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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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Spier I, Yin X, Richardson M, Pineda M, Laner A, Ritter D, Boyle J, Mur P, Hansen TVO, Shi X, Mahmood K, Plazzer JP, Ognedal E, Nordling M, Farrington SM, Yamamoto G, Baert-Desurmont S, Martins A, Borras E, Tops C, Webb E, Beshay V, Genuardi M, Pesaran T, Capellá G, Tavtigian SV, Latchford A, Frayling IM, Plon SE, Greenblatt M, Macrae FA, Aretz S. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genet Med 2024; 26:100992. [PMID: 37800450 PMCID: PMC10922469 DOI: 10.1016/j.gim.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. METHODS Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. RESULTS The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). CONCLUSION The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
| | - Xiaoyu Yin
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | | | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | | | - Deborah Ritter
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Julie Boyle
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Australia; Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
| | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | | | | | | | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sean V Tavtigian
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Andrew Latchford
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | - Ian M Frayling
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, United Kingdom
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Marc Greenblatt
- Larner College of Medicine, University of Vermont, Burlington, VT
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
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Iizuka D, Sasatani M, Ishikawa A, Daino K, Hirouchi T, Kamiya K. Newly discovered genomic mutation patterns in radiation-induced small intestinal tumors of ApcMin/+ mice. PLoS One 2023; 18:e0292643. [PMID: 37824459 PMCID: PMC10569626 DOI: 10.1371/journal.pone.0292643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
Among the small intestinal tumors that occur in irradiated mice of the established mouse model B6/B6-Chr18MSM-F1 ApcMin/+, loss of heterozygosity analysis can be utilized to estimate whether a deletion in the wild-type allele containing the Adenomatous polyposis coli (Apc) region (hereafter referred to as Deletion), a duplication in the mutant allele with a nonsense mutation at codon 850 of Apc (Duplication), or no aberration (Unidentified) has occurred. Previous research has revealed that the number of Unidentified tumors tends to increase with the radiation dose. In the present study, we investigated the molecular mechanisms underlying the development of an Unidentified tumor type in response to radiation exposure. The mRNA expression levels of Apc were significantly lower in Unidentified tumors than in normal tissues. We focused on epigenetic suppression as the mechanism underlying this decreased expression; however, hypermethylation of the Apc promoter region was not observed. To investigate whether deletions occur that cannot be captured by loss of heterozygosity analysis, we analyzed chromosome 18 using a customized array comparative genomic hybridization approach designed to detect copy-number changes in chromosome 18. However, the copy number of the Apc region was not altered in Unidentified tumors. Finally, gene mutation analysis of the Apc region using next-generation sequencing suggested the existence of a small deletion (approximately 3.5 kbp) in an Unidentified tumor from a mouse in the irradiated group. Furthermore, nonsense and frameshift mutations in Apc were found in approximately 30% of the Unidentified tumors analyzed. These results suggest that radiation-induced Unidentified tumors arise mainly due to decreased Apc expression of an unknown regulatory mechanism that does not depend on promoter hypermethylation, and that some tumors may result from nonsense mutations which are as-yet undefined point mutations.
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Affiliation(s)
- Daisuke Iizuka
- Department of Radiation Effects Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Megumi Sasatani
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Atsuko Ishikawa
- Department of Radiation Effects Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kazuhiro Daino
- Department of Radiation Effects Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tokuhisa Hirouchi
- Department of Radiobiology, Institute for Environmental Sciences, Rokkasho, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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Jinda W, Moungthard H, Limwongse C, Pithukpakorn M, Saelee P, Pokkasup N, Khunpukdee S, Sukthaworn S, Jumpasri J. Identification of Genomic Alterations in Thai Patients With Colorectal Cancer Using Next-Generation Sequencing-Based Multigene Cancer Panel. Cureus 2023; 15:e39067. [PMID: 37323311 PMCID: PMC10267666 DOI: 10.7759/cureus.39067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is one of the leading causes of death and illness in the general population. Although the incidence of CRC is steadily decreasing worldwide, it is being diagnosed more in individuals under 50 years of age. Multiple disease-causing variants have been reported to be involved in the development of CRC. This study aimed to investigate the molecular and clinical characteristics of Thai patients with CRC. Methods NGS-based multigene cancer panel testing was performed on 21 unrelated patients. Target enrichment was performed using a custom-designed Ion AmpliSeq on-demand panel. Thirty-six genes associated with CRC and other cancer were analyzed for variant detection. Results Sixteen variants (five nonsense, eight missense, two deletions, and one duplication) in nine genes were identified in 12 patients. Eight (66.7%) patients harboring disease-causing deleterious variants in genes APC, ATM, BRCA2, MSH2, and MUTYH. One of the eight patients also carried additional heterozygous variants in genes ATM, BMPR1A, and MUTYH. In addition, four patients carried variants of uncertain significance in genes APC, MLH1, MSH2, STK11, and TP53. Among all detected genes, APC was the most frequent causative gene observed in CRC patients, which is consistent with previous reports. Conclusion This study demonstrated the comprehensive molecular and clinical characterization of CRC patients. These findings showed the benefits of using multigene cancer panel sequencing for pathogenic gene detection and showed the prevalence of genetic aberrations in Thai patients with CRC.
