Identification of DNA-protein interactions and enhancer activity at the 5' end of the upstream regulatory region in human papillomavirus type 11

We have examined the 5' end of the noncoding region of the genome of a human papillomavirus, HPV-11, for regulatory elements using permissive host cells. This region of unknown function in the upstream regulatory region (URR) is known to have unusual DNA structure and frequently contains rearrangements which are associated with some more virulent isolates. This 5' 269-bp fragment was found to exhibit both specific DNA-protein binding using laryngeal papilloma protein extracts and enhancer activity in normal and papillomatous primary laryngeal cells. The viral DNA flanks the L1 open reading frame and does not contain the viral E2 binding site. Three distinct protein binding sites are contained in a 50-bp region of the fragment. This fragment, as a whole, functions as an enhancer in primary laryngeal and papilloma cells when ligated to the SV40 promoter and SV40 T-antigen gene. We conclude that this part of the noncoding region of the papillomaviruses has elements characteristic of regulatory elements in cells permissive for infection by these viruses.     

Human papillomavirus type 13 and pygmy chimpanzee papillomavirus type 1: comparison of the genome organizations

Human papillomavirus type 13(HPV-13) is associated with oral focal epithelial hyperplasia (FEH) in humans. A recent epidemic of a FEH-like disease in a pygmy chimpanzee (Pan paniscus) colony allowed us to clone a novel papillomavirus genome. To assess the homology between HPV-13 and the pygmy chimpanzee papillomavirus type 1 (PCPV-1), the complete nucleotide sequences of both FEH-related viruses were determined. In both viruses, all eight major open reading frames were located on one strand and the genomic organization was similar to that of other mucosal papillomaviruses. The genomes of PCPV-1 and HPV-13 showed extensive overall sequence homology (85%). They could be classified, using phylogenetic analysis, together with HPV types 6, 11, 43, and 44 in a group associated with benign orogenital lesions. These data indicate that two phylogenetically related papillomaviruses can elicit similar pathology in different primate host species, reflecting viral genomic similarities.     

An epidermotropic canine papillomavirus with malignant potential contains an E5 gene and establishes a unique genus

A novel canine papillomavirus, CfPV-2, was cloned from a footpad lesion of a golden retriever. Unlike the known canine oral papillomavirus (COPV), which has a double-stranded DNA genome size of 8607 bps, the genome of CfPV-2 is 8101 bps. Some of this size difference is due to an abbreviated early-late region (ELR), which is 1200 bps shorter than that of COPV. However, CfPV-2 has other differences from COPV, including the presence of an E5 ORF between the E2 gene and the ELR and an enlarged E4 ORF (one of the largest PV E4 open reading frames). The genome of CfPV-2 shares low homology with all the other papillomaviruses and, even in the most highly conserved ORF of L1, the nucleotide sequence shares only 57% homology with COPV. Due to this highly divergent DNA sequence, CfPV-2 establishes a new PV genus, with its closest phylogenetic relatives being amongst the Xi and Gamma genuses. CfPV-2 also has unique biological features; it induces papillomas on footpads and interdigital regions which, if infection is persistent, can progress to highly metastatic squamous cell carcinoma. CfPV-2 does not induce oral papillomas in immunocompetent animals and antibodies generated against COPV and CfPV-2 are type-specific. The availability of a new canine papillomavirus with differing genetic and biological properties now makes it possible to study type-specific host immune responses, tissue tropism and the comparative analysis of viral gene functions in the dog.     

Detection of HPV-2 and identification of novel mutations by whole genome sequencing from biopsies of two patients with multiple cutaneous horns.

BACKGROUND: Human papillomavirus-2 (HPV-2) is generally associated with common warts. The association of cutaneous horns with HPV-2 infection has never been reported. OBJECTIVES: To identify the papillomavirus (PV) type(s) involved in cutaneous horns and analysis the genomes of these viruses. STUDY DESIGN: We screened biopsies from two patients with multiple cutaneous horns using PV type-specific PCR assays, and sequenced the whole genomes of the viruses by a PCR-by-PCR strategy. Sequence comparison with the reference genome and its closely related PVs in the same phylogenetic group was performed to identify sequence variation across the genome(s) of newly detected PV(s). RESULTS: Two strains of HPV-2 were identified from the biopsies of two patients respectively. No double or multiple infections were detected. Novel mutations were found in the HPV-2 genome, located both in the coding and non-coding regions. Amino acid changes occurred only in E1 and E7 ORFs. The two strains also shared several mutations at the same positions. CONCLUSIONS: Each patient was infected with a single strain of HPV-2 that developed unique mutations; HPV-2 may play a role in the onset and development of cutaneous horns; amino acid changes in functionally significant viral proteins may confer differential pathogenic risks.     

