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Singh AK, Talseth-Palmer B, McPhillips M, Lavik LAS, Xavier A, Drabløs F, Sjursen W. Targeted sequencing of genes associated with the mismatch repair pathway in patients with endometrial cancer. PLoS One 2020; 15:e0235613. [PMID: 32634176 PMCID: PMC7340288 DOI: 10.1371/journal.pone.0235613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/19/2020] [Indexed: 01/28/2023] Open
Abstract
Germline variants inactivating the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 cause Lynch syndrome that implies an increased cancer risk, where colon and endometrial cancer are the most frequent. Identification of these pathogenic variants is important to identify endometrial cancer patients with inherited increased risk of new cancers, in order to offer them lifesaving surveillance. However, several other genes are also part of the MMR pathway. It is therefore relevant to search for variants in additional genes that may be associated with cancer risk by including all known genes involved in the MMR pathway. Next-generation sequencing was used to screen 22 genes involved in the MMR pathway in constitutional DNA extracted from full blood from 199 unselected endometrial cancer patients. Bioinformatic pipelines were developed for identification and functional annotation of variants, using several different software tools and custom programs. This facilitated identification of 22 exonic, 4 UTR and 9 intronic variants that could be classified according to pathogenicity. This study has identified several germline variants in genes of the MMR pathway that potentially may be associated with an increased risk for cancer, in particular endometrial cancer, and therefore are relevant for further investigation. We have also developed bioinformatics strategies to analyse targeted sequencing data, including low quality data and genomic regions outside of the protein coding exons of the relevant genes.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
| | - Bente Talseth-Palmer
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- School of Biomedical Science and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
- Department of Research and Development, Møre og Romsdal Hospital Trust, Molde, Norway
| | - Mary McPhillips
- NSW Health Pathology, Molecular Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | | | - Alexandre Xavier
- School of Biomedical Science and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
| | - Wenche Sjursen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
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2
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Cervelli T, Lodovichi S, Bellè F, Galli A. Yeast-based assays for the functional characterization of cancer-associated variants of human DNA repair genes. MICROBIAL CELL 2020; 7:162-174. [PMID: 32656256 PMCID: PMC7328678 DOI: 10.15698/mic2020.07.721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Technological advances are continuously revealing new genetic variants that are often difficult to interpret. As one of the most genetically tractable model organisms, yeast can have a central role in determining the consequences of human genetic variation. DNA repair gene mutations are associated with many types of cancers, therefore the evaluation of the functional impact of these mutations is crucial for risk assessment and for determining therapeutic strategies. Owing to the evolutionary conservation of DNA repair pathways between human cells and the yeast Saccharomyces cerevisiae, several functional assays have been developed. Here, we describe assays for variants of human genes belonging to the major DNA repair pathways divided in functional assays for human genes with yeast orthologues and human genes lacking a yeast orthologue. Human genes with orthologues can be studied by introducing the correspondent human mutations directly in the yeast gene or expressing the human gene carrying the mutations; while the only possible approach for human genes without a yeast orthologue is the heterologous expression. The common principle of these approaches is that the mutated gene determines a phenotypic alteration that can vary according to the gene studied and the domain of the protein. Here, we show how the versatility of yeast can help in classifying cancer-associated variants.
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Affiliation(s)
- Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Francesca Bellè
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
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3
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Mercatanti A, Lodovichi S, Cervelli T, Galli A. CRIMEtoYHU: a new web tool to develop yeast-based functional assays for characterizing cancer-associated missense variants. FEMS Yeast Res 2018; 17:4562592. [PMID: 29069390 DOI: 10.1093/femsyr/fox078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
Evaluation of the functional impact of cancer-associated missense variants is more difficult than for protein-truncating mutations and consequently standard guidelines for the interpretation of sequence variants have been recently proposed. A number of algorithms and software products were developed to predict the impact of cancer-associated missense mutations on protein structure and function. Importantly, direct assessment of the variants using high-throughput functional assays using simple genetic systems can help in speeding up the functional evaluation of newly identified cancer-associated variants. We developed the web tool CRIMEtoYHU (CTY) to help geneticists in the evaluation of the functional impact of cancer-associated missense variants. Humans and the yeast Saccharomyces cerevisiae share thousands of protein-coding genes although they have diverged for a billion years. Therefore, yeast humanization can be helpful in deciphering the functional consequences of human genetic variants found in cancer and give information on the pathogenicity of missense variants. To humanize specific positions within yeast genes, human and yeast genes have to share functional homology. If a mutation in a specific residue is associated with a particular phenotype in humans, a similar substitution in the yeast counterpart may reveal its effect at the organism level. CTY simultaneously finds yeast homologous genes, identifies the corresponding variants and determines the transferability of human variants to yeast counterparts by assigning a reliability score (RS) that may be predictive for the validity of a functional assay. CTY analyzes newly identified mutations or retrieves mutations reported in the COSMIC database, provides information about the functional conservation between yeast and human and shows the mutation distribution in human genes. CTY analyzes also newly found mutations and aborts when no yeast homologue is found. Then, on the basis of the protein domain localization and functional conservation between yeast and human, the selected variants are ranked by the RS. The RS is assigned by an algorithm that computes functional data, type of mutation, chemistry of amino acid substitution and the degree of mutation transferability between human and yeast protein. Mutations giving a positive RS are highly transferable to yeast and, therefore, yeast functional assays will be more predictable. To validate the web application, we have analyzed 8078 cancer-associated variants located in 31 genes that have a yeast homologue. More than 50% of variants are transferable to yeast. Incidentally, 88% of all transferable mutations have a reliability score >0. Moreover, we analyzed by CTY 72 functionally validated missense variants located in yeast genes at positions corresponding to the human cancer-associated variants. All these variants gave a positive RS. To further validate CTY, we analyzed 3949 protein variants (with positive RS) by the predictive algorithm PROVEAN. This analysis shows that yeast-based functional assays will be more predictable for the variants with positive RS. We believe that CTY could be an important resource for the cancer research community by providing information concerning the functional impact of specific mutations, as well as for the design of functional assays useful for decision support in precision medicine.
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Affiliation(s)
- Alberto Mercatanti
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, via G. Moruzzi 1, 56124 Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, via G. Moruzzi 1, 56124 Pisa, Italy
- PhD program in Clinical and Translational Science, University of Pisa, Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, via G. Moruzzi 1, 56124 Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, via G. Moruzzi 1, 56124 Pisa, Italy
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4
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Oligonucleotide-directed mutagenesis screen to identify pathogenic Lynch syndrome-associated MSH2 DNA mismatch repair gene variants. Proc Natl Acad Sci U S A 2016; 113:4128-33. [PMID: 26951660 DOI: 10.1073/pnas.1520813113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA oligonucleotides can achieve targeted base-pair substitution with modest efficiency but high precision. We show that "oligo targeting" can be used effectively to study missense mutations in DNA mismatch repair (MMR) genes. Inherited inactivating mutations in DNA MMR genes are causative for the cancer predisposition Lynch syndrome (LS). Although overtly deleterious mutations in MMR genes can clearly be ascribed as the cause of LS, the functional implications of missense mutations are often unclear. We developed a genetic screen to determine the pathogenicity of these variants of uncertain significance (VUS), focusing on mutator S homolog 2 (MSH2). VUS were introduced into the endogenous Msh2 gene of mouse embryonic stem cells by oligo targeting. Subsequent selection for MMR-deficient cells using the guanine analog 6-thioguanine allowed the detection of MMR-abrogating VUS. The screen was able to distinguish weak and strong pathogenic variants from polymorphisms and was used to investigate 59 Msh2 VUS. Nineteen of the 59 VUS were identified as pathogenic. Functional assays revealed that 14 of the 19 detected variants fully abrogated MMR activity and that five of the detected variants attenuated MMR activity. Implementation of the screen in clinical practice allows proper counseling of mutation carriers and treatment of their tumors.
