Alteration of a sequence with homology to human endogenous retrovirus (HERV-K) in primary human glioma: implications for viral repeat mediated rearrangement

We had earlier demonstrated that a comparison of DNA fingerprinting profiles of tumor and corresponding normal DNA from the same patient by random amplified polymorphic DNA (RAPD) analysis can readily demonstrate alterations in tumor DNA Gene 206 (1998) 45 and J. Neuro Oncol. 48 (2000) 1]. These alterations could be used to identify changes in tumor DNA where the prior identity of the locus was not known. In this study, we report the identification, cloning and characterization of a RAPD amplified fragment which was lost in a glioma, a grade IV glioblastoma multiforme (GBM). Comparison of the RAPD profile of tumor and corresponding leucocyte DNA revealed several differences between the two. These included a band of 443 bases, which was demonstrated in the normal, but not in tumor DNA. On sequencing, this band was found to be homologous with a group of SINE sequences, which are probably derived from the human endogenous retrovirus-K (HERV-K). Homology search also reveals that HERV-K-derived sequences are interspersed, amongst others, in the tumor suppressor gene BRCA2 and the DNA repair gene XRCC1. Of particular interest is the inverted repeat pattern of HERV-derived sequences in the genes. While not demonstrating a cause effect relationship, this highlights the possible role of such virus-derived sequences in gene inactivation by recombination during tumorigenesis.