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Affiliation(s)
- Worapoj Jinda
- Division of Research and Technology Assessment, National Cancer Institute, Bangkok, THA
| | - Hathaiwan Moungthard
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | - Chanin Limwongse
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, THA
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, THA
| | - Pensri Saelee
- Division of Research and Technology Assessment, National Cancer Institute, Bangkok, THA
| | - Nareerat Pokkasup
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | - Saipan Khunpukdee
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | | | - Jaruphan Jumpasri
- Division of Policy and Medical Strategy Development, National Cancer Institute, Bangkok, THA
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Kaissarian NM, Meyer D, Kimchi-Sarfaty C. Synonymous Variants: Necessary Nuance in our Understanding of Cancer Drivers and Treatment Outcomes. J Natl Cancer Inst 2022; 114:1072-1094. [PMID: 35477782 PMCID: PMC9360466 DOI: 10.1093/jnci/djac090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Once called "silent mutations" and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.
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Affiliation(s)
- Nayiri M Kaissarian
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
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Cai D, He F, Xu X, Xiong F, Zhang L. APC c.4621C>T variant causing Gardner's syndrome in a Han Chinese family may be inherited through maternal mosaicism. Exp Ther Med 2021; 21:488. [PMID: 33790997 PMCID: PMC8005673 DOI: 10.3892/etm.2021.9919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/15/2020] [Indexed: 12/03/2022] Open
Abstract
Gardner's syndrome is a rare autosomal dominant hereditary disease that is characterized by multiple colorectal polyps combined with extra-colonic presentation (such as osteoma or desmoid tumors) of familial adenomatous polyposis syndrome. Gardner's syndrome is caused by the mutation of the adenomatous polyposis coli (APC) gene, which is located at 5q21. The aim of the current study was to investigate the APC gene mutations present in a Han Chinese family diagnosed with Gardner's syndrome. The 38-year-old proband presented with clinical symptoms, and was later diagnosed with Gardner's syndrome. Genomic DNA was extracted from the peripheral venous blood of 150 normal controls as well as the family members of the proband. Analysis of the respective APC gene sequences was performed using PCR amplification and Sanger sequencing. Pathogenesis associated with the APC mutation was investigated using reverse-transcription quantitative PCR and determined through bioinformatics approaches. Haplotype analysis was performed to identify the genetic source of the mutation(s). In the initial screening for APC variants, the APC c.4621C>T variant was detected in the proband and his son, but was not detected in the proband's affected mother. The mRNA expression changed significantly according to age and the presence of the mutation in the blood of the patients. Haplotype analysis suggested the presence of maternal mosaicism for this mutation. Haplotype analysis revealed that the APC c.4621C>T variant in a patient with Gardner's syndrome was most likely derived from his mother through mosaicism. These results indicate the necessity to verify the possibility of gonadal mosaicism when a proband diagnosed with Gardner's syndrome appears to exhibit a de novo mutation.
