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Disciglio V, Forte G, Fasano C, Sanese P, Lepore Signorile M, De Marco K, Grossi V, Cariola F, Simone C. APC Splicing Mutations Leading to In-Frame Exon 12 or Exon 13 Skipping Are Rare Events in FAP Pathogenesis and Define the Clinical Outcome. Genes (Basel) 2021; 12:genes12030353. [PMID: 33670833 PMCID: PMC7997234 DOI: 10.3390/genes12030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is caused by germline mutations in the tumor suppressor gene APC. To date, nearly 2000 APC mutations have been described in FAP, most of which are predicted to result in truncated protein products. Mutations leading to aberrant APC splicing have rarely been reported. Here, we characterized a novel germline heterozygous splice donor site mutation in APC exon 12 (NM_000038.5: c.1621_1626+7del) leading to exon 12 skipping in an Italian family with the attenuated FAP (AFAP) phenotype. Moreover, we performed a literature meta-analysis of APC splicing mutations. We found that 119 unique APC splicing mutations, including the one described here, have been reported in FAP patients, 69 of which have been characterized at the mRNA level. Among these, only a small proportion (9/69) results in an in-frame protein, with four mutations causing skipping of exon 12 or 13 with loss of armadillo repeat 2 (ARM2) and 3 (ARM3), and five mutations leading to skipping of exon 5, 7, 8, or (partially) 9 with loss of regions not encompassing known functional domains. The APC splicing mutations causing skipping of exon 12 or 13 considered in this study cluster with the AFAP phenotype and reveal a potential molecular mechanism of pathogenesis in FAP disease.
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Affiliation(s)
- Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
- Correspondence: (V.D.); (C.S.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
- Department of Biomedical Sciences and Human Oncology (DIMO), Medical Genetics, University of Bari Aldo Moro, 70124 Bari, Italy
- Correspondence: (V.D.); (C.S.)
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Wang D, Zhang Z, Li Y, Xu C, Yu Y, Li M, Chen C, Zhang X. Adenomatous Polyposis Coli Gene Mutations in 22 Chinese Pedigrees with Familial Adenomatous Polyposis. Med Sci Monit 2019; 25:3796-3803. [PMID: 31113927 PMCID: PMC6542301 DOI: 10.12659/msm.913911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP), which has a very high tendency of progression to colorectal cancer, is mainly caused by mutations of the adenomatous polyposis coli (APC) gene. This study systematically screened the APC mutations and observed the correlation of APC mutations with clinical manifestations of FAP. Material/Methods Eighty subjects (probands and their family members of 22 FAP pedigrees) were enrolled, underwent abdominal ultrasound, computed tomography, and colonoscopic examinations, and were assessed for APC mutations between January 2010 and June 2015 at Tianjin Union Medical Center. Peripheral blood was collected from subjects, and DNA was extracted and screened for APC mutations using multiplex ligation-dependent probe amplification for large-fragment deletions or PCR-denaturing high-performance liquid chromatography with DNA sequencing for micromutations. Results Nineteen of 22 FAP pedigrees were found to have mutations of APC, and 17 types APC mutations were identified. All the mutations were heterozygosity with autosomal dominant inheritance. APC mutations included 8 caused by frameshift, 3 by aberrant splicing, 2 by missense mutation, 2 by nonsense mutation, and 2 by large-fragment deletion. Frameshift mutation was the most common type of APC mutation, and Coding DNA Sequence 15 was the most common mutation site. Five novel APC mutations, including 1 with large-fragment deletion, were identified. Conclusions We systematically screened 17 mutations of APC from 22 Chinese pedigrees with FAP. This study will broaden the spectrum of known APC germline mutations and help understand the types and distribution of APC mutations among Chinese patients with FAP.
