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a Vasiljevi
Department of Laboratory Medicine, Division of Medical Microbiology, Lund University, University Hospital, Malmö, Sweden
Correspondence
Ola Forslund
Ola.forslund{at}med.lu.se
| ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers for the sequences of isolates HPV-107 (FA85), HPV-110 (FA5), HPV-111 (FA51) and FA75[KI88-03] determined in this work are EF422221, EU410348, EU410349 and EU410347, respectively.
| INTRODUCTION |
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Non-melanoma skin cancers (NMSCs), comprising basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), are the most prevalent malignancies in the Caucasian population (Oberyszyn, 2008
; Stern, 1999
). SCC accounts for up to 20 % of all deaths from skin cancer, whereas BCC has a relatively good prognosis (Ramos et al., 2004
). Epidemiological studies have established a causal association between UV radiation and NMSC, as well as that fair skin and the immune status of the host are important risk factors (Boukamp, 2005
; Preston & Stern, 1992
; Reichrath, 2006
). In addition, as cutaneous HPV infection is more prevalent at sun-exposed sites and, as the viral proteins affect the apoptotic pathway of the cell, infection is proposed to be a co-factor to UV irradiation in the development of NMSC (Forslund et al., 2007
; Jackson et al., 2000
).
NMSCs are common on sun-exposed sites in patients with the rare inherited genetic disease epidermodysplasia verruciformis (Jablonska & Majewski, 1994
). These patients are highly susceptible to HPV infections (Kremsdorf et al., 1984
; Orth et al., 1978
), predominantly HPV-5 and -8, which belong to the genus Betapapillomavirus (Pfister, 2003
; Pfister & Ter Schegget, 1997
). These viruses are detectable both in skin cancers and in specimens of healthy skin from the general population (Antonsson et al., 2003a
; Astori et al., 1998
; Harwood & Proby, 2002
), but a recent study has found that betapapillomaviruses of species 1 tend to be associated with benign skin lesions, whilst betapapillomaviruses of species 2 are more commonly found in skin cancers (Forslund et al., 2007
). Four viruses of species 2 that were found in SCC samples in this recent study were the isolates FA5, FA51, FA7 and FA85, which had previously also been detected in samples from healthy skin (Antonsson et al., 2003a
, b
; Forslund et al., 1999
).
The fact that many putative HPVs remain uncharacterized significantly impairs our ability to study the biological significance of the cutaneous viruses in more detail. Therefore, we characterized the four betapapillomavirus isolates previously found in skin cancers (Forslund et al., 2007
) and investigated whether these viruses were medically significant by assaying their prevalence and viral load among patients with skin lesions.
| METHODS |
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Sequence analysis.
The cloned DNA of HPV-107 was used as template in primer-walking sequencing reactions. Clones containing the complete genomes of HPV-110 and -111 and FA75[KI88-03] were used in an EZ-Tn <TET-1> (Epicentre Biotechnologies) insertion reaction according to the kit manual. Briefly, 10 µl mix containing 0.2 µg plasmid, 0.025 pmol EZ-Tn5 <TET-1> transposon, 1 µl buffer and 1 µl transposase was incubated for 2 h at 37 °C. One microlitre of stop solution was added and the mix was incubated at 70 °C for 10 min. Two microlitres of the mix was used for transformation of One Shot TOP10 chemically competent Escherichia coli (Invitrogen). At least 30 colonies were picked and the plasmids sequenced using transposon-specific primers. Sequencing was carried out using an ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems) and analysed on a 3730 automated sequencer (Applied Biosystems). The sequences were overlapped using BioEdit version 7.0.1 (Hall, 1999
). The ORF of each protein was identified using BioEdit and proteins were compared with available amino acid sequences in GenBank using the BLAST server.
