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Splice Variants but not Mutations of DNA Polymerase ß Are Common in Bladder Cancer

Molecular and Genetic Epidemiology Group [T. E. T., J. A. T.] and Cancer and Aging Group [J. I. R.], The Laboratory of Molecular Carcinogenesis, The National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Section of Medical Genetics and Molecular Medicine, The Children’s Mercy Hospital and Clinic, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108 [P. K. R.]

DNA polymerase ß (POLß) is a highly conserved protein that functions in base excision repair. Loss of the POLß locus on chromosome 8p is a frequent event in bladder cancer, and loss of POLß function could hinder DNA repair leading to a mutator phenotype. Both point mutations and large intragenic deletions of POLß have been reported from analysis of various tumor cDNAs but not from genomic DNA. We noticed that the breakpoints of the presumed rearrangements were delineated by exon-exon junctions, which could instead be consistent with alternative splicing of POLß mRNA. We tested the hypothesis that the reported intragenic deletion were splice variants by screening genomic DNA of human bladder tumors, bladder cancer cell lines, and normal bladder tissues for mutations or deletions in exons 1–14, exon , and the promoter region of POLß. We found no evidence of somatic mutations or deletions in our sample set, although two polymorphisms were identified. Examination of cDNA from a subset of the original sample set revealed that truncated forms of POLß were surprisingly common. Forty-eight of 89 (54%) sequenced cDNA clones had large deletions, each beginning and/or ending exactly at exon-exon junctions. Because these deletions occur at exon-exon junctions and are seen in cDNA but not genomic DNA, they are consistent with alternative mRNA splicing. We describe 12 different splicing events occurring in 18 different combinations. Loss of exon 2 was the most frequent, being found in 42 of 49 (86%) of the variant sequenced clones. The splice variants appear to be somewhat more common and variable in bladder cancer cell lines and tumor tissues but occur at a high frequency in normal bladder tissues as well. We examine alternative splicing in terms of the information content of splice donor and acceptor site sequences, and discuss possible explanations for the predominant splicing event, the loss of exon 2.

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