Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms

• Published in: PloS one Vol. 8; no. 11; p. e81194
• Main Authors: De Lellis, Laura, Aceto, Gitana Maria, Curia, Maria Cristina, Catalano, Teresa, Mammarella, Sandra, Veschi, Serena, Fantini, Fabiana, Battista, Pasquale, Stigliano, Vittoria, Messerini, Luca, Mareni, Cristina, Sala, Paola, Bertario, Lucio, Radice, Paolo, Cama, Alessandro
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20.11.2013; Public Library of Science (PLoS)
• Subjects: Adaptor Proteins, Signal Transducing - genetics; Adenomatous polyposis coli; Aging; Algorithms; Alleles; Alternative Splicing; Analysis; Antigens, Neoplasm - genetics; Cancer; Cell adhesion & migration; Cell Adhesion Molecules - genetics; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms, Hereditary Nonpolyposis - diagnosis; Colorectal Neoplasms, Hereditary Nonpolyposis - genetics; Defects; Diagnostic systems; DNA Methylation; DNA Mismatch Repair - genetics; DNA-Binding Proteins - genetics; Epithelial Cell Adhesion Molecule; Gene expression; Gene Expression Regulation, Neoplastic; Gene rearrangement; Genes; Genetic aspects; Genetic disorders; Genetic screening; Genetic Testing; Genomics; Germ-Line Mutation; Humans; Medical diagnosis; Medicine; Methylation; Microsatellite instability; Mismatch repair; MMR protein; Multivariate analysis; Mutation; MutL Protein Homolog 1; MutS Homolog 2 Protein - genetics; Nuclear Proteins - genetics; Pathology; Patients; Pharmacy; Promoter Regions, Genetic; Screening; Stability; Tumors; Italy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0081194

The identification of germline variants predisposing to hereditary nonpolyposis colorectal cancer (HNPCC) is crucial for clinical management of carriers, but several probands remain negative for such variants or bear variants of uncertain significance (VUS). Here we describe the results of integrative molecular analyses in 132 HNPCC patients providing evidences for improved genetic testing of HNPCC with traditional or next generation methods. Patients were screened for: germline allele-specific expression (ASE), nucleotide variants, rearrangements and promoter methylation of mismatch repair (MMR) genes; germline EPCAM rearrangements; tumor microsatellite instability (MSI) and immunohistochemical (IHC) MMR protein expression. Probands negative for pathogenic variants of MMR genes were screened for germline APC and MUTYH sequence variants. Most germline defects identified were sequence variants and rearrangements of MMR genes. Remarkably, altered germline ASE of MMR genes was detected in 8/22 (36.5%) probands analyzed, including 3 cases negative at other screenings. Moreover, ASE provided evidence for the pathogenic role and guided the characterization of a VUS shared by 2 additional probands. No germline MMR gene promoter methylation was observed and only one EPCAM rearrangement was detected. In several cases, tumor IHC and MSI diverged from germline screening results. Notably, APC or biallelic MUTYH germline defects were identified in 2/19 probands negative for pathogenic variants of MMR genes. Our results show that ASE complements gDNA-based analyses in the identification of MMR defects and in the characterization of VUS affecting gene expression, increasing the number of germline alterations detected. An appreciable fraction of probands negative for MMR gene variants harbors APC or MUTYH variants. These results indicate that germline ASE analysis and screening for APC and MUTYH defects should be included in HNPCC diagnostic algorithms.