1
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Fukui K, Fujii Y, Yano T. Identification of a Catalytic Lysine Residue Conserved Among GHKL ATPases: MutL, GyrB, and MORC. J Mol Biol 2024; 436:168575. [PMID: 38641238 DOI: 10.1016/j.jmb.2024.168575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
DNA mismatch repair endonuclease MutL is a member of GHKL ATPase superfamily. Mutations of MutL homologs are causative of a hereditary cancer, Lynch syndrome. We characterized MutL homologs from human and a hyperthermophile, Aquifex aeolicus, (aqMutL) to reveal the catalytic mechanism for the ATPase activity. Although involvement of a basic residue had not been conceived in the catalytic mechanism, analysis of the pH dependence of the aqMutL ATPase activity revealed that the reaction is catalyzed by a residue with an alkaline pKa. Analyses of mutant aqMutLs showed that Lys79 is the catalytic residue, and the corresponding residues were confirmed to be critical for activities of human MutL homologs, on the basis of which a catalytic mechanism for MutL ATPase is proposed. These and other results described here would contribute to evaluating the pathogenicity of Lynch syndrome-associated missense mutations. Furthermore, it was confirmed that the catalytic lysine residue is conserved among DNA gyrases and microrchidia ATPases, other members of GHKL ATPases, indicating that the catalytic mechanism proposed here is applicable to these members of the superfamily.
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Affiliation(s)
- Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan.
| | - Yuki Fujii
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan.
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2
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Rath A, Radecki AA, Rahman K, Gilmore RB, Hudson JR, Cenci M, Tavtigian SV, Grady JP, Heinen CD. A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants. Hum Mutat 2022; 43:2295-2307. [PMID: 36054288 PMCID: PMC9772141 DOI: 10.1002/humu.24462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. However, previous assays are limited due to the model system employed, the manner of gene expression, or the environment in which function is assessed. Here, we developed a human cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene. Using clustered regularly interspaced short palindromic repeats gene editing, we knocked in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact on RNA and protein, including their ability to prevent microsatellite instability and instigate a DNA damage response. A statistical clustering analysis determined the range of functions associated with known pathogenic or benign variants, and linear regression was performed using existing odds in favor of pathogenicity scores for these control variants to calibrate our functional assay results. By converting the functional outputs into a single odds in favor of pathogenicity score, variant classification expert panels can use these results to readily reassess these VUS. Ultimately, this information will guide proper diagnosis and disease management for suspected Lynch syndrome patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | | | - Kaussar Rahman
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Rachel B. Gilmore
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Jonathan R. Hudson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Matthew Cenci
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - James P. Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, CT
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3
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Mahdouani M, Ben Ahmed S, Hmila F, Rais H, Ben Sghaier R, Saad H, Ben Said M, Masmoudi S, Hmida D, Brieger A, Zeuzem S, Saad A, Gribaa M, Plotz G. Functional characterization of MLH1 missense variants unveils mechanisms of pathogenicity and clarifies role in cancer. PLoS One 2022; 17:e0278283. [PMID: 36454741 PMCID: PMC9714755 DOI: 10.1371/journal.pone.0278283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/28/2022] [Indexed: 12/05/2022] Open
Abstract
Lynch syndrome is a heritable condition caused by a heterozygous germline inactivating mutation of the DNA mismatch repair (MMR) genes, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants, for which the clinical significance is unclear in many cases. We have identified three MLH1 missense alterations (p.(Glu736Lys), p.(Pro640Thr) and p.(Leu73Pro)) in six individuals from large Tunisian families. For none of these alterations, a classification of pathogenicity was available, consequently diagnosis, predictive testing and targeted surveillance in affected families was impossible. We therefore performed functional laboratory testing using a system testing stability as well as catalytic activity that includes clinically validated reference variants. Both p.(Leu73Pro) and p.(Pro640Thr) were found to be non-functional due to severe defects in protein stability and catalytic activity. In contrast, p.(Glu736Lys) was comparable to the wildtype protein and therefore considered a neutral substitution. Analysis of residue conservation and of the structural roles of the substituted residues corroborated these findings. In conjunction with the available clinical data, two variants fulfil classification criteria for class 4 "likely pathogenic". The findings of this work clarify the mechanism of pathogenicity of two unclear MLH1 variants and enables predictive testing and targeted surveillance in members of carrier families worldwide.
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Affiliation(s)
- Marwa Mahdouani
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Slim Ben Ahmed
- Department of Oncology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Fahmi Hmila
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
- Department of General and Digestive Surgery, Farhat Hached University Hospital, Sousse, Tunisia
| | - Henda Rais
- Medical Service, Salah Azaiez Institute, Tunis, Tunisia
| | - Rihab Ben Sghaier
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Hanene Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Dorra Hmida
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Angela Brieger
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Ali Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Moez Gribaa
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
- * E-mail:
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4
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CNOT6: A Novel Regulator of DNA Mismatch Repair. Cells 2022; 11:cells11030521. [PMID: 35159331 PMCID: PMC8833972 DOI: 10.3390/cells11030521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mismatch repair (MMR) is a highly conserved pathway that corrects both base–base mispairs and insertion-deletion loops (IDLs) generated during DNA replication. Defects in MMR have been linked to carcinogenesis and drug resistance. However, the regulation of MMR is poorly understood. Interestingly, CNOT6 is one of four deadenylase subunits in the conserved CCR4-NOT complex and it targets poly(A) tails of mRNAs for degradation. CNOT6 is overexpressed in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and androgen-independent prostate cancer cells, which suggests that an altered expression of CNOT6 may play a role in tumorigenesis. Here, we report that a depletion of CNOT6 sensitizes human U2OS cells to N-methyl-N′nitro-N-nitrosoguanidine (MNNG) and leads to enhanced apoptosis. We also demonstrate that the depletion of CNOT6 upregulates MMR and decreases the mutation frequency in MMR-proficient cells. Furthermore, the depletion of CNOT6 increases the stability of mRNA transcripts from MMR genes, leading to the increased expression of MMR proteins. Our work provides insight into a novel CNOT6-dependent mechanism for regulating MMR.
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Ijsselsteijn R, van Hees S, Drost M, Jansen JG, de Wind N. Induction of mismatch repair deficiency, compromised DNA damage signaling and compound hypermutagenesis by a dietary mutagen in a cell-based model for Lynch Syndrome. Carcinogenesis 2021; 43:160-169. [PMID: 34919656 PMCID: PMC8947211 DOI: 10.1093/carcin/bgab108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/21/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The prevalent cancer predisposition Lynch syndrome (LS, OMIM #120435) is caused by an inherited heterozygous defect in any of the four core DNA mismatch repair (MMR) genes MSH2, MSH6, MLH1 or PMS2. MMR repairs errors by the replicative DNA polymerases in all proliferating tissues. Its deficiency, following somatic loss of the wild type copy, results in a spontaneous mutator phenotype that underlies the rapid development of, predominantly, colorectal cancer (CRC) in LS. Here we have addressed the hypothesis that aberrant responses of intestinal stem cells to diet-derived mutagens may be causally involved in the restricted cancer tropism of LS. To test this we have generated a panel of isogenic mouse embryonic stem (mES) cells with heterozygous or homozygous disruption of multiple MMR genes and investigated their responses to the common dietary mutagen and carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Our data reveal that PhIP can inactivate the wild type allele of heterozygous mES cells via the induction of either loss of heterozygosity (LOH) or intragenic mutations. Moreover, while protective DNA damage signaling (DDS) is compromised, PhIP induces more mutations in Msh2, Mlh1, Msh6 or Pms2-deficient mES cells than in wild type cells. Combined with their spontaneous mutator phenotypes, this results in a compound hypermutator phenotype. Together, these results indicate that dietary mutagens may promote CRC development in LS at multiple levels, providing a rationale for dietary modifications in the management of LS.