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5
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Niroula A, Vihinen M. Classification of Amino Acid Substitutions in Mismatch Repair Proteins Using PON-MMR2. Hum Mutat 2015; 36:1128-34. [PMID: 26333163 DOI: 10.1002/humu.22900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022]
Abstract
Variations in mismatch repair (MMR) system genes are causative of Lynch syndrome and other cancers. Thousands of variants have been identified in MMR genes, but the clinical relevance is known for only a small proportion. Recently, the InSiGHT group classified 2,360 MMR variants into five classes. One-third of variants, majority of which is nonsynonymous variants, remain to be of uncertain clinical relevance. Computational tools can be used to prioritize variants for disease relevance investigations. Previously, we classified 248 MMR variants as likely pathogenic and likely benign using PON-MMR. We have developed a novel tool, PON-MMR2, which is trained on a larger and more reliable dataset. In performance comparison, PON-MMR2 outperforms both generic tolerance prediction methods as well as methods optimized for MMR variants. It achieves accuracy and MCC of 0.89 and 0.78, respectively, in cross-validation and 0.86 and 0.69, respectively, on an independent test dataset. We classified 354 class 3 variants in InSiGHT database as well as all possible amino acid substitutions in four MMR proteins. Likely harmful variants mainly appear in the protein core, whereas likely benign variants are on the surface. PON-MMR2 is a highly reliable tool to prioritize variants for functional analysis. It is freely available at http://structure.bmc.lu.se/PON-MMR2/.
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Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science, Lund University, BMC B13, Lund, SE, 22184, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, Lund, SE, 22184, Sweden
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6
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Kraus C, Rau TT, Lux P, Erlenbach-Wünsch K, Löhr S, Krumbiegel M, Thiel CT, Stöhr R, Agaimy A, Croner RS, Stürzl M, Hohenberger W, Hartmann A, Reis A. Comprehensive screening for mutations associated with colorectal cancer in unselected cases reveals penetrant and nonpenetrant mutations. Int J Cancer 2014; 136:E559-68. [PMID: 25142776 DOI: 10.1002/ijc.29149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/17/2014] [Accepted: 07/25/2014] [Indexed: 12/14/2022]
Abstract
Germline mutation testing in patients with colorectal cancer (CRC) is offered only to a subset of patients with a clinical presentation or tumor histology suggestive of familial CRC syndromes, probably underestimating familial CRC predisposition. The aim of our study was to determine whether unbiased screening of newly diagnosed CRC cases with next generation sequencing (NGS) increases the overall detection rate of germline mutations. We analyzed 152 consecutive CRC patients for germline mutations in 18 CRC-associated genes using NGS. All patients were also evaluated for Bethesda criteria and all tumors were investigated for microsatellite instability, immunohistochemistry for mismatch repair proteins and the BRAF*V600E somatic mutation. NGS based sequencing identified 27 variants in 9 genes in 23 out of 152 patients studied (18%). Three of them were already reported as pathogenic and 12 were class 3 germline variants with an uncertain prediction of pathogenicity. Only 1 of these patients fulfilled Bethesda criteria and had a microsatellite instable tumor and an MLH1 germline mutation. The others would have been missed with current approaches: 2 with a MSH6 premature termination mutation and 12 uncertain, potentially pathogenic class 3 variants in APC, MLH1, MSH2, MSH6, MSH3 and MLH3. The higher NGS mutation detection rate compared with current testing strategies based on clinicopathological criteria is probably due to the large genetic heterogeneity and overlapping clinical presentation of the various CRC syndromes. It can also identify apparently nonpenetrant germline mutations complicating the clinical management of the patients and their families.
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Affiliation(s)
- Cornelia Kraus
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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7
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Challenges in assessing pathogenicity based on frequency of variants in mismatch repair genes: an extreme case of a MSH2 variant and a meta-analysis. Gene 2014; 546:421-4. [PMID: 24933000 DOI: 10.1016/j.gene.2014.06.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 04/30/2014] [Accepted: 06/13/2014] [Indexed: 11/21/2022]
Abstract
The clinical interpretation of variants in mismatch repair (MMR) genes associated with Lynch syndrome can be confusing when the functional nature of the variant is not clearly defined. We report an extreme case where a polymorphism in the MSH2 gene which had a low minor allele frequency, was misclassified as a mutation based on low evidential methods in the database and previous publications. We expanded this experience to perform a systematic meta-analysis in order to investigate other variants that have potentially been misclassified. Our results suggested that the interpretation of pathogenicity should be more cautious and emphasized the need for solid validation through multiple analyses including functional analysis for variants in MMR genes.
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8
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Sijmons RH, Greenblatt MS, Genuardi M. Gene variants of unknown clinical significance in Lynch syndrome. An introduction for clinicians. Fam Cancer 2014; 12:181-7. [PMID: 23525798 DOI: 10.1007/s10689-013-9629-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clinicians referring patients for genetic testing for Lynch syndrome will sooner or later receive results for DNA Mismatch Repair (MMR) genes reporting DNA changes that are unclear from a clinical point of view. These changes are referred to as variants of unknown, or unclear, clinical significance (VUS). In contrast to clearly pathogenic mutations, VUS do not firmly diagnose Lynch syndrome at the molecular level and cannot be used to identify with certainty any of the patients' asymptomatic relatives as Lynch syndrome mutation carriers. The International database that collects MMR gene variants ( www.insight-group.org/mutations ) already lists more than 1,000 different VUSs and these variants are likely the tip of the iceberg. This paper aims at introducing non-geneticist clinicians to the topic of clinical MMR gene variant interpretation. Many lines of evidence are being used to classify VUS. Some are already familiar to clinicians and others may be less familiar but are expected to become important in clinical genetics in the coming years. Clinicians can play an important role in collecting the data needed to interpret the MMR variants detected in their patients.
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Affiliation(s)
- Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, The Netherlands.
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9
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Kidane D, Chae WJ, Czochor J, Eckert KA, Glazer PM, Bothwell ALM, Sweasy JB. Interplay between DNA repair and inflammation, and the link to cancer. Crit Rev Biochem Mol Biol 2014; 49:116-39. [PMID: 24410153 DOI: 10.3109/10409238.2013.875514] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA damage and repair are linked to cancer. DNA damage that is induced endogenously or from exogenous sources has the potential to result in mutations and genomic instability if not properly repaired, eventually leading to cancer. Inflammation is also linked to cancer. Reactive oxygen and nitrogen species (RONs) produced by inflammatory cells at sites of infection can induce DNA damage. RONs can also amplify inflammatory responses, leading to increased DNA damage. Here, we focus on the links between DNA damage, repair, and inflammation, as they relate to cancer. We examine the interplay between chronic inflammation, DNA damage and repair and review recent findings in this rapidly emerging field, including the links between DNA damage and the innate immune system, and the roles of inflammation in altering the microbiome, which subsequently leads to the induction of DNA damage in the colon. Mouse models of defective DNA repair and inflammatory control are extensively reviewed, including treatment of mouse models with pathogens, which leads to DNA damage. The roles of microRNAs in regulating inflammation and DNA repair are discussed. Importantly, DNA repair and inflammation are linked in many important ways, and in some cases balance each other to maintain homeostasis. The failure to repair DNA damage or to control inflammatory responses has the potential to lead to cancer.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics
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10
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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11
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Functional analysis in mouse embryonic stem cells reveals wild-type activity for three MSH6 variants found in suspected Lynch syndrome patients. PLoS One 2013; 8:e74766. [PMID: 24040339 PMCID: PMC3769292 DOI: 10.1371/journal.pone.0074766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 08/06/2013] [Indexed: 02/02/2023] Open
Abstract
Lynch syndrome confers an increased risk to various types of cancer, in particular early onset colorectal and endometrial cancer. Mutations in mismatch repair (MMR) genes underlie Lynch syndrome, with the majority of mutations found in MLH1 and MSH2. Mutations in MSH6 have also been found but these do not always cause a clear cancer predisposition phenotype and MSH6-defective tumors often do not show the standard characteristics of MMR deficiency, such as microsatellite instability. In particular, the consequences of MSH6 missense mutations are challenging to predict, which further complicates genetic counseling. We have previously developed a method for functional characterization of MSH2 missense mutations of unknown significance. This method is based on endogenous gene modification in mouse embryonic stem cells using oligonucleotide-directed gene targeting, followed by a series of functional assays addressing the MMR functions. Here we have adapted this method for the characterization of MSH6 missense mutations. We recreated three MSH6 variants found in suspected Lynch syndrome families, MSH6-P1087R, MSH6-R1095H and MSH6-L1354Q, and found all three to behave like wild type MSH6. Thus, despite suspicion for pathogenicity from clinical observations, our approach indicates these variants are not disease causing. This has important implications for counseling of mutation carriers.
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12
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Clinical correlation and molecular evaluation confirm that the MLH1 p.Arg182Gly (c.544A>G) mutation is pathogenic and causes Lynch syndrome. Fam Cancer 2013; 11:509-18. [PMID: 22773173 DOI: 10.1007/s10689-012-9544-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Approximately 25 % of mismatch repair (MMR) variants are exonic nucleotide substitutions. Some result in the substitution of one amino acid for another in the protein sequence, so-called missense variants, while others are silent. The interpretation of the effect of missense and silent variants as deleterious or neutral is challenging. Pre-symptomatic testing for clinical use is not recommended for relatives of individuals with variants classified as 'of uncertain significance'. These relatives, including non-carriers, are considered at high-risk as long as the contribution of the variant to disease causation cannot be determined. This results in continuing anxiety, and the application of potentially unnecessary screening and prophylactic interventions. We encountered a large Irish Lynch syndrome kindred that carries the c.544A>G (p.Arg182Gly) alteration in the MLH1 gene and we undertook to study the variant. The clinical significance of the variant remains unresolved in the literature. Data are presented on cancer incidence within five kindreds with the same germline missense variant in the MLH1 MMR gene. Extensive testing of relevant family members in one kindred, a review of the literature, review of online MMR mutation databases and use of in silico phenotype prediction tools were undertaken to study the significance of this variant. Clinical, histological, immunohistochemical and molecular evidence from these families and other independent clinical and scientific evidence indicates that the MLH1 p.Arg182Gly (c.544A>G) change causes Lynch syndrome and supports reclassification of the variant as pathogenic.
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13
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Pérez-Cabornero L, Infante M, Velasco E, Lastra E, Miner C, Durán M. Evaluating the effect of unclassified variants identified in MMR genes using phenotypic features, bioinformatics prediction, and RNA assays. J Mol Diagn 2013; 15:380-90. [PMID: 23523604 DOI: 10.1016/j.jmoldx.2013.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 11/16/2022] Open
Abstract
Lynch syndrome is caused by mutations in one of the mismatch-repair system (MMR) genes. A major difficulty in diagnosis and management of Lynch syndrome is the existence of unclassified genetic variants (UVs) with unknown clinical significance, especially mutations with new descriptions and missense-type nucleotide substitutions. We evaluated the pathogenicity of 20 such mutations (6 in MLH1, 4 in MSH2, and 7 in MSH6) found in Spanish patients suspected of Lynch syndrome. The UVs were tested for evidence of MMR defect in tumor samples and were evaluated for co-occurrence with a pathogenic mutation, the cosegregation of the variant with the disease; where sufficient data were available, in silico resources at the protein level and mRNA analysis were used to assess the putative effect on the splicing mechanism. To evaluate the frequency of these UVs in the general population, a case--control study was also performed. Five variants were identified with similar frequencies in both cases and controls, suggesting a nonpathogenic effect in patients. In contrast, abnormal splicing mutations were detected in a high proportion of patients [3/20 (15%)]. In this study, we classified 15 of the 20 UVs: six variants with strong evidence of pathogenicity and nine variants that should be considered neutral variants. Clinical significance of the other five remains unknown.
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Affiliation(s)
- Lucia Pérez-Cabornero
- Cancer Genetics Laboratory, Institute of Biology and Molecular Genetics, University of Valladolid, Valladolid, Spain
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Bozzao C, Lastella P, Stella A. Anticipation in lynch syndrome: where we are where we go. Curr Genomics 2012; 12:451-65. [PMID: 22547953 PMCID: PMC3219841 DOI: 10.2174/138920211797904070] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/08/2011] [Accepted: 07/20/2011] [Indexed: 02/06/2023] Open
Abstract
Lynch syndrome (LS) is the most common form of inherited predisposition to develop cancer mainly in the colon and endometrium but also in other organ sites. Germline mutations in DNA mismatch repair (MMR) gene cause the transmission of the syndrome in an autosomal dominant manner. The management of LS patients is complicated by the large variation in age at cancer diagnosis which requires these patients to be enrolled in surveillance protocol starting as early as in their second decade of life. Several environmental and genetic factors have been proposed to explain this phenotypic heterogeneity, but the molecular mechanisms remain unknown. Although the presence of genetic anticipation in Lynch syndrome has been suspected since 15 years, only recently the phenomenon has been increasingly reported to be present in different cancer genetic syndromes including LS. While the biological basis of earlier cancer onset in successive generations remains poorly known, recent findings point to telomere dynamics as a mechanism significantly contributing to genetic anticipation in Lynch syndrome and in other familial cancers. In this review, we summarize the clinical and molecular features of Lynch syndrome, with a particular focus on the latest studies that have investigated the molecular mechanisms of genetic anticipation.
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Affiliation(s)
- Cristina Bozzao
- Medical Genetics Unit, Department of Biomedicine in Childhood, Università degli Studi di Bari "Aldo Moro", Bari, Italy
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Rasmussen LJ, Heinen CD, Royer-Pokora B, Drost M, Tavtigian S, Hofstra RMW, de Wind N. Pathological assessment of mismatch repair gene variants in Lynch syndrome: past, present, and future. Hum Mutat 2012; 33:1617-25. [PMID: 22833534 DOI: 10.1002/humu.22168] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 07/11/2012] [Indexed: 12/12/2022]
Abstract
Lynch syndrome (LS) is caused by germline mutations in DNA mismatch repair (MMR) genes and is the most prevalent hereditary colorectal cancer syndrome. A significant proportion of variants identified in MMR and other common cancer susceptibility genes are missense or noncoding changes whose consequences for pathogenicity cannot be easily interpreted. Such variants are designated as "variants of uncertain significance" (VUS). Management of LS can be significantly improved by identifying individuals who carry a pathogenic variant and thus benefit from screening, preventive, and therapeutic measures. Also, identifying family members that do not carry the variant is important so they can be released from the intensive surveillance. Determining which genetic variants are pathogenic and which are neutral is a major challenge in clinical genetics. The profound mechanistic knowledge on the genetics and biochemistry of MMR enables the development and use of targeted assays to evaluate the pathogenicity of variants found in suspected patients with LS. We describe different approaches for the functional analysis of MMR gene VUS and propose development of a validated diagnostic framework. Furthermore, we call attention to common misconceptions about functional assays and endorse development of an integrated approach comprising validated assays for diagnosis of VUS in patients suspected of LS.
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Affiliation(s)
- Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark.
