1
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Scott A, Hernandez F, Chamberlin A, Smith C, Karam R, Kitzman JO. Saturation-scale functional evidence supports clinical variant interpretation in Lynch syndrome. Genome Biol 2022; 23:266. [PMID: 36550560 PMCID: PMC9773515 DOI: 10.1186/s13059-022-02839-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is a cancer predisposition syndrome affecting more than 1 in every 300 individuals worldwide. Clinical genetic testing for LS can be life-saving but is complicated by the heavy burden of variants of uncertain significance (VUS), especially missense changes. RESULT To address this challenge, we leverage a multiplexed analysis of variant effect (MAVE) map covering >94% of the 17,746 possible missense variants in the key LS gene MSH2. To establish this map's utility in large-scale variant reclassification, we overlay it on clinical databases of >15,000 individuals with LS gene variants uncovered during clinical genetic testing. We validate these functional measurements in a cohort of individuals with paired tumor-normal test results and find that MAVE-based function scores agree with the clinical interpretation for every one of the MSH2 missense variants with an available classification. We use these scores to attempt reclassification for 682 unique missense VUS, among which 34 scored as deleterious by our function map, in line with previously published rates for other cancer predisposition genes. Combining functional data and other evidence, ten missense VUS are reclassified as pathogenic/likely pathogenic, and another 497 could be moved to benign/likely benign. Finally, we apply these functional scores to paired tumor-normal genetic tests and identify a subset of patients with biallelic somatic loss of function, reflecting a sporadic Lynch-like Syndrome with distinct implications for treatment and relatives' risk. CONCLUSION This study demonstrates how high-throughput functional assays can empower scalable VUS resolution and prospectively generate strong evidence for variant classification.
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Affiliation(s)
- Anthony Scott
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Felicia Hernandez
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA
| | - Adam Chamberlin
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA
| | - Cathy Smith
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Rachid Karam
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jacob O. Kitzman
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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2
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Singh S, Sharma S, Baranwal M. Identification of SNPs in hMSH3/MSH6 interaction domain affecting the structure and function of MSH2 protein. Biotechnol Appl Biochem 2022; 69:2454-2465. [PMID: 34837403 DOI: 10.1002/bab.2295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
MutS homolog 2 (MSH2) is a mismatch repair gene that plays a critical role in DNA repair pathways, and its mutations are associated with different cancers. The present study aimed to find out the single nucleotide polymorphisms (SNPs) of MSH2 protein associated with causing structural and functional changes leading to the development of cancer with the help of computational tools. Four different tools for predicting deleterious SNPs (SIFT, PROVEAN, PANTHER, and PolyPhen), two tools each for identifying disease association (PhD-SNP and SNP&GO) and estimating stability (I-mutant and MUPro) were employed. Homology modeling, energy minimization, and root mean square deviation calculation were used to estimate structural variations. Twenty-seven SNPs and five SNPs (double amino acid change) were identified based on a consensus approach that might be associated with the structural and functional change in MSH2 protein. Molecular docking reveals that six SNPs affect the interaction of MSH2 and MSH6. Twelve identified SNPs were reported to be linked with hereditary nonpolyposis, colorectal cancer, and Lynch syndrome. Further, selected SNPs need to be validated in an in vitro system for their precise association with cancer predisposition.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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3
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Britton BM, London JA, Martin-Lopez J, Jones ND, Liu J, Lee JB, Fishel R. Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA. J Biol Chem 2022; 298:102505. [PMID: 36126773 PMCID: PMC9597889 DOI: 10.1016/j.jbc.2022.102505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022] Open
Abstract
MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.
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Affiliation(s)
- Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - James A London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Juana Martin-Lopez
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Nathan D Jones
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.
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4
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Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, A I ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Grabsch HI, Fullwood MJ, Teh TB, Bi X, Kaneda A, Li S, Tan P. Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer. Cancer Res 2022; 82:2538-2551. [PMID: 35583999 DOI: 10.1158/0008-5472.can-21-2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer. Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage gastric cancer MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced gastric cancers was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient gastric cancers also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extraterminal motif (BET) inhibition. Our results reveal a role for MSH2 in gastric cancer epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies. SIGNIFICANCE DNA repair protein MSH2 binds and regulates cell adhesion genes by enabling enhancer-promoter interactions, and loss of MSH2 causes deficient cell adhesion and bromodomain and extraterminal motif inhibitor synthetic lethality in gastric cancer.