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Affiliation(s)
- Robbert Ijsselsteijn
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandrine van Hees
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jacob G Jansen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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6
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Ollodart AR, Yeh CLC, Miller AW, Shirts BH, Gordon AS, Dunham MJ. Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 2021; 218:iyab058. [PMID: 33848333 PMCID: PMC8225350 DOI: 10.1093/genetics/iyab058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 01/01/2023] Open
Abstract
Despite the fundamental importance of mutation rate as a driving force in evolution and disease risk, common methods to assay mutation rate are time-consuming and tedious. Established methods such as fluctuation tests and mutation accumulation experiments are low-throughput and often require significant optimization to ensure accuracy. We established a new method to determine the mutation rate of many strains simultaneously by tracking mutation events in a chemostat continuous culture device and applying deep sequencing to link mutations to alleles of a DNA-repair gene. We applied this method to assay the mutation rate of hundreds of Saccharomyces cerevisiae strains carrying mutations in the gene encoding Msh2, a DNA repair enzyme in the mismatch repair pathway. Loss-of-function mutations in MSH2 are associated with hereditary nonpolyposis colorectal cancer, an inherited disorder that increases risk for many different cancers. However, the vast majority of MSH2 variants found in human populations have insufficient evidence to be classified as either pathogenic or benign. We first benchmarked our method against Luria-Delbrück fluctuation tests using a collection of published MSH2 missense variants. Our pooled screen successfully identified previously characterized nonfunctional alleles as high mutators. We then created an additional 185 human missense variants in the yeast ortholog, including both characterized and uncharacterized alleles curated from ClinVar and other clinical testing data. In a set of alleles of known pathogenicity, our assay recapitulated ClinVar's classification; we then estimated pathogenicity for 157 variants classified as uncertain or conflicting reports of significance. This method is capable of studying the mutation rate of many microbial species and can be applied to problems ranging from the generation of high-fidelity polymerases to measuring the frequency of antibiotic resistance emergence.
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Affiliation(s)
- Anja R Ollodart
- Molecular Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Chiann-Ling C Yeh
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Aaron W Miller
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Adam S Gordon
- Department of Pharmacology, Northwestern University, Chicago, IL 60208, USA
| | - Maitreya J Dunham
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
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7
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Cerretelli G, Ager A, Arends MJ, Frayling IM. Molecular pathology of Lynch syndrome. J Pathol 2020; 250:518-531. [PMID: 32141610 DOI: 10.1002/path.5422] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) is characterised by predisposition to colorectal, endometrial, and other cancers and is caused by inherited pathogenic variants affecting the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. It is probably the most common predisposition to cancer, having an estimated prevalence of between 1/100 and 1/180. Resources such as the International Society for Gastrointestinal Hereditary Cancer's MMR gene variant database, the Prospective Lynch Syndrome Database (PLSD), and the Colon Cancer Family Register (CCFR), as well as pathological and immunological studies, are enabling advances in the understanding of LS. These include defined criteria by which to interpret gene variants, the function of MMR in the normal control of apoptosis, definition of the risks of the various cancers, and the mechanisms and pathways by which the colorectal and endometrial tumours develop, including the critical role of the immune system. Colorectal cancers in LS can develop along three pathways, including flat intramucosal lesions, which depend on the underlying affected MMR gene. This gives insights into the limitations of colonoscopic surveillance and highlights the need for other forms of anti-cancer prophylaxis in LS. Finally, it shows that the processes of autoimmunisation and immunoediting fundamentally constrain the development of tumours in LS and explain the efficacy of immune checkpoint blockade therapy in MMR-deficient tumours. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Guia Cerretelli
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ann Ager
- Division of Infection and Immunity, School of Medicine and Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Mark J Arends
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ian M Frayling
- Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, UK
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González-Acosta M, Hinrichsen I, Fernández A, Lázaro C, Pineda M, Plotz G, Capellá G. Validation of an in Vitro Mismatch Repair Assay Used in the Functional Characterization of Mismatch Repair Variants. J Mol Diagn 2019; 22:376-385. [PMID: 31881334 DOI: 10.1016/j.jmoldx.2019.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/27/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022] Open
Abstract
A significant proportion of DNA-mismatch repair (MMR) variants are classified as of unknown significance, precluding diagnosis. The in vitro MMR assay is used to assess their MMR capability, likely the most important function of an MMR protein. However, the robustness of the assay, crucial for its use in the clinical setting, has been rarely evaluated. The aim of the present work was to validate an in vitro MMR assay approach to the functional characterization of MMR variants, as a first step to meeting quality standards of diagnostic laboratories. The MMR assay was optimized by testing a variety of reagents and experimental conditions. Reference materials and standard operating procedures were established. To determine the intra- and interexperimental variability of the assay and its reproducibility among centers, independent transfections of six previously characterized MLH1 variants were performed in two independent laboratories. Reagents and conditions optimal for performing the in vitro MMR assay were determined. The validated assay demonstrated no significant intra- or interexperimental variability and good reproducibility between centers. We set up a robust in vitro MMR assay that can provide relevant in vitro functional evidence for MMR variant pathogenicity assessment, eventually improving the molecular diagnosis of hereditary cancer syndromes associated with MMR deficiency.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inga Hinrichsen
- Biomedical Research Laboratory, Department of Internal Medicine 1, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Anna Fernández
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Gabriel Capellá
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.
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9
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Ben Sghaier R, Jansen AML, Bdioui A, Van Wezel T, Ksiaa M, Elgolli L, Ben Fatma L, Ben Ahmed S, Azzouz MM, Hellara O, Elghali A, Darbel F, Skandrani K, Mokkni M, Gdissa A, Ltaief R, Saad A, Hmila F, Gribaa M, Morreau H. Targeted next generation sequencing screening of Lynch syndrome in Tunisian population. Fam Cancer 2019; 18:343-348. [PMID: 31114938 DOI: 10.1007/s10689-019-00130-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A high colorectal cancer (CRC) incidence is observed in Tunisia, with a relatively high proportion of patients developing CRC before the age of 40. While this suggests a genetic susceptibility, only a few Tunisian Lynch Syndrome families have been described. In this study we aimed to identify the underlying genetic cause in 32 patients with early onset CRC and/or a positive family history. Of twenty-four patients' tumor or biopsies could be analyzed with immunohistochemical staining to detect loss of expression of one of the MMR proteins. Ten tumors showed loss of expression, of which one tumor was from a patient where a germline pathogenic MSH2 variant was detected previously with Sanger sequencing. Next generation sequencing of the MMR, POLE and POLD1 genes was performed in leukocyte and tumor DNA of the remaining nine patients, as well as in two patients with MMR-proficient tumors, but with severe family history. In six of 11 patients a germline variant was detected in MLH1 (n = 5) or MSH2 (n = 1). Two of six patients were from the same family and both were found to carry a novel in-frame MLH1 deletion, predicted to affect MLH1 function. All MLH1 variant carriers had loss of heterozygosity with retention of the variant in the tumors, while a somatic pathogenic variant was detected in the patient with the germline MSH2 variant.
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Affiliation(s)
- Rihab Ben Sghaier
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia.
