Isabel Rodriguez from the National Cancer Institute, USA spoke at the Nanopore Community Meeting 2022 on “Analysis of viral and human oncogene expression in human papillomavirus-driven cancer.” Rodriguez shared that human pipillomavirus (HPV) is responsible for almost all cervical cancer cases, the fourth most common cancer worldwide. I also didn’t realize that the incidence is the highest in low and middle-income countries. HPV is also a preventable disease because there is a vaccine. HPV is a sexually transmitted infection with over 200 HPV types, according to what Rodriguez shared. Rodriguez explained that the use of Oxford Nanopore Technologies (ONT) sequencing, the ~7900 base pair circular DNA virus can be sequenced. Reads can be mapped in cell lines and also in humans. Rodriguez and colleagues examined a panel of 22 cell lines with diverse ancestry and HPV types. The methods used for tumor and direct cell lines were DNA and RNA extraction and sequencing on the GridION. Direct RNA reads, whole genome sequencing, and other methods were used. The virus integration sites were identified in each cell line. The team noticed that in some cell lines HPV can turn on or off genes. They noticed that for nearly all cell lines there was one gene that is highly expressed, suggesting there is one gene of oncogenic importance for all HPV lines studied. The research team also found cell lines without HPV gene expression. Comparing all cell lines with high-risk HPV, these rarely had RB1 or TP53 mutations. This work, Rodriguez concluded, established the largest collection of cervical cell lines. This session introduced the work needed to sequence cell lines in order to learn about HPV integration and oncogenesis.
