The Papillomavirus Episteme: a major update to the papillomavirus sequence database

Doorslaer, Koenraad Van; Li, Zhiwen; Xirasagar, Sandhya; Maes, Piet; Kaminsky, David A.; Liou, David; Sun, Qiang; Kaur, Ramandeep; Huyen, Yentram; McBride, Alison A.

doi:10.1093/nar/gkw879

Cited by 343 publications

(362 citation statements)

References 45 publications

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“…Libraries were then hybridized to the custom HPV capture probes for 72 h using the Roche target enrichment protocol following manufacture instructions and sequenced on one Illumina HiSeq 2500 lane (Illumina, San Diego, CA) using the paired end 150 bp sequencing mode. After sequencing, we aligned adaptor‐cleaned, QC‐passed, de‐duplicated, paired end reads to a custom human (GRCh37/hg19) plus HPV reference genome containing 143 alpha genus HPV types from the Papillomavirus Episteme using Burrows‐Wheeler Aligner (BWA) . Junction fragments were computationally identified using a combination of programs; Delly and SplazerS, both of which specify a combined read pair discordancy and split read analysis.…”

Section: Methodsmentioning

confidence: 99%

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV‐negative cervical cancer

Arsdale

Patterson

Maggi

et al. 2019

Genes Chromosomes & Cancer

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Cervical carcinogenesis, the second leading cause of cancer death in women worldwide, is caused by multiple types of human papillomaviruses (HPVs). To investigate a possible role for HPV in a cervical carcinoma that was HPV‐negative by PCR testing, we performed HPV DNA hybridization capture plus massively parallel sequencing. This detected a subgenomic, URR‐E6‐E7‐E1 segment of HPV70 DNA, a type not generally associated with cervical cancer, inserted in an intron of the B‐cell lymphoma/leukemia 11B (BCL11B) gene in the human genome. Long range DNA sequencing confirmed the virus and flanking BCL11B DNA structures including both insertion junctions. Global transcriptomic analysis detected multiple, alternatively spliced, HPV70‐BCL11B, fusion transcripts with fused open reading frames. The insertion and fusion transcripts were present in an intraepithelial precursor phase of tumorigenesis. These results suggest oncogenicity of HPV70, identify novel BCL11B variants with potential oncogenic implications, and underscore the advantages of thorough genomic analyses to elucidate insights into HPV‐associated tumorigenesis.

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Section: Methodsmentioning

confidence: 99%

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV‐negative cervical cancer

Arsdale

Patterson

Maggi

et al. 2019

Genes Chromosomes & Cancer

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“…To date, over 200 human papillomavirus (HPV) types have been isolated and fully characterized (https://pave.niaid.nih.gov) [1]. Based on the identity of the L1 major capsid gene sequence, HPVs are classified into 5 genera (Alpha [α]-, Beta [β]-, Gamma [γ]-, Mu [µ]-, and Nu [ν]-HPVs), which are further subdivided into species designated by a number.…”

Section: Structure and Classification Of Human Papillomavirusmentioning

confidence: 99%

Beta Human Papillomavirus and Associated Diseases

et al. 2019

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The cutaneous human papillomavirus (HPV), mostly from β- and γ-HPV genus, is ubiquitously distributed throughout the human body and may be part of the commensal flora. The association of β-HPVs and cutaneous squamous cell carcinoma (cSCC) development was initially reported in patients with the rare genetic disorder Epidermodysplasia verruciformis. Likewise, immunosuppressed organ transplant recipients have an increased susceptibility to β-HPV infections in the skin as well as to cSCC development. Although ultraviolet radiation (UVR) is the main risk factor of cSCC, experimental data points toward β-HPVs as co-carcinogens, which appear to be required solely at early stages of skin carcinogenesis by facilitating the accumulation of UVR-induced DNA mutations. Several epidemiological studies relying on different biomarkers of β-HPV infections have also been conducted in immunocompetent individuals to access their association with cSCC development. Additionally, in vivo and in vitro studies are presenting cumulative evidence that E6 and E7 proteins from specific β-HPVs exhibit transforming activities and may collaborate with different environmental factors in promoting carcinogenesis. Nevertheless, further research is crucial to better understand the pathological implications of the broad distribution of these HPVs.

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“…HPV sequences were downloaded from pave.niaid.nih.gov (Van Doorslaer et al, 2017). Length-scaled transcript per million (TPM) values for each transcript were M A N U S C R I P T…”

Section: Bioinformatics Processingmentioning

confidence: 99%

Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis

Lukowski

Tuong

Nöske

et al. 2018

Journal of Investigative Dermatology

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Persistent human papillomavirus (HPV) infection is responsible for at least 5% of human malignancies. Most HPV-associated cancers are initiated by the HPV16 genotype, as confirmed by detection of integrated HPV DNA in cells of oral and anogenital epithelial cancers. However, single-cell RNA-sequencing (scRNA-seq) may enable prediction of HPV involvement in carcinogenesis at other sites. We conducted scRNA-seq on keratinocytes from a mouse transgenic for the E7 gene of HPV16, and showed sensitive and specific detection of HPV16-E7 mRNA, predominantly in basal keratinocytes. We showed that increased E7 mRNA copy number per cell was associated with increased expression of E7 induced genes. This technique enhances detection of active viral transcription in solid tissue and may clarify possible linkage of HPV infection to development of squamous cell carcinoma.

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The Papillomavirus Episteme: a major update to the papillomavirus sequence database

Cited by 343 publications

References 45 publications

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV‐negative cervical cancer

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV‐negative cervical cancer

Beta Human Papillomavirus and Associated Diseases

Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis

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