| | | | - Ahlem Bdioui
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Tom Van Wezel
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - Mehdi Ksiaa
- Gastroenterology Department, Sahloul Hospital, Sousse, Tunisia
| | | | - Leila Ben Fatma
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Slim Ben Ahmed
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | - Olfa Hellara
- Gastroenterology Department, Fatouma Bourguiba Hospital, Monastir, Tunisia
| | - Amine Elghali
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | | | - Moncef Mokkni
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ameni Gdissa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Rached Ltaief
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ali Saad
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Fahmi Hmila
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Moez Gribaa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Hans Morreau
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
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10
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Valle L, Vilar E, Tavtigian SV, Stoffel EM. Genetic predisposition to colorectal cancer: syndromes, genes, classification of genetic variants and implications for precision medicine. J Pathol 2019; 247:574-588. [PMID: 30584801 PMCID: PMC6747691 DOI: 10.1002/path.5229] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Abstract
This article reviews genes and syndromes associated with predisposition to colorectal cancer (CRC), with an overview of gene variant classification. We include updates on the application of preventive and therapeutic measures, focusing on the use of non-steroidal anti-inflammatory drugs (NSAIDs) and immunotherapy. Germline pathogenic variants in genes conferring high or moderate risk to cancer are detected in 6-10% of all CRCs and 20% of those diagnosed before age 50. CRC syndromes can be subdivided into nonpolyposis and polyposis entities, the most common of which are Lynch syndrome and familial adenomatous polyposis, respectively. In addition to known and novel genes associated with highly penetrant CRC risk, identification of pathogenic germline variants in genes associated with moderate-penetrance cancer risk and/or hereditary cancer syndromes not traditionally linked to CRC may have an impact on genetic testing, counseling, and surveillance. The use of multigene panels in genetic testing has exposed challenges in the classification of variants of uncertain significance. We provide an overview of the main classification systems and strategies for improving these. Finally, we highlight approaches for integrating chemoprevention in the care of individuals with genetic predisposition to CRC and use of targeted agents and immunotherapy for treatment of mismatch repair-deficient and hypermutant tumors. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Eduardo Vilar
- Departments of Clinical Cancer Prevention, GI Medical Oncology and Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Elena M. Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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11
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D'Arcy BM, Blount J, Prakash A. Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene. Hum Mutat 2019; 40:458-471. [PMID: 30653781 DOI: 10.1002/humu.23708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/28/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited disorder that is associated with an increased predisposition to certain cancers caused by loss-of-function mutations in one of four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, or PMS2). The diagnosis of LS is often challenged by the identification of missense mutations where the functional effects are not known. These are termed variants of uncertain significance (VUSs) and account for 20%-30% of noncoding and missense mutations. VUSs cause ambiguity during clinical diagnosis and hinder implementation of appropriate medical management. In the current study, we focus on the functional and biological consequences of two nonsynonymous VUSs in PMS2. These variants, c.620G>A and c.123_131delGTTAGTAGA, result in the alteration of glycine 207 to glutamate (p.Gly207Glu) and the deletion of amino acid residues 42-44 (p.Leu42_Glu44del), respectively. While the PMS2 p.Gly207Glu variant retains in vitro MMR and ATPase activities, PMS2 p.Leu42_Glu44del appears to lack such capabilities. Structural and biophysical characterization using circular dichroism, small-angle X-ray scattering, and X-ray crystallography of the N-terminal domain of the PMS2 variants indicate that the p.Gly207Glu variant is properly folded similar to the wild-type enzyme, whereas p.Leu42_Glu44del is disordered and prone to aggregation.
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Affiliation(s)
- Brandon M D'Arcy
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
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12
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Shuen AY, Lanni S, Panigrahi GB, Edwards M, Yu L, Campbell BB, Mandel A, Zhang C, Zhukova N, Alharbi M, Bernstein M, Bowers DC, Carroll S, Cole KA, Constantini S, Crooks B, Dvir R, Farah R, Hijiya N, George B, Laetsch TW, Larouche V, Lindhorst S, Luiten RC, Magimairajan V, Mason G, Mason W, Mordechai O, Mushtaq N, Nicholas G, Oren M, Palma L, Pedroza LA, Ramdas J, Samuel D, Wolfe Schneider K, Seeley A, Semotiuk K, Shamvil A, Sumerauer D, Toledano H, Tomboc P, Wierman M, Van Damme A, Lee YY, Zapotocky M, Bouffet E, Durno C, Aronson M, Gallinger S, Foulkes WD, Malkin D, Tabori U, Pearson CE. Functional Repair Assay for the Diagnosis of Constitutional Mismatch Repair Deficiency From Non-Neoplastic Tissue. J Clin Oncol 2019; 37:461-470. [PMID: 30608896 DOI: 10.1200/jco.18.00474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Constitutional mismatch repair deficiency (CMMRD) is a highly penetrant cancer predisposition syndrome caused by biallelic mutations in mismatch repair (MMR) genes. As several cancer syndromes are clinically similar, accurate diagnosis is critical to cancer screening and treatment. As genetic diagnosis is confounded by 15 or more pseudogenes and variants of uncertain significance, a robust diagnostic assay is urgently needed. We sought to determine whether an assay that directly measures MMR activity could accurately diagnose CMMRD. PATIENTS AND METHODS In vitro MMR activity was quantified using a 3'-nicked G-T mismatched DNA substrate, which requires MSH2-MSH6 and MLH1-PMS2 for repair. We quantified MMR activity from 20 Epstein-Barr virus-transformed lymphoblastoid cell lines from patients with confirmed CMMRD. We also tested 20 lymphoblastoid cell lines from patients who were suspected for CMMRD. We also characterized MMR activity from patients with neurofibromatosis type 1, Li-Fraumeni syndrome, polymerase proofreading-associated cancer syndrome, and Lynch syndrome. RESULTS All CMMRD cell lines had low MMR activity (n = 20; mean, 4.14 ± 1.56%) relative to controls (n = 6; mean, 44.00 ± 8.65%; P < .001). Repair was restored by complementation with the missing protein, which confirmed MMR deficiency. All cases of patients with suspected CMMRD were accurately diagnosed. Individuals with Lynch syndrome (n = 28), neurofibromatosis type 1 (n = 5), Li-Fraumeni syndrome (n = 5), and polymerase proofreading-associated cancer syndrome (n = 3) had MMR activity that was comparable to controls. To accelerate testing, we measured MMR activity directly from fresh lymphocytes, which yielded results in 8 days. CONCLUSION On the basis of the current data set, the in vitro G-T repair assay was able to diagnose CMMRD with 100% specificity and sensitivity. Rapid diagnosis before surgery in non-neoplastic tissues could speed proper therapeutic management.
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Affiliation(s)
- Andrew Y Shuen
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stella Lanni
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Lisa Yu
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brittany B Campbell
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ariane Mandel
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cindy Zhang
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nataliya Zhukova
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Mark Bernstein
- 4 Dalhousie University Faculty of Medicine, Halifax, Nova Scotia, Canada
| | - Daniel C Bowers
- 5 University of Texas Southwestern Medical Center, Dallas, TX.,6 Children's Health, Dallas, TX
| | | | - Kristina A Cole
- 8 Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA
| | - Shlomi Constantini
- 9 Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,10 Tel Aviv University, Tel Aviv, Israel
| | - Bruce Crooks
- 4 Dalhousie University Faculty of Medicine, Halifax, Nova Scotia, Canada
| | - Rina Dvir
- 10 Tel Aviv University, Tel Aviv, Israel.,11 Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Roula Farah
- 12 Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Nobuko Hijiya
- 13 Ann & Robert H. Lurie Children's Hospital/Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ben George
- 14 Medical College of Wisconsin, Milwaukee, WI
| | - Theodore W Laetsch
- 5 University of Texas Southwestern Medical Center, Dallas, TX.,6 Children's Health, Dallas, TX
| | | | | | | | | | - Gary Mason
- 19 Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Warren Mason
- 1 University of Toronto, Toronto, Ontario, Canada.,20 Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Garth Nicholas
- 23 Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | - Laura Palma
- 25 McGill University Health Centre, Montréal, Quebec, Canada
| | - Luis Alberto Pedroza
- 26 Baylor College of Medicine and Texas Children's Hospital, Houston, TX.,27 Universidad San Francisco de Quito, Quito, Ecuador
| | | | | | - Kami Wolfe Schneider
- 30 Children's Hospital Colorado, Aurora, CO.,31 University of Colorado, Anschutz Medical Campus, Aurora, CO
| | | | | | | | - David Sumerauer
- 34 University Hospital Motol, Charles University, Prague, Czech Republic
| | - Helen Toledano
- 11 Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | | | | | - An Van Damme
- 36 Université Catholique de Louvain, Brussels, Belgium
| | - Yi-Yen Lee
- 37 Taipei Veterans General Hospital, Taipei, Republic of China
| | - Michal Zapotocky
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada.,34 University Hospital Motol, Charles University, Prague, Czech Republic
| | - Eric Bouffet
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Durno
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada.,32 Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Steve Gallinger
- 32 Mount Sinai Hospital, Toronto, Ontario, Canada.,38 Toronto General Hospital, Toronto, Ontario, Canada
| | | | - David Malkin
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Uri Tabori
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christopher E Pearson
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
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13
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A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome. Genet Med 2018; 21:1486-1496. [PMID: 30504929 DOI: 10.1038/s41436-018-0372-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/07/2018] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data. METHODS Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay. The assay was calibrated by regression analysis followed by symmetric cross-validation and Bayesian integration with in silico predictions of pathogenicity. CIMRA assay reproducibility was assessed in four laboratories. RESULTS Concordance between the training runs met our prespecified validation criterion. The CIMRA assay alone correctly classified 65% of variants, with only 3% discordant classification. Bayesian integration with in silico predictions of pathogenicity increased the proportion of correctly classified variants to 87%, without changing the discordance rate. Interlaboratory results were highly reproducible. CONCLUSION The CIMRA assay accurately predicts pathogenic and benign MMR gene variants. Quantitative combination of assay results with in silico analysis correctly classified the majority of variants. Using this calibration, CIMRA assay results can be integrated into the diagnostic algorithm for MMR gene variants.