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16
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Belvederesi L, Bianchi F, Loretelli C, Bracci R, Cascinu S, Cellerino R. Sub-cellular localization analysis of MSH6 missense mutations does not reveal an overt MSH6 nuclear transport impairment. Fam Cancer 2012; 11:675-80. [PMID: 22851212 DOI: 10.1007/s10689-012-9558-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nearly one-third of the identified MSH6 germline mutations deal with single amino acid substitutions. For an effective genetic counselling it is necessary to clearly elucidate by functional tools the specific sub-processes underlying the mismatch repair (MMR) misfunctioning in MSH6 non-truncating mutants. Since the MMR repair pathway occurs in the nucleus, we suppose the impairment of MutSα nuclear trafficking to be a possible Lynch syndrome susceptibility causative mechanism. In the present study the MMR status of the tumour, the main clinical features of mutation carriers and population data associated to the MSH6 missense variants, were complemented with computational data about tolerability predictions and amino acid substitution conservation. The selected panel of ten potentially pathogenic MSH6 mutations was analyzed in a homologous expression system for possible deleterious effects on nucleo-cytoplasmic shuttling through the assessment of the sub-cellular localization of the corresponding mutated proteins. Localization analysis results do not reveal an apparent role of MSH6 missense mutations in nuclear import impairment and provide the first hint to exclude the MSH6 nuclear translocation sub-process as a possible causative mechanisms of MMR misfunctioning.
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Andersen SD, Liberti SE, Lützen A, Drost M, Bernstein I, Nilbert M, Dominguez M, Nyström M, Hansen TVO, Christoffersen JW, Jäger AC, de Wind N, Nielsen FC, Tørring PM, Rasmussen LJ. Functional characterization ofMLH1missense variants identified in lynch syndrome patients. Hum Mutat 2012; 33:1647-55. [DOI: 10.1002/humu.22153] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 06/03/2012] [Indexed: 01/30/2023]
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18
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Heinen CD, Juel Rasmussen L. Determining the functional significance of mismatch repair gene missense variants using biochemical and cellular assays. Hered Cancer Clin Pract 2012; 10:9. [PMID: 22824075 PMCID: PMC3434035 DOI: 10.1186/1897-4287-10-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/28/2012] [Indexed: 12/15/2022] Open
Abstract
With the discovery that the hereditary cancer susceptibility disease Lynch syndrome (LS) is caused by deleterious germline mutations in the DNA mismatch repair (MMR) genes nearly 20 years ago, genetic testing can now be used to diagnose this disorder in patients. A definitive diagnosis of LS can direct how clinicians manage the disease as well as prevent future cancers for the patient and their families. A challenge emerges, however, when a germline missense variant is identified in a MMR gene in a suspected LS patient. The significance of a single amino acid change in these large repair proteins is not immediately obvious resulting in them being designated variants of uncertain significance (VUS). One important strategy for resolving this uncertainty is to determine whether the variant results in a non-functional protein. The ability to reconstitute the MMR reaction in vitro has provided an important experimental tool for studying the functional consequences of VUS. However, beyond this repair assay, a number of other experimental methods have been developed that allow us to test the effect of a VUS on discrete biochemical steps or other aspects of MMR function. Here, we describe some of these assays along with the challenges of using such assays to determine the functional consequences of MMR VUS which, in turn, can provide valuable insight into their clinical significance. With increased gene sequencing in patients, the number of identified VUS has expanded dramatically exacerbating this problem for clinicians. However, basic science research laboratories around the world continue to expand our knowledge of the overall MMR molecular mechanism providing new opportunities to understand the functional significance, and therefore pathogenic significance, of VUS.
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Affiliation(s)
- Christopher D Heinen
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, 233 Farmington Avenue, ML3101 Farmington, CT, USA.
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Borràs E, Pineda M, Brieger A, Hinrichsen I, Gómez C, Navarro M, Balmaña J, Ramón y Cajal T, Torres A, Brunet J, Blanco I, Plotz G, Lázaro C, Capellá G. Comprehensive functional assessment of MLH1 variants of unknown significance. Hum Mutat 2012; 33:1576-88. [PMID: 22736432 DOI: 10.1002/humu.22142] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/15/2022]
Abstract
Lynch syndrome is associated with germline mutations in DNA mismatch repair (MMR) genes. Up to 30% of DNA changes found are variants of unknown significance (VUS). Our aim was to assess the pathogenicity of eight MLH1 VUS identified in patients suspected of Lynch syndrome. All of them are novel or not previously characterized. For their classification, we followed a strategy that integrates family history, tumor pathology, and control frequency data with a variety of in silico and in vitro analyses at RNA and protein level, such as MMR assay, MLH1 and PMS2 expression, and subcellular localization. Five MLH1 VUS were classified as pathogenic: c.[248G>T(;)306G>C], c.[780C>G;788A>C], and c.791-7T>A affected mRNA processing, whereas c.218T>C (p.L73P) and c.244A>G [corrected] (p.T82A) impaired MMR activity. Two other VUS were considered likely neutral: the silent c.702G>A variant did not affect mRNA processing or stability, and c.974G>A (p.R325Q) did not influence MMR function. In contrast, variant c.25C>T (p.R9W) could not be classified, as it associated with intermediate levels of MMR activity. Comprehensive functional assessment of MLH1 variants was useful in their classification and became relevant in the diagnosis and genetic counseling of carrier families.
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Affiliation(s)
- Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Spain
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20
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Valentin MD, da Silva FC, dos Santos EMM, Lisboa BG, de Oliveira LP, Ferreira FDO, Gomy I, Nakagawa WT, Aguiar Junior S, Redal M, Vaccaro C, Valle AD, Sarroca C, Carraro DM, Rossi BM. Characterization of germline mutations of MLH1 and MSH2 in unrelated south American suspected Lynch syndrome individuals. Fam Cancer 2012; 10:641-7. [PMID: 21681552 DOI: 10.1007/s10689-011-9461-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant syndrome that predisposes individuals to development of cancers early in life. These cancers are mainly the following: colorectal, endometrial, ovarian, small intestine, stomach and urinary tract cancers. LS is caused by germline mutations in DNA mismatch repair genes (MMR), mostly MLH1 and MSH2, which are responsible for more than 85% of known germline mutations. To search for germline mutations in MLH1 and MSH2 genes in 123 unrelated South American suspected LS patients (Bethesda or Amsterdam Criteria) DNA was obtained from peripheral blood, and PCR was performed followed by direct sequencing in both directions of all exons and intron-exon junctions regions of the MLH1 and MSH2 genes. MLH1 or MSH2 pathogenic mutations were found in 28.45% (34/123) of the individuals, where 25/57 (43.85%) fulfilled Amsterdam I, II and 9/66 (13.63%) the Bethesda criteria. The mutations found in both genes were as follows: nonsense (35.3%), frameshift (26.47%), splicing (23.52%), and missense (9%). Thirteen alterations (35.14%) were described for the first time. The data reported in this study add new information about MLH1 and MSH2 gene mutations and contribute to better characterize LS in Brazil, Uruguay and Argentina. The high rate of novel mutations demonstrates the importance of defining MLH1 and MSH2 mutations in distinct LS populations.
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Affiliation(s)
- Mev Dominguez Valentin
- Laboratory of Genomics and Molecular Biology, Centro Internacional de Pesquisa e Ensino, A.C.Camargo Hospital, São Paulo, Brazil.
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21
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Monteiro Santos EM, Valentin MD, Carneiro F, de Oliveira LP, de Oliveira Ferreira F, Junior SA, Nakagawa WT, Gomy I, de Faria Ferraz VE, da Silva Junior WA, Carraro DM, Rossi BM. Predictive models for mutations in mismatch repair genes: implication for genetic counseling in developing countries. BMC Cancer 2012; 12:64. [PMID: 22321913 PMCID: PMC3305354 DOI: 10.1186/1471-2407-12-64] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 02/09/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is the most common form of inherited predisposition to colorectal cancer (CRC), accounting for 2-5% of all CRC. LS is an autosomal dominant disease characterized by mutations in the mismatch repair genes mutL homolog 1 (MLH1), mutS homolog 2 (MSH2), postmeiotic segregation increased 1 (PMS1), post-meiotic segregation increased 2 (PMS2) and mutS homolog 6 (MSH6). Mutation risk prediction models can be incorporated into clinical practice, facilitating the decision-making process and identifying individuals for molecular investigation. This is extremely important in countries with limited economic resources. This study aims to evaluate sensitivity and specificity of five predictive models for germline mutations in repair genes in a sample of individuals with suspected Lynch syndrome. METHODS Blood samples from 88 patients were analyzed through sequencing MLH1, MSH2 and MSH6 genes. The probability of detecting a mutation was calculated using the PREMM, Barnetson, MMRpro, Wijnen and Myriad models. To evaluate the sensitivity and specificity of the models, receiver operating characteristic curves were constructed. RESULTS Of the 88 patients included in this analysis, 31 mutations were identified: 16 were found in the MSH2 gene, 15 in the MLH1 gene and no pathogenic mutations were identified in the MSH6 gene. It was observed that the AUC for the PREMM (0.846), Barnetson (0.850), MMRpro (0.821) and Wijnen (0.807) models did not present significant statistical difference. The Myriad model presented lower AUC (0.704) than the four other models evaluated. Considering thresholds of ≥ 5%, the models sensitivity varied between 1 (Myriad) and 0.87 (Wijnen) and specificity ranged from 0 (Myriad) to 0.38 (Barnetson). CONCLUSIONS The Barnetson, PREMM, MMRpro and Wijnen models present similar AUC. The AUC of the Myriad model is statistically inferior to the four other models.
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22
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Drost M, Zonneveld JBM, van Hees S, Rasmussen LJ, Hofstra RMW, de Wind N. A rapid and cell-free assay to test the activity of lynch syndrome-associated MSH2 and MSH6 missense variants. Hum Mutat 2011; 33:488-94. [PMID: 22102614 DOI: 10.1002/humu.22000] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/15/2011] [Indexed: 12/31/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant disorder that predisposes to colon, endometrial, and other cancers. LS is caused by a heterozygous germline mutation in one of the DNA mismatch repair (MMR) genes. A significant proportion of all mutations found in suspected LS patients comprises single amino acid alterations. The pathogenicity of these variants of uncertain significance (VUS) is difficult to assess, precluding diagnosis of carriers and their relatives. Here we present a rapid cell-free assay to investigate MMR activity of MSH2 or MSH6 VUS. We used this assay to analyze a series of MSH2 and MSH6 VUS, selected from the Leiden Open Variation Database. Whereas a significant fraction of the MSH2 VUS has lost MMR activity, suggesting pathogenicity, the large majority of the MSH6 VUS appears MMR proficient. We anticipate that this assay will be an important tool in the development of a comprehensive and widely applicable diagnostic procedure for LS-associated VUS.
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Affiliation(s)
- Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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23
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Cyr JL, Brown GD, Stroop J, Heinen CD. The predicted truncation from a cancer-associated variant of the MSH2 initiation codon alters activity of the MSH2-MSH6 mismatch repair complex. Mol Carcinog 2011; 51:647-58. [PMID: 21837758 DOI: 10.1002/mc.20838] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 06/24/2011] [Accepted: 07/11/2011] [Indexed: 12/15/2022]
Abstract
Lynch syndrome (LS) is caused by germline mutations in DNA mismatch repair (MMR) genes. MMR recognizes and repairs DNA mismatches and small insertion/deletion loops. Carriers of MMR gene variants have a high risk of developing colorectal, endometrial, ovarian, and other extracolonic carcinomas. We report on an ovarian cancer patient who carries a germline MSH2 c.1A>C variant which alters the translation initiation codon. Mutations affecting the MSH2 start codon have been described previously for LS-related malignancies. However, the patients often lack a clear family history indicative of LS and their tumors often fail to display microsatellite instability, a hallmark feature of LS. Therefore, the pathogenicity of start codon variants remains undefined. Loss of the MSH2 start codon has been predicted to result in a truncated protein translated from a downstream in-frame AUG that would lack the first 25 amino acids. We therefore purified recombinant MSH2(NΔ25)-MSH6 and MSH2(NΔ25)-MSH3 to examine their DNA lesion recognition and adenosine nucleotide processing functions in vitro. We found that the MSH2(NΔ25) mutant confers distinct biochemical defects on MSH2-MSH6, but does not have a significant effect on MSH2-MSH3. We confirmed that expression of the MSH2 c.1A>C cDNA results in the production of multiple protein products in human cells that may include the truncated and full-length forms of MSH2. An in vivo MMR assay revealed a slight reduction in MMR efficiency in these cells. These data suggest that mutation of the MSH2 initiation codon, while not a strong, high-risk disease allele, may have a moderate impact on disease phenotype.
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Affiliation(s)
- Jennifer L Cyr
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030-3101, USA
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Wielders EAL, Dekker RJ, Holt I, Morris GE, te Riele H. Characterization of MSH2 variants by endogenous gene modification in mouse embryonic stem cells. Hum Mutat 2011; 32:389-96. [PMID: 21309037 DOI: 10.1002/humu.21448] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/21/2010] [Indexed: 12/30/2022]
Abstract
Mutations in the mismatch repair gene MSH2 underlie hereditary nonpolyposis colorectal cancer (Lynch syndrome). Whereas disruptive mutations are overtly pathogenic, the implications of missense mutations found in sporadic colorectal cancer patients or in suspected Lynch syndrome families are often unknown. Adequate genetic counseling of mutation carriers requires phenotypic characterization of the variant allele. We present a novel approach to functionally characterize MSH2 missense mutations. Our approach involves introduction of the mutation into the endogenous gene of murine embryonic stem cells (ESC) by oligonucleotide-directed gene modification, a technique we recently developed in our lab. Subsequently, the mismatch repair capacity of mutant ESC is determined using a set of validated functional assays. We have evaluated four clinically relevant MSH2 variants and found one to completely lack mismatch repair capacity while three behaved as wild-type MSH2 and can therefore be considered as polymorphisms. Our approach contributes to an adequate risk assessment of mismatch repair missense mutations. We have also shown that oligonucleotide-directed gene modification provides a straightforward approach to recreate allelic variants in the endogenous gene in murine ESC. This approach can be extended to other hereditary conditions.
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Affiliation(s)
- Eva A L Wielders
- The Netherlands Cancer Institute, Division of Molecular Biology, Amsterdam, The Netherlands
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25
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Non-truncating hMLH1 variants identified in Slovenian gastric cancer patients are not associated with Lynch Syndrome: a functional analysis report. Fam Cancer 2010; 10:255-63. [DOI: 10.1007/s10689-010-9409-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Drost M, Zonneveld JEBM, van Dijk L, Morreau H, Tops CM, Vasen HFA, Wijnen JT, de Wind N. A cell-free assay for the functional analysis of variants of the mismatch repair protein MLH1. Hum Mutat 2010; 31:247-53. [PMID: 20020535 DOI: 10.1002/humu.21180] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The hereditary colon and endometrium cancer predisposition Lynch Syndrome (also called HNPCC) is caused by a germ-line mutation in one of the DNA mismatch repair (MMR) genes. A significant fraction of the gene alterations detected in suspected Lynch Syndrome patients is comprised of amino acid substitutions. The relevance for cancer risk of these variants is difficult to assess, as currently no time- and cost-effective, validated, and widely applicable functional assays for the measurement of MMR activity are available. Here we describe a rapid, cell-free, and easily quantifiable MMR activity assay for the diagnostic assessment of variants of the MLH1 MMR protein. This assay allows the parallel generation and functional analysis of a series of variants of the MLH1 protein in vitro using readily available, or preprepared, reagents. Using this assay we have tested 26 MLH1 variants and of these, 15 had lost activity. These results are in concordance with those obtained from first-generation assays and with in silico and pathology data. After its multifocal technical and clinical validation this assay could have great impact for the diagnosis and counseling of carriers of an MLH1 variant and their relatives.
