1
|
Chan JM, Clendenning M, Joseland S, Georgeson P, Mahmood K, Joo JE, Walker R, Como J, Preston S, Chai SM, Chu YL, Meyers AL, Pope BJ, Duggan D, Fink JL, Macrae FA, Rosty C, Winship IM, Jenkins MA, Buchanan DD. Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family. Fam Cancer 2024; 23:9-21. [PMID: 38063999 PMCID: PMC10869370 DOI: 10.1007/s10689-023-00351-2] [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: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 02/17/2024]
Abstract
Genetic susceptibility to familial colorectal cancer (CRC), including for individuals classified as Familial Colorectal Cancer Type X (FCCTX), remains poorly understood. We describe a multi-generation CRC-affected family segregating pathogenic variants in both BRCA1, a gene associated with breast and ovarian cancer and RNF43, a gene associated with Serrated Polyposis Syndrome (SPS). A single family out of 105 families meeting the criteria for FCCTX (Amsterdam I family history criteria with mismatch repair (MMR)-proficient CRCs) recruited to the Australasian Colorectal Cancer Family Registry (ACCFR; 1998-2008) that underwent whole exome sequencing (WES), was selected for further testing. CRC and polyp tissue from four carriers were molecularly characterized including a single CRC that underwent WES to determine tumor mutational signatures and loss of heterozygosity (LOH) events. Ten carriers of a germline pathogenic variant BRCA1:c.2681_2682delAA p.Lys894ThrfsTer8 and eight carriers of a germline pathogenic variant RNF43:c.988 C > T p.Arg330Ter were identified in this family. Seven members carried both variants, four of which developed CRC. A single carrier of the RNF43 variant met the 2019 World Health Organization (WHO2019) criteria for SPS, developing a BRAF p.V600 wildtype CRC. Loss of the wildtype allele for both BRCA1 and RNF43 variants was observed in three CRC tumors while a LOH event across chromosome 17q encompassing both genes was observed in a CRC. Tumor mutational signature analysis identified the homologous recombination deficiency (HRD)-associated COSMIC signatures SBS3 and ID6 in a CRC for a carrier of both variants. Our findings show digenic inheritance of pathogenic variants in BRCA1 and RNF43 segregating with CRC in a FCCTX family. LOH and evidence of BRCA1-associated HRD supports the importance of both these tumor suppressor genes in CRC tumorigenesis.
Collapse
Affiliation(s)
- James M Chan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Shuyi Marci Chai
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Yen Lin Chu
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron L Meyers
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Duggan
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - J Lynn Fink
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Queensland University of Technology, Brisbane, QLD, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Envoi Pathology, Brisbane, QLD, Australia
- School of Medicine, University of Queensland, Herston, QLD, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Mark A Jenkins
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia.
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia.
| |
Collapse
|
2
|
Olkinuora AP, Mayordomo AC, Kauppinen AK, Cerliani MB, Coraglio M, Collia ÁK, Gutiérrez A, Alvarez K, Cassana A, Lopéz-Köstner F, Jauk F, García-Rivello H, Ristimäki A, Koskenvuo L, Lepistö A, Nieminen TT, Vaccaro CA, Pavicic WH, Peltomäki P. Mono- and biallelic germline variants of DNA glycosylase genes in colon adenomatous polyposis families from two continents. Front Oncol 2022; 12:870863. [DOI: 10.3389/fonc.2022.870863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, biallelic germline variants of the DNA glycosylase genes MUTYH and NTHL1 were linked to polyposis susceptibility. Significant fractions remain without a molecular explanation, warranting searches for underlying causes. We used exome sequencing to investigate clinically well-defined adenomatous polyposis cases and families from Finland (N=34), Chile (N=21), and Argentina (N=12), all with known susceptibility genes excluded. Nine index cases (13%) revealed germline variants with proven or possible pathogenicity in the DNA glycosylase genes, involving NEIL1 (mono- or biallelic) in 3 cases, MUTYH (monoallelic) in 3 cases, NTHL1 (biallelic) in 1 case, and OGG1 (monoallelic) in 2 cases. NTHL1 was affected with the well-established, pathogenic c.268C>T, p.(Gln90Ter) variant. A recurrent heterozygous NEIL1 c.506G>A, p.(Gly169Asp) variant was observed in two families. In a Finnish family, the variant occurred in trans with a truncating NEIL1 variant (c.821delT). In an Argentine family, the variant co-occurred with a genomic deletion of exons 2 – 11 of PMS2. Mutational signatures in tumor tissues complied with biological functions reported for NEIL1. Our results suggest that germline variants in DNA glycosylase genes may occur in a non-negligible proportion of unexplained colon polyposis cases and may predispose to tumor development.
Collapse
|
3
|
Djursby M, Hansen TVO, Wadt KAW, Madsen MB, Berchtold LA, Lautrup CK, Markholt S, Jensen UB, Krogh LN, Lundsgaard M, Gerdes AM, Nilbert M, Therkildsen C. Clinical implications of genetic testing in familial intermediate and late-onset colorectal cancer. Hum Genet 2022; 141:1925-1933. [PMID: 35904628 DOI: 10.1007/s00439-022-02470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
Abstract
The genetic background of familial, late-onset colorectal cancer (CRC) (i.e., onset > age 50 years) has not been studied as thoroughly as other subgroups of familial CRC, and the proportion of families with a germline genetic predisposition to CRC remains to be defined. To define the contribution of known or suggested CRC predisposition genes to familial late-onset CRC, we analyzed 32 well-established or candidate CRC predisposition genes in 75 families with late-onset CRC. We identified pathogenic or likely pathogenic variants in five patients in MSH6 (n = 1), MUTYH (monoallelic; n = 2) and NTHL1 (monoallelic; n = 2). In addition, we identified a number of variants of unknown significance in particular in the lower penetrant Lynch syndrome-associated mismatch repair (MMR) gene MSH6 (n = 6). In conclusion, screening using a comprehensive cancer gene panel in families with accumulation of late-onset CRC appears not to have a significant clinical value due to the low level of high-risk pathogenic variants detected. Our data suggest that only patients with abnormal MMR immunohistochemistry (IHC) or microsatellite instability (MSI) analyses, suggestive of Lynch syndrome, or a family history indicating another cancer predisposition syndrome should be prioritized for such genetic evaluations. Variants in MSH6 and MUTYH have previously been proposed to be involved in digenic or oligogenic hereditary predisposition to CRC. Accumulation of variants in MSH6 and monoallelic, pathogenic variants in MUTYH in our study indicates that digenic or oligogenic inheritance might be involved in late-onset CRC and warrants further studies of complex types of inheritance.
