Comparative in silico analyses and experimental validation of novel splice site and missense mutations in the genes MLH1 and MSH2

• Published in: Journal of cancer research and clinical oncology Vol. 136; no. 1; pp. 123 - 134
• Main Authors: Betz, Beate, Theiss, Stephan, Aktas, Murat, Konermann, Carolin, Goecke, Timm O, Möslein, Gabriela, Schaal, Heiner, Royer-Pokora, Brigitte
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 2010; Springer-Verlag; Springer; Springer Nature B.V
• Subjects: Adaptor Proteins, Signal Transducing - genetics; Algorithms; Antineoplastic agents; Base Sequence; Biological and medical sciences; Cancer Research; Colorectal cancer; Colorectal Neoplasms, Hereditary Nonpolyposis - genetics; Computational Biology - methods; DNA Mutational Analysis; Exons - genetics; Gastroenterology. Liver. Pancreas. Abdomen; Genes; Genetic disorders; Hematology; Humans; Internal Medicine; Medical sciences; Medicine; Medicine & Public Health; Molecular Sequence Data; Mutation; Mutation, Missense; MutL Protein Homolog 1; MutS Homolog 2 Protein - genetics; Nuclear Proteins - genetics; Oncology; Original Paper; Pharmacology. Drug treatments; Reverse Transcriptase Polymerase Chain Reaction; RNA Splice Sites - genetics; RNA Splicing; Stomach. Duodenum. Small intestine. Colon. Rectum. Anus; Tumors; Missense mutations; HNPCC; Splice site mutations; Exonic splicing enhancer; Validation; Hereditary nonpolyposis colorectal cancer; Rectal disease; Splicing; Malignant tumor; MLH1; Genetic disease; Repair gene; Colonic disease; Missense mutation; MSH2; Analysis; Digestive diseases; Intestinal disease; Genetics; In silico; Comparative study; Cancer
• ISSN: 0171-5216; 1432-1335
• DOI: 10.1007/s00432-009-0643-z

Hereditary non-polyposis colorectal cancer, an autosomal dominant predisposition to colorectal cancer and other malignancies, is caused by inactivating mutations of DNA mismatch repair genes, mainly MLH1 and MSH2. Missense mutations affect protein structure or function, but may also cause aberrant splicing, if located within splice sites (ss) or cis-acting sequences of splicing regulatory proteins, i.e., exonic splicing enhancers or exonic splicing silencers. Despite significant progress of ss scoring algorithms, the prediction for the impact of mutations on splicing is still unsatisfactory. For this study, we assessed ten ss and nine missense mutations outside ss in MLH1 and MSH2, including eleven newly identified mutations, and experimentally analyzed their effect at the RNA level. We additionally tested and compared the reliability of several web-based programs for the prediction of splicing outcome for these mutations.