title: A comprehensive haplotype analysis of the XPC genomic sequence reveals a cluster of genetic variants associated with sensitivity to tobacco-smoke mutagens.
abstract: The impact of single-nucleotide polymorphisms (SNPs) of the DNA repair gene XPC on DNA repair capacity (DRC) and genotoxicity has not been comprehensively determined. We constructed a comprehensive haplotype map encompassing all common XPC SNPs and evaluated the effect of Bayesian-inferred haplotypes on DNA damage associated with tobacco smoking, using chromosome aberrations (CA) as a biomarker. We also used the mutagen-sensitivity assay, in which mutagen-induced CA in cultured lymphocytes are determined, to evaluate the haplotype effects on DRC. We hypothesized that if certain XPC haplotypes have functional effects, a correlation between these haplotypes and baseline and/or mutagen-induced CA would exist. Using HapMap and single nucleotide polymorphism (dbSNP) databases, we identified 92 SNPs, of which 35 had minor allele frequencies >or= 0.05. Bayesian inference and subsequent phylogenetic analysis identified 21 unique haplotypes, which segregated into six distinct phylogenetically grouped haplotypes (PGHs A-F). A SNP tagging approach used identified 11 tagSNPs representing these 35 SNPs (r(2) = 0.80). We utilized these tagSNPs to genotype a population of smokers matched to nonsmokers (n = 123). Haplotypes for each individual were reconstituted and PGH designations were assigned. Relationships between XPC haplotypes and baseline and/or mutagen-induced CA were then evaluated. We observed significant interaction among smoking and PGH-C (p = 0.046) for baseline CA where baseline CA was 3.5 times higher in smokers compared to nonsmokers. Significant interactions among smoking and PGH-D (p = 0.023) and PGH-F (p = 0.007) for mutagen-induced CA frequencies were also observed. These data indicate that certain XPC haplotypes significantly alter CA and DRC in smokers and, thus, can contribute to cancer risk.
authors.affiliation: Department of Obstetrics and Gynecology, The University of Texas Medical Branch, Galveston, Texas 77555 1062, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Rondelli
authors.forename: Randa A
authors.initials: RA
authors.lastname: El-Zein
authors.forename: Jeffrey K
authors.initials: JK
authors.lastname: Wickliffe
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Etzel
authors.forename: Sherif Z
authors.initials: SZ
authors.lastname: Abdel-Rahman
mesh_terms: D000328:Adult; D000368:Aged; D002470:Cell Survival / Q000187:drug effects; D002478:Cells, Cultured; D002874:Chromosome Mapping; D004249:DNA Damage; D004260:DNA Repair / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D006801:Humans; D008214:Lymphocytes / Q000187:drug effects / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D009153:Mutagens / Q000633:toxicity*; D020641:Polymorphism, Single Nucleotide; D012906:Smoke / Q000009:adverse effects*; D055815:Young Adult
chemical_list: D004268:DNA-Binding Proteins; D009153:Mutagens; D012906:Smoke; C086984:XPC protein, human