BACKGROUND: Altered germline expression of genes may represent a powerful marker of genetic or epigenetic predisposition to cancer or other diseases. METHODS: We developed and validated a method of nonfluorescent primer extension that uses a single dideoxynucleotide and denaturing HPLC (DHPLC) to analyze the relative allele expression. We devised 5 independent assays for measuring allele-specific expression (ASE) to exploit different markers of mismatch repair genes MLH1 [mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)] and MSH2 [mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)]. We initially confirmed method reproducibility with genomic DNA (gDNA) from individuals heterozygous for a frequent single-nucleotide polymorphism in the MLH1 gene. After this preliminary validation with gDNA, we confirmed assay reproducibility with cDNA templates from control individuals. Relative allele expression was estimated by comparing the heights of the peaks corresponding to the 2 alleles. Results obtained with gDNA templates were used to normalize cDNA results. RESULTS: With these DHPLC-based primer-extension assays, we detected and confirmed a 5-fold imbalance in MLH1 allele expression in a mutation-negative patient with hereditary nonpolyposis colorectal cancer and in another patient with a modest degree of imbalance in MLH1 expression. Among control individuals, the relative expression of MLH1 alleles displayed a narrow range of variation. CONCLUSIONS: Independent DHPLC-based primer-extension assays for measuring and confirming ASE can be developed for different sequence variants of interest. This DHPLC application provides a cost-effective method for detecting ASE in cases for which conventional screening fails to detect pathogenic mutations in candidate genes and may be applicable for confirming ASE revealed by other methods, such as those used for transcriptome-wide analyses. .
BACKGROUND: Altered germline expression of genes may represent a powerful marker of genetic or epigenetic predisposition to cancer or other diseases. METHODS: We developed and validated a method of nonfluorescent primer extension that uses a single dideoxynucleotide and denaturing HPLC (DHPLC) to analyze the relative allele expression. We devised 5 independent assays for measuring allele-specific expression (ASE) to exploit different markers of mismatch repair genes MLH1 [mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)] and MSH2 [mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)]. We initially confirmed method reproducibility with genomic DNA (gDNA) from individuals heterozygous for a frequent single-nucleotide polymorphism in the MLH1 gene. After this preliminary validation with gDNA, we confirmed assay reproducibility with cDNA templates from control individuals. Relative allele expression was estimated by comparing the heights of the peaks corresponding to the 2 alleles. Results obtained with gDNA templates were used to normalize cDNA results. RESULTS: With these DHPLC-based primer-extension assays, we detected and confirmed a 5-fold imbalance in MLH1 allele expression in a mutation-negative patient with hereditary nonpolyposis colorectal cancer and in another patient with a modest degree of imbalance in MLH1 expression. Among control individuals, the relative expression of MLH1 alleles displayed a narrow range of variation. CONCLUSIONS: Independent DHPLC-based primer-extension assays for measuring and confirming ASE can be developed for different sequence variants of interest. This DHPLC application provides a cost-effective method for detecting ASE in cases for which conventional screening fails to detect pathogenic mutations in candidate genes and may be applicable for confirming ASE revealed by other methods, such as those used for transcriptome-wide analyses. .
Authors: Maria Cristina Curia; Sabrina De Iure; Laura De Lellis; Serena Veschi; Sandra Mammarella; Marquitta J White; Jacquelaine Bartlett; Angelo Di Iorio; Cristina Amatetti; Marco Lombardo; Patrizia Di Gregorio; Pasquale Battista; Renato Mariani-Costantini; Scott M Williams; Alessandro Cama Journal: Gastroenterology Date: 2011-10-10 Impact factor: 22.682
Authors: Gitana Maria Aceto; Fabiana Fantini; Sabrina De Iure; Marta Di Nicola; Giandomenico Palka; Rosa Valanzano; Patrizia Di Gregorio; Vittoria Stigliano; Maurizio Genuardi; Pasquale Battista; Alessandro Cama; Maria Cristina Curia Journal: J Exp Clin Cancer Res Date: 2015-10-28
Authors: Laura De Lellis; Gitana Maria Aceto; Maria Cristina Curia; Teresa Catalano; Sandra Mammarella; Serena Veschi; Fabiana Fantini; Pasquale Battista; Vittoria Stigliano; Luca Messerini; Cristina Mareni; Paola Sala; Lucio Bertario; Paolo Radice; Alessandro Cama Journal: PLoS One Date: 2013-11-20 Impact factor: 3.240