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Affiliation(s)
- Decheng Cai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fei He
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Leitao Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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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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Jansen AML, Goel A. Mosaicism in Patients With Colorectal Cancer or Polyposis Syndromes: A Systematic Review. Clin Gastroenterol Hepatol 2020; 18:1949-1960. [PMID: 32147591 PMCID: PMC7725418 DOI: 10.1016/j.cgh.2020.02.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Somatic mosaicism, in which variants arise post-zygotically and are therefore not present in all cells in the body, may be an underestimated cause of colorectal cancer (CRC) and polyposis syndromes. We performed a systematic review to provide a comprehensive overview of somatic mosaicism in patients with CRC and polyposis syndromes. METHODS We searched PubMed through March 2018 to identify reports of mosaicism in patients with CRC or polyposis syndromes. We divided the final set of studies into 3 subgroups describing APC mosaicism, mosaicism in other CRC susceptibility genes, and epigenetic mosaicism. RESULTS Of the 232 articles identified in our systematic search, 46 met the criteria for further analysis. Of these, 35 studies described mosaic variants or epimutations in patients with CRC or polyposis syndromes. Nineteen studies described APC mosaicism, comprising a total of 57 patients. Six described mosaicism in genes associated with familial CRC syndromes, such as Lynch and Cowden syndromes. Ten studies described epigenetic mosaicism, sometimes resulting from a germline variant (such as deletion of EPCAM). CONCLUSIONS We found that somatic mosaicism is underdiagnosed but critical for determining the clinical management of patients with de novo polyposis who possibly carry mosaic APC variants, and present a decision tree for the clinical management of these patients. Mosaicism in genes associated with susceptibility to CRC contributes to development of other familial CRC syndromes. Heritable epigenetic mosaicism is likely underestimated and could have a dominant pattern of inheritance. However, the inheritance of primary mosaic epimutations, without an underlying genetic cause, is complex and not fully understood.
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Affiliation(s)
- Anne Maria Lucia Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California.
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APC and MUTYH Analysis in FAP Patients: A Novel Mutation in APC Gene and Genotype-Phenotype Correlation. Genes (Basel) 2018; 9:genes9070322. [PMID: 29954149 PMCID: PMC6071208 DOI: 10.3390/genes9070322] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
APC and MUTYH genes are mutated in 70⁻90% and 10⁻30% of familial adenomatous polyposis cases (FAP) respectively. An association between mutation localization and FAP clinical phenotype is reported. The aims of this study were to determine APC and MUTYH mutational status in a small cohort of FAP patients and to evaluate the genotype-phenotype correlation in mutated patients. Here, we report the identification of a novel APC germline mutation, c.510_511insA. Overall, mutational analysis showed pathogenic mutations in 6/10 patients: 5/10 in APC and 1/10 in MUTYH. Additionally, we found three variants of unknown significance in MUTYH gene that showed no evidence of possible splicing defects by in silico analysis. Molecular analysis was also extended to family members of mutated patients. A genotype-phenotype correlation was observed for colonic signs whereas a variation of disease onset age was revealed for the same mutation. Moreover, we found an intrafamilial variability of FAP onset age. Regarding extracolonic manifestations, the development of desmoid tumors was related to surgery and not to mutation position, while a genotype-phenotype correspondence was observed for the onset of thyroid or gastric cancer. These findings can be useful in association to clinical data for early surveillance and suitable treatment of FAP patients.
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Alternative splicing within the Wnt signaling pathway: role in cancer development. Cell Oncol (Dordr) 2016; 39:1-13. [PMID: 26762488 DOI: 10.1007/s13402-015-0266-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Wnt signaling cascade plays a fundamental role in embryonic development, adult tissue regeneration, homeostasis and stem cell maintenance. Abnormal Wnt signaling has been found to be prevalent in various human cancers. Also, a role of Wnt signaling in the regulation of alternative splicing of several cancer-related genes has been established. In addition, accumulating evidence suggests the existence of multiple splice isoforms of Wnt signaling cascade components, including Wnt ligands, receptors, components of the destruction complex and transcription activators/suppressors. The presence of multiple Wnt signaling-related isoforms may affect the functionality of the Wnt pathway, including its deregulation in cancer. As such, specific Wnt pathway isoform components may serve as therapeutic targets or as biomarkers for certain human cancers. Here, we review the role of alternative splicing of Wnt signaling components during the onset and progression of cancer. CONCLUSIONS Splice isoforms of components of the Wnt signaling pathway play distinct roles in cancer development. Isoforms of the same component may function in a tissue- and/or cancer-specific manner. Splice isoform expression analyses along with deregulated Wnt signaling pathway analyses may be of help to design efficient diagnostic and therapeutic strategies.