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Affiliation(s)
- Mark Drost
- Departments of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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27
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van Riel E, Ausems MG, Hogervorst FB, Kluijt I, van Gijn ME, van Echtelt J, Scheidel-Jacobse K, Hennekam EF, Stulp RP, Vos YJ, Offerhaus GJA, Menko FH, Gille JJ. A novel pathogenic MLH1 missense mutation, c.112A > C, p.Asn38His, in six families with Lynch syndrome. Hered Cancer Clin Pract 2010; 8:7. [PMID: 20704743 PMCID: PMC2927519 DOI: 10.1186/1897-4287-8-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 08/12/2010] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND An unclassified variant (UV) in exon 1 of the MLH1 gene, c.112A > C, p.Asn38His, was found in six families who meet diagnostic criteria for Lynch syndrome. The pathogenicity of this variant was unknown. We aim to elucidate the pathogenicity of this MLH1 variant in order to counsel these families adequately and to enable predictive testing in healthy at-risk relatives. METHODS We studied clinical data, microsatellite instability and immunohistochemical staining of MMR proteins, and performed genealogy, haplotype analysis and DNA testing of control samples. RESULTS The UV showed co-segregation with the disease in all families. All investigated tumors showed a microsatellite instable pattern. Immunohistochemical data were variable among tested tumors. Three families had a common ancestor and all families originated from the same geographical area in The Netherlands. Haplotype analysis showed a common haplotype in all six families. CONCLUSIONS We conclude that the MLH1 variant is a pathogenic mutation and genealogy and haplotype analysis results strongly suggest that it is a Dutch founder mutation. Our findings imply that predictive testing can be offered to healthy family members. The immunohistochemical data of MMR protein expression show that interpreting these results in case of a missense mutation should be done with caution.
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Affiliation(s)
- Els van Riel
- Department of Medical Genetics, University Medical Centre Utrecht, Lundlaan 6, Utrecht, The Netherlands.
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28
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Kantelinen J, Kansikas M, Korhonen MK, Ollila S, Heinimann K, Kariola R, Nyström M. MutSbeta exceeds MutSalpha in dinucleotide loop repair. Br J Cancer 2010; 102:1068-73. [PMID: 20160730 PMCID: PMC2844022 DOI: 10.1038/sj.bjc.6605531] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The target substrates of DNA mismatch recognising factors MutSalpha (MSH2+MSH6) and MutSbeta (MSH2+MSH3) have already been widely researched. However, the extent of their functional redundancy and clinical substance remains unclear. Mismatch repair (MMR)-deficient tumours are strongly associated with microsatellite instability (MSI) and the degree and type of MSI seem to be dependent on the MMR gene affected, and is linked to its substrate specificities. Deficiency in MSH2 and MSH6 is associated with both mononucleotide and dinucleotide repeat instability. Although no pathogenic MSH3 mutations have been reported, its deficiency is also suggested to cause low dinucleotide repeat instability. METHODS To assess the substrate specificities and functionality of MutSalpha and MutSbeta we performed an in vitro MMR assay using three substrate constructs, GT mismatch, 1 and 2 nucleotide insertion/deletion loops (IDLs) in three different cell lines. RESULTS Our results show that though MutSalpha alone seems to be responsible for GT and IDL1 repair, MutSalpha and MutSbeta indeed have functional redundancy in IDL2 repair and in contrast with earlier studies, MutSbeta seems to exceed MutSalpha. CONCLUSION The finding is clinically relevant because the strong role of MutSbeta in IDL2 repair indicates MSH3 deficiency in tumours with low dinucleotide and no mononucleotide repeat instability.
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Affiliation(s)
- J Kantelinen
- Department of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, Helsinki, Finland
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A cancer-associated DNA polymerase delta variant modeled in yeast causes a catastrophic increase in genomic instability. Proc Natl Acad Sci U S A 2009; 107:157-62. [PMID: 19966286 DOI: 10.1073/pnas.0907526106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate DNA synthesis by the replicative DNA polymerases alpha, delta, and epsilon is critical for genome stability in eukaryotes. In humans, over 20 SNPs were reported that result in amino-acid changes in Poldelta or Polepsilon. In addition, Poldelta variants were found in colon-cancer cell lines and in sporadic colorectal carcinomas. Using the yeast-model system, we examined the functional consequences of two cancer-associated Poldelta mutations and four polymorphisms affecting well-conserved regions of Poldelta or Polepsilon. We show that the R696W substitution in Poldelta (analog of the R689W change in the human cancer-cell line DLD-1) is lethal in haploid and homozygous diploid yeast. The cell death results from a catastrophic increase in spontaneous mutagenesis attributed to low-fidelity DNA synthesis by Poldelta-R696W. Heterozygotes survive, and the mutation rate depends on the relative expression level of wild-type versus mutant alleles. Based on these observations, we propose that the mutation rate in heterozygous human cells could be regulated by transient changes in gene expression leading to a temporary excess of Poldelta-R689W. The similarities between the mutational spectra of the yeast strains producing Poldelta-R696W and DLD-1 cells suggest that the altered Poldelta could be responsible for a significant proportion of spontaneous mutations in this cancer cell line. These results suggest that the highly error-prone Poldelta-R689W could contribute to cancer initiation and/or progression in humans.
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Arnold S, Buchanan DD, Barker M, Jaskowski L, Walsh MD, Birney G, Woods MO, Hopper JL, Jenkins MA, Brown MA, Tavtigian SV, Goldgar DE, Young JP, Spurdle AB. Classifying MLH1 and MSH2 variants using bioinformatic prediction, splicing assays, segregation, and tumor characteristics. Hum Mutat 2009; 30:757-70. [PMID: 19267393 PMCID: PMC2707453 DOI: 10.1002/humu.20936] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reliable methods for predicting functional consequences of variants in disease genes would be beneficial in the clinical setting. This study was undertaken to predict, and confirm in vitro, splicing aberrations associated with mismatch repair (MMR) variants identified in familial colon cancer patients. Six programs were used to predict the effect of 13 MLH1 and 6 MSH2 gene variants on pre-mRNA splicing. mRNA from cycloheximide-treated lymphoblastoid cell lines of variant carriers was screened for splicing aberrations. Tumors of variant carriers were tested for microsatellite instability and MMR protein expression. Variant segregation in families was assessed using Bayes factor causality analysis. Amino acid alterations were examined for evolutionary conservation and physicochemical properties. Splicing aberrations were detected for 10 variants, including a frameshift as a minor cDNA product, and altered ratio of known alternate splice products. Loss of splice sites was well predicted by splice-site prediction programs SpliceSiteFinder (90%) and NNSPLICE (90%), but consequence of splice site loss was less accurately predicted. No aberrations correlated with ESE predictions for the nine exonic variants studied. Seven of eight missense variants had normal splicing (88%), but only one was a substitution considered neutral from evolutionary/physicochemical analysis. Combined with information from tumor and segregation analysis, and literature review, 16 of 19 variants were considered clinically relevant. Bioinformatic tools for prediction of splicing aberrations need improvement before use without supporting studies to assess variant pathogenicity. Classification of mismatch repair gene variants is assisted by a comprehensive approach that includes in vitro, tumor pathology, clinical, and evolutionary conservation data.
