Sequencing HPV for biomarker discovery
Background
Human papillomavirus (HPV) is the etiological agent of cervical cancer and other anogenital malignancies and cancer of the head/neck. Typically, HPV infections are transient and clear within relatively short time, typically 1-2 years. Persistent HPV infections, however, may last for years and can lead to the progressive transformation into cancer. Why typically benign infections develop into malign states remains unknown.
More than 200 HPV types are characterized. Of these, fourteen carcinogenic HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 are responsible for nearly all HPV-induced cancers.
Read more about HPV research at the cancer registry here.
Methodology development
High throughput HPV genotyping by NGS technology may increase sensitivity and specificity in both clinical end epidemiological contexts. We have developed a labour and cost effective genotyping protocol with improved analytical sensitivity and specificity. In addition to identifying carcinogenic and other HPV types, our protocol allows the characterization of nucleotide diversity in the target gene relevant for the study of pathogen evolution and vaccine escape.
HPV genotyping for cancer risk prediction is most often based on the gene encoding the viral capsid; the yardstick for HPV taxonomy. However, causal links between viral variants and cancer development are to be found elsewhere in the viral genome. We have therefore developed a HPV whole genome sequencing (HPV-WGS) approach for ultimate resolution in ongoing searches for associations between viral variants and cancer development.
arch group has uncovered that HPV populations within a patient is much more variable than previously known. We wish to investigate this variability, how it changes through an infection within the same patients and if some variants have a higher likelihood of developing cancer. To achieve this we will whole genome sequence high-risk HPV types from thousands of clinical cervical samples and investigate the dynamic relationship between HPV mutations, length of infection and risk of cancer.
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Lagström S, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Sci Rep. 2019 Jan 24;9(1):524. doi: 10.1038/s41598-018-36669-6. PMID: 30679491; PMCID: PMC6345795.
Dube Mandishora RS, Gjøtterud KS, Lagström S, Stray-Pedersen B, Duri K, Chin'ombe N, Nygård M, Christiansen IK, Ambur OH, Chirenje MZ, Rounge TB. Intra-host sequence variability in human papillomavirus. Papillomavirus Res. 2018 Jun;5:180-191. doi: 10.1016/j.pvr.2018.04.006. Epub 2018 Apr 30. PMID: 29723682; PMCID: PMC6047465.
Dube Mandishora RS, Christiansen IK, Chin'ombe N, Duri K, Ngara B, Rounge TB, Meisal R, Ambur OH, Palefsky JM, Stray-Pedersen B, Chirenje ZM. Genotypic diversity of anogenital human papillomavirus in women attending cervical cancer screening in Harare, Zimbabwe. J Med Virol. 2017 Sep;89(9):1671-1677. doi: 10.1002/jmv.24825. Epub 2017 Jun 15. PMID: 28390142.
Meisal R, Rounge TB, Christiansen IK, Eieland AK, Worren MM, Molden TF, Kommedal Ø, Hovig E, Leegaard TM, Ambur OH. HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization. PLoS One. 2017 Jan 3;12(1):e0169074. doi: 10.1371/journal.pone.0169074. PMID: 28045981; PMCID: PMC5207713.