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Esplin ED, Snyder MP. Genomic era diagnosis and management of hereditary and sporadic colon cancer. World J Clin Oncol 2014; 5:1036-1047. [PMID: 25493239 PMCID: PMC4259930 DOI: 10.5306/wjco.v5.i5.1036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/21/2014] [Accepted: 05/16/2014] [Indexed: 02/06/2023] Open
Abstract
The morbidity and mortality attributable to heritable and sporadic carcinomas of the colon are substantial and affect children and adults alike. Despite current colonoscopy screening recommendations colorectal adenocarcinoma (CRC) still accounts for almost 140000 cancer cases yearly. Familial adenomatous polyposis (FAP) is a colon cancer predisposition due to alterations in the adenomatous polyposis coli gene, which is mutated in most CRC. Since the beginning of the genomic era next-generation sequencing analyses of CRC continue to improve our understanding of the genetics of tumorigenesis and promise to expand our ability to identify and treat this disease. Advances in genome sequence analysis have facilitated the molecular diagnosis of individuals with FAP, which enables initiation of appropriate monitoring and timely intervention. Genome sequencing also has potential clinical impact for individuals with sporadic forms of CRC, providing means for molecular diagnosis of CRC tumor type, data guiding selection of tumor targeted therapies, and pharmacogenomic profiles specifying patient specific drug tolerances. There is even a potential role for genomic sequencing in surveillance for recurrence, and early detection, of CRC. We review strategies for diagnostic assessment and management of FAP and sporadic CRC in the current genomic era, with emphasis on the current, and potential for future, impact of genome sequencing on the clinical care of these conditions.
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Spier I, Horpaopan S, Vogt S, Uhlhaas S, Morak M, Stienen D, Draaken M, Ludwig M, Holinski-Feder E, Nöthen MM, Hoffmann P, Aretz S. Deep intronic APC mutations explain a substantial proportion of patients with familial or early-onset adenomatous polyposis. Hum Mutat 2012; 33:1045-50. [PMID: 22431159 DOI: 10.1002/humu.22082] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/05/2012] [Indexed: 01/13/2023]
Abstract
To uncover pathogenic deep intronic variants in patients with colorectal adenomatous polyposis, in whom no germline mutation in the APC or MUTYH genes can be identified by routine diagnostics, we performed a systematic APC messenger RNA analysis in 125 unrelated mutation-negative cases. Overall, we identified aberrant transcripts in 8% of the patients (familial cases 30%; early-onset manifestation 21%). In eight of them, two different out-of-frame pseudoexons were found consisting of a 167-bp insertion from intron 4 in five families with a shared founder haplotype and a 83-bp insertion from intron 10 in three patients. The pseudoexon formation was caused by three different heterozygous germline mutations, which are supposed to activate cryptic splice sites. In conclusion, a few deep intronic mutations contribute substantially to the APC mutation spectrum. Complementary DNA analysis and/or target sequencing of intronic regions should be considered as an additional mutation discovery approach in polyposis patients.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25,Bonn, Germany.
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Inactivation of promoter 1B of APC causes partial gene silencing: evidence for a significant role of the promoter in regulation and causative of familial adenomatous polyposis. Oncogene 2011; 30:4977-89. [PMID: 21643010 PMCID: PMC3240859 DOI: 10.1038/onc.2011.201] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Familial adenomatous polyposis (FAP) is caused by germline mutations in the adenomatous polyposis coli (APC) gene. Two promoters, 1A and 1B, have been recognized in APC, and 1B is thought to have a minor role in the regulation of the gene. We have identified a novel deletion encompassing half of this promoter in the largest family (Family 1) of the Swedish Polyposis Registry. The mutation leads to an imbalance in allele-specific expression of APC, and transcription from promoter 1B was highly impaired in both normal colorectal mucosa and blood from mutation carriers. To establish the significance of promoter 1B in normal colorectal mucosa (from controls), expression levels of specific transcripts from each of the promoters, 1A and 1B, were examined, and the expression from 1B was significantly higher compared with 1A. Significant amounts of transcripts generated from promoter 1B were also determined in a panel of 20 various normal tissues examined. In FAP-related tumors, the APC germline mutation is proposed to dictate the second hit. Mutations leaving two or three out of seven 20-amino-acid repeats in the central domain of APC intact seem to be required for tumorigenesis. We examined adenomas from mutation carriers in Family 1 for second hits in the entire gene without any findings, however, loss of the residual expression of the deleterious allele was observed. Three major conclusions of significant importance in relation to the function of APC can be drawn from this study; (i) germline inactivation of promoter 1B is disease causing in FAP; (ii) expression of transcripts from promoter 1B is generated at considerable higher levels compared with 1A, demonstrating a hitherto unknown importance of 1B; (iii) adenoma formation in FAP, caused by impaired function of promoter 1B, does not require homozygous inactivation of APC allowing for alternative genetic models as basis for adenoma formation.
