Viral regulatory region sequence variations in kidney tissue obtained from patients with BK virus nephropathy

Background. The polyomavirus genome contains a noncoding control region (NCCR), which is believed to contain the enhancer elements that are important activators of viral transcription. We hypothesized that DNA sequence variations in this region play a role in the pathogenesis of BK virus allograft nephropathy (BKVAN). Methods. Tissue sections were prepared from 26 paraffin-embedded biopsies with BKVAN obtained from 15 patients. The sections were lysed in a proteinase K buffer and subjected to DNA sequencing using Big Dye cycle sequencing reactions run on an automated DNA sequencer (ABI310). NCCR anatomy was compared to the genomic sequence of archetype BKV strain WW. Results. Twelve putative transcription factor binding sites showed nucleotide substitutions, deletions, or duplications in at least one of the biopsies studied. Changes were most commonly found in binding sites for granulocyte/macrophage stimulating factor promoter (24/26 biopsies) and nuclear factor-I (NF-I) transcription factor (21/22 biopsies). Less frequent changes were seen at other binding sites, including T antigen (3/22 biopsies) and the cytomegalovirus immediate early (CMV IE-1) promoter (3/22 biopsies). Five biopsies showed complex rearrangements reminiscent of those described in JC virus-associated progressive multifocal leukoencephalopathy. Conclusion. The regulatory region of BKV shows sequence heterogeneity in biopsy tissue with viral nephropathy. Sequence variations frequently affect putative transcription factor binding sites, with potential implications for promoter activity related to genes important in viral replication. Architectural rearrangements were found in some cases but did not appear to be a prerequisite for the pathogenesis of BKVAN.