Characterization of cDNAs of spliced HPV-11 E2 mRNA and other HPV mRNAs recovered via retrovirus-mediated gene transfer

Human papillomaviruses (HPVs) are associated with hyperproliferations of cutaneous or mucosal epithelium. These viruses cannot be propagated in any cell culture system. Because cloning cDNA copies of HPV mRNAs recovered from human lesions has met with only very limited success, the characterization of HPV mRNAs has been problematic. Using the Moloney murine leukemia virus vector system (C.L. Cepko, B.E. Roberts, and R.C. Mulligan, 1984, Cell 37, 1053-1062), we have recovered cDNAs of spliced E2 mRNAs of human papillomavirus type 11 and additional mRNAs of type 11 and type 18 and determined the utilization of open reading frames (ORFs) in the DNA sequences. The recovery of cDNA copies of messages with splice sites identical to those previously described strongly suggests that the newly characterized splice donors and acceptors are also authentic. The HPV-11 E2 cDNA contains the intact E6 and E7 ORFs and the beginning of the E1 ORF in the first exon, which is then spliced from nt 847 to the second exon at nt 2622, 100 nucleotides upstream from the initiation codon for the E2 ORF. The initiation codon in the E1 ORF is followed by four additional in-frame AUG triplets and an in-frame termination codon positioned 30 nucleotides upstream from the initiation codon for the E2 protein. The authenticity of this putative E2 cDNA was shown by its ability to provide enhancer transactivating activity in chloramphenicol acetyltransferase (CAT) assays in several cell lines. A mutation in the genomic DNA at this splice acceptor site eliminates its activity, demonstrating that the splice is essential for the expression of the E2 protein. We conclude that the translation of the HPV-11 E2 protein requires internal initiation.     

Intraepithelial DNA immunisation with a plasmid encoding a codon optimised COPV E1 gene sequence,but not the wild-type gene sequence completely protects against mucosal challenge with infectious COPV in beagles

DNA plasmids encoding the open reading frames of canine oral papillomavirus (COPV) nonstructural early genes E1, E2, or E7 protein were delivered into both oral mucosal and cutaneous epithelial sites in beagle dogs using particle-mediated immunotherapeutic delivery (PMID) technology. Control dogs were vaccinated with plasmid encoding either hepatitis B virus surface antigen (HBVs) or COPV L1. Using a prophylactic immunisation protocol, a priming dose of plasmid DNA was followed by a booster dose 6 weeks later. Four weeks after boost, all dogs were challenged with infectious COPV particles. Following viral challenge, as shown previously (M. A. Stanley et al., 2001, Vaccine 19, 2783-2792), mucosal papillomas developed in the negative-control HBVs vaccinated dogs, but all animals in the COPV L1 group were fully protected from disease development. In the early gene-vaccinated groups five of six in the E1-vaccinated dogs, two of six in E2-vaccinated dogs, and three of six in the E7-vaccinated beagles developed oral papillomas. Compared to the HBVs negative-control group the oral papillomas that did develop in the early-gene vaccinated beagles were significantly smaller, shorter in duration, and fewer in number. Taken together the disease burden was markedly reduced and this was statistically significant. In a second experiment one group of animals was vaccinated with plasmid encoding the wild-type COPV E1 gene, and a separate group was vaccinated with plasmid encoding a synthetic codon-optimised COPV E1 gene sequence. None of the codon-optimised E1-vaccinated animals developed papillomas at any challenge site. However, all animals vaccinated with wild-type E1 had papillomas. These data suggest that immunisation by PMID with papillomavirus early genes can significantly impact upon subsequent disease development and that full protection can be achieved using improved vectors encoding codon-optimised gene sequences perhaps emphasizing the importance of antigen load in the generation of protective responses to papillomavirus proteins.     

