title: Alteration of a sequence with homology to human endogenous retrovirus (HERV-K) in primary human glioma: implications for viral repeat mediated rearrangement.
abstract: 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.
authors.affiliation: Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, 110029, New Delhi, India.
authors.forename: A
authors.initials: A
authors.lastname: Misra
authors.forename: K
authors.initials: K
authors.lastname: Chosdol
authors.forename: C
authors.initials: C
authors.lastname: Sarkar
authors.forename: A K
authors.initials: AK
authors.lastname: Mahapatra
authors.forename: S
authors.initials: S
authors.lastname: Sinha
mesh_terms: D001483:Base Sequence; D001932:Brain Neoplasms / Q000235:genetics* / Q000821:virology*; D003001:Cloning, Molecular; D004260:DNA Repair / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics* / Q000302:isolation & purification; D004279:DNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D004268:DNA-Binding Proteins / Q000235:genetics; D020077:Endogenous Retroviruses / Q000235:genetics* / Q000302:isolation & purification; D024522:Genes, BRCA2; D005909:Glioblastoma / Q000235:genetics* / Q000821:virology*; D006801:Humans; D008969:Molecular Sequence Data; D019105:Random Amplified Polymorphic DNA Technique; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements; D000076105:X-ray Repair Cross Complementing Protein 1
chemical_list: D004273:DNA, Neoplasm; D004279:DNA, Viral; D004268:DNA-Binding Proteins; D000076105:X-ray Repair Cross Complementing Protein 1; C000619371:XRCC1 protein, human