title: Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms.
abstract: 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.
authors.affiliation: Department of Pharmacy, "G. d'Annunzio" University, Chieti, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: De Lellis
authors.forename: Gitana Maria
authors.initials: GM
authors.lastname: Aceto
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Curia
authors.forename: Teresa
authors.initials: T
authors.lastname: Catalano
authors.forename: Sandra
authors.initials: S
authors.lastname: Mammarella
authors.forename: Serena
authors.initials: S
authors.lastname: Veschi
authors.forename: Fabiana
authors.initials: F
authors.lastname: Fantini
authors.forename: Pasquale
authors.initials: P
authors.lastname: Battista
authors.forename: Vittoria
authors.initials: V
authors.lastname: Stigliano
authors.forename: Luca
authors.initials: L
authors.lastname: Messerini
authors.forename: Cristina
authors.initials: C
authors.lastname: Mareni
authors.forename: Paola
authors.initials: P
authors.lastname: Sala
authors.forename: Lucio
authors.initials: L
authors.lastname: Bertario
authors.forename: Paolo
authors.initials: P
authors.lastname: Radice
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cama
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D000465:Algorithms; D000483:Alleles; D017398:Alternative Splicing; D000951:Antigens, Neoplasm / Q000235:genetics; D015815:Cell Adhesion Molecules / Q000235:genetics; D003123:Colorectal Neoplasms, Hereditary Nonpolyposis / Q000175:diagnosis* / Q000235:genetics*; D019175:DNA Methylation; D053843:DNA Mismatch Repair / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D000071858:Epithelial Cell Adhesion Molecule; D015972:Gene Expression Regulation, Neoplastic; D005820:Genetic Testing; D018095:Germ-Line Mutation; D006801:Humans; D000070957:MutL Protein Homolog 1; D051718:MutS Homolog 2 Protein / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D000951:Antigens, Neoplasm; D015815:Cell Adhesion Molecules; D004268:DNA-Binding Proteins; D000071858:Epithelial Cell Adhesion Molecule; C094443:G-T mismatch-binding protein; C501486:MLH1 protein, human; D009687:Nuclear Proteins; D000070957:MutL Protein Homolog 1; D051718:MutS Homolog 2 Protein