Collapse
Affiliation(s)
- Malene Djursby
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Thomas van Overeem 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
| | - Karin A W Wadt
- 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
| | - Majbritt Busk Madsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lukas Adrian Berchtold
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte Kvist Lautrup
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Sara Markholt
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Malene Lundsgaard
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Anne Marie Gerdes
- 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
| | - Mef Nilbert
- Clinical Research Centre, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark.,Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Christina Therkildsen
- Clinical Research Centre, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark.,HNPCC Register, Gastro Unit, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark
| |
Collapse
|
4
|
Dell'Elice A, Cini G, Fornasarig M, Armelao F, Barana D, Bianchi F, Casalis Cavalchini GC, Maffè A, Mammi I, Pedroni M, Percesepe A, Sorrentini I, Tibiletti M, Maestro R, Quaia M, Viel A. Filling the gap: A thorough investigation for the genetic diagnosis of unsolved polyposis patients with monoallelic MUTYH pathogenic variants. Mol Genet Genomic Med 2021; 9:e1831. [PMID: 34704405 PMCID: PMC8683633 DOI: 10.1002/mgg3.1831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/23/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022] Open
Abstract
Backgrounds MUTYH‐associated polyposis (MAP) is an autosomal recessive disease caused by biallelic pathogenic variants (PV) of the MUTYH gene. The aim of this study was to investigate the genetic causes of unexplained polyposis patients with monoallelic MUTYH PV. The analysis focused on 26 patients with suspected MAP, belonging to 23 families. Ten probands carried also one or more additional MUTYH variants of unknown significance. Methods Based on variant type and on the collected clinical and molecular data, these variants were reinterpreted by applying the ACMG/AMP rules. Moreover, supplementary analyses were carried out to investigate the presence of other variants and copy number variations in the coding and promoter regions of MUTYH, as well as other polyposis genes (APC, NTHL1, POLE, POLD1, MSH3, RNF43, and MCM9). Results We reclassified 4 out of 10 MUTYH variants as pathogenic or likely pathogenic, thus supporting the diagnosis of MAP in only four cases. Two other patients belonging to the same family showed a previously undetected deletion of the APC gene promoter. No PVs were found in the other investigated genes. However, 6 out of the 18 remaining families are still interesting MAP candidates, due to the co‐presence of a class 3 MUTYH variant that could be reinterpreted in the next future. Conclusion Several efforts are necessary to fully elucidate the genetic etiology of suspected MAP patients, especially those with the most severe polyposis/tumor phenotype. Clinical data, tumor molecular profile, family history, and polyposis inheritance mode may guide variant interpretation and address supplementary studies.
Collapse
Affiliation(s)
- Anastasia Dell'Elice
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giulia Cini
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Mara Fornasarig
- Unit of Oncologic Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Franco Armelao
- U.O. Multizonale Gastroenterologia ed Endoscopia Digestiva, Ospedale Santa Chiara, Azienda Provinciale per i Servizi sanitari, Trento, Italy
| | - Daniela Barana
- Oncology Unit, Local Health and Social Care Unit, ULSS8 Berica, Montecchio Maggiore, Italy
| | - Francesca Bianchi
- Clinica Oncologica e Centro Regionale di Genetica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | | | - Antonella Maffè
- S.S. Genetica e Biologia Molecolare, S.C. Interaziendale Laboratorio Analisi Chimico Cliniche e Microbiologia, ASO S Croce e Carle, Cuneo, Italy
| | - Isabella Mammi
- Medical Genetics Unit, Dolo General Hospital, Venezia, Italy
| | - Monica Pedroni
- Dipartimento di Scienze Mediche e Chirurgiche Materno-Infantili e dell'Adulto, Università di Modena e Reggio Emilia, Modena, Italy
| | | | | | - Mariagrazia Tibiletti
- Department of Pathology, Circolo Hospital ASST Settelaghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Roberta Maestro
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Michele Quaia
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| |
Collapse
|
5
|
Olkinuora AP, Peltomäki PT, Aaltonen LA, Rajamäki K. From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet 2021; 30:R206-R224. [PMID: 34329396 PMCID: PMC8490010 DOI: 10.1093/hmg/ddab208] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9-26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.
Collapse
Affiliation(s)
- Alisa P Olkinuora
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi T Peltomäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
6
|
Toh M, Ngeow J. Homologous Recombination Deficiency: Cancer Predispositions and Treatment Implications. Oncologist 2021; 26:e1526-e1537. [PMID: 34021944 PMCID: PMC8417864 DOI: 10.1002/onco.13829] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) is a highly accurate DNA repair mechanism. Several HR genes are established cancer susceptibility genes with clinically actionable pathogenic variants (PVs). Classically, BRCA1 and BRCA2 germline PVs are associated with significant breast and ovarian cancer risks. Patients with BRCA1 or BRCA2 PVs display worse clinical outcomes but respond better to platinum-based chemotherapies and poly-ADP ribose polymerase inhibitors, a trait termed "BRCAness." With the advent of whole-exome sequencing and multigene panels, PVs in other HR genes are increasingly identified among familial cancers. As such, several genes such as PALB2 are reclassified as cancer predisposition genes. But evidence for cancer risks remains unclear for many others. In this review, we will discuss cancer predispositions and treatment implications beyond BRCA1 and BRCA2, with a focus on 24 HR genes: 53BP1, ATM, ATR, ATRIP, BARD1, BLM, BRIP1, DMC1, MRE11A, NBN, PALB2, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RIF1, RMI1, RMI2, RPA1, TOP3A, TOPBP1, XRCC2, and XRCC3. IMPLICATIONS FOR PRACTICE: This review provides a comprehensive reference for readers to quickly identify potential cancer predisposing homologous recombination (HR) genes, and to generate research questions for genes with inconclusive evidence. This review also evaluates the "BRCAness" of each HR member. Clinicians can refer to these discussions to identify potential candidates for future clinical trials.
Collapse
Affiliation(s)
- MingRen Toh
- Duke–National University of Singapore Medical SchoolSingapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer CenterSingapore
- Lee Kong Chian School of Medicine, Nanyang Technological UniversitySingapore
| |
Collapse
|
7
|
Exome sequencing of early-onset patients supports genetic heterogeneity in colorectal cancer. Sci Rep 2021; 11:11135. [PMID: 34045552 PMCID: PMC8159954 DOI: 10.1038/s41598-021-90590-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/12/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is a complex disease that can be caused by a spectrum of genetic variants ranging from low to high penetrance changes, that interact with the environment to determine which individuals will develop the disease. In this study, we sequenced 20 early-onset CRC patients to discover novel genetic variants that could be linked to the prompt disease development. Eight genes, CHAD, CHD1L, ERCC6, IGTB7, PTPN13, SPATA20, TDG and TGS1, were selected and re-sequenced in a further 304 early onset CRC patients to search for rare, high-impact variants. Although we found a recurring truncating variant in the TDG gene shared by two independent patients, the results obtained did not help consolidate any of the candidates as promising CRC predisposing genes. However, we found that potential risk alleles in our extended list of candidate variants have a tendency to appear at higher numbers in younger cases. This supports the idea that CRC onset may be oligogenic in nature and may show molecular heterogeneity. Further, larger and robust studies are thus needed to unravel the genetics behind early-onset CRC development, coupled with novel functional analyses and omic approaches that may offer complementary insight.