Therapeutic immunisation with COPV early genes by epithelial DNA delivery

Following challenge with COPV (canine oral papillomavirus), DNA plasmids encoding COPV L1, E1 or E2 protein were delivered into oral mucosal and cutaneous sites in beagles using particle-mediated immunotherapeutic delivery (PMID). Two weeks post-challenge, a priming dose of 8 microg DNA was delivered followed by a booster dose after a further two weeks. A group of control dogs were vaccinated using plasmid DNA encoding Hepatitis B virus surface (HBVs) gene. All of the control animals developed warts at the vast majority of sites (94%). All of the animals given wild type L1, E1, or E2 developed warts at most sites (88%, 75%, and 88%, respectively). The animals given codon optimised E2 however, were protected from wart growth with only one tiny lesion seen on a single animal that persisted for only a few days. The E1 codon optimised group was also significantly protected with a far lower number of smaller warts (48%) that persisted for a shorter duration. These data suggest that therapeutic immunisation by PMID with papillomavirus early genes is effective and emphasizes the importance of antigen load in the generation of protective responses to papillomavirus proteins.     

A subtype of human papillomavirus 5 (HPV-5b) and its subgenomic segment amplified in a carcinoma: nucleotide sequences and genomic organizations.

A subtype of human papillomavirus 5 (HPV-5b) is closely associated with carcinomas in the disease epidermodysplasia verruciformis (EV). The complete genome was cloned from virus particles in benign lesions of a patient with EV and sequenced: it was 7779 nucleotides long and consisted of six open reading frames (ORFs) (E6, E7, E1, E2, E4, and E5) in the early region, three ORFs (L2, L3, and L1) in the late region, and a noncoding region, all existing on one DNA strand. The 40% segment of the HPV-5b genome specifically amplified in carcinomas was cloned from a primary carcinoma of the same EV patient and sequenced: it was 3143 nucleotides long and corresponded to a segment of the original HPV-5b genome containing the entire sequences of E6, E7, and the noncoding region and portions of E1 and L1. Compared to the whole genomic DNA, no mutations were detected in this probable malignancy-associated viral subgenomic segment cloned from carcinoma. These results suggest that amplification of the viral segment containing E6, E7, and the noncoding region may play a role in the malignant conversion of HPV-5b-infected benign lesions and that mutations in these genes or regions are not necessarily required.     

Protection of beagle dogs from mucosal challenge with canine oral papillomavirus by immunization with recombinant adenoviruses expressing codon-optimized early genes

Replication-deficient adenoviral (rAd5) vaccines containing codon-optimized E1, E2, E4, and E7 genes of canine oral papillomavirus (COPV) were tested singly or in combination to determine which vaccines could protect against mucosal challenge with COPV. In three studies, groups of 4-6 beagle dogs were immunized subcutaneously (s.c.) with 10(11) rAd5 at 8-10 weeks and 4-6 weeks prior to challenge with infectious COPV particles at multiple oral mucosal sites. Control dogs were immunized with equivalent doses of rAd5 expressing human papillomavirus (HPV) type 16 L1 (rAd5-HPV-16 L1). In the first study, complete protection from COPV-induced papillomas was achieved by immunization with rAd5 vaccine combinations expressing either E1 + E2 or E1 + E2 + E4 + E7; whereas two of six dogs immunized with rAd5-E4 + rAd5-E7 and six of six rAd5-HPV16-L1-immunized control dogs developed oral papillomas. In two subsequent studies, rAd5-E1 and rAd5-E2 vaccines were tested singly or in combination to assess levels of protective immunity to COPV challenge. Subcutaneous immunization with either one or two doses of rAd5 expressing the COPV E1 and E2 genes could protect > 90% of challenged dogs from wart formation. In contrast, all eight dogs immunized with rAd5-HPV-16 L1 developed papillomas at multiple sites. Protection was accompanied by significant IFN-gamma responses to COPV E1 and E2 peptides. Partial protection was conferred by two immunizations with either rAd5-E1 (6 of 9 protected) or rAd5-E2 (8 of 9 protected). These data indicate that rAd5 expressing papillomavirus E1 and E2 proteins can induce strong protective responses even in outbred populations under practical immunization conditions.     