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Affiliation(s)
- Sven Arnold
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Daniel D. Buchanan
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Melissa Barker
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Lesley Jaskowski
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Michael D. Walsh
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Genevieve Birney
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Michael O. Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - John L. Hopper
- Centre for Genetic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Mark A. Jenkins
- Centre for Genetic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Melissa A. Brown
- School of Medicine, and School of Molecular and Microbial Sciences, University of Queensland, Brisbane
| | | | - David E. Goldgar
- Department of Dermatology, University of Utah, Salt Lake City, Utah, USA
| | - Joanne P. Young
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B. Spurdle
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
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31
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Machado AMD, Figueiredo C, Touati E, Máximo V, Sousa S, Michel V, Carneiro F, Nielsen FC, Seruca R, Rasmussen LJ. Helicobacter pylori infection induces genetic instability of nuclear and mitochondrial DNA in gastric cells. Clin Cancer Res 2009; 15:2995-3002. [PMID: 19383819 DOI: 10.1158/1078-0432.ccr-08-2686] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE Helicobacter pylori is a major cause of gastric carcinoma. To investigate a possible link between bacterial infection and genetic instability of the host genome, we examined the effect of H. pylori infection on known cellular repair pathways in vitro and in vivo. Moreover, various types of genetic instabilities in the nuclear and mitochondrial DNA (mtDNA) were examined. EXPERIMENTAL DESIGN We observed the effects of H. pylori infection on a gastric cell line (AGS), on C57BL/6 mice, and on individuals with chronic gastritis. In AGS cells, the effect of H. pylori infection on base excision repair and mismatch repair (MMR) was analyzed by reverse transcription-PCR, Western blot, and activity assays. In mice, MMR expression was analyzed by reverse transcription-PCR and the CA repeat instabilities were examined by Mutation Detection Enhancement gel electrophoresis. Mutation spectra in AGS cells and chronic gastritis tissue were determined by PCR, single-stranded conformation polymorphism, and sequencing. H. pylori vacA and cagA genotyping was determined by multiplex PCR and reverse hybridization. RESULTS Following H. pylori infection, the activity and expression of base excision repair and MMR are down-regulated both in vitro and in vivo. Moreover, H. pylori induces genomic instability in nuclear CA repeats in mice and in mtDNA of AGS cells and chronic gastritis tissue, and this effect in mtDNA is associated with bacterial virulence. CONCLUSIONS Our results suggest that H. pylori impairs central DNA repair mechanisms, inducing a transient mutator phenotype, rendering gastric epithelial cells vulnerable to the accumulation of genetic instability and thus contributing to gastric carcinogenesis in infected individuals.
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Kaput J, Cotton RGH, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MRN, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SGE, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AMO, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS. Planning the human variome project: the Spain report. Hum Mutat 2009; 30:496-510. [PMID: 19306394 PMCID: PMC5879779 DOI: 10.1002/humu.20972] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.
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Affiliation(s)
- Jim Kaput
- Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, Jefferson, Arkansas 72079, USA.
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Kaufmann A, Vogt S, Uhlhaas S, Stienen D, Kurth I, Hameister H, Mangold E, Kötting J, Kaminsky E, Propping P, Friedl W, Aretz S. Analysis of rare APC variants at the mRNA level: six pathogenic mutations and literature review. J Mol Diagn 2009; 11:131-9. [PMID: 19196998 DOI: 10.2353/jmoldx.2009.080129] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In monogenic disorders, the functional evaluation of rare, unclassified variants helps to assess their pathogenic relevance and can improve differential diagnosis and predictive testing. We characterized six rare APC variants in patients with familial adenomatous polyposis at the mRNA level. APC variants c.531 + 5G>C and c.532-8G>A in intron 4, c.1409-2_1409delAGG in intron 10, c.1548G>A in exon 11, and a large duplication of exons 10 and 11 result in a premature stop codon attributable to aberrant transcripts whereas the variant c.1742A>G leads to the in-frame deletion of exon 13 and results in the removal of a functional motif. Mutation c.1548G>A was detected in the index patient but not in his affected father, suggesting mutational mosaicism. A literature review shows that most of the rare APC variants detected by routine diagnostics and further analyzed at the transcript level were evaluated as pathogenic. The majority of rare APC variants, particularly those located close to exon-intron boundaries, could be classified as pathogenic because of aberrant splicing. Our study shows that the characterization of rare variants at the mRNA level is crucial for the evaluation of pathogenicity and underlying mutational mechanisms, and could lead to better treatment modalities.
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34
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Current World Literature. Curr Opin Obstet Gynecol 2009; 21:101-9. [DOI: 10.1097/gco.0b013e3283240745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Tournier I, Vezain M, Martins A, Charbonnier F, Baert-Desurmont S, Olschwang S, Wang Q, Buisine MP, Soret J, Tazi J, Frébourg T, Tosi M. A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects. Hum Mutat 2009; 29:1412-24. [PMID: 18561205 DOI: 10.1002/humu.20796] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Numerous unclassified variants (UVs) have been found in the mismatch repair genes MLH1 and MSH2 involved in hereditary nonpolyposis colorectal cancer (HNPCC or Lynch syndrome). Some of these variants may have an effect on pre-mRNA splicing, either by altering degenerate positions of splice site sequences or by affecting intronic or exonic splicing regulatory sequences such as exonic splicing enhancers (ESEs). In order to determine the consequences of UVs on splicing, we used a functional assay of exon inclusion. For each variant, mutant and wild-type exons to be tested were PCR-amplified from patient genomic DNA together with approximately 150 bp of flanking sequences and were inserted into a splicing reporter minigene. After transfection into HeLa cells, the effects on splicing were evaluated by RT-PCR analysis and systematic sequencing. A total of 22 UVs out of 85 different variant alleles examined in 82 families affected splicing, including four exonic variants that affected putative splicing regulatory elements. We analyzed short stretches spanning the latter variants by cloning them into the ESE-dependent central exon of a three-exon splicing minigene and we showed in cell transfection experiments that the wild-type sequences indeed contain functional ESEs. We then used this construct to query for ESE elements in the MLH1 or MSH2 regions affected by 14 previously reported exonic splicing mutations and showed that they also contain functional ESEs. These splicing assays represent a valuable tool for the interpretation of UVs and should contribute to the optimization of the molecular diagnosis of the Lynch syndrome and of other genetic diseases.
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Affiliation(s)
- Isabelle Tournier
- Inserm U614, Federate Institute for Multidisciplinary Research on Peptides, Faculty of Medicine, University of Rouen, Department of Genetics and Institute for Biomedical Research, Rouen University Hospital, Rouen, France
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Ollila S, Dermadi Bebek D, Jiricny J, Nyström M. Mechanisms of pathogenicity in human MSH2 missense mutants. Hum Mutat 2008; 29:1355-63. [PMID: 18951462 DOI: 10.1002/humu.20893] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The human mismatch repair (MMR) gene MSH2 is the second most frequently mutated hereditary nonpolyposis colorectal cancer (HNPCC) susceptibility locus. Given that missense mutations account for 17% of all identified alterations in this gene, the study of their pathogenicity is of increasing importance. Previously, we showed that pathogenic MSH2 missense mutations typically impaired the repair activity of the protein. In this study, we took advantage of its crystal structure and attempted to correlate the mismatch binding and ATP-catalyzed mismatch release activities with the location of 18 nontruncating MSH2 mutations. We observed that the MMR-deficient mutations situated in the amino-terminal connector and lever domains of MSH2 (V161D, G162R, G164R, L173P, L187P, C333Y, and D603N) affected protein stability, whereas mutations in the ATPase domain (A636P, G674A, C697F, I745_I746del, and E749 K) mainly caused defects in mismatch binding or release. Of the MMR-proficient variants, four (T33P, A272 V, G322D, and V923E) showed slightly reduced mismatch binding and/or release efficiencies compared to wild-type (WT) protein, while two variants (N127S and A834 T) showed no defects in the assays. Similar to our biochemical data, the mutations that affected protein stability were associated with an absence of the protein in tumors in immunohistochemical (IHC) analyses. In contrast, the protein with the mutation E749 K, which abrogates MMR but not protein stability, is well expressed in tumors. In conclusion, pathogenic missense mutations in MSH2 may interfere with different mechanisms that tend to cluster in separate protein domains with varying effects on protein stability, which could be taken into account when interpreting IHC data.
