title: Viral regulatory region sequence variations in kidney tissue obtained from patients with BK virus nephropathy.
abstract: 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 (ABI 310). 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA. randhawapa@msx.upmc.edu
authors.forename: Parmjeet
authors.initials: P
authors.lastname: Randhawa
authors.forename: Debbie
authors.initials: D
authors.lastname: Zygmunt
authors.forename: Ron
authors.initials: R
authors.lastname: Shapiro
authors.forename: Abhay
authors.initials: A
authors.lastname: Vats
authors.forename: K
authors.initials: K
authors.lastname: Weck
authors.forename: P
authors.initials: P
authors.lastname: Swalsky
authors.forename: Sydney
authors.initials: S
authors.lastname: Finkelstein
mesh_terms: D001739:BK Virus / Q000235:genetics* / Q000472:pathogenicity; D004279:DNA, Viral / Q000032:analysis; D006801:Humans; D007668:Kidney / Q000821:virology; D007674:Kidney Diseases / Q000601:surgery / Q000821:virology*; D016030:Kidney Transplantation; D027601:Polyomavirus Infections / Q000821:virology*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D014412:Tumor Virus Infections / Q000821:virology*; D014774:Virulence
chemical_list: D004279:DNA, Viral