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Bonilla C, Lefèvre JH, Winney B, Johnstone E, Tonks S, Colas C, Day T, Hutnik K, Boumertit A, Midgley R, Kerr D, Parc Y, Bodmer WF. Cyclin D1 rare variants in UK multiple adenoma and early-onset colorectal cancer patients. J Hum Genet 2010; 56:58-63. [PMID: 21107342 DOI: 10.1038/jhg.2010.144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We examined the influence that rare variants and low-frequency polymorphisms in the cancer candidate gene CCND1 have on the development of multiple intestinal adenomas and the early onset of colorectal cancer. Individuals with <100 multiple polyps and patients with colorectal cancer diagnosed before 50 years of age were recruited in UK, and screened for sequence changes in the coding and regulatory regions of CCND1. A set of about 800 UK control individuals was genotyped for the variants discovered in the cases. Variants in the promoter, intron-exon boundaries and untranslated regions of the CCND1 gene had higher frequencies in cases than in controls. Five of these variants were typed in a set of French multiple adenoma and early-onset patients, who also showed higher allele frequencies than UK controls. When pooled together, variants with frequencies lower than 1% conferred an increased risk of disease that was significant in the multiple adenoma group (odds ratio (OR) 2.2; 95% confidence interval, 1.1-4.4; P = 0.03). Most variants had a putative functional effect when assessed in silico. We conclude that rare variants of CCND1 are risk factors for colorectal cancer, with considerably larger effects than common polymorphisms, and as such should be systematically evaluated in susceptibility studies.
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Affiliation(s)
- Carolina Bonilla
- Department of Clinical Pharmacology, University of Oxford, Headington, Oxford, UK
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Heinen CD. Genotype to phenotype: analyzing the effects of inherited mutations in colorectal cancer families. Mutat Res 2010; 693:32-45. [PMID: 19766128 PMCID: PMC2891646 DOI: 10.1016/j.mrfmmm.2009.09.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
With improvements to DNA sequencing technologies, including the advent of massively parallel sequencing to perform "deep sequencing" of tissue samples, the ability to determine all of the nucleotide variations in a tumor becomes a possibility. This information will allow us to more fully understand the heterogeneity within each tumor, as well as to identify novel genes involved in cancer development. However, the new challenge that arises will be to interpret the pathogenic significance of each genetic variant. The enormity and complexity of this challenge can be demonstrated by focusing on just the genes involved in the hereditary colon cancer syndromes, familial adenomatous polyposis (FAP) and hereditary non-polyposis coli (HNPCC). The genes responsible for each disease were identified almost two decades ago -APC for FAP and the MMR genes for HNPCC - and a large number of germline variations have been identified in these genes in hereditary cancer patients. However, relating the effect of an individual genotype to phenotype is not always straightforward. This review focuses on the roles of the APC and MMR genes in tumor development and the work that has been done to relate different variants in each gene to functional aberrations and ultimately tumorigenesis. By considering the work that has already been done on two well-defined diseases with clear genetic associations, one can begin to understand the challenges that lie ahead as new genes and gene mutations are discovered through tumor sequencing.
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Affiliation(s)
- Christopher D Heinen
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA.
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Castellsagué E, González S, Guinó E, Stevens KN, Borràs E, Raymond VM, Lázaro C, Blanco I, Gruber SB, Capellá G. Allele-specific expression of APC in adenomatous polyposis families. Gastroenterology 2010; 139:439-47, 447.e1. [PMID: 20434453 PMCID: PMC2910837 DOI: 10.1053/j.gastro.2010.04.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 03/24/2010] [Accepted: 04/21/2010] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Germline mutations in the APC gene cause of most cases of familial adenomatous polyposis (FAP) and a lesser proportion of attenuated FAP (AFAP). Systematic analysis of APC at the RNA level could provide insight into the pathogenicity of identified mutations and the molecular basis of FAP/AFAP in families without identifiable mutations. Here, we analyzed the prevalence of imbalances in the allelic expression of APC in polyposis families with germline mutations in the gene and without detectable mutations in APC and/or MUTYH. METHODS Allele-specific expression (ASE) was determined by single nucleotide primer extension using an exon 11 polymorphism as an allele-specific marker. In total, 52 APC-mutation-positive (36 families) and 24 APC/MUTYH-mutation-negative (23 families) informative patients were analyzed. Seventy-six controls also were included. RESULTS Of the APC-mutation-positive families, most of those in whom the mutation was located before the last exon of the gene (12 of 14) had ASE imbalance, which is consistent with a mechanism of nonsense-mediated decay. Of the APC/MUTYH-mutation-negative families, 2 (9%) had ASE imbalance, which might cause the disease. Normal allele expression was restored shortly after lymphocytes were cultured with puromycin, supporting a 'nonsense-mediated' hypothesis. CONCLUSIONS ASE analysis might be used to determine the pathogenesis of some cases of FAP and AFAP in which APC mutations are not found. ASE also might be used to prioritize the order in which different areas of APC are tested. RNA-level studies are important for the molecular diagnosis of FAP.
