Human papilloma viruses and cervical tumours: mapping of integration sites and analysis of adjacent cellular sequences

BACKGROUND: In cervical tumours the integration of human papilloma viruses (HPV) transcripts often results in the generation of transcripts that consist of hybrids of viral and cellular sequences. Mapping data using a variety of techniques has demonstrated that HPV integration occurred without obvious specificity into human genome. However, these techniques could not demonstrate whether integration resulted in the generation of transcripts encoding viral or viral-cellular sequences. The aim of this work was to map the integration sites of HPV DNA and to analyse the adjacent cellular sequences. METHODS: Amplification of the INTs was done by the APOT technique. The APOT products were sequenced according to standard protocols. The analysis of the sequences was performed using BLASTN program and public databases. To localise the INTs PCR-based screening of GeneBridge4-RH-panel was used. RESULTS: Twelve cellular sequences adjacent to integrated HPV16 (INT markers) expressed in squamous cell cervical carcinomas were isolated. For 11 INT markers homologous human genomic sequences were readily identified and 9 of these showed significant homologies to known genes/ESTs. Using the known locations of homologous cDNAs and the RH-mapping techniques, mapping studies showed that the INTs are distributed among different human chromosomes for each tumour sample and are located in regions with the high levels of expression. CONCLUSIONS: Integration of HPV genomes occurs into the different human chromosomes but into regions that contain highly transcribed genes. One interpretation of these studies is that integration of HPV occurs into decondensed regions, which are more accessible for integration of foreign DNA

Cosmid contig and cDNA map of the human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia

We constructed a fine physical map of human chromosome 13q14 region between D13S1168 and D13S25 loci consisting of cosmid and cDNA clones. This interval had been shown to be in the center of the genome region frequently lost in a human blood malignancy known as B-cell chronic lymphocytic leukemia (BCLL), Mapping of the genome region is a step in searching for a putative tumor suppressor gene for BCLL. A chr13-specific cosmid library (LA13NC01) was screened with four YAC and seven WI-STS markers belonging to the above 13q14 interval, yielding a cosmid subset of more than 400 clones representing the region. Cosmids between D13S1168 and D13S25 loci were arranged in contigs. Seven different clones were found in cDNA libraries by hybridization screening with YAC ICRF66c1 and two cosmids covering the D13S319 locus, which is the central point for BCLL-associated deletions, The cDNA clones were mapped against the contigous cosmids