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Affiliation(s)
- Dan Wang
- Department of Pathology, Tianjin Medical University General Hospital, Tianjin, China (mainland)
| | - Zhao Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Yuwei Li
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Chen Xu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Yongjun Yu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Mingsen Li
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Chao Chen
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China (mainland)
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Synonymous mutation adenomatous polyposis coliΔ486s affects exon splicing and may predispose patients to adenomatous polyposis coli/mutY DNA glycosylase mutation‑negative familial adenomatous polyposis. Mol Med Rep 2018; 18:4931-4939. [PMID: 30272267 PMCID: PMC6236305 DOI: 10.3892/mmr.2018.9495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant-inherited colorectal cancer. Recent advances in genetics have indicated that the majority of patients with FAP carry germline mutations of the adenomatous polyposis coli (APC) and mutY DNA glycosylase (MUTYH) genes. However, a large subset of families with a history of FAP have undetectable pathogenic alterations, termed APC/MUTYH mutation-negative FAP. To investigate the germline mutations in the APC and MUTYH genes in Chinese patients with FAP, 13 unrelated patients were enrolled. Through genetic sequencing, four known pathogenic alterations (Lys1061LysfsTer2, Glu1309AspfsTer4, Arg283Ter and Ser1196Ter) of APC and two novel disease-associated pathogenic mutations (Tyr152Ter and Ter522Gly) in MUTYH were identified in six individuals. For samples that did not present with pathogenic alterations, the functional effects of missense, synonymous and intronic mutations were analyzed using bioinformatics tools and databases. Bioinformatics prediction suggested that the synonymous mutation Tyr486Tyr in APC (APC∆486s) was likely a disease-causing polymorphism and may have induced the exon skipping of APC. A hybrid mini-gene assay was performed, which confirmed that the synonymous single nucleotide polymorphism APC∆486s induced major splicing defects with skipping of exon 12 in APC. The data of the present study suggested that the synonymous polymorphism APC∆486s was a potential pathogenic alteration that predisposed APC/MUTYH mutation-negative patients to FAP.
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Novel mutations and phenotypic associations identified through APC, MUTYH, NTHL1, POLD1, POLE gene analysis in Indian Familial Adenomatous Polyposis cohort. Sci Rep 2017; 7:2214. [PMID: 28533537 PMCID: PMC5440391 DOI: 10.1038/s41598-017-02319-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
Colo-Rectal Cancer is a common cancer worldwide with 5-10% cases being hereditary. Familial Adenomatous Polyposis (FAP) syndrome is due to germline mutations in the APC or rarely MUTYH gene. NTHL1, POLD1, POLE have been recently reported in previously unexplained FAP cases. Unlike the Caucasian population, FAP phenotype and its genotypic associations have not been widely studied in several geoethnic groups. We report the first FAP cohort from South Asia and the only non-Caucasian cohort with comprehensive analysis of APC, MUTYH, NTHL1, POLD1, POLE genes. In this cohort of 112 individuals from 53 FAP families, we detected germline APC mutations in 60 individuals (45 families) and biallelic MUTYH mutations in 4 individuals (2 families). No NTHL1, POLD1, POLE mutations were identified. Fifteen novel APC mutations and a new Indian APC mutational hotspot at codon 935 were identified. Eight very rare FAP phenotype or phenotypes rarely associated with mutations outside specific APC regions were observed. APC genotype-phenotype association studies in different geo-ethnic groups can enrich the existing knowledge about phenotypic consequences of distinct APC mutations and guide counseling and risk management in different populations. A stepwise cost-effective mutation screening approach is proposed for genetic testing of south Asian FAP patients.
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Ben-Salem S, Sobreira N, Akawi NA, Al-Shamsi AM, John A, Pramathan T, Valle D, Ali BR, Al-Gazali L. Gonadal mosaicism in ARID1B gene causes intellectual disability and dysmorphic features in three siblings. Am J Med Genet A 2015; 170A:156-61. [PMID: 26395437 PMCID: PMC5448135 DOI: 10.1002/ajmg.a.37405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023]
Abstract
The gene encoding the AT-rich interaction domain-containing protein 1B (ARID1B) has recently been shown to be one of the most frequently mutated genes in patients with intellectual disability (ID). The phenotypic spectrums associated with variants in this gene vary widely ranging for mild to severe non-specific ID to Coffin-Siris syndrome. In this study, we evaluated three children from a consanguineous Emirati family affected with ID and dysmorphic features. Genomic DNA from all affected siblings was analyzed using CGH array and whole-exome sequencing (WES). Based on a recessive mode of inheritance, homozygous or compound heterozygous variants shared among all three affected children could not be identified. However, further analysis revealed a heterozygous variant (c.4318C>T; p.Q1440*) in the three affected children in an autosomal dominant ID causing gene, ARID1B. This variant was absent in peripheral blood samples obtained from both parents and unaffected siblings. Therefore, we propose that the most likely explanation for this situation is that one of the parents is a gonadal mosaic for the variant. To the best of our knowledge, this is the first report of a gonadal mosaicism inheritance of an ARID1B variant leading to familial ID recurrence.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nadia A Akawi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aisha M Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thachillath Pramathan