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Affiliation(s)
- Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Gao Bin Chen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Hematology-Oncology, National University Health System, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Yi Xiang See
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manjie Xing
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Zhimei Li
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Chern Han Yong
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Aparna Anand
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Lai Fong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | | | - Javier Yu Peng Koh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Heike I Grabsch
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tean Bin Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
| | - Xuezhi Bi
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Bioprocessing Technology Institute, Singapore, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
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5
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Rath A, Mishra A, Ferreira VD, Hu C, Omerza G, Kelly K, Hesse A, Reddi HV, Grady JP, Heinen CD. Functional interrogation of Lynch syndrome-associated MSH2 missense variants via CRISPR-Cas9 gene editing in human embryonic stem cells. Hum Mutat 2019; 40:2044-2056. [PMID: 31237724 DOI: 10.1002/humu.23848] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) predisposes patients to cancer and is caused by germline mutations in the DNA mismatch repair (MMR) genes. Identifying the deleterious mutation, such as a frameshift or nonsense mutation, is important for confirming an LS diagnosis. However, discovery of a missense variant is often inconclusive. The effects of these variants of uncertain significance (VUS) on disease pathogenesis are unclear, though understanding their impact on protein function can help determine their significance. Laboratory functional studies performed to date have been limited by their artificial nature. We report here an in-cellulo functional assay in which we engineered site-specific MSH2 VUS using clustered regularly interspaced short palindromic repeats-Cas9 gene editing in human embryonic stem cells. This approach introduces the variant into the endogenous MSH2 loci, while simultaneously eliminating the wild-type gene. We characterized the impact of the variants on cellular MMR functions including DNA damage response signaling and the repair of DNA microsatellites. We classified the MMR functional capability of eight of 10 VUS providing valuable information for determining their likelihood of being bona fide pathogenic LS variants. This human cell-based assay system for functional testing of MMR gene VUS will facilitate the identification of high-risk LS patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
| | - Akriti Mishra
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | | | - Chaoran Hu
- Department of Statistics, University of Connecticut, Storrs, Connecticut.,Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Gregory Omerza
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Kevin Kelly
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Andrew Hesse
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Honey V Reddi
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - James P Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Christopher D Heinen
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
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6
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Bonjoch L, Mur P, Arnau-Collell C, Vargas-Parra G, Shamloo B, Franch-Expósito S, Pineda M, Capellà G, Erman B, Castellví-Bel S. Approaches to functionally validate candidate genetic variants involved in colorectal cancer predisposition. Mol Aspects Med 2019; 69:27-40. [PMID: 30935834 DOI: 10.1016/j.mam.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Most next generation sequencing (NGS) studies identified candidate genetic variants predisposing to colorectal cancer (CRC) but do not tackle its functional interpretation to unequivocally recognize a new hereditary CRC gene. Besides, germline variants in already established hereditary CRC-predisposing genes or somatic variants share the same need when trying to categorize those with relevant significance. Functional genomics approaches have an important role in identifying the causal links between genetic architecture and phenotypes, in order to decipher cellular function in health and disease. Therefore, functional interpretation of identified genetic variants by NGS platforms is now essential. Available approaches nowadays include bioinformatics, cell and molecular biology and animal models. Recent advances, such as the CRISPR-Cas9, ZFN and TALEN systems, have been already used as a powerful tool with this objective. However, the use of cell lines is of limited value due to the CRC heterogeneity and its close interaction with microenvironment. Access to tridimensional cultures or organoids and xenograft models that mimic the in vivo tissue architecture could revolutionize functional analysis. This review will focus on the application of state-of-the-art functional studies to better tackle new genes involved in germline predisposition to this neoplasm.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Bahar Shamloo
- Molecular Biology, Genetics, and Bioengineering Department, Legacy Research Institute, Portland, OR, USA
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Batu Erman
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain.
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7
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Kim D, Fishel R, Lee JB. Coordinating Multi-Protein Mismatch Repair by Managing Diffusion Mechanics on the DNA. J Mol Biol 2018; 430:4469-4480. [PMID: 29792877 PMCID: PMC6388638 DOI: 10.1016/j.jmb.2018.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
Abstract
DNA mismatch repair (MMR) corrects DNA base-pairing errors that occur during DNA replication. MMR catalyzes strand-specific DNA degradation and resynthesis by dynamic molecular coordination of sequential downstream pathways. The temporal and mechanistic order of molecular events is essential to insure interactions in MMR that occur over long distances on the DNA. Biophysical real-time studies of highly conserved components on mismatched DNA have shed light on the mechanics of MMR. Single-molecule imaging has visualized stochastically coordinated MMR interactions that are based on thermal fluctuation-driven motions. In this review, we describe the role of diffusivity and stochasticity in MMR beginning with mismatch recognition through strand-specific excision. We conclude with a perspective of the possible research directions that should solve the remaining questions in MMR.
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Affiliation(s)
- Daehyung Kim
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea; Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 37673, Korea.