Conservation of HPV-16 E6/E7 ORF sequences in a cervical carcinoma.

A cervical carcinoma that contained human papillomavirus (HPV)-16 homologous DNA was analyzed. Each tumor cell genome contained a single, incomplete copy of HPV-16 DNA. The E6 and E7 open reading frames (ORFs) were completely conserved relative to other published HPV-16 sequences. Much of the non-coding region (NCR) was free of base changes, including complete conservation of several regulatory elements. Multiple mutations were identified in the remaining integrated HPV-16 DNA, which was composed of parts of the L1 and E1 ORFs. The extraordinary conservation of the E6/E7 DNA sequence, as compared with other regions of the integrated HPV-16 DNA, supports the role of E6/E7 in tumorigenesis.     

Regression of canine oral papillomas is associated with infiltration of CD4+ and CD8+ lymphocytes

Canine oral papillomavirus (COPV) infection is used in vaccine development against mucosal papillomaviruses. The predictable, spontaneous regression of the papillomas makes this an attractive system for analysis of cellular immunity. Immunohistochemical analysis of the timing and phenotype of immune cell infiltration revealed a marked influx of leukocytes during wart regression, including abundant CD4+ and CD8+ cells, with CD4+ cells being most numerous. Comparison of these findings, and those of immunohistochemistry using TCRalphabeta-, TCRgammadelta-, CD1a-, CD1c-, CD11a-, CD11b-, CD11c-, CD18-, CD21-, and CD49d-specific monoclonal antibodies, with previously published work in the human, ox, and rabbit models revealed important differences between these systems. Unlike bovine papillomavirus lesions, those of COPV do not have a significant gamma/delta T-cell infiltrate. Furthermore, COPV lesions had numerous CD4+ cells, unlike cottontail rabbit papillomavirus lesions. The lymphocyte infiltrate in the dog resembled that in human papillomavirus lesions, indicating that COPV is an appropriate model for human papillomavirus immunity.     

Nucleotide sequence of human papillomavirus (HPV) type 41: an unusual HPV type without a typical E2 binding site consensus sequence.

The complete nucleotide sequence of human papillomavirus type 41 (HPV-41) has been determined. HPV-41 was originally isolated from a facial wart, but its DNA has subsequently been detected in some skin carcinomas and premalignant keratoses (Grimmel et al., Int. J. Cancer, 1988, 41, 5-9; de Villiers, Grimmel and Neumann, unpublished results). The analysis of the cloned HPV-41 nucleic acid reveals that its genome organisation is characteristic as for other papillomavirus types. Yet, the analysis indicates at the same time that this virus is most distantly related to all other types of human-pathogenic papillomaviruses sequenced thus far and appears to identify HPV-41 as the first member of a new subgroup of HPV. The overall nucleotide homology to other sequenced HPV types is below 50%. The closest other HPV type is represented by HPV-18, sharing 49% identical nucleotides. The typical E2 binding sequence ACCN6GGT, found in all papillomaviruses analyzed to date, does not occur in the URR of the HPV-41 genome. Modified E2 binding sequences, as described for BPV 1 (Li et al., Genes Dev. 1989, 3, 510-526), are located in the domain proximal to the E6 ORF. These are ACCN6GTT, AACN6GGT and the two perfect palindromic sequences AACGAATTCGTT.     

Antibodies to human papillomavirus type-16 in human sera as revealed by the use of prokaryotically expressed viral gene products.

Open reading frames of human papillomaviruses were expressed in Escherichia coli as beta-galactosidase fusion proteins. These bacterially derived papillomaviral gene products were used to examine sera from 67 women (63 healthy subjects, 4 patients with genital carcinoma) for antibodies to papillomavirus type-16 antigens (E1, E2, E4, E5, E6, E7, L1, L2) and the L2 proteins of HPV-6b and HPV-18 by Western-blot analysis. The serologic data were compared with cytological findings classified according to Papanicolaou and with nucleic acid hybridization data from cervical smears of the same individuals. Twenty-three of the normal individuals showed antibodies exclusively directed against L2 gene products; whereas in the sera from the four genital cancer patients, antibodies to the early gene products E4 and/or E7 could be detected. In one case these antibodies were found to be combined with antibodies to L2 of HPV-16 and -18 and in another case with those to E1 and E2 of HPV-16. In none of the sera examined could antibodies to L1, E5 or E6 be identified. Three of the antibody positive normal women were found to be also positive for HPV-16/18 DNA, while all of the 40 seronegative women were HPV-16/18 DNA negative. These data indicate that serology may be a valuable means to study the epidemiology of genital human papillomavirus infection.     