Collapse
|
8
|
Moscatello C, Di Nicola M, Veschi S, Di Gregorio P, Cianchetti E, Stuppia L, Battista P, Cama A, Curia MC, Aceto GM. Relationship between MUTYH, OGG1 and BRCA1 mutations and mRNA expression in breast and ovarian cancer predisposition. Mol Clin Oncol 2020; 14:15. [PMID: 33343895 PMCID: PMC7725208 DOI: 10.3892/mco.2020.2177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
The aetiology of breast and ovarian cancer (BC/OC) is multi-factorial. At present, the involvement of base excision repair (BER) glycosylases (MUTYH and OGG1) in BC/OC predisposition is controversial. The present study investigated whether germline mutation status and mRNA expression of two BER genes, MUTHY and OGG1, were correlated with BRCA1 in 59 patients with BC/OC and 50 matched population controls. In addition, to evaluate the relationship between MUTYH, OGG1 and BRCA1, their possible mutual modulation and correlation among mutational spectrum, gene expression and demographic characteristics were evaluated. The results identified 18 MUTYH and OGG1 variants, of which 4 were novel (2 MUTYH and 2 OGG1) in 44 of the 59 patients. In addition, two pathogenic mutations were identified: OGG1 p.Arg46Gln, detected in a patient with BC and a family history of cancer, and MUTYH p.Val234Gly in a patient with OC, also with a family history of cancer. A significant reduced transcript expression in MUTYH was observed (P=0.033) in cases, and in association with the presence of rare variants in the same gene (P=0.030). A significant correlation in the expression of the two BER genes was observed in cases (P=0.004), whereas OGG1 and BRCA1 was significantly correlated in cases (P=0.001) compared with controls (P=0.010). The results of the present study indicated that the relationship among mutational spectrum, gene expression and demographic characteristics may improve the genetic diagnosis and primary prevention of at-risk individuals belonging to families with reduced mRNA expression, regardless of mutation presence.
Collapse
Affiliation(s)
- Carmelo Moscatello
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Marta Di Nicola
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Serena Veschi
- Department of Pharmacy, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Patrizia Di Gregorio
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Ettore Cianchetti
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Liborio Stuppia
- Immunohaematology and Transfusional Medicine Service, 'SS. Annunziata' Hospital, I-66100 Chieti, Italy
| | - Pasquale Battista
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Alessandro Cama
- Department of Pharmacy, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Gitana Maria Aceto
- Department of Medical, Oral and Biotechnological Sciences, 'G. d'Annunzio' University of Chieti-Pescara, I-66100 Chieti, Italy
| |
Collapse
|
9
|
Byrjalsen A, Hansen TVO, Stoltze UK, Mehrjouy MM, Barnkob NM, Hjalgrim LL, Mathiasen R, Lautrup CK, Gregersen PA, Hasle H, Wehner PS, Tuckuviene R, Sackett PW, Laspiur AO, Rossing M, Marvig RL, Tommerup N, Olsen TE, Scheie D, Gupta R, Gerdes A, Schmiegelow K, Wadt K. Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes. PLoS Genet 2020; 16:e1009231. [PMID: 33332384 PMCID: PMC7787686 DOI: 10.1371/journal.pgen.1009231] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/06/2021] [Accepted: 10/28/2020] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Historically, cancer predisposition syndromes (CPSs) were rarely established for children with cancer. This nationwide, population-based study investigated how frequently children with cancer had or were likely to have a CPS. METHODS Children (0-17 years) in Denmark with newly diagnosed cancer were invited to participate in whole-genome sequencing of germline DNA. Suspicion of CPS was assessed according to Jongmans'/McGill Interactive Pediatric OncoGenetic Guidelines (MIPOGG) criteria and familial cancer diagnoses were verified using population-based registries. RESULTS 198 of 235 (84.3%) eligible patients participated, of whom 94/198 (47.5%) carried pathogenic variants (PVs) in a CPS gene or had clinical features indicating CPS. Twenty-nine of 198 (14.6%) patients harbored a CPS, of whom 21/198 (10.6%) harbored a childhood-onset and 9/198 (4.5%) an adult-onset CPS. In addition, 23/198 (11.6%) patients carried a PV associated with biallelic CPS. Seven of the 54 (12.9%) patients carried two or more variants in different CPS genes. Seventy of 198 (35.4%) patients fulfilled the Jongmans' and/or MIPOGG criteria indicating an underlying CPS, including two of the 9 (22.2%) patients with an adult-onset CPS versus 18 of the 21 (85.7%) patients with a childhood-onset CPS (p = 0.0022), eight of the additional 23 (34.8%) patients with a heterozygous PV associated with biallelic CPS, and 42 patients without PVs. Children with a central nervous system (CNS) tumor had family members with CNS tumors more frequently than patients with other cancers (11/44, p = 0.04), but 42 of 44 (95.5%) cases did not have a PV in a CPS gene. CONCLUSION These results demonstrate the value of systematically screening pediatric cancer patients for CPSs and indicate that a higher proportion of childhood cancers may be linked to predisposing germline variants than previously supposed.
Collapse
Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas V. O. Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik K. Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Mana M. Mehrjouy
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Nanna Moeller Barnkob
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Lisa L. Hjalgrim
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - René Mathiasen
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | | | - Henrik Hasle
- Department of Paediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Peder S. Wehner
- Department of Paediatric Hematology and Oncology, H. C. Andersen Children’s Hospital, Odense University Hospital, Odense, Denmark
| | - Ruta Tuckuviene
- Department of Paediatrics and Adolescent Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - Peter Wad Sackett
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Adrian O. Laspiur
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Tina Elisabeth Olsen
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ramneek Gupta
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Anne–Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- * E-mail:
| |
Collapse
|
10
|
Djursby M, Madsen MB, Frederiksen JH, Berchtold LA, Therkildsen C, Willemoe GL, Hasselby JP, Wikman F, Okkels H, Skytte AB, Nilbert M, Wadt K, Gerdes AM, van Overeem Hansen T. New Pathogenic Germline Variants in Very Early Onset and Familial Colorectal Cancer Patients. Front Genet 2020; 11:566266. [PMID: 33193653 PMCID: PMC7541943 DOI: 10.3389/fgene.2020.566266] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/24/2020] [Indexed: 12/30/2022] Open
Abstract
A genetic diagnosis facilitates personalized cancer treatment and clinical care of relatives at risk, however, although 25% of colorectal cancer cases are familial, around 95% of the families are genetically unresolved. In this study, we performed gene panel analysis on germline DNA of 32 established or candidate colorectal cancer predisposing genes in 149 individuals from either families with an accumulation of colorectal cancers or families with only one sporadic case of very early onset colorectal cancer (≤40 years at diagnosis). We identified pathogenic or likely pathogenic genetic variants in 10.1% of the participants in genes such as APC, POLE, MSH2 or PMS2. The MSH2 variant, c.2168C>T, p.(Ser723Phe) was previously described as a variant of unknown significance, but we have now reclassified it to be likely pathogenic. The POLE variant, c.1089C>A, p.(Asn363Lys) was identified in a patient with three metachronous colorectal cancers from age 28 and turned out to be de novo. One pathogenic PMS2 variant was novel. We also identified a number of highly interesting variants of unknown significance in APC, BUB1, TP53 and RPS20. The RPS20 variant is novel and was found in a large Amsterdam I positive family with a multi tumor phenotype including 12 cases of CRC from as early as age 24. This variant was found to segregate with cancer in the family and multiple in silico tools predict it to be pathogenic. Our data further support the shift from phenotypic-based cancer panels to large panels including all established genes involved in hereditary cancer syndromes or (targeted) whole genome sequencing. Additionally, identification of a likely disease-predisposing variant in RPS20 expands the phenotypic spectrum of RPS20-related cancers and emphasize that this gene is relevant to include in colorectal cancer gene panels.
Collapse
Affiliation(s)
- Malene Djursby
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Majbritt B Madsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jane H Frederiksen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lukas A Berchtold
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christina Therkildsen
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Gro L Willemoe
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jane P Hasselby
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Friedrik Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Okkels
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mef Nilbert
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| |
Collapse
|
11
|
Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
Collapse
Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| |
Collapse
|
12
|
Schubert SA, Ruano D, Tiersma Y, Drost M, de Wind N, Nielsen M, van Hest LP, Morreau H, de Miranda NFCC, van Wezel T. Digenic inheritance of MSH6 and MUTYH variants in familial colorectal cancer. Genes Chromosomes Cancer 2020; 59:697-701. [PMID: 32615015 PMCID: PMC7689793 DOI: 10.1002/gcc.22883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
We describe a family severely affected by colorectal cancer (CRC) where whole-exome sequencing identified the coinheritance of the germline variants encoding MSH6 p.Thr1100Met and MUTYH p.Tyr179Cys in, at least, three CRC patients diagnosed before 60 years of age. Digenic inheritance of monoallelic MSH6 variants of uncertain significance and MUTYH variants has been suggested to predispose to Lynch syndrome-associated cancers; however, cosegregation with disease in the familial setting has not yet been established. The identification of individuals carrying multiple potential cancer risk variants is expected to rise with the increased application of whole-genome sequencing and large multigene panel testing in clinical genetic counseling of familial cancer patients. Here we demonstrate the coinheritance of monoallelic variants in MSH6 and MUTYH consistent with cosegregation with CRC, further supporting a role for digenic inheritance in cancer predisposition.
Collapse
Affiliation(s)
| | - Dina Ruano
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Yvonne Tiersma
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Mark Drost
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Niels de Wind
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maartje Nielsen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Liselotte P. van Hest
- Department of Clinical GeneticsAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Hans Morreau
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | | | - Tom van Wezel
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| |
Collapse
|
13
|
Terradas M, Capellá G, Valle L. Dominantly Inherited Hereditary Nonpolyposis Colorectal Cancer Not Caused by MMR Genes. J Clin Med 2020; 9:jcm9061954. [PMID: 32585810 PMCID: PMC7355797 DOI: 10.3390/jcm9061954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/30/2022] Open
Abstract
In the past two decades, multiple studies have been undertaken to elucidate the genetic cause of the predisposition to mismatch repair (MMR)-proficient nonpolyposis colorectal cancer (CRC). Here, we present the proposed candidate genes according to their involvement in specific pathways considered relevant in hereditary CRC and/or colorectal carcinogenesis. To date, only pathogenic variants in RPS20 may be convincedly linked to hereditary CRC. Nevertheless, accumulated evidence supports the involvement in the CRC predisposition of other genes, including MRE11, BARD1, POT1, BUB1B, POLE2, BRF1, IL12RB1, PTPN12, or the epigenetic alteration of PTPRJ. The contribution of the identified candidate genes to familial/early onset MMR-proficient nonpolyposis CRC, if any, is extremely small, suggesting that other factors, such as the accumulation of low risk CRC alleles, shared environmental exposures, and/or gene-environmental interactions, may explain the missing heritability in CRC.
Collapse
Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-93-260-7145
| |
Collapse
|
14
|
Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
Collapse
Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
| |
Collapse
|
15
|
Henn J, Spier I, Adam RS, Holzapfel S, Uhlhaas S, Kayser K, Plotz G, Peters S, Aretz S. Diagnostic yield and clinical utility of a comprehensive gene panel for hereditary tumor syndromes. Hered Cancer Clin Pract 2019; 17:5. [PMID: 30680046 PMCID: PMC6343270 DOI: 10.1186/s13053-018-0102-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/12/2018] [Indexed: 12/31/2022] Open
Abstract
Background In a considerable number of patients with a suspected hereditary tumor syndrome (HTS), no underlying germline mutation is detected in the most likely affected genes. The present study aimed to establish and validate a large gene panel for HTS, and determine its diagnostic yield and clinical utility. Methods The study cohort comprised 173 patients with suspected, but unexplained, HTS (group U) and 64 HTS patients with a broad spectrum of known germline mutations (group K). All patients in group U presented with early age at onset, multiple tumors, and/or a familial clustering of various tumor types; no germline mutation had been identified during routine diagnostics. Sequencing of leukocyte DNA was performed for the 94 HTS genes of the Illumina TruSight™Cancer Panel and 54 additional HTS genes. Results The sensitivity of the panel to identify known germline variants was 99.6%. In addition to known mutations, a total of 192 rare, potentially pathogenic germline variants in 86 genes were identified. Neither the proportion of rare variants per patient (group K: 0.9 variants; group U: 0.8 variants) nor the proportion of variants in the most frequently mutated, moderately penetrant genes CHEK2 and ATM showed significant inter-group difference. Four of the five patients from group U with a truncating CHEK2 mutation had thyroid cancer, pointing to a broader tumor spectrum in patients with pathogenic CHEK2 variants. In 22% of patients from group K, a further potential causative variant was identified. Here, the most interesting finding was an NF1 nonsense mutation in a child with a known TP53 frameshift mutation. In 17% of patients from group U, potential causative variants were identified. In three of these patients (2%), mutations in PMS2, PTEN, or POLD1 were considered to be causative. In both groups, incidental findings with presumptive predictive value were generated. Conclusions The gene panel identified the genetic cause in some prescreened, unexplained HTS patients and generated incidental findings. Some patients harbored predicted pathogenic mutations in more than one established HTS gene, rendering interpretation of the respective alterations challenging. Established moderate risk genes showed an almost equal distribution among patients with known and unexplained disease.