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8
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Graham WJ, Putnam CD, Kolodner RD. The properties of Msh2-Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair. J Biol Chem 2018; 293:18055-18070. [PMID: 30237169 PMCID: PMC6254361 DOI: 10.1074/jbc.ra118.005439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/17/2018] [Indexed: 11/30/2022] Open
Abstract
DNA mismatch repair (MMR) corrects mispaired DNA bases and small insertion/deletion loops generated by DNA replication errors. After binding a mispair, the eukaryotic mispair recognition complex Msh2–Msh6 binds ATP in both of its nucleotide-binding sites, which induces a conformational change resulting in the formation of an Msh2–Msh6 sliding clamp that releases from the mispair and slides freely along the DNA. However, the roles that Msh2–Msh6 sliding clamps play in MMR remain poorly understood. Here, using Saccharomyces cerevisiae, we created Msh2 and Msh6 Walker A nucleotide–binding site mutants that have defects in ATP binding in one or both nucleotide-binding sites of the Msh2–Msh6 heterodimer. We found that these mutations cause a complete MMR defect in vivo. The mutant Msh2–Msh6 complexes exhibited normal mispair recognition and were proficient at recruiting the MMR endonuclease Mlh1–Pms1 to mispaired DNA. At physiological (2.5 mm) ATP concentration, the mutant complexes displayed modest partial defects in supporting MMR in reconstituted Mlh1–Pms1-independent and Mlh1–Pms1-dependent MMR reactions in vitro and in activation of the Mlh1–Pms1 endonuclease and showed a more severe defect at low (0.1 mm) ATP concentration. In contrast, five of the mutants were completely defective and one was mostly defective for sliding clamp formation at high and low ATP concentrations. These findings suggest that mispair-dependent sliding clamp formation triggers binding of additional Msh2–Msh6 complexes and that further recruitment of additional downstream MMR proteins is required for signal amplification of mispair binding during MMR.
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Affiliation(s)
| | - Christopher D Putnam
- From the Ludwig Institute for Cancer Research San Diego,; Departments of Medicine and
| | - Richard D Kolodner
- From the Ludwig Institute for Cancer Research San Diego,; Cellular and Molecular Medicine,; Moores-UCSD Cancer Center, and; Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, California 92093-0669.
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9
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Hanne J, Britton BM, Park J, Liu J, Martín-López J, Jones N, Schoffner M, Klajner P, Bundschuh R, Lee JB, Fishel R. MutS homolog sliding clamps shield the DNA from binding proteins. J Biol Chem 2018; 293:14285-14294. [PMID: 30072380 DOI: 10.1074/jbc.ra118.002264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/31/2018] [Indexed: 11/06/2022] Open
Abstract
Sliding clamps on DNA consist of evolutionarily conserved enzymes that coordinate DNA replication, repair, and the cellular DNA damage response. MutS homolog (MSH) proteins initiate mismatch repair (MMR) by recognizing mispaired nucleotides and in the presence of ATP form stable sliding clamps that randomly diffuse along the DNA. The MSH sliding clamps subsequently load MutL homolog (MLH/PMS) proteins that form a second extremely stable sliding clamp, which together coordinate downstream MMR components with the excision-initiation site that may be hundreds to thousands of nucleotides distant from the mismatch. Specific or nonspecific binding of other proteins to the DNA between the mismatch and the distant excision-initiation site could conceivably obstruct the free diffusion of these MMR sliding clamps, inhibiting their ability to initiate repair. Here, we employed bulk biochemical analysis, single-molecule fluorescence imaging, and mathematical modeling to determine how sliding clamps might overcome such hindrances along the DNA. Using both bacterial and human MSH proteins, we found that increasing the number of MSH sliding clamps on a DNA decreased the association of the Escherichia coli transcriptional repressor LacI to its cognate promoter LacO. Our results suggest a simple mechanism whereby thermal diffusion of MSH sliding clamps along the DNA alters the association kinetics of other DNA-binding proteins over extended distances. These observations appear generally applicable to any stable sliding clamp that forms on DNA.
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Affiliation(s)
- Jeungphill Hanne
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Brooke M Britton
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Jonghyun Park
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea
| | - Jiaquan Liu
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Juana Martín-López
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Nathan Jones
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210.,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Matthew Schoffner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Piotr Klajner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Ralf Bundschuh
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, .,Department of Physics, The Ohio State University, Columbus, Ohio 43210.,Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, and
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea, .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784 Korea
| | - Richard Fishel
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, .,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
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10
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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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11
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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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12
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Lee JB, Cho WK, Park J, Jeon Y, Kim D, Lee SH, Fishel R. Single-molecule views of MutS on mismatched DNA. DNA Repair (Amst) 2014; 20:82-93. [PMID: 24629484 PMCID: PMC4245035 DOI: 10.1016/j.dