Updated: Feb 1, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive
Ayslan C Brant1, Albert N Menezes2, Shayany P Felix3
1Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil; Post-Graduate Program in Genetics, Universidade Federal do Rio de Janeiro (UFRJ), Brazil.
Abstract:
Scarce data are available on the expression of papillomavirus genome and the frequency of alternatively spliced E6E7 mRNAs in invasive cervical cancer. We carried out a comprehensive characterization of HPV expression by RNA-Seq analysis in 22 invasive cervical cancer with HPV16 or HPV18, characterizing the presence of integrated/episomal viral DNA, the integration sites in human genome and the proportion of alternative splicing products of E6 and E7 genes. The expression patterns suggested the presence of episomal and/or integrated viral DNA, with integration detected in most tumors, frequently occurring within human genes in HPV18+ and in intergenic regions in HPV16+ tumors. Alternative splicing of E6E7 transcripts showed E6*I as the most frequent isoform for both viral types, followed by E6*II and E6/E7 (unspliced) transcripts in HPV16+, and by E6/E7 in HPV18+ tumors. Previously described E6*VI and E6*V transcript isoforms for HPV16, and E6*X for HPV18, were rare or not detected.
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