Collapse
Affiliation(s)
- Jonas Henn
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
| | - Isabel Spier
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany.,2Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Ronja S Adam
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany.,3Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Stefanie Holzapfel
- 2Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany.,4Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Siegfried Uhlhaas
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
| | - Katrin Kayser
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
| | - Guido Plotz
- 5Department of Medicine I, Biomedical Research Laboratory, University of Frankfurt, Frankfurt, Germany
| | - Sophia Peters
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
| | - Stefan Aretz
- 1Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany.,2Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| |
Collapse
|
16
|
Mur P, Jemth AS, Bevc L, Amaral N, Navarro M, Valdés-Mas R, Pons T, Aiza G, Urioste M, Valencia A, Lázaro C, Moreno V, Puente XS, Stenmark P, Warpman-Berglund U, Capellá G, Helleday T, Valle L. Germline variation in the oxidative DNA repair genes NUDT1 and OGG1 is not associated with hereditary colorectal cancer or polyposis. Hum Mutat 2018; 39:1214-1225. [PMID: 29900613 DOI: 10.1002/humu.23564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023]
Abstract
The causal association of NUDT1 (=MTH1) and OGG1 with hereditary colorectal cancer (CRC) remains unclear. Here, we sought to provide additional evidence for or against the causal contribution of NUDT1 and OGG1 mutations to hereditary CRC and/or polyposis. Mutational screening was performed using pooled DNA amplification and targeted next-generation sequencing in 529 families (441 uncharacterized MMR-proficient familial nonpolyposis CRC and 88 polyposis cases). Cosegregation, in silico analyses, in vitro functional assays, and case-control associations were carried out to characterize the identified variants. Five heterozygous carriers of novel (n = 1) or rare (n = 4) NUDT1 variants were identified. In vitro deleterious effects were demonstrated for c.143G>A p.G48E (catalytic activity and protein stability) and c.403G>T p.G135W (protein stability), although cosegregation data in the carrier families were inconclusive or nonsupportive. The frequency of missense, loss-of-function, and splice-site NUDT1 variants in our familial CRC cohort was similar to the one observed in cancer-free individuals, suggesting lack of association with CRC predisposition. No OGG1 pathogenic mutations were identified. Our results suggest that the contribution of NUDT1 and OGG1 germline mutations to hereditary CRC and to polyposis is inexistent or, at most, negligible. The inclusion of these genes in routine genetic testing is not recommended.
Collapse
Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Luka Bevc
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nuno Amaral
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rafael Valdés-Mas
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO) and Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Alfonso Valencia
- Life Science Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, School of Medicine, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ulrika Warpman-Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| |
Collapse
|
17
|
Ciavarella M, Miccoli S, Prossomariti A, Pippucci T, Bonora E, Buscherini F, Palombo F, Zuntini R, Balbi T, Ceccarelli C, Bazzoli F, Ricciardiello L, Turchetti D, Piazzi G. Somatic APC mosaicism and oligogenic inheritance in genetically unsolved colorectal adenomatous polyposis patients. Eur J Hum Genet 2018; 26:387-395. [PMID: 29367705 PMCID: PMC5839046 DOI: 10.1038/s41431-017-0086-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 10/26/2017] [Accepted: 11/13/2017] [Indexed: 12/27/2022] Open
Abstract
Germline variants in the APC gene cause familial adenomatous polyposis. Inherited variants in MutYH, POLE, POLD1, NTHL1, and MSH3 genes and somatic APC mosaicism have been reported as alternative causes of polyposis. However, ~30-50% of cases of polyposis remain genetically unsolved. Thus, the aim of this study was to investigate the genetic causes of unexplained adenomatous polyposis. Eight sporadic cases with >20 adenomatous polyps by 35 years of age or >50 adenomatous polyps by 55 years of age, and no causative germline variants in APC and/or MutYH, were enrolled from a cohort of 56 subjects with adenomatous colorectal polyposis. APC gene mosaicism was investigated on DNA from colonic adenomas by Sanger sequencing or Whole Exome Sequencing (WES). Mosaicism extension to other tissues (peripheral blood, saliva, hair follicles) was evaluated using Sanger sequencing and/or digital PCR. APC second hit was investigated in adenomas from mosaic patients. WES was performed on DNA from peripheral blood to identify additional polyposis candidate variants. We identified APC mosaicism in 50% of patients. In three cases mosaicism was restricted to the colon, while in one it also extended to the duodenum and saliva. One patient without APC mosaicism, carrying an APC in-frame deletion of uncertain significance, was found to harbor rare germline variants in OGG1, POLQ, and EXO1 genes. In conclusion, our restrictive selection criteria improved the detection of mosaic APC patients. In addition, we showed for the first time that an oligogenic inheritance of rare variants might have a cooperative role in sporadic colorectal polyposis onset.
Collapse
Affiliation(s)
- Michele Ciavarella
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Sara Miccoli
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Anna Prossomariti
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Elena Bonora
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Buscherini
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Flavia Palombo
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Tiziana Balbi
- Pathology Unit, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Claudio Ceccarelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Franco Bazzoli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Luigi Ricciardiello
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
| | - Daniela Turchetti
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
| | - Giulia Piazzi
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
| |
Collapse
|
18
|
DeRycke MS, Gunawardena S, Balcom JR, Pickart AM, Waltman LA, French AJ, McDonnell S, Riska SM, Fogarty ZC, Larson MC, Middha S, Eckloff BW, Asmann YW, Ferber MJ, Haile RW, Gallinger S, Clendenning M, Rosty C, Win AK, Buchanan DD, Hopper JL, Newcomb PA, Le Marchand L, Goode EL, Lindor NM, Thibodeau SN. Targeted sequencing of 36 known or putative colorectal cancer susceptibility genes. Mol Genet Genomic Med 2017; 5:553-569. [PMID: 28944238 PMCID: PMC5606870 DOI: 10.1002/mgg3.317] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mutations in several genes predispose to colorectal cancer. Genetic testing for hereditary colorectal cancer syndromes was previously limited to single gene tests; thus, only a very limited number of genes were tested, and rarely those infrequently mutated in colorectal cancer. Next-generation sequencing technologies have made it possible to sequencing panels of genes known and suspected to influence colorectal cancer susceptibility. METHODS Targeted sequencing of 36 known or putative CRC susceptibility genes was conducted for 1231 CRC cases from five subsets: (1) Familial Colorectal Cancer Type X (n = 153); (2) CRC unselected by tumor immunohistochemical or microsatellite stability testing (n = 548); (3) young onset (age <50 years) (n = 333); (4) proficient mismatch repair (MMR) in cases diagnosed at ≥50 years (n = 68); and (5) deficient MMR CRCs with no germline mutations in MLH1, MSH2, MSH6, or PMS2 (n = 129). Ninety-three unaffected controls were also sequenced. RESULTS Overall, 29 nonsense, 43 frame-shift, 13 splice site, six initiator codon variants, one stop codon, 12 exonic deletions, 658 missense, and 17 indels were identified. Missense variants were reviewed by genetic counselors to determine pathogenicity; 13 were pathogenic, 61 were not pathogenic, and 584 were variants of uncertain significance. Overall, we identified 92 cases with pathogenic mutations in APC,MLH1,MSH2,MSH6, or multiple pathogenic MUTYH mutations (7.5%). Four cases with intact MMR protein expression by immunohistochemistry carried pathogenic MMR mutations. CONCLUSIONS Results across case subsets may help prioritize genes for inclusion in clinical gene panel tests and underscore the issue of variants of uncertain significance both in well-characterized genes and those for which limited experience has accumulated.