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14
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Suerink M, Ripperger T, Messiaen L, Menko FH, Bourdeaut F, Colas C, Jongmans M, Goldberg Y, Nielsen M, Muleris M, van Kouwen M, Slavc I, Kratz C, Vasen HF, Brugiѐres L, Legius E, Wimmer K. Constitutional mismatch repair deficiency as a differential diagnosis of neurofibromatosis type 1: consensus guidelines for testing a child without malignancy. J Med Genet 2018; 56:53-62. [PMID: 30415209 DOI: 10.1136/jmedgenet-2018-105664] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a rare childhood cancer predisposition syndrome caused by biallelic germline mutations in one of four mismatch-repair genes. Besides very high tumour risks, CMMRD phenotypes are often characterised by the presence of signs reminiscent of neurofibromatosis type 1 (NF1). Because NF1 signs may be present prior to tumour onset, CMMRD is a legitimate differential diagnosis in an otherwise healthy child suspected to have NF1/Legius syndrome without a detectable underlying NF1/SPRED1 germline mutation. However, no guidelines indicate when to counsel and test for CMMRD in this setting. Assuming that CMMRD is rare in these patients and that expected benefits of identifying CMMRD prior to tumour onset should outweigh potential harms associated with CMMRD counselling and testing in this setting, we aimed at elaborating a strategy to preselect, among children suspected to have NF1/Legius syndrome without a causative NF1/SPRED1 mutation and no overt malignancy, those children who have a higher probability of having CMMRD. At an interdisciplinary workshop, we discussed estimations of the frequency of CMMRD as a differential diagnosis of NF1 and potential benefits and harms of CMMRD counselling and testing in a healthy child with no malignancy. Preselection criteria and strategies for counselling and testing were developed and reviewed in two rounds of critical revisions. Existing diagnostic CMMRD criteria were adapted to serve as a guideline as to when to consider CMMRD as differential diagnosis of NF1/Legius syndrome. In addition, counselling and testing strategies are suggested to minimise potential harms.
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Affiliation(s)
- Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Fred H Menko
- Family Cancer Clinic, Antoni van Leeuwenhoek Hospital and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Franck Bourdeaut
- Département d'Oncologie Pédiatrique et d'Adolescents Jeunes Adultes, Institut Curie, Paris, France
| | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris Sciences Lettres Research University, Paris, France.,Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Marjolijn Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yael Goldberg
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martine Muleris
- Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Mariëtte van Kouwen
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Irene Slavc
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
| | - Christian Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Hans F Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laurence Brugiѐres
- Children and Adolescent Oncology Department, Gustave Roussy Cancer Institute, Villejuif, France
| | - Eric Legius
- Department of Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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15
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McGillivray P, Clarke D, Meyerson W, Zhang J, Lee D, Gu M, Kumar S, Zhou H, Gerstein M. Network Analysis as a Grand Unifier in Biomedical Data Science. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013444] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biomedical data scientists study many types of networks, ranging from those formed by neurons to those created by molecular interactions. People often criticize these networks as uninterpretable diagrams termed hairballs; however, here we show that molecular biological networks can be interpreted in several straightforward ways. First, we can break down a network into smaller components, focusing on individual pathways and modules. Second, we can compute global statistics describing the network as a whole. Third, we can compare networks. These comparisons can be within the same context (e.g., between two gene regulatory networks) or cross-disciplinary (e.g., between regulatory networks and governmental hierarchies). The latter comparisons can transfer a formalism, such as that for Markov chains, from one context to another or relate our intuitions in a familiar setting (e.g., social networks) to the relatively unfamiliar molecular context. Finally, key aspects of molecular networks are dynamics and evolution, i.e., how they evolve over time and how genetic variants affect them. By studying the relationships between variants in networks, we can begin to interpret many common diseases, such as cancer and heart disease.
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Affiliation(s)
- Patrick McGillivray
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - William Meyerson
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Jing Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | - Sushant Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Holly Zhou
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
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16
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Blount J, Prakash A. The changing landscape of Lynch syndrome due to PMS2 mutations. Clin Genet 2018; 94:61-69. [PMID: 29286535 PMCID: PMC5995637 DOI: 10.1111/cge.13205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations.
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Affiliation(s)
- Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
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17
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Köger N, Paulsen L, López-Kostner F, Della Valle A, Vaccaro CA, Palmero EI, Alvarez K, Sarroca C, Neffa F, Kalfayan PG, Gonzalez ML, Rossi BM, Reis RM, Brieger A, Zeuzem S, Hinrichsen I, Dominguez-Valentin M, Plotz G. Evaluation of MLH1 variants of unclear significance. Genes Chromosomes Cancer 2018. [PMID: 29520894 DOI: 10.1002/gcc.22536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in silico predictions on structure and conservation. Additionally, we collected all available clinical information of the families to come to a conclusion concerning their pathogenic potential and facilitate clinical diagnosis in the affected families. We provide evidence that four of the alterations are causative for Lynch syndrome, four are likely neutral and one shows compromised activity which can currently not be classified with respect to its pathogenic potential. The work demonstrates that biochemical testing, corroborated by congruent evolutionary and structural information, can serve to reliably classify uncertain variants when other data are insufficient.
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Affiliation(s)
- Nicole Köger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Lea Paulsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | | | - Adriana Della Valle
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Edenir Inêz Palmero
- Barretos Cancer Hospital, Molecular Oncology Research Center, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, São Paulo, Brazil
| | - Karin Alvarez
- Laboratorio de Oncología y Genética Molecular, Clínica Los Condes, Santiago, Chile
| | - Carlos Sarroca
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | - Florencia Neffa
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Maria Laura Gonzalez
- Hereditary Cancer Program (PROCANHE), Hospital Italiano, Buenos Aires, Argentina
| | | | - Rui Manuel Reis
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany.,Life and Health Sciences Q5 753 Research Institute (ICVS), Health Sciences School, University of Minho, Braga, 754, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, 755, Portugal
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Inga Hinrichsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
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18
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Tricarico R, Kasela M, Mareni C, Thompson BA, Drouet A, Staderini L, Gorelli G, Crucianelli F, Ingrosso V, Kantelinen J, Papi L, De Angioletti M, Berardi M, Gaildrat P, Soukarieh O, Turchetti D, Martins A, Spurdle AB, Nyström M, Genuardi M. Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants. Hum Mutat 2016; 38:64-77. [PMID: 27629256 DOI: 10.1002/humu.23117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/04/2016] [Accepted: 09/09/2016] [Indexed: 01/15/2023]
Abstract
Pathogenicity assessment of DNA variants in disease genes to explain their clinical consequences is an integral component of diagnostic molecular testing. The International Society for Gastrointestinal Hereditary Tumors (InSiGHT) has developed specific criteria for the interpretation of mismatch repair (MMR) gene variants. Here, we performed a systematic investigation of 24 MLH1 and MSH2 variants. The assessments were done by analyzing population frequency, segregation, tumor molecular characteristics, RNA effects, protein expression levels, and in vitro MMR activity. Classifications were confirmed for 15 variants and changed for three, and for the first time determined for six novel variants. Overall, based on our results, we propose the introduction of some refinements to the InSiGHT classification rules. The proposed changes have the advantage of homogenizing the InSIGHT interpretation criteria with those set out by the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium for the BRCA1/BRCA2 genes. We also observed that the addition of only few clinical data was sufficient to obtain a more stable classification for variants considered as "likely pathogenic" or "likely nonpathogenic." This shows the importance of obtaining as many as possible points of evidence for variant interpretation, especially from the clinical setting.
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Affiliation(s)
- Rossella Tricarico
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mariann Kasela
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | | | - Bryony A Thompson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Aurélie Drouet
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Lucia Staderini
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Greta Gorelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Francesca Crucianelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Valentina Ingrosso
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Jukka Kantelinen
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Maria De Angioletti
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy.,ICCOM-CNR, Sesto Fiorentino, Italy
| | - Margherita Berardi
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy
| | - Pascaline Gaildrat
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Omar Soukarieh
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Daniela Turchetti
- Medical Genetics, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alexandra Martins
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Minna Nyström
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Institute of Genomic Medicine, A. Gemelli School of Medicine, Medical Genetics Unit, Catholic University of the Sacred Heart, Rome, Italy
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19
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van der Klift HM, Mensenkamp AR, Drost M, Bik EC, Vos YJ, Gille HJJP, Redeker BEJW, Tiersma Y, Zonneveld JBM, García EG, Letteboer TGW, Olderode-Berends MJW, van Hest LP, van Os TA, Verhoef S, Wagner A, van Asperen CJ, Ten Broeke SW, Hes FJ, de Wind N, Nielsen M, Devilee P, Ligtenberg MJL, Wijnen JT, Tops CMJ. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome. Hum Mutat 2016; 37:1162-1179. [PMID: 27435373 DOI: 10.1002/humu.23052] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 01/01/2023]
Abstract
Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are applied to overcome problematic PMS2 mutation analysis due to the presence of pseudogenes and frequent gene conversion events. Here, we determined PMS2 mutation detection yield and mutation spectrum in a nationwide cohort of 396 probands. Furthermore, we studied concordance between tumor IHC/MSI (immunohistochemistry/microsatellite instability) profile and mutation carrier state. Overall, we found 52 different pathogenic PMS2 variants explaining 121 Lynch syndrome and nine CMMRD patients. In vitro mismatch repair assays suggested pathogenicity for three missense variants. Ninety-one PMS2 mutation carriers (70%) showed isolated loss of PMS2 in their tumors, for 31 (24%) no or inconclusive IHC was available, and eight carriers (6%) showed discordant IHC (presence of PMS2 or loss of both MLH1 and PMS2). Ten cases with isolated PMS2 loss (10%; 10/97) harbored MLH1 mutations. We confirmed that recently improved mutation analysis provides a high yield of PMS2 mutations in patients with isolated loss of PMS2 expression. Application of universal tumor prescreening methods will however miss some PMS2 germline mutation carriers.
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Affiliation(s)
- Heleen M van der Klift
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands. .,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yvonne J Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hans J J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Bert E J W Redeker
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - José B M Zonneveld
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Encarna Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Tom G W Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maran J W Olderode-Berends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Theo A van Os
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Senno Verhoef
- Netherlands Cancer Institute, Amsterdam, The Netherlands.,Clinical Genetics Service, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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20
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Peña-Diaz J, Rasmussen LJ. Approaches to diagnose DNA mismatch repair gene defects in cancer. DNA Repair (Amst) 2015; 38:147-154. [PMID: 26708048 DOI: 10.1016/j.dnarep.2015.11.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 08/12/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance of MMR gene alterations in human disease.
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Affiliation(s)
- Javier Peña-Diaz
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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21
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Heinen CD. Mismatch repair defects and Lynch syndrome: The role of the basic scientist in the battle against cancer. DNA Repair (Amst) 2015; 38:127-134. [PMID: 26710976 DOI: 10.1016/j.dnarep.2015.11.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 08/21/2015] [Accepted: 11/30/2015] [Indexed: 12/24/2022]
Abstract
We have currently entered a genomic era of cancer research which may soon lead to a genomic era of cancer treatment. Patient DNA sequencing information may lead to a personalized approach to managing an individual's cancer as well as future cancer risk. The success of this approach, however, begins not necessarily in the clinician's office, but rather at the laboratory bench of the basic scientist. The basic scientist plays a critical role since the DNA sequencing information is of limited use unless one knows the function of the gene that is altered and the manner by which a sequence alteration affects that function. The role of basic science research in aiding the clinical management of a disease is perhaps best exemplified by considering the case of Lynch syndrome, a hereditary disease that predisposes patients to colorectal and other cancers. This review will examine how the diagnosis, treatment and even prevention of Lynch syndrome-associated cancers has benefitted from extensive basic science research on the DNA mismatch repair genes whose alteration underlies this condition.
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Affiliation(s)
- Christopher D Heinen
- Center for Molecular Medicine and Neag Comprehensive Cancer Center, University of Connecticut Health, Farmington, CT 06030, USA.
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22
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23
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Hinrichsen I, Schäfer D, Langer D, Köger N, Wittmann M, Aretz S, Steinke V, Holzapfel S, Trojan J, König R, Zeuzem S, Brieger A, Plotz G. Functional testing strategy for coding genetic variants of unclear significance in MLH1 in Lynch syndrome diagnosis. Carcinogenesis 2014; 36:202-11. [PMID: 25477341 DOI: 10.1093/carcin/bgu239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lynch syndrome is caused by inactivating mutations in the MLH1 gene, but genetic variants of unclear significance frequently preclude diagnosis. Functional testing can reveal variant-conferred defects in gene or protein function. Based on functional defect frequencies and clinical applicability of test systems, we developed a functional testing strategy aimed at efficiently detecting pathogenic defects in coding MLH1 variants. In this strategy, tests of repair activity and expression are prioritized over analyses of subcellular protein localization and messenger RNA (mRNA) formation. This strategy was used for four unclear coding MLH1 variants (p.Asp41His, p.Leu507Phe, p.Gln689Arg, p.Glu605del + p.Val716Met). Expression was analyzed using a transfection system, mismatch repair (MMR) activity by complementation in vitro, mRNA formation by reverse transcriptase-PCR in carrier lymphocyte mRNA, and subcellular localization with dye-labeled fusion constructs. All tests included clinically meaningful controls. The strategy enabled efficient identification of defects in two unclear variants: the p.Asp41His variant showed loss of MMR activity, whereas the compound variant p.Glu605del + p.Val716Met had a defect of expression. This expression defect was significantly stronger than the pathogenic expression reference variant analyzed in parallel, therefore the defect of the compound variant is also pathogenic. Interestingly, the expression defect was caused additively by both of the compound variants, at least one of which is non-pathogenic when occurring by itself. Tests were neutral for p.Leu507Phe and p.Gln689Arg, and the results were consistent with available clinical data. We finally discuss the improved sensitivity and efficiency of the applied strategy and its limitations in analyzing unclear coding MLH1 variants.
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Affiliation(s)
- Inga Hinrichsen
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Dieter Schäfer
- Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany
| | - Deborah Langer
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Nicole Köger
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Margarethe Wittmann
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Verena Steinke
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Jörg Trojan
- Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Rainer König
- Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Angela Brieger
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
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24
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Dominguez-Valentin M, Drost M, Therkildsen C, Rambech E, Ehrencrona H, Angleys M, Lau Hansen T, de Wind N, Nilbert M, Juel Rasmussen L. Functional implications of the p.Cys680Arg mutation in the MLH1 mismatch repair protein. Mol Genet Genomic Med 2014; 2:352-5. [PMID: 25077178 PMCID: PMC4113276 DOI: 10.1002/mgg3.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 12/15/2022] Open
Abstract
In clinical genetic diagnostics, it is difficult to predict whether genetic mutations that do not greatly alter the primary sequence of the encoded protein causing unknown functional effects on cognate proteins lead to development of disease. Here, we report the clinical identification of c.2038 T>C missense mutation in exon 18 of the human MLH1 gene and biochemically characterization of the p.Cys680Arg mutant MLH1 protein to implicate it in the pathogenicity of the Lynch syndrome (LS). We show that the mutation is deficient in DNA mismatch repair and, therefore, contributing to LS in the carriers.
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Affiliation(s)
- Mev Dominguez-Valentin
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden ; The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center Leiden, The Netherlands
| | - Christina Therkildsen
- The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Eva Rambech
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University Lund, Sweden
| | - Maria Angleys
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
| | - Thomas Lau Hansen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
| | - Niels de Wind
- Department of Toxicogenetics, Leiden University Medical Center Leiden, The Netherlands
| | - Mef Nilbert
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden ; The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
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25
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Nagel ZD, Chaim IA, Samson LD. Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research. DNA Repair (Amst) 2014; 19:199-213. [PMID: 24780560 DOI: 10.1016/j.dnarep.2014.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.
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Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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26
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Parsons MT, Whiley PJ, Beesley J, Drost M, de Wind N, Thompson BA, Marquart L, Hopper JL, Jenkins MA, Brown MA, Tucker K, Warwick L, Buchanan DD, Spurdle AB. Consequences of germline variation disrupting the constitutional translational initiation codon start sites of MLH1 and BRCA2: Use of potential alternative start sites and implications for predicting variant pathogenicity. Mol Carcinog 2013; 54:513-22. [PMID: 24302565 DOI: 10.1002/mc.22116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/03/2013] [Accepted: 11/07/2013] [Indexed: 12/21/2022]
Abstract
Variants that disrupt the translation initiation sequences in cancer predisposition genes are generally assumed to be deleterious. However, few studies have validated these assumptions with functional and clinical data. Two cancer syndrome gene variants likely to affect native translation initiation were identified by clinical genetic testing: MLH1:c.1A>G p.(Met1?) and BRCA2:c.67+3A>G. In vitro GFP-reporter assays were conducted to assess the consequences of translation initiation disruption on alternative downstream initiation codon usage. Analysis of MLH1:c.1A>G p.(Met1?) showed that translation was mostly initiated at an in-frame position 103 nucleotides downstream, but also at two ATG sequences downstream. The protein product encoded by the in-frame transcript initiating from position c.103 showed loss of in vitro mismatch repair activity comparable to known pathogenic mutations. BRCA2:c.67+3A>G was shown by mRNA analysis to result in an aberrantly spliced transcript deleting exon 2 and the consensus ATG site. In the absence of exon 2, translation initiated mostly at an out-of-frame ATG 323 nucleotides downstream, and to a lesser extent at an in-frame ATG 370 nucleotides downstream. Initiation from any of the downstream alternative sites tested in both genes would lead to loss of protein function, but further clinical data is required to confirm if these variants are associated with a high cancer risk. Importantly, our results highlight the need for caution in interpreting the functional and clinical consequences of variation that leads to disruption of the initiation codon, since translation may not necessarily occur from the first downstream alternative start site, or from a single alternative start site.
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Affiliation(s)
- Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Phillip J Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Niels de Wind
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Louise Marquart
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - John L Hopper
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia.,School of Public Health, Seoul National University, Seoul, Korea
| | - Mark A Jenkins
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | | | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, Sydney, Australia
| | - Linda Warwick
- ACT Genetics Service, The Canberra Hospital, Canberra, Australia
| | - Daniel D Buchanan
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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27
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Drost M, Koppejan H, de Wind N. Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene. Hum Mutat 2013; 34:1477-80. [PMID: 24027009 DOI: 10.1002/humu.22426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/05/2013] [Indexed: 01/14/2023]
Abstract
Lynch syndrome (LS) is a common cancer predisposition caused by an inactivating mutation in one of four DNA mismatch repair (MMR) genes. Frequently a variant of uncertain significance (VUS), rather than an obviously pathogenic mutation, is identified in one of these genes. The inability to define pathogenicity of such variants precludes targeted healthcare. Here, we have modified a cell-free assay to test VUS in the MMR gene PMS2 for functional activity. We have analyzed nearly all VUS in PMS2 found thus far and describe loss of MMR activity for five, suggesting the applicability of the assay for diagnosis of LS.
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Affiliation(s)
- Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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28
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Farrell MP, Hughes DJ, Drost M, Wallace AJ, Cummins RJ, Fletcher TA, Meany MA, Kay EW, de Wind N, Power DG, Andrews EJ, Green AJ, Gallagher DJ. Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity. Fam Cancer 2013; 12:741-7. [PMID: 23712482 DOI: 10.1007/s10689-013-9652-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic testing of an Irish kindred identified an exonic nucleotide substitution c.1664T>C (p.Leu555Pro) in the MLH1 mismatch repair (MMR) gene. This previously unreported variant is classified as a "variant of uncertain significance" (VUS). Immunohistochemical (IHC) analysis and microsatellite instability (MSI) studies, genetic testing, a literature and online MMR mutation database review, in silico phenotype prediction tools, and an in vitro MMR activity assay were used to study the clinical significance of this variant. The MLH1 c.1664T>C (p.Leu555Pro) VUS co-segregated with three cases of classic Lynch syndrome-associated malignancies over two generations, with consistent loss of MLH1 and PMS2 protein expression on IHC, and evidence of the MSI-High mutator phenotype. The leucine at position 555 is well conserved across a number of species, and this novel variant has not been reported as a normal polymorphism in the general population. In silico and in vitro analyses suggest that this variant may have a deleterious effect on the MLH1 protein and abrogate MMR activity. Evidence from clinical, histological, immunohistochemical, and molecular genetic data suggests that MLH1 c.1664T>C (p.Leu555Pro) is likely to be the pathogenic cause of Lynch syndrome in this family.
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Affiliation(s)
- M P Farrell
- Cancer Genetics Department, Mater Private Hospital, 73 Eccles St, Dublin 7, Ireland,
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29
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Genetic screens to identify pathogenic gene variants in the common cancer predisposition Lynch syndrome. Proc Natl Acad Sci U S A 2013; 110:9403-8. [PMID: 23690608 DOI: 10.1073/pnas.1220537110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In many individuals suspected of the common cancer predisposition Lynch syndrome, variants of unclear significance (VUS), rather than an obviously pathogenic mutations, are identified in one of the DNA mismatch repair (MMR) genes. The uncertainty of whether such VUS inactivate MMR, and therefore are pathogenic, precludes targeted healthcare for both carriers and their relatives. To facilitate the identification of pathogenic VUS, we have developed an in cellulo genetic screen-based procedure for the large-scale mutagenization, identification, and cataloging of residues of MMR genes critical for MMR gene function. When a residue identified as mutated in an individual suspected of Lynch syndrome is listed as critical in such a reverse diagnosis catalog, there is a high probability that the corresponding human VUS is pathogenic. To investigate the applicability of this approach, we have generated and validated a prototypic reverse diagnosis catalog for the MMR gene MutS Homolog 2 (Msh2) by mutagenizing, identifying, and cataloging 26 deleterious mutations in 23 amino acids. Extensive in vivo and in vitro analysis of mutants listed in the catalog revealed both recessive and dominant-negative phenotypes. Nearly half of these critical residues match with VUS previously identified in individuals suspected of Lynch syndrome. This aids in the assignment of pathogenicity to these human VUS and validates the approach described here as a diagnostic tool. In a wider perspective, this work provides a model for the translation of personalized genomics into targeted healthcare.
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30
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Abstract
The mismatch repair (MMR) system detects non-Watson-Crick base pairs and strand misalignments arising during DNA replication and mediates their removal by catalyzing excision of the mispair-containing tract of nascent DNA and its error-free resynthesis. In this way, MMR improves the fidelity of replication by several orders of magnitude. It also addresses mispairs and strand misalignments arising during recombination and prevents synapses between nonidentical DNA sequences. Unsurprisingly, MMR malfunction brings about genomic instability that leads to cancer in mammals. But MMR proteins have recently been implicated also in other processes of DNA metabolism, such as DNA damage signaling, antibody diversification, and repair of interstrand cross-links and oxidative DNA damage, in which their functions remain to be elucidated. This article reviews the progress in our understanding of the mechanism of replication error repair made during the past decade.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland.