DNA sequence of the HPV-16 E5 ORF and the structural conservation of its encoded protein

Infection of cervical epithelium by human papillomavirus type 16 (HPV-16) appears to be closely associated with the development of cervical dysplasia and carcinoma. By inference from genetic and biochemical studies of the bovine papillomavirus, the E5 ORF of the human papillomaviruses is anticipated to encode a "transforming" protein. In an effort to compare the E5 ORF of HPV-16 with other human papillomaviruses and bovine papillomavirus, we sequenced this region from a new isolate of HPV-16 which was derived from extrachromosomal viral DNA within a premalignant cervical lesion (cervical intraepithelial neoplasia, grade III, or CIN III). In addition, we also sequenced the original isolate of HPV-16 (derived from integrated viral DNA by Durst et al. [Proc. Natl. Acad. Sci. USA 80, 3812-3815 (1983)] and sequenced by Seedorf et al. [Virology 145, 181-185 (1985)]. Both HPV-16 isolates contained an additional nucleotide (T) at bp 3906. This nucleotide addition caused a frameshift in the E5 ORF such that it now contains an initiation codon at bp 3849; the frameshift also alters the predicted E5 NH2 terminus but retains the original COOH half of the protein. E5 proteins encoded by several HPVs which infect the genital region (e.g., types 6, 11, 16, 18, 33) exhibit a conserved trimodal hydrophobic structure, but not a conserved amino acid sequence.     

Cloning and molecular characterization of an oral papillomavirus of domestic rabbits

DNA obtained from New Zealand white rabbit oral papillomas was analyzed for the presence of papillomavirus DNA. The viral genome was cloned as three separate subclones, which were each mapped and oriented with respect to one another. Comparisons with other papillomavirus DNAs by Southern blot hybridization under various conditions of stringency revealed a strong area of conservation among the DNAs of the rabbit oral papillomavirus (ROPV) and CRPV, HPV-1a, HPV-16, and BPV-5, but not with 12 other papillomavirus DNAs. This region, which spans the junction of the presumptive E2 and L2 open reading frames of ROPV, was sequenced and compared to other known papillomavirus sequences. These analyses revealed a high degree of DNA homology in the C-terminal E2 and N-terminal L2 regions between ROPV and both HPV-1a and CRPV. The homology with HPV-16 was limited to the L2 open reading frame. The predicted amino acid sequences of each region were also compared and bore out the same conclusions. In addition, no E5 open reading frame was detected in the ROPV sequence.     

Genomic characterisation of Felis catus papillomavirus 4, a novel papillomavirus detected in the oral cavity of a domestic cat

Three papillomaviruses (PVs) from the domestic cat have been fully sequenced so far including Felis domesticus PV-1 (FdPV-1), FdPV-2, and a recently described Felis catus PV-3 (FcaPV-4). In the current article, we describe the full genomic sequence of a fourth PV from the domestic cat. This PV was amplified from the oral cavity of a cat with severe gingivitis. However, the aetiological involvement of FcaPV-4 in development of lesions observed in this cat remains uncertain. The complete genome of the novel virus comprised 7,616 bp and was predicted to encode five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) genes, with the organisation typical for PVs. The L1 showed 65.1 % nucleotide sequence identity to L1 of FcaPV-3 and approximately 60 % identity to L1 of canine tau-papillomaviruses CPV-2 and CPV-7. The novel virus clustered with FcaPV-3, CPV-2 and CPV-7 on a phylogenetic tree constructed from a concatenated alignment of 3,013 bp from E1, E2, L1 and L2. Based on the genomic and phylogenetic data, we propose that the novel virus is classified as a distinct species within the same genus as FcaPV-3. We also propose that both viruses are classified within the genus Taupapillomavirus, although this classification may need to be re-visited after more tau-PV genomes become available.