Collapse
Affiliation(s)
- Melissa S. DeRycke
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Shanaka Gunawardena
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Jessica R. Balcom
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Angela M. Pickart
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Lindsey A. Waltman
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Amy J. French
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Shannon McDonnell
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Shaun M. Riska
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Zachary C. Fogarty
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Melissa C. Larson
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Sumit Middha
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | | | - Yan W. Asmann
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFlorida
| | - Matthew J. Ferber
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Robert W. Haile
- Division of OncologyDepartment of MedicineStanford UniversityStanfordCalifornia
| | | | - Mark Clendenning
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Christophe Rosty
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
- Envoi Specialist PathologistsHerstonQueenslandAustralia
- School of MedicineUniversity of QueenslandHerstonQueenslandAustralia
| | - Aung K. Win
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
- Genetic Medicine and Familial Cancer CentreThe Royal Melbourne HospitalParkvilleVictoriaAustralia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
- Genetic Medicine and Familial Cancer CentreThe Royal Melbourne HospitalParkvilleVictoriaAustralia
| | - John L. Hopper
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
| | - Polly A. Newcomb
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashington
| | - Loic Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHawaii
| | - Ellen L. Goode
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | | | | |
Collapse
|
19
|
Hahn MM, de Voer RM, Hoogerbrugge N, Ligtenberg MJL, Kuiper RP, van Kessel AG. The genetic heterogeneity of colorectal cancer predisposition - guidelines for gene discovery. Cell Oncol (Dordr) 2016; 39:491-510. [PMID: 27279102 PMCID: PMC5121185 DOI: 10.1007/s13402-016-0284-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a cumulative term applied to a clinically and genetically heterogeneous group of neoplasms that occur in the bowel. Based on twin studies, up to 45 % of the CRC cases may involve a heritable component. Yet, only in 5-10 % of these cases high-penetrant germline mutations are found (e.g. mutations in APC and DNA mismatch repair genes) that result in a familial aggregation and/or an early onset of the disease. Genome-wide association studies have revealed that another ~5 % of the CRC cases may be explained by a cumulative effect of low-penetrant risk factors. Recent attempts to identify novel genetic factors using whole exome and whole genome sequencing has proven to be difficult since the remaining, yet to be discovered, high penetrant CRC predisposing genes appear to be rare. In addition, most of the moderately penetrant candidate genes identified so far have not been confirmed in independent cohorts. Based on literature examples, we here discuss how careful patient and cohort selection, candidate gene and variant selection, and corroborative evidence may be employed to facilitate the discovery of novel CRC predisposing genes. CONCLUSIONS The picture emerges that the genetic predisposition to CRC is heterogeneous, involving complex interplays between common and rare (inter)genic variants with different penetrances. It is anticipated, however, that the use of large clinically well-defined patient and control datasets, together with improved functional and technical possibilities, will yield enough power to unravel this complex interplay and to generate accurate individualized estimates for the risk to develop CRC.
Collapse
Affiliation(s)
- M M Hahn
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R M de Voer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - M J L Ligtenberg
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R P Kuiper
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - A Geurts van Kessel
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| |
Collapse
|
20
|
Aceto GM, Fantini F, De Iure S, Di Nicola M, Palka G, Valanzano R, Di Gregorio P, Stigliano V, Genuardi M, Battista P, Cama A, Curia MC. Correlation between mutations and mRNA expression of APC and MUTYH genes: new insight into hereditary colorectal polyposis predisposition. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:131. [PMID: 26511139 PMCID: PMC4625907 DOI: 10.1186/s13046-015-0244-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/19/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Transcript dosage imbalance may influence the transcriptome. To gain insight into the role of altered gene expression in hereditary colorectal polyposis predisposition, in the present study we analyzed absolute and allele-specific expression (ASE) of adenomatous polyposis coli (APC) and mutY Homolog (MUTYH) genes. METHODS We analyzed DNA and RNA extracted from peripheral blood mononuclear cells (PBMC) of 49 familial polyposis patients and 42 healthy blood donors selected according similar gender and age. Patients were studied for germline alterations in both genes using dHPLC, MLPA and automated sequencing. APC and MUTYH mRNA expression levels were investigated by quantitative Real-Time PCR (qRT-PCR) analysis using TaqMan assay and by ASE assays using dHPLC-based primer extension. RESULTS Twenty out of 49 patients showed germline mutations: 14 in APC gene and six in MUTYH gene. Twenty-nine patients did not show mutations in both genes. Results from qRT-PCR indicated that gene expression of both APC and MUTYH was reduced in patients analyzed. In particular, a significant reduction in APC expression was observed in patients without APC germline mutation vs control group (P < 0.05) while APC expression in the mutation carrier patients, although lower compared to control individuals, did not show statistical significance. On the other hand a significant reduced MUTYH expression was detected in patients with MUTYH mutations vs control group (P < 0.05). Altered ASE of APC was detected in four out of eight APC mutation carriers. In particular one case showed a complete loss of one allele. Among APC mutation negative cases, 4 out of 13 showed a moderate ASE. ASE of MUTYH did not show any altered expression in the cases analyzed. Spearman's Rho Test analysis showed a positive and significant correlation between APC and MUTYH genes both in cases and in controls (P = 0.020 and P < 0.001). CONCLUSIONS APC and MUTYH showed a reduced germline expression, not always corresponding to gene mutation. Expression of APC is decreased in mutation negative cases and this appears to be a promising indicator of FAP predisposition, while for MUTYH gene, mutation is associated to reduced mRNA expression. This study could improve the predictive genetic diagnosis of at-risk individuals belonging to families with reduced mRNA expression regardless of presence of mutation.
Collapse
Affiliation(s)
- Gitana Maria Aceto
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Fabiana Fantini
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Sabrina De Iure
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Marta Di Nicola
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Giandomenico Palka
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Rosa Valanzano
- Department of Clinical Physiopathology, University of Florence, Florence, Italy.
| | - Patrizia Di Gregorio
- Immunohaematology and Transfusional Medicine Service, "SS. Annunziata" Hospital, Chieti, Italy.
| | - Vittoria Stigliano
- Division of Gastroenterology and Digestive Endoscopy, Regina Elena National Cancer Institute, Rome, Italy.
| | - Maurizio Genuardi
- Institute of Medical Genetics, "A. Gemelli" School of Medicine, Catholic University of the Sacred Heart, Rome, Italy.
| | - Pasquale Battista
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| | - Alessandro Cama
- Department of Pharmacy, "G. d'Annunzio" University, Chieti, Italy.
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, Chieti, Italy.
| |
Collapse
|
21
|
Jurgens J, Ling H, Hetrick K, Pugh E, Schiettecatte F, Doheny K, Hamosh A, Avramopoulos D, Valle D, Sobreira N. Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 2015; 17:782-8. [PMID: 25569433 PMCID: PMC4496331 DOI: 10.1038/gim.2014.196] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/01/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE In March 2013 the American College of Medical Genetics and Genomics published a list of 56 genes with the recommendation that pathogenic and likely pathogenic variants detected incidentally by clinical sequencing be reported to patients. As an initial step in determining the practical consequences of this recommendation in the research setting, we searched for variants in these genes in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. METHODS We identified rare, nonsynonymous, and splicing single-nucleotide variants and insertions/deletions and assessed variant classification using the Human Gene Mutation, Emory, and ClinVar databases. We analyzed the burden of mutation in each of the 56 genes and determined which variants should be reported to patients. RESULTS Our filtering resulted in 249 distinct variants, with a mean of 1.69 variants per individual. Half of these were novel missense mutations not classified by any of the three reference databases. Of 101 variants listed in the Human Gene Mutation Database, 48 were also in ClinVar and 3 were also in Emory; half of these shared variants were classified discordantly between databases. Some genes consistently had greater variation than others. In total, 0.86% of individuals had a reportable incidental variant. CONCLUSION These observations demonstrate some current challenges of assessing phenotypic consequences of incidental variants for counseling patients.