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31
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Hinrichsen I, Brieger A, Trojan J, Zeuzem S, Nilbert M, Plotz G. Expression defect size among unclassified MLH1 variants determines pathogenicity in Lynch syndrome diagnosis. Clin Cancer Res 2013; 19:2432-41. [PMID: 23403630 DOI: 10.1158/1078-0432.ccr-12-3299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Lynch syndrome is caused by a germline mutation in a mismatch repair gene, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants with unclear clinical significance. The functionality of these variants can be tested in the laboratory, but the results cannot be used for clinical diagnosis. We therefore aimed to establish a laboratory test that can be applied clinically. EXPERIMENTAL DESIGN We assessed the expression, stability, and mismatch repair activity of 38 MLH1 missense variants and determined the pathogenicity status of recurrent variants using clinical data. RESULTS Four recurrent variants were classified as neutral (K618A, H718Y, E578G, V716M) and three as pathogenic (A681T, L622H, P654L). All seven variants were proficient in mismatch repair but showed defects in expression. Quantitative PCR, pulse-chase, and thermal stability experiments confirmed decreases in protein stability, which were stronger in the pathogenic variants. The minimal cellular MLH1 concentration for mismatch repair was determined, which corroborated that strongly destabilized variants can cause repair deficiency. Loss of MLH1 tumor immunostaining is consistently reported in carriers of the pathogenic variants, showing the impact of this protein instability on these tumors. CONCLUSIONS Expression defects are frequent among MLH1 missense variants, but only severe defects cause Lynch syndrome. The data obtained here enabled us to establish a threshold for distinguishing tolerable (clinically neutral) from pathogenic expression defects. This threshold allows the translation of laboratory results for uncertain MLH1 variants into pathogenicity statements for diagnosis, thereby improving the targeting of cancer prevention measures in affected families.
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Affiliation(s)
- Inga Hinrichsen
- Medizinische Klinik 1, Biomedical Research Laboratory, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
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Bouwman P, Jonkers J. The effects of deregulated DNA damage signalling on cancer chemotherapy response and resistance. Nat Rev Cancer 2012; 12:587-98. [PMID: 22918414 DOI: 10.1038/nrc3342] [Citation(s) in RCA: 446] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tumours with specific DNA repair defects can be completely dependent on back-up DNA repair pathways for their survival. This dependence can be exploited therapeutically to induce synthetic lethality in tumour cells. For instance, homologous recombination (HR)-deficient tumours can be effectively targeted by DNA double-strand break-inducing agents. However, not all HR-defective tumours respond equally well to this type of therapy. Tumour cells may acquire resistance by invoking biochemical mechanisms that reduce drug action or by acquiring additional alterations in DNA damage response pathways. A thorough understanding of these processes is important for predicting treatment response and for the development of novel treatment strategies that prevent the emergence of therapy-resistant tumours.
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Affiliation(s)
- Peter Bouwman
- Division of Molecular Pathology and Cancer Systems Biology Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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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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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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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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Ali H, Olatubosun A, Vihinen M. Classification of mismatch repair gene missense variants with PON-MMR. Hum Mutat 2012; 33:642-50. [PMID: 22290698 DOI: 10.1002/humu.22038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Numerous mismatch repair (MMR) gene variants have been identified in Lynch syndrome and other cancer patients, but knowledge about their pathogenicity is frequently missing. The diagnosis and treatment of patients would benefit from knowing which variants are disease related. Bioinformatic approaches are well suited to the problem and can handle large numbers of cases. Functional effects were revealed based on literature for 168 MMR missense variants. Performance of numerous prediction methods was tested with this dataset. Among the tested tools, only the results of tolerance prediction methods correlated to functional information, however, with poor performance. Therefore, a novel consensus-based predictor was developed. The novel prediction method, pathogenic-or-not mismatch repair (PON-MMR), achieved accuracy of 0.87 and Matthews correlation coefficient of 0.77 on the experimentally verified variants. When applied to 616 MMR cases with unknown effects, 81 missense variants were predicted to be pathogenic and 167 neutral. With PON-MMR, the number of MMR missense variants with unknown effect was reduced by classifying a large number of cases as likely pathogenic or benign. The results can be used, for example, to prioritize cases for experimental studies and assist in the classification of cases.
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Affiliation(s)
- Heidi Ali
- Institute of Biomedical Technology, FI-33014 University of Tampere, Finland
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Kantelinen J, Kansikas M, Candelin S, Hampel H, Smith B, Holm L, Kariola R, Nyström M. Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients. Hum Mutat 2012; 33:1294-301. [PMID: 22581703 DOI: 10.1002/humu.22119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 04/19/2012] [Indexed: 12/24/2022]
Abstract
Mismatch repair (MMR) malfunction causes the accumulation of mismatches in the genome leading to genomic instability and cancer. The inactivation of an MMR gene (MSH2, MSH6, MLH1, or PMS2) with an inherited mutation causes Lynch syndrome (LS), a dominant susceptibility to cancer. MMR gene variants of uncertain significance (VUS) may be pathogenic mutations, which cause LS, may result in moderately increased cancer risks, or may be harmless polymorphisms. Our study suggests that an inherited MMR VUS individually assessed as proficient may, however, in a pair with another MMR VUS found in the same colorectal cancer (CRC) patient have a concomitant contribution to the MMR deficiency. Here, eight pairs of MMR gene variants found in cancer patients were functionally analyzed in an in vitro MMR assay. Although the other pairs do not suggest a compound deficiency, the MSH2 VUS pair c.380A>G/c.982G>C (p.Asn127Ser/p.Ala328Pro), which nearly halves the repair capability of the wild-type MSH2 protein, is presumed to increase the cancer risk considerably. Moreover, two MSH6 variants, c.1304T>C (p.Leu435Pro) and c.1754T>C (p.Leu585Pro), were shown to be MMR deficient. The role of one of the most frequently reported MMR gene VUS, MSH2 c.380A>G (p.Asn127Ser), is especially interesting because its concomitant defect with another variant could finally explain its recurrent occurrence in CRC patients.
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Affiliation(s)
- Jukka Kantelinen
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Xiao Y, Jung C, Marx AD, Winkler I, Wyman C, Lebbink JHG, Friedhoff P, Cristovao M. Generation of DNA nanocircles containing mismatched bases. Biotechniques 2012; 51:259-62, 264-5. [PMID: 21988692 DOI: 10.2144/000113749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 08/25/2011] [Indexed: 11/23/2022] Open
Abstract
The DNA mismatch repair (MMR) system recognizes and repairs errors that escaped the proofreading function of DNA polymerases. To study molecular details of the MMR mechanism, in vitro biochemical assays require specific DNA substrates carrying mismatches and strand discrimination signals. Current approaches used to generate MMR substrates are time-consuming and/or not very flexible with respect to sequence context. Here we report an approach to generate small circular DNA containing a mismatch (nanocircles). Our method is based on the nicking of PCR products resulting in single-stranded 3' overhangs, which form DNA circles after annealing and ligation. Depending on the DNA template, one can generate mismatched circles containing a single hemimethylated GATC site (for use with the bacterial system) and/or nicking sites to generate DNA circles nicked in the top or bottom strand (for assays with the bacterial or eukaryotic MMR system). The size of the circles varied (323 to 1100 bp), their sequence was determined by the template DNA, and purification of the circles was achieved by ExoI/ExoIII digestion and/or gel extraction. The quality of the nanocircles was assessed by scanning-force microscopy and their suitability for in vitro repair initiation was examined using recombinant Escherichia coli MMR proteins.
