title: The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma.
abstract: Many variants of uncertain functional significance in cancer susceptibility genes lie in regulatory regions, and clarifying their association with disease risk poses significant challenges. We studied 17 germline variants (nine of which were novel) in the CDKN2A 5'UTR with independent approaches, which included mono and bicistronic reporter assays, Western blot of endogenous protein, and allelic representation after polysomal profiling to investigate their impact on CDKN2A mRNA translation regulation. Two of the novel variants (c.-27del23, c.-93-91delAGG) were classified as causal mutations (score ≥3), along with the c.-21C>T, c.-34G>T, and c.-56G>T, which had already been studied by a subset of assays. The novel c.-42T>A as well as the previously described c.-67G>C were classified as potential mutations (score 1 or 2). The remaining variants (c.-14C>T, c.-20A>G, c.-25C>T+c.-180G>A, c.-30G>A, c.-40C>T, c.-45G>A, c.-59C>G, c.-87T>A, c.-252A>T) were classified as neutral (score 0). In conclusion, we found evidence that nearly half of the variants found in this region had a negative impact on CDKN2A mRNA translation, supporting the hypothesis that 5'UTR can act as a cellular Internal Ribosome Entry Site (IRES) to modulate p16(INK) (4a) translation.
authors.affiliation: Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.|Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: Virginia
authors.initials: V
authors.lastname: Andreotti
authors.affiliation: Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Bisio
authors.affiliation: Department of Biopathology and INSERM U1186, Gustave Roussy, Villejuif, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Bressac-de Paillerets
authors.affiliation: Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Harland
authors.affiliation: Department of Biopathology and INSERM U1186, Gustave Roussy, Villejuif, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Cabaret
authors.affiliation: Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK.
authors.forename: Julia
authors.initials: J
authors.lastname: Newton-Bishop
authors.affiliation: Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.|Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: Lorenza
authors.initials: L
authors.lastname: Pastorino
authors.affiliation: Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.|Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: William
authors.initials: W
authors.lastname: Bruno
authors.affiliation: NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Bertorelli
authors.affiliation: NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: De Sanctis
authors.affiliation: Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Provenzani
authors.affiliation: Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Menin
authors.affiliation: Mutagenesis Unit, IRCCS AOU San Martino -IST, Genoa, Italy.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Fronza
authors.affiliation: Medical Oncology Unit, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Queirolo
authors.affiliation: Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Spitale
authors.affiliation: Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.|Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Bianchi-Scarrà
authors.affiliation: Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Inga
authors.affiliation: Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.|Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Ghiorzo
mesh_terms: D020121:5' Untranslated Regions; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000096:biosynthesis / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D006801:Humans; D008297:Male; D008545:Melanoma / Q000235:genetics* / Q000378:metabolism; D010375:Pedigree; D010442:Peptide Chain Initiation, Translational / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D019941:Cyclin-Dependent Kinase Inhibitor p16
keywords: 5′ untranslated region; CDKN2A; germline mutation; melanoma susceptibility; polysomal imbalance; reporter assays; variants with unknown functional significance