The clones and corresponding complete sequences were submitted to the International Reference Centre for Papillomaviruses at the German Cancer Research Centre, Heidelberg, Germany, where they were labelled: HPV-107 (FA85) (GenBank accession no. EF422221 [GenBank] ), HPV-110 (FA5) (GenBank accession no. EU410348 [GenBank] ) and HPV-111 (FA51) (GenBank accession no. EU410349 [GenBank] ). The sequence of FA75[KI88-03] was identical to an unpublished HPV type previously submitted to the Reference Center and was therefore deposited as isolate FA75[KI88-03] (GenBank accession no. EU410347 [GenBank] ).
Phylogenetic analysis.
Phylogenetic analysis was based on an L1 ORF alignment made using the CLUSTAL W multiple alignment in BioEdit of HPV-107, -110 and -111 and FA75[KI88-03] and all other betapapillomavirus types from species 2, as well as HPV-5, -49, -92 and -96. A neighbour-joining tree was generated using MEGA version 4 (Tamura et al., 2007
) using 500 bootstrap replications and the Kimura two-parameter model.
Patient panel.
Stripped (Forslund et al., 2004
) lesions and healthy skin biopsies from patients with the diagnoses AK (n=50), seborrhoeic keratosis (SK) (n=45), BCC (n=118) and SCC (n=50) were collected from 263 immunocompetent patients attending dermatology clinics in Sweden. Healthy skin biopsies were collected 10–15 cm from the lesion or proximally to the ear, depending on the location of the lesion. The samples were selected from a larger series of 489 patients (Forslund et al., 2007
) and all four skin-lesion groups were matched for age and sex. All four groups had a mean age of 76±1 years. The distribution between men and women was 56±1 and 44±1 %, respectively, within each group.
The DNA from each biopsy was extracted using a phenol-free method (Forslund et al., 1999
). To ensure the quality of the extracted DNA, all samples were checked for the presence of the β-globin gene (Hazard et al., 2006
). Swab samples from the tops of the lesions (before stripping) were collected in 1 ml saline (Forslund et al., 2004
).
Real-time PCR.
Primers and probes for quantitative PCR (Table 1
) were designed in the L1 region, using Primer Express version 2.0 (Applied Biosystems).
Calculations of virus copy numbers for standard curves were based on spectrophotometric measurement of a plasmid containing the L1 ORF of HPV-107 and plasmids containing the FA fragments (the FA fragment constitutes about 30 % of the L1 ORF and is generated by primers FAP59 and FAP64; Forslund et al., 1999
) of HPV-110 and -111 and FA75[KI88-03]. For the establishment of standard curves, serial logarithmic dilutions covering a range of 6 logs (from 105 copies to one copy per reaction) were employed using a solution of human placental DNA (10 ng µl–1) as diluent.
Primers and probes were tested for cross-hybridization with closely related types within species 2 of the genus Betapapillomavirus. The 25 µl PCR mixture contained 3.5 mM MgCl2 (Applied Biosystems), 1x Reaction buffer (Applied Biosystems), 0.2 mM each dNTP (Roche Diagnostics), 0.2 µM each primer (Cybergene; Table 1
), 0.04 µM Taqman probe (Cybergene; Table 1
), 0.625 U AmpliTaq Gold polymerase (Applied Biosystems) and 2.5 µl sample. Real-time PCR was carried out in a GeneAmp 5700 SDS (Applied Biosystems), using the following parameters: 2 min at 50 °C and 10 min at 95 °C, followed by 40 cycles of 15 s at 95 °C and 1 min at 60 °C. Human placental DNA (10 ng µl–1) and water (both from Sigma) were used as non-template controls in each run. The same parameters were used for the patient samples, which were diluted 1 : 2 in TE buffer before analysis. All samples positive for HPV-107, -110 or -111 or FA75[KI88-03] in the real-time PCRs were verified in triplicate using undiluted samples. The coefficient of variation (CV) for each sample was based on these verification runs. In addition, these amplicons were cloned and sequenced.
In order to determine the viral load, the number of cells in each sample was determined by quantification of the β-globin gene as described previously (Hazard et al., 2006
). For all lesion biopsies found to be positive for any of the novel types, a swab sample taken from the top of the lesion before stripping was also analysed.
Statistical analysis.
Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated by comparing proportions using StatCalc within Epi Info version 3.4.3 (CDC, Atlanta, GA, USA). A two-sided Mann–Whitney U-test was used to test differences in viral load (SPSS version 16.0).
Study approval.
This study was approved by the ethics committees of Karolinska Institute and Lund University, Sweden. All patients gave informed consent.
| RESULTS |
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Real-time PCR
In order to verify the specificity of primers and probes, plasmid titration series ranging from 105 copies down to one copy per sample of plasmids containing HPV-9, -15, -17, -22, -23, -37 and -38 were all tested in real-time PCRs using the specific primers and probes for HPV-107, -110 and -111 and FA75[KI88-03]. No cross-reactivity was detected. Plasmid titration series with HPV-107, -110 and -111 and FA75[KI88-03] showed that the PCR assays had sensitivities of one viral copy per reaction (data not shown).
The presence and quantity of each HPV type are described in Table 4
. A total of 19 patients (7.2 %) were positive for one or more of the investigated types in their healthy or lesion biopsy. Seventeen patients (6.5 %) harboured at least one HPV type in the lesion, whereas seven patients (2.7 %) harboured HPV in healthy skin (Table 4
) (OR 2.53, 95 % CI 0.97–6.84). Viral load was investigated in biopsies from the HPV-positive lesions and corresponding swabs from the top of lesions, as well as in biopsies from HPV-positive healthy skin. Twelve out of 20 swab samples were HPV positive for the same virus as the lesion, and overall the viral loads were higher on top of the lesions (P<0.001) (Table 4
). Furthermore, the viral loads did not differ between healthy skin and tumour biopsies (P=0.42). Amongst the lesions, the highest viral load was detected in an SK with three copies per cell, and the viral loads were significantly higher than in AK lesions (SK vs AK: P=0.03; SK vs BCC: P=0.10; SK vs SCC: P=0.25). No other differences in viral load were detected (AK vs BCC: P=0.72; AK vs SCC: P=0.41; BCC vs SCC: P=0.80).
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Considering the four viruses together, they were most frequently detected in AK lesions (6/50), which was significantly more often than in all healthy skin samples (7/263) (OR 5.0, 95 % CI 1.4–17.5). The prevalences in the other lesions were not significantly different from the prevalence in healthy skin: SK: OR 1.7, 95 % CI 0.3–8.5; BCC: OR 1.6, 95 % CI 0.4–5.8; SCC: OR 2.3, 95 % CI 0.5–10.5.
| DISCUSSION |
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The viral loads in the HPV-positive patients were low, ranging from one viral copy per
35 000 cells to three copies per cell, a trend also observed by other groups (Bens et al., 1998
; Meyer et al., 2001
; Weissenborn et al., 2005
). We found that SK lesions harboured higher amounts of virus than AK; however, due to the small number of observations, this finding requires further investigation. Also, when only minute amounts of virus are present, the possibility that results may reflect contamination rather than actual infection needs to be considered, in particular with regard to the remarkable viral loads of cutaneous HPV-88 described recently (Kullander et al., 2008
). We found that many HPV-positive lesions contained higher amounts of virus on top of the lesion than in the lesion itself, in line with previous reports (Forslund et al., 2004
). Surprisingly, in our study we also found lesions that contained significant amounts of virus even though HPV DNA was not detected on top of the lesion. Speculatively, the lack of detectable superficial HPV DNA might be due to an impaired productive life cycle in these lesions. In addition, a possible reason for the absence of HPV in the SK samples from the top of the lesion could be that the irregular anatomy of this lesion type makes it difficult to swab its entire surface, consequently leading to failure in detection.
In conclusion, the characterization of HPV-107, HPV-110, HPV-111 and HPV isolate FA75[KI88-03] expands our knowledge of the heterogeneity of members of species 2 of the genus Betapapillomavirus. However, a large number of additional putative types exist within this species and much more effort will be required to elucidate fully the medical implications of these viruses.
| ACKNOWLEDGEMENTS |
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Received 7 March 2008;
accepted 15 June 2008.
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