Collapse
Affiliation(s)
- Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kurt Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | | | - Kimberly Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
22
|
Shia J. Evolving approach and clinical significance of detecting DNA mismatch repair deficiency in colorectal carcinoma. Semin Diagn Pathol 2015; 32:352-61. [PMID: 25716099 DOI: 10.1053/j.semdp.2015.02.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The last two decades have seen significant advancement in our understanding of colorectal tumors with DNA mismatch repair (MMR) deficiency. The ever-emerging revelations of new molecular and genetic alterations in various clinical conditions have necessitated constant refinement of disease terminology and classification. Thus, a case with the clinical condition of hereditary non-polyposis colorectal cancer as defined by the Amsterdam criteria may be one of Lynch syndrome characterized by a germline defect in one of the several MMR genes, one of the yet-to-be-defined "Lynch-like syndrome" if there is evidence of MMR deficiency in the tumor but no detectable germline MMR defect or tumor MLH1 promoter methylation, or "familial colorectal cancer type X" if there is no evidence of MMR deficiency. The detection of these conditions carries significant clinical implications. The detection tools and strategies are constantly evolving. The Bethesda guidelines symbolize a selective approach that uses clinical information and tumor histology as the basis to select high-risk individuals. Such a selective approach has subsequently been found to have limited sensitivity, and is thus gradually giving way to the alternative universal approach that tests all newly diagnosed colorectal cancers. Notably, the universal approach also has its own limitations; its cost-effectiveness in real practice, in particular, remains to be determined. Meanwhile, technological advances such as the next-generation sequencing are offering the promise of direct genetic testing for MMR deficiency at an affordable cost probably in the near future. This article reviews the up-to-date molecular definitions of the various conditions related to MMR deficiency, and discusses the tools and strategies that have been used in detecting these conditions. Special emphasis will be placed on the evolving nature and the clinical importance of the disease definitions and the detection strategies.
Collapse
Affiliation(s)
- Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065.
| |
Collapse
|
23
|
Guarinos C, Juárez M, Egoavil C, Rodríguez-Soler M, Pérez-Carbonell L, Salas R, Cubiella J, Rodríguez-Moranta F, de-Castro L, Bujanda L, Serradesanferm A, Nicolás-Pérez D, Herráiz M, Fernández-Bañares F, Herreros-de-Tejada A, Aguirre E, Balmaña J, Rincón ML, Pizarro A, Polo-Ortiz F, Castillejo A, Alenda C, Payá A, Soto JL, Jover R. Prevalence and characteristics of MUTYH-associated polyposis in patients with multiple adenomatous and serrated polyps. Clin Cancer Res 2014; 20:1158-68. [PMID: 24470512 DOI: 10.1158/1078-0432.ccr-13-1490] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The present study aimed to determine the prevalence of MUTYH mutations in patients with multiple colonic polyps and to explore the best strategy for diagnosing MUTYH-associated polyposis (MAP) in these patients. EXPERIMENTAL DESIGN This study included 405 patients with at least 10 colonic polyps each. All cases were genetically tested for the three most frequent MUTYH mutations. Whole-gene analysis was performed in heterozygous patients and in 216 patients lacking the three most frequent mutations. Polyps from 56 patients were analyzed for the KRAS-Gly12Cys and BRAF V600E somatic mutations. RESULTS Twenty-seven (6.7%) patients were diagnosed with MAP, of which 40.8% showed serrated polyps. The sensitivity of studying only the three common variants was 74.1%. Of 216 patients without any monoallelic mutation in common variants, whole-gene analysis revealed biallelic pathogenic mutation in only one. G396D mutation was associated with serrated lesions and older age at diagnosis. There was a strong association between germinal MUTYH mutation and KRAS Gly12Cys somatic mutation in polyps. BRAF V600E mutation was found in 74% of serrated polyps in MUTYH-negative patients and in none of the polyps of MAP patients. CONCLUSIONS We observed a low frequency of MUTYH mutations among patients with multiple adenomatous and serrated polyps. The MAP phenotype frequently included patients with serrated polyps, especially when G396D mutation was involved. Our results show that somatic molecular markers of polyps can be useful in identifying MAP cases and support the need for the complete MUTYH gene analysis only in patients heterozygous for recurrent variants.
Collapse
Affiliation(s)
- Carla Guarinos
- Authors' Affiliations: Unidad de Investigación, Departments of Pathology, and Gastroenterology, Hospital General Universitario, Alicante; Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Ourense; Department of Gastroenterology, Bellvitge University Hospital; Institut de Malaties Digestives i Metabòliques, CIBERehd, Hospital Clínic; Department of Oncology, Hospital Vall d'Hebrón, Barcelona; Gastroenterology Department, Complexo Hospitalario de Vigo, Vigo; Department of Gastroenterology, Hospital Donostia, CIBERehd, Universidad del País Vasco, San Sebastián; Department of Gastroenterology, Hospital Universitario de Canarias, La Laguna, Tenerife; Department of Gastroenterology, Clínica Universitaria de Navarra, Pamplona; Department of Gastroenterology, Hospital Mútua de Terrassa, Terrassa; Department of Gastroenterology, Hospital Puerta de Hierro, Madrid; Department of Oncology, Hospital Arnau de Vilanova, Lleida; Department of Gastroenterology, Hospital Bidasoa, Irún; Department of Gastroenterology, Hospital Universitario Virgen del Rocío, Sevilla; Department of Gastroenterology, Hospital Basurto, Bilbao; Department of Molecular Genetics, Hospital General Universitario, Elche, Spain; and Gastrointestinal Cancer Research Laboratory, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
He H, Han D, Feng H, Qu H, Song S, Bai B, Zhang Z. Involvement of and interaction between WNT10A and EDA mutations in tooth agenesis cases in the Chinese population. PLoS One 2013; 8:e80393. [PMID: 24312213 PMCID: PMC3842385 DOI: 10.1371/journal.pone.0080393] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 10/02/2013] [Indexed: 11/18/2022] Open
Abstract
Background Dental agenesis is the most common, often heritable, developmental anomaly in humans. Although WNT10A gene mutations are known to cause rare syndromes associated with tooth agenesis, including onycho-odontodermal dysplasia (OODD), Schöpf-Schulz-Passarge syndrome (SSPS), hypohidrotic ectodermal dysplasia (HED), and more than half of the cases of isolated oligodontia recently, the genotype-phenotype correlations and the mode of inheritance of WNT10A mutations remain unclear. The phenotypic expression with WNT10A mutations shows a high degree of variability, suggesting that other genes might function with WNT10A in regulating ectodermal organ development. Moreover, the involvement of mutations in other genes, such as EDA, which is also associated with HED and isolated tooth agenesis, is not clear. Therefore, we hypothesized that EDA mutations interact with WNT10A mutations to play a role in tooth agenesis. Additionally, EDA, EDAR, and EDARADD encode signaling molecules in the Eda/Edar/NF-κB signaling pathways, we also checked EDAR and EDARADD in this study. Methods WNT10A, EDA, EDAR and EDARADD were sequenced in 88 patients with isolated oligodontia and 26 patients with syndromic tooth agenesis. The structure of two mutated WNT10A and two mutated EDA proteins was analyzed. Results Digenic mutations of both WNT10A and EDA were identified in 2 of 88 (2.27%) isolated oligodontia cases and 4 of 26 (15.38%) syndromic tooth agenesis cases. No mutation in EDAR or EDARADD gene was found. Conclusions WNT10A and EDA digenic mutations could result in oligodontia and syndromic tooth agenesis in the Chinese population. Moreover, our results will greatly expand the genotypic spectrum of tooth agenesis.