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Lee YT, Liu CJ, Hu YW, Teng CJ, Tzeng CH, Yeh CM, Chen TJ, Lin JK, Lin CC, Lan YT, Wang HS, Yang SH, Jiang JK, Chen WS, Lin TC, Chang SC, Chen MH, Teng HW, Liu JH, Yen CC. Incidence of Second Primary Malignancies Following Colorectal Cancer: A Distinct Pattern of Occurrence Between Colon and Rectal Cancers and Association of Co-Morbidity with Second Primary Malignancies in a Population-Based Cohort of 98,876 Patients in Taiwan. Medicine (Baltimore) 2015; 94:e1079. [PMID: 26131831 PMCID: PMC4504576 DOI: 10.1097/md.0000000000001079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The purpose of this study is to determine the features of second primary malignancies (SPMs) among patients with prior colorectal cancer (CRC) using a nationwide population-based dataset.Patients with CRC newly diagnosed between 1996 and 2011, and >1 year of follow-up were recruited from the Taiwan National Health Insurance database. Standardized incidence ratios (SIRs) of SPMs in patients with CRC were calculated.During the 16-year study period, 4259 SPMs developed among 98,876 CRC patients. The median duration of follow-up was 4.03 years. The SIR for all SPMs was 1.13 (95% confidence interval = 1.10-1.17). Compared with the general population, a higher incidence of thyroid, prostate, ovarian, and hematologic malignancies developed among patients with colon cancer, whereas the risk for bone and soft tissue cancers increased among patients with rectal cancer. The risk for breast, bladder, kidney, lung, and uterine cancers was significantly higher in patients with colon and rectal cancers than the general population. The risk for liver and biliary tract cancers declined in patients with rectal cancer. Based on multivariate analysis among patients with CRC, age ≥70 years, men, chronic obstructive pulmonary disease (COPD), cirrhosis, and dyslipidemia were independent predictors of an SPM.In conclusion, patients with CRC were at increased risk for a second cancer. The pattern of SPMs was distinct between patients with colon and rectal cancer. Age, men, COPD, cirrhosis, and dyslipidemia were independent risk factors for SPMs. Surveillance and education should be provided for survivors with respect to risk for SPMs.
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Affiliation(s)
- Yu-Ting Lee
- From the Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (Y-TL, C-JL, C-HT, M-HC, H-WT, C-CY); National Yang-Ming University School of Medicine, Taipei, Taiwan (Y-TL, C-JL, , Y-WH, C-JT, C-HT, T-JC, J-KL, C-CL, Y-TL, H-SW, S-HY, J-KJ, W-SC, T-CL, S-CC, M-HC, H-WT, J-HL, C-CY); Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan (Y-WH, J-HL); Division of Oncology and Hematology, Department of Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan (C-JT); Department of Family Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C-MY, T-JC); and Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan (J-KL, C-CL, Y-TL, H-SW, S-HY, J-KJ, W-SC, T-CL, S-CC)
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MUTYH-associated polyposis (MAP): evidence for the origin of the common European mutations p.Tyr179Cys and p.Gly396Asp by founder events. Eur J Hum Genet 2013; 22:923-9. [PMID: 23361220 DOI: 10.1038/ejhg.2012.309] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/20/2012] [Accepted: 12/28/2012] [Indexed: 12/18/2022] Open
Abstract
MUTYH-associated polyposis (MAP) is an autosomal recessive adenomatous polyposis caused by biallelic germline mutations of the base-excision-repair gene MUTYH. In MAP patients of European origin, the combined allele frequency of the mutations p.Tyr179Cys and p.Gly396Asp ranges between 50 and 82%, while these mutations have not been identified in Far Eastern Asian populations, supporting the hypothesis that a founder effect has occurred at some point in European history. To investigate the natural history of the two common European MUTYH alleles, we genotyped six gene-flanking microsatellite markers in 80 unrelated Italian and German MAP patients segregating one or both mutations and calculated their age in generations (g) by using DMLE+2.2 software. Three distinct common haplotypes, one for p.Tyr179Cys and two for p.Gly396Asp, were identified. Estimated mutation ages were 305 g (95% CS: 271-418) for p.Tyr179Cys and 350 g (95% CS: 313-435) for p.Gly396Asp. These results provide evidence for strong founder effects and suggest that the p.Tyr179Cys and p.Gly396Asp mutations derive from ancestors who lived between 5-8 thousand years and 6-9 thousand years B.C., respectively.
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