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Affiliation(s)
- Ester Castellsagué
- Translational Research Laboratory, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
| | - Sara González
- Translational Research Laboratory, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
| | - Elisabet Guinó
- Bioinformatics and Biostatistics Unit, Department of Epidemiology, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
| | - Kristen N. Stevens
- Department of Epidemiology, University of Michigan, Ann Arbor MI 48109, Michigan, USA
| | - Ester Borràs
- Translational Research Laboratory, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
| | - Victoria M. Raymond
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI 48109, Michigan, USA
| | - Conxi Lázaro
- Translational Research Laboratory, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
| | - Ignacio Blanco
- Cancer Genetic Counseling Program, IDIBELL-Institut Català d’Oncologia, Barcelona, Spain
| | - Stephen B. Gruber
- Department of Internal Medicine, Epidemiology, and Human Genetics, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor MI 48109, Michigan, USA
| | - Gabriel Capellá
- Translational Research Laboratory, IDIBELL-Institut Català d’Oncologia, Barcelona 08907, Spain
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Clinical relevance of rare germline sequence variants in cancer genes: evolution and application of classification models. Curr Opin Genet Dev 2010; 20:315-23. [PMID: 20456937 DOI: 10.1016/j.gde.2010.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 12/11/2022]
Abstract
Multifactorial models developed for BRCA1/2 variant classification have proved very useful for delineating BRCA1/2 variants associated with very high risk of cancer, or with little clinical significance. Recent linkage of this quantitative assessment of risk to clinical management guidelines has provided a basis to standardize variant reporting, variant classification and management of families with such variants, and can theoretically be applied to any disease gene. As proof of principle, the multifactorial approach already shows great promise for application to the evaluation of mismatch repair gene variants identified in families with suspected Lynch syndrome. However there is need to be cautious of the noted limitations and caveats of the current model, some of which may be exacerbated by differences in ascertainment and biological pathways to disease for different cancer syndromes.
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Large intron 14 rearrangement in APC results in splice defect and attenuated FAP. Hum Genet 2009; 127:359-69. [PMID: 20033212 DOI: 10.1007/s00439-009-0776-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
Abstract
Familial adenomatous polyposis [FAP (OMIM 175100)] is an autosomal dominant colorectal cancer predisposition syndrome characterized by hundreds to thousands of colonic polyps and, if untreated by a combination of screening and/or surgical intervention, an approximately 99% lifetime risk of colorectal cancer. A subset of FAP patients develop an attenuated form of the condition characterized by lower numbers of colonic polyps (highly variable, but generally less than 100) and a lower lifetime risk of colorectal cancer, on the order of 70%. We report the diagnosis of three attenuated FAP families due to a 1.4-kb deletion within intron 14 of APC, originally reported clinically as a variant of unknown significance (VUS). Sequence analysis suggests that this arose through an Alu-mediated recombination event with a locus on chromosome 6q22.1. This mutation is inherited by family members who presented with an attenuated FAP phenotype, with variable age of onset and severity. Sequence analysis of mRNA revealed an increase in the level of aberrant splicing of exon 14, resulting in the generation of an exon 13-exon 15 splice-form that is predicted to lead to a frameshift and protein truncation at codon 673. The relatively mild phenotypic presentation and the intra-familial variation are consistent with the leaky nature of exon 14 splicing in normal APC. The inferred founder of these three families may account for as yet undetected affected branches of this kindred. This and similar types of intronic mutations may account for a significant proportion of FAP cases where APC clinical analysis fails because of the current limitations of testing options.
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