Collapse
Affiliation(s)
- Huiying He
- Department of Prosthodontics, School and Hospital of Stomatology, Peking University, Beijing, China
| | - Dong Han
- Department of Prosthodontics, School and Hospital of Stomatology, Peking University, Beijing, China
| | - Hailan Feng
- Department of Prosthodontics, School and Hospital of Stomatology, Peking University, Beijing, China
- * E-mail:
| | - Hong Qu
- College of Life Sciences, Peking University, Beijing, China
| | - Shujuan Song
- Department of Genetics, Peking University Health Science Center, Beijing, China
| | - Baojing Bai
- Department of Prosthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Zhenting Zhang
- Department of Prosthodontics, School of Stomatology, Capital Medical University, Beijing, China
| |
Collapse
|
25
|
De Lellis L, Aceto GM, Curia MC, Catalano T, Mammarella S, Veschi S, Fantini F, Battista P, Stigliano V, Messerini L, Mareni C, Sala P, Bertario L, Radice P, Cama A. Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms. PLoS One 2013; 8:e81194. [PMID: 24278394 PMCID: PMC3835792 DOI: 10.1371/journal.pone.0081194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/09/2013] [Indexed: 01/27/2023] Open
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.
Collapse
Affiliation(s)
- Laura De Lellis
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
| | - Gitana Maria Aceto
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Teresa Catalano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Serena Veschi
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Fabiana Fantini
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Pasquale Battista
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Vittoria Stigliano
- Department of Gastroenterology, Unit of Hereditary Colorectal Cancer, National Cancer Institute, Regina Elena (IRE), Rome, Italy
| | - Luca Messerini
- Section of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Cristina Mareni
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Paola Sala
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucio Bertario
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular bases of genetic risk and genetic testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandro Cama
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
- * E-mail:
| |
Collapse
|
26
|
Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 407] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
Collapse
Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | | |
Collapse
|
27
|
Smith CG, West H, Harris R, Idziaszczyk S, Maughan TS, Kaplan R, Richman S, Quirke P, Seymour M, Moskvina V, Steinke V, Propping P, Hes FJ, Wijnen J, Cheadle JP. Role of the Oxidative DNA Damage Repair Gene OGG1 in Colorectal Tumorigenesis. ACTA ACUST UNITED AC 2013; 105:1249-53. [DOI: 10.1093/jnci/djt183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
28
|
Abstract
Digenic inheritance (DI) is the simplest form of inheritance for genetically complex diseases. By contrast with the thousands of reports that mutations in single genes cause human diseases, there are only dozens of human disease phenotypes with evidence for DI in some pedigrees. The advent of high-throughput sequencing (HTS) has made it simpler to identify monogenic disease causes and could similarly simplify proving DI because one can simultaneously find mutations in two genes in the same sample. However, through 2012, I could find only one example of human DI in which HTS was used; in that example, HTS found only the second of the two genes. To explore the gap between expectation and reality, I tried to collect all examples of human DI with a narrow definition and characterise them according to the types of evidence collected, and whether there has been replication. Two strong trends are that knowledge of candidate genes and knowledge of protein–protein interactions (PPIs) have been helpful in most published examples of human DI. By contrast, the positional method of genetic linkage analysis, has been mostly unsuccessful in identifying genes underlying human DI. Based on the empirical data, I suggest that combining HTS with growing networks of established PPIs may expedite future discoveries of human DI and strengthen the evidence for them.
Collapse
|
29
|
Mazzei F, Viel A, Bignami M. Role of MUTYH in human cancer. Mutat Res 2013; 743-744:33-43. [PMID: 23507534 DOI: 10.1016/j.mrfmmm.2013.03.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 06/01/2023]
Abstract
MUTYH, a human ortholog of MutY, is a post-replicative DNA glycosylase, highly conserved throughout evolution, involved in the correction of mismatches resulting from a faulty replication of the oxidized base 8-hydroxyguanine (8-oxodG). In particular removal of adenine from A:8-oxodG mispairs by MUTYH activity is followed by error-free base excision repair (BER) events, leading to the formation of C:8-oxodG base pairs. These are the substrate of another BER enzyme, the OGG1 DNA glycosylase, which then removes 8-oxodG from DNA. Thus the combined action of OGG1 and MUTYH prevents oxidative damage-induced mutations, i.e. GC->TA transversions. Germline mutations in MUTYH are associated with a recessively heritable colorectal polyposis, now referred to as MUTYH-associated polyposis (MAP). Here we will review the phenotype(s) associated with MUTYH inactivation from bacteria to mammals, the structure of the MUTYH protein, the molecular mechanisms of its enzymatic activity and the functional characterization of MUTYH variants. The relevance of these results will be discussed to define the role of specific human mutations in colorectal cancer risk together with the possible role of MUTYH inactivation in sporadic cancer.
Collapse
Affiliation(s)
- Filomena Mazzei
- Department of Environment, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Alessandra Viel
- Experimental Oncology 1, Centro di Riferimento Oncologico, IRCCS, Via F.Gallini 2, 33081 Aviano, PN, Italy
| | - Margherita Bignami
- Department of Environment, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy.
| |
Collapse
|
30
|
Chen HJ, Lin Q, Zeng L, Yang BL. Recent advances in molecular diagnosis of hereditary nonpolyposis colorectal cancer. Shijie Huaren Xiaohua Zazhi 2012; 20:2806-2811. [DOI: 10.11569/wcjd.v20.i29.2806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) is a dominant autosomal genetic syndrome, accounting for 5%-10% of all colorectal cancers. It is caused by inactivating germ-line mutations of DNA mismatch repair (MMR) genes, including hMLH1, hMSH2, hMSH6, hPMS2, and hPMS1. HNPCC shows a tendency towards early age at onset, multiplicity of tumors, right-sided colon involvement, characteristic tumor pathology, and spectrum of extracolonic tumors. The diagnosis of HNPCC mainly relies on history and genetic linkage analysis. Patients meeting the Amsterdam criteria or Bethesda guidelines should undergo detection of microsatellite instability and immunohistochemistry analysis of hMSH2 and hMLH1 expression. If one of the two detections yields a positive result, molecular genetic testing for germline mutations of MMR genes should be taken into consideration.
Collapse
|