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Affiliation(s)
- Yu Xiao
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
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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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41
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Tomsic J, Liyanarachchi S, Hampel H, Morak M, Thomas BC, Raymond VM, Chittenden A, Schackert HK, Gruber SB, Syngal S, Viel A, Holinski-Feder E, Thibodeau SN, de la Chapelle A. An American founder mutation in MLH1. Int J Cancer 2011; 130:2088-95. [PMID: 21671475 DOI: 10.1002/ijc.26233] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 05/19/2011] [Indexed: 01/10/2023]
Abstract
Mutations in the mismatch repair genes cause Lynch syndrome (LS), conferring high risk of colorectal, endometrial and some other cancers. After the same splice site mutation in the MLH1 gene (c.589-2A>G) had been observed in four ostensibly unrelated American families with typical LS cancers, its occurrence in comprehensive series of LS cases (Mayo Clinic, Germany and Italy) was determined. It occurred in 10 out of 995 LS mutation carriers (1.0%) diagnosed in the Mayo Clinic diagnostic laboratory. It did not occur among 1,803 cases tested for MLH1 mutations by the German HNPCC consortium, while it occurred in three probands and an additional five family members diagnosed in Italy. In the U.S., the splice site mutation occurs on a large (∼4.8 Mb) shared haplotype that also harbors the variant c.2146G>A, which predicts a missense change in codon 716 referred to here as V716M. In Italy, it occurs on a different, shorter shared haplotype (∼2.2 Mb) that does not carry V716M. The V716M variant was found to be present by itself in the U.S., German and Italian populations with individuals sharing a common haplotype of 280 kb, allowing us to calculate that the variant arose around 5,600 years ago (225 generations; 95% confidence interval 183-272). The splice site mutation in America arose or was introduced some 450 years ago (18 generations; 95% confidence interval 14-23); it accounts for 1.0% all LS in the Unites States and can be readily screened for.
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Affiliation(s)
- Jerneja Tomsic
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Abstract
PURPOSE Lynch syndrome is a genetic disease that predisposes to colorectal tumors, caused by mutation in mismatch repair genes. The use of genetic tests to identify mutation carriers does not always give perfectly clear results, as happens when an unclassified variant is found. This study aimed to define the pathogenic role of 35 variants present in MSH2, MLH1, MSH6, and PMS2 genes identified in our 15-year case study. METHODS We collected clinical and molecular data of all carriers, and then we analyzed the variants pathogenic role with web tools and molecular analyses. Using a Bayesian approach, we derived a posterior probability of pathogenicity and classified each variant according to a standardized five-class system. RESULTS The MSH2 p.Pro349Arg, p.Met688Arg, the MLH1 p.Gly67Arg, p.Thr82Ala, p.Lys618Ala, the MSH6 p.Ala1236Pro, and the PMS2 p.Arg20Gln were classified as pathogenic, and the MSH2 p.Cys697Arg and the PMS2 p.Ser46Ile were classified as likely pathogenic. Seven variants were likely nonpathogenic, 3 were nonpathogenic, and 16 remained uncertain. CONCLUSION Quantitative assessment of several parameters and their integration in a multifactorial likelihood model is the method of choice for classifying the variants. As such classifications can be associated with surveillance and testing recommendations, the results and the method developed in our study can be useful for helping laboratory geneticists in evaluation of genetic tests and clinicians in the management of carriers.
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Kohonen-Corish MRJ, Macrae F, Genuardi M, Aretz S, Bapat B, Bernstein IT, Burn J, Cotton RGH, den Dunnen JT, Frebourg T, Greenblatt MS, Hofstra R, Holinski-Feder E, Lappalainen I, Lindblom A, Maglott D, Møller P, Morreau H, Möslein G, Sijmons R, Spurdle AB, Tavtigian S, Tops CMJ, Weber TK, de Wind N, Woods MO. Deciphering the colon cancer genes--report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010. Hum Mutat 2011; 32:491-4. [PMID: 21387463 DOI: 10.1002/humu.21450] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 01/09/2011] [Indexed: 12/12/2022]
Abstract
The Human Variome Project (HVP) has established a pilot program with the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) to compile all inherited variation affecting colon cancer susceptibility genes. An HVP-InSiGHT Workshop was held on May 10, 2010, prior to the HVP Integration and Implementation Meeting at UNESCO in Paris, to review the progress of this pilot program. A wide range of topics were covered, including issues relating to genotype-phenotype data submission to the InSiGHT Colon Cancer Gene Variant Databases (chromium.liacs.nl/LOVD2/colon_cancer/home.php). The meeting also canvassed the recent exciting developments in models to evaluate the pathogenicity of unclassified variants using in silico data, tumor pathology information, and functional assays, and made further plans for the future progress and sustainability of the pilot program.
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Kim YM, Choe CG, Cho SK, Jung IH, Chang WY, Cho M. Three novel germline mutations in MLH1 and MSH2 in families with Lynch syndrome living on Jeju island, Korea. BMB Rep 2011; 43:693-7. [PMID: 21034533 DOI: 10.5483/bmbrep.2010.43.10.693] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominant syndrome characterized by predisposition to early-onset cancers. HNPCC is caused by heterozygous loss-of-function mutations within the mismatch repair genes MLH1, MSH2, MSH6, PMS1, and PMS2. We genotyped the MLH1 and MSH2 genes in patients suffering from Lynch syndrome and in 11 unrelated patients who were diagnosed with colorectal cancer and had subsequently undergone surgery. Five Lynch syndrome patients carried germline mutations in MLH1 or MSH2. Two of these were identified as known mutations in MLH1: deletion of exon 10 and a point mutation (V384D). The remaining three patients exhibited novel mutations: a duplication (937_942dupGAAGTT) in MLH1; deletion of exons 8, 9, and 10; and a point mutation in MLH1 (F396I) combined with multiple missense mutations in MSH2 (D295G, K808E, Q855P, and I884T). The findings underline the importance of efficient pre-screening of conspicuous cases.
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Affiliation(s)
- Young Mee Kim
- Department of Biochemistry, Institute of Medical Science, Jeju National University, Jeju 690-756, Korea
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Perera S, Li B, Tsitsikotas S, Ramyar L, Pollett A, Semotiuk K, Bapat B. A novel and rapid method of determining the effect of unclassified MLH1 genetic variants on differential allelic expression. J Mol Diagn 2010; 12:757-64. [PMID: 20864636 DOI: 10.2353/jmoldx.2010.090240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Germline mutations in mismatch repair genes predispose patients to Lynch Syndrome and the majority of these mutations have been detected in two key genes, MLH1 and MSH2. In particular, about a third of the missense variants identified in MLH1 are of unknown clinical significance. Using the PeakPicker software program, we have conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances. Lymphocyte RNA extracted from patients harboring known MLH1 variants was used to quantify the ratio of variant to wild-type transcript, while patient lymphocyte DNA was used to establish baseline allelic expression levels. Our analysis indicated that the missense variants c.350C>T, c.793C>T, and c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were all associated with significantly unbalanced allelic expression. However, the variants c.55A>T and c.2246T>C did not demonstrate an allelic imbalance. These results illustrate a novel and efficient method to investigate the pathogenicity of unclassified genetic variants discovered in mismatch repair genes, as well as genes implicated in other inherited diseases. In addition, the PeakPicker methodology has the potential to be applied in the diagnostic setting, which, in conjunction with results from other assays, will help increase both the accuracy and efficiency of genetic testing of colorectal cancer, as well as other inherited diseases.
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Affiliation(s)
- Sheron Perera
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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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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Clinical relevance of rare germline sequence variants in cancer genes: evolution and application of classification models. Curr Opin Genet Dev 2010; 20:315-23. [PMID: 20456937 DOI: 10.1016/j.gde.2010.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 12/11/2022]
Abstract
Multifactorial models developed for BRCA1/2 variant classification have proved very useful for delineating BRCA1/2 variants associated with very high risk of cancer, or with little clinical significance. Recent linkage of this quantitative assessment of risk to clinical management guidelines has provided a basis to standardize variant reporting, variant classification and management of families with such variants, and can theoretically be applied to any disease gene. As proof of principle, the multifactorial approach already shows great promise for application to the evaluation of mismatch repair gene variants identified in families with suspected Lynch syndrome. However there is need to be cautious of the noted limitations and caveats of the current model, some of which may be exacerbated by differences in ascertainment and biological pathways to disease for different cancer syndromes.
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