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Inst för laboratoriemedicin / Dept of Laboratory Medicine
Doi
Abstract
The increasing prevalence of skin cancer results in that it will soon equal that of all other
cancers combined. Sun exposure is a well-known risk factor for its development, but
despite the growing public awareness of the harmful consequences of ultraviolet
radiation, the cancer incidence continues to increase, implying that other factors might
also have a role in promoting this disease.
Data from immunosuppressed patients reveals a 100-fold increased incidence of nonmelanoma skin carcinoma (NMSC), but an infectious etiology has not been established.
However, certain human papillomaviruses (HPVs) have previously been detected in this
type of cancer.
We applied high throughput sequencing to different skin lesions in order to assess which
organisms were present. Most viral reads (>95%) belonged to human papillomavirus.
Traditionally, viral detection was performed using PCR methods. We used degenerate
“general” HPV primers and multiplexed novel “specific” HPV primers in order to
amplify a broad number of HPVs by PCR. This method showed a very high sensitivity,
but the HPV types with low similarity to the primer sequences might have escaped
amplification. Therefore, we performed an unbiased approach based on non-PCR whole
genome amplification, independent of sequence information, in order to detect those
“escaping” HPV types, as well as to determine if other viruses were present in the
samples.
Overall, we identified almost 100 putative novel HPV types in total, and characterized 4
novel HPV types (HPV 197, 200, 201 and 202). Most of the HPV types were detected in
very few patients each, and at a very low viral load (below 0.5 copies/cell), except for
HPV 197, which was the most commonly found virus in skin tumors (37.4% of skin
lesions). Despite the higher sensitivity of PCR methods, the unbiased approach detected
HPV in 37/40 condyloma acuminata that had been reported as “HPV-negative” with
specific PCR techniques. Certain HPV types, including HPV 197, were not detected by
PCR and only by non-PCR based methods. Therefore, more unbiased PCR-independent
methods are needed to describe which organisms are most commonly present in skin
lesions.
The work in this thesis has expanded our knowledge of the wide genomic diversity of
HPV on the skin, and finds that PCR-independent methods are needed to describe which
organisms are most commonly present in skin lesions. Further studies are needed to assess
any possible role of viral infections in skin cancer, elucidation of mechanistic effects and
determine the direction of causality of any associations
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