The early detection of frameshift mutations induced by a food-borne carcinogen in rats: a new tool for molecular epidemiology

Development of allele-specific PCR and RT-PCR assays for clustered resistance genes using a potato late blight resistance transgene as a model

Members of the NBS-LRR gene family impart resistance to a wide variety of pathogens and are often found clustered within a plant genome. This clustering of homologous sequences can complicate PCR-based characterizations, especially the study of transgenes. We have developed allele-specific PCR and RT-PCR assays for the potato late blight resistance gene RB. Our assay utilizes two approaches toward primer design, allowing discrimination between the RB transgene and both the endogenous RB gene and numerous RB homeologs. First, a reverse primer was designed to take advantage of an indel present in the RB transgene but absent in rb susceptibility alleles, enhancing specificity for the transgene, though not fully discriminating against RB homeologs. Second, a forward primer was designed according to the principles of mismatch amplification mutation assay (MAMA) PCR, targeting SNPs introduced during the cloning of RB. Together, the indel reverse primer and the MAMA forward primer provide an assay that is highly specific for the RB transgene, being capable of distinguishing the transgene from all RB endogenous gene copies and from all RB paralogs in a diverse collection of wild and cultivated potato genotypes. These primers have been successfully multiplexed with primers of an internal control. The multiplexed assay is useful for both PCR and RT-PCR applications. Double MAMA-PCR, in which both PCR primers target separate transgene-specific SNPs, was also tested and shown to be equally specific for the RB transgene. We propose extending the use of MAMA for the characterization of resistance transgenes.

Highlights of the eighth international conference on carcinogenic/mutagenic N-substituted aryl compounds

Research in the 20th century initially identified arylamines as causative factors in occupational carcinogenesis, especially bladder cancer, and subsequently identified arylamines as a major class of mutagens/carcinogens in the environment and diet that are potential risk factors in a variety of human cancers. Current research focuses on understanding of mechanisms of arylamine carcinogenesis, such as the role of metabolic processing, DNA adduct formation, and mutagenesis, and learning more about the molecular alterations in carcinomas induced by these compounds. Furthermore, research to identify human exposures, including developing more sensitive methods for analyzing environmental samples and identifying suitable biomarkers are important aspects of contemporary investigations. In addition, better evaluation of the risk of these compounds in human cancer especially with regard to the impact of genetic polymorphisms is a major focus of research in this field. Although current population studies have sometimes been described as equivocal, improved tools for epidemiology, refined human biomonitoring methods and collaborative endeavors to study multiple population groups now provide a better means to ultimately define the role of arylamines in human carcinogenesis. The purpose of the Eighth International Conference on Carcinogenic/Mutagenic N-Substituted Aryl Compounds, held in Washington, DC, 12-14 November 2001, was to explore the current scope of studies on arylamine carcinogenesis among scientists in basic research and epidemiology and to discuss future research priorities. With the intent of providing a view to the current field of research on aromatic amines, this review presents a synopsis of the Proceedings of the Eighth International Conference and highlights the manuscripts contained in this special issue of Mutation Research.

Detecting rare mutations associated with cancer risk

For more than a decade, investigators have been searching for a means of determining the risk of individuals developing cancer by detecting rare oncogenic mutations. The accumulation of mutations and the clonal evolvement of tumors provide opportunities for monitoring disease development and intervening prior to the presentation of clinical symptoms, or determining the risk of disease relapse during remission. A number of techniques, mostly polymerase chain reaction (PCR)-based, have been developed that enable the detection of rare oncogenic mutations within the range of 10(-2) to 10(-4) wild-type cells. Only a handful of procedures enable the detection of intragenic single base mutations at one mutant in 10-6 or better. These ultra-sensitive mutation detection techniques have produced some interesting results regarding single base mutation spectra and frequencies in p53, Harvey-ras, N-ras, and other reporter genes and DNA sequences in human tissues. Although there is evidence that some individuals may harbor cells or clones expressing genomic instability, the connection with the processes of carcinogenesis is still tenuous. There remains a need for rigorous epidemiological studies employing these ultra-sensitive mutation detection procedures. Since genomic instability is considered key to tumor development, the relevance of the detection of hypermutable clones in individuals is discussed in the context of cancer risk.

Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA

The carcinogenic heterocyclic amine (HA) 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is formed during the cooking of various meats. To enable structure/activity studies aimed at understanding how DNA damaged by a member of the HA class of compounds can ultimately lead to cancer, we have determined the first solution structure of an 11-mer duplex containing the C8-dG adduct formed by reaction with N-acetoxy-PhIP. A slow conformational exchange is observed in which the PhIP ligand either intercalates into the DNA helix by denaturing and displacing the modified base pair (main form) or is located outside the helix in a minimally perturbed B-DNA duplex (minor form). In the main base-displaced intercalation structure, the minor groove is widened, and the major groove is compressed at the lesion site because of the location of the bulky PhIP-N-methyl and phenyl ring in the minor groove; this distortion causes significant bending of the helix. The PhIP phenyl ring interacts with the phosphodiester-sugar ring backbone of the complementary strand and its fast rotation with respect to the intercalated imidazopyridine ring causes substantial distortions at this site, such as unwinding and bulging-out of the strand. The glycosidic torsion angle of the [PhIP]dG residue is syn, and the displaced guanine base is directed toward the 3' end of the modified strand. This study contributes, to our knowledge, the first structural information on the biologically relevant HA class to a growing body of knowledge about how conformational similarities and differences for a variety of types of lesions can influence protein interactions and ultimately biological outcome.

Early detection of 2-amino-1-methyl-6-phenylimidazo (4,5-b)pyridine(PhIP)-induced mutations within the Apc gene of rat colon

A large proportion of human cancers result from exposure of individuals to environmental or occupational carcinogens. The early detection of carcinogen-induced mutations is a prerequisite for the identification of individuals at risk for developing cancer. Short G-rich repetitive sequences have been previously identified as hot-spots for frameshift mutagenesis induced by a large variety of carcinogens belonging to several families of widespread environmental pollutants. In order to test if these sequences, when mutated, might serve as biomarkers for carcinogen exposure, we designed a sensitive PCR-based strategy that allows the detection of rare mutational events within a whole genome. 2-Amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP), the most abundant carcinogenic heterocyclic amine generated in cooked meat, induces mammary and colon carcinoma in F344 rats. About 25% of male rats exposed to 400 p.p.m. PhIP in the diet for >43 weeks present colon tumors with specific -1G mutations within 5'-GGGA-3' sequences of the APC: gene. Using our PCR assay we have assessed the occurrence of such specific events in rats exposed to PhIP for only 1, 2, 4 and 6 weeks. A specific amplification signal was already observed in the 1 week-treated population and increases in a treatment time-dependent manner. These data validate this approach for the early detection of mutations and demonstrate its usefulness for molecular epidemiology and early diagnosis.