A new approach for the evaluation of the human papillomavirus type 16 variability with high resolution melting analysis.

Studies on the variability of human papillomavirus (HPV) type 16 are based mostly on DNA sequencing of the viral oncogenes E6 and E7. In order to simplify variant identification, high resolution melting (HRM) analysis, which has been shown to distinguish amplicons differing in a single nucleotide, was employed. Optimised HRM analysis was applied to 255 anogenital samples positive for HPV 16. The E6/E7 region of the HPV 16 genome was amplified using nested PCR with subsequent melting of the amplicons. Samples giving ambiguous melting profiles were melted again in the presence of reference HPV 16 DNA to define and confirm the novel melting profiles. Out of 219 samples of Croatian origin, 65 reference variants, 119 E6-360G variants and 35 novel melting profiles were found. Samples containing unusual profiles were sequenced for identification. In addition, a subset of samples with two common variants, 23 reference and 34 E6-350G variants, was also sequenced to confirm the findings of high resolution melting. Concordance between the melting analysis and sequencing was 93.9%, while HRM sensitivity and specificity were 92.9% and 94.7%, respectively. This study showed that HRM analysis can be useful for the identification of HPV 16 variants. The HRM method will be useful in low resource settings as it saves considerable time and resources compared to sequencing.

Gorlin syndrome patient with large deletion in 9q22.32-q22.33 detected by quantitative multiplex fluorescent PCR.

BACKGROUND: Gorlin syndrome is a rare autosomal-dominant disorder characterized by a wide range of developmental abnormalities and various tumors. The syndrome is caused by mutations in PTCH1, a tumor suppressor gene located at 9q22.32. We describe a Gorlin syndrome case with typical features of the syndrome and no mutations in PTCH1, but with a large deletion of the 9q22 region that has rarely been described. OBJECTIVE: To fully characterize the large deletion in the patient. METHODS: In order to map the size and position of the deletion, we developed quantitative multiplex fluorescent PCR with polymorphic markers surrounding the PTCH1 gene, followed by long-range PCR and sequencing. RESULTS: The deleted segment of 4.5 Mb in the 9q22.32-q22.33 region was determined, and included the entire PTCH1, its promoter and 22 OMIM genes. CONCLUSION: We suggest that screening for large deletions should be included in standard mutation screening for Gorlin syndrome patients.

Involvement of p16 and PTCH in pathogenesis of melanoma and basal cell carcinoma.

The involvement of two tumor suppressors p16 and Ptch in pathogenesis of cutaneous melanomas and basal cell carcinomas (BCCs) was studied through expression of Ptch and p16 and genetic alterations in 9p21 region (p16) and in 9q22.3 region (PTCH) of chromosome 9. Immunohistochemical analyses of paraffin-embedded tissues with Ptch and p16 antibodies, typing for 9q22-q31 and 9p21 region with polymorphic markers and p16 and Ptch mutation detection was done. Higher expression of p16 and Ptch in melanoma and BCC of the skin was frequently detected in studied cases. However, allelic loss of PTCH region occurs more frequently in BCCs than loss of heterozygosity of p16 region. Both types of tumors, BCCs and melanomas, suggest involvement of Hh-Gli signaling pathway, but using different mechanisms.

New sequence variants in BRCA1 and BRCA2 genes detected by high-resolution melting analysis in an elderly healthy female population in Croatia.

BACKGROUND: Mutations in BRCA1 and BRCA2 genes are associated with family predisposition to breast and ovarian cancer. Novel screening methods are required for efficient and rapid detection of sequence variants in cancer patients and their family members. METHODS: The screening for variants in the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2 in Croatia was performed by a high-resolution melting approach, which is based on differences in melting curves caused by variations in nucleotide sequence. This is the first screening in Croatia on elderly healthy women with no family history of cancer. BRCA1 screening was performed on 220 and BRCA2 screening on 115 samples. RESULTS: In a population well beyond the average age of breast/ovarian cancer onset, 21 different sequence variants in the BRCA1 gene (one novel: c.5193+49_50delTA) and 36 variants in the BRCA2 gene (7 novel: c.459A>C, c.3318C>A, c.4412_ 4414delGAA, c.4790C>A, c.6264T>C, c.9087G>A, and c.9864A>G) were detected. CONCLUSIONS: Nine BRCA1 and seven BRCA2 known variants appeared with such high frequencies that they could be declared as harmless in this population. Eight BRCA1 high frequency variants, located further from the promoter region, appear to be strongly correlated. Three novel variants that changed the amino acid sequence of the BRCA2 protein (two missense base substitutions, c.3318C>A and c.4790C>A, and one codon deletion c.4412_4414delGAA), appearing only once, were predicted to have no potential effect on protein structure and function.

Hedgehog-Patched pathway aberrations in a malignant triton tumor case study.

Transition from malignant schwannoma to malignant triton tumor is analyzed in a case report on a patient with recurring cancers and suspected familial predisposition. It is hypothesized that rhabdomyoblastic differentiation, which distinguishes triton from schwannoma, might be attributable to Hedgehog-Patched pathway malfunctioning. Loss of one Patched gene allele was found in the tissue of advanced triton, but the retained allele had no exon or promoter mutations. Protein levels at early cancer stages indicated possible Patched response to the pathway activation in the first occurrence of triton tumor. Later, in the recurring triton, Patched expression was several times lower than in the control tissue, suggesting that haploinsufficiency was aided by silencing of the remaining allele, although its promoter was not hypermethylated. These findings may justify further investigation of the Hedgehog-Patched pathway role in triton malignancies, especially because of the recent research on the therapeutical potential of the pathway.

The Patched gene is epigenetically regulated in ovarian dermoids and fibromas, but not in basocellular carcinomas.

The Hedgehog/Patched signaling pathway plays a prominent role during mammalian development but it is also involved in oncogenic transformation. We investigated the methylation status of the Patched promotor in a set of basocellular carcinomas of the skin and ovarian tumors as an alternative to mutational causes of the pathway deregulation. Our aim was to define a possible role of genetic and/or epigenetic mechanisms of Hedgehog/Patched signal transduction in the development of these tumors. Bisulfite-converted DNA from tumors and from matched healthy tissue was amplified by a specific PCR and the CpG-rich regions of the Patched promoter were sequenced. Two promoter regions showed statistically significant hypermethylation compared to healthy controls in ovarian tumors; more significantly in the region in the vicinity of Gli1-binding sites and less significantly in the region containing the ATG codon. But, in basocellular carcinomas of the skin we observed no difference in methylation, suggesting different mechanisms of neoplasia in these tumors.