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Affiliation(s)
- Saara Ollila
- Department of Biological and Environmental Sciences, Genetics, University of Helsinki, Helsinki, Finland
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37
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Ou J, Niessen RC, Vonk J, Westers H, Hofstra RMW, Sijmons RH. A database to support the interpretation of human mismatch repair gene variants. Hum Mutat 2008; 29:1337-41. [PMID: 18951442 DOI: 10.1002/humu.20907] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Germline mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, or PMS2 can cause Lynch syndrome. This syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC), is an autosomal dominantly-inherited disorder predominantly characterized by colorectal and endometrial cancer. Truncating MMR gene mutations generally offer a clear handle for genetic counseling and allow for presymptomatic testing. In contrast, the clinical implications of most missense mutations and small in-frame deletions detected in patients suspected of having Lynch syndrome are unclear. We have constructed an online database, the Mismatch Repair Gene Unclassified Variants Database (www.mmruv.info), for information on the results of functional assays and other findings that may help in classifying these MMR gene variants. Ideally, such mutations should be clinically classified by a broad expert panel rather than by the individual database curators. In addition, the different MMR gene mutation databases could be interlinked or combined to increase user-friendliness and avoid unnecessary overlap between them. Both activities are presently being organized by the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org).
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Affiliation(s)
- Jianghua Ou
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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38
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Couch FJ, Rasmussen LJ, Hofstra R, Monteiro ANA, Greenblatt MS, de Wind N. Assessment of functional effects of unclassified genetic variants. Hum Mutat 2008; 29:1314-26. [PMID: 18951449 PMCID: PMC2771414 DOI: 10.1002/humu.20899] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been extensively characterized at the functional level, few assays based on functional properties of the encoded proteins have been established for the purpose of predicting the contribution of rare inherited variants to disease. Much of the difficulty in establishing predictive functional assays stems from the technical complexity of the assays. However, perhaps the most challenging aspect of functional assay development for clinical testing purposes is the absolute requirement for validation of the sensitivity and specificity of the assays and the determination of positive predictive values (PPVs) and negative predictive values (NPVs) of the assays relative to a "gold standard" measure of disease predisposition. In this commentary, we provide examples of some of the functional assays under development for several cancer predisposition genes (BRCA1, BRCA2, CDKN2A, and mismatch repair [MMR] genes MLH1, MSH2, MSH6, and PMS2) and present a detailed review of the issues associated with functional assay development. We conclude that validation is paramount for all assays that will be used for clinical interpretation of inherited variants of any gene, but note that in certain circumstances information derived from incompletely validated assays may be valuable for classification of variants for clinical purposes when used to supplement data derived from other sources.
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Affiliation(s)
- Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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39
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Goldgar DE, Easton DF, Byrnes GB, Spurdle AB, Iversen ES, Greenblatt MS. Genetic evidence and integration of various data sources for classifying uncertain variants into a single model. Hum Mutat 2008; 29:1265-72. [PMID: 18951437 PMCID: PMC2936773 DOI: 10.1002/humu.20897] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic testing often results in the finding of a variant whose clinical significance is unknown. A number of different approaches have been employed in the attempt to classify such variants. For some variants, case-control, segregation, family history, or other statistical studies can provide strong evidence of direct association with cancer risk. For most variants, other evidence is available that relates to properties of the protein or gene sequence. In this work we propose a Bayesian method for assessing the likelihood that a variant is pathogenic. We discuss the assessment of prior probability, and how to combine the various sources of data into a statistically valid integrated assessment with a posterior probability of pathogenicity. In particular, we propose the use of a two-component mixture model to integrate these various sources of data and to estimate the parameters related to sensitivity and specificity of specific kinds of evidence. Further, we discuss some of the issues involved in this process and the assumptions that underpin many of the methods used in the evaluation process.
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Affiliation(s)
- David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah 84132-2409, USA.
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40
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Greenblatt MS, Brody LC, Foulkes WD, Genuardi M, Hofstra RMW, Olivier M, Plon SE, Sijmons RH, Sinilnikova O, Spurdle AB. Locus-specific databases and recommendations to strengthen their contribution to the classification of variants in cancer susceptibility genes. Hum Mutat 2008; 29:1273-81. [PMID: 18951438 PMCID: PMC3446852 DOI: 10.1002/humu.20889] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Locus-specific databases (LSDBs) are curated collections of sequence variants in genes associated with disease. LSDBs of cancer-related genes often serve as a critical resource to researchers, diagnostic laboratories, clinicians, and others in the cancer genetics community. LSDBs are poised to play an important role in disseminating clinical classification of variants. The IARC Working Group on Unclassified Genetic Variants has proposed a new system of five classes of variants in cancer susceptibility genes. However, standards are lacking for reporting and analyzing the multiple data types that assist in classifying variants. By adhering to standards of transparency and consistency in the curation and annotation of data, LSDBs can be critical for organizing our understanding of how genetic variation relates to disease. In this article we discuss how LSDBs can accomplish these goals, using existing databases for BRCA1, BRCA2, MSH2, MLH1, TP53, and CDKN2A to illustrate the progress and remaining challenges in this field. We recommend that: 1) LSDBs should only report a conclusion related to pathogenicity if a consensus has been reached by an expert panel. 2) The system used to classify variants should be standardized. The Working Group encourages use of the five class system described in this issue by Plon and colleagues. 3) Evidence that supports a conclusion should be reported in the database, including sources and criteria used for assignment. 4) Variants should only be classified as pathogenic if more than one type of evidence has been considered. 5) All instances of all variants should be recorded.
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Affiliation(s)
- Marc S Greenblatt
- Vermont Cancer Center and Department of Medicine, University of Vermont, Burlington, Vermont 05405, USA.
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Cyr JL, Heinen CD. Hereditary cancer-associated missense mutations in hMSH6 uncouple ATP hydrolysis from DNA mismatch binding. J Biol Chem 2008; 283:31641-8. [PMID: 18790734 DOI: 10.1074/jbc.m806018200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hereditary nonpolyposis colorectal cancer is caused by germline mutations in DNA mismatch repair genes. The majority of cases are associated with mutations in hMSH2 or hMLH1; however, about 12% of cases are associated with alterations in hMSH6. The hMSH6 protein forms a heterodimer with hMSH2 that is capable of recognizing a DNA mismatch. The heterodimer then utilizes its adenosine nucleotide processing ability in an, as of yet, unclear mechanism to facilitate communication between the mismatch and a distant strand discrimination site. The majority of reported mutations in hMSH6 are deletions or truncations that entirely eliminate the function of the protein; however, nearly a third of the reported variations are missense mutations whose functional significance is unclear. We analyzed seven cancer-associated single amino acid alterations in hMSH6 distributed throughout the functional domains of the protein to determine their effect on the biochemical activity of the hMSH2-hMSH6 heterodimer. Five alterations affect mismatch-stimulated ATP hydrolysis activity providing functional evidence that missense variants of hMSH6 can disrupt mismatch repair function and may contribute to disease. Of the five mutants that affect mismatch-stimulated ATP hydrolysis, only two (R976H and H1248D) affect mismatch recognition. Thus, three of the mutants (G566R, V878A, and D803G) appear to uncouple the mismatch binding and ATP hydrolysis activities of the heterodimer. We also demonstrate that these three mutations alter ATP-dependent conformation changes of hMSH2-hMSH6, suggesting that cancer-associated mutations in hMSH6 can disrupt the intramolecular signaling that coordinates mismatch binding with adenosine nucleotide processing.
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Affiliation(s)
- Jennifer L Cyr
- Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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42
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Ollila S, Bebek DD, Greenblatt M, Nyström M. Uncertain pathogenicity of MSH2
variants N127S and G322D challenges their classification. Int J Cancer 2008; 123:720-4. [DOI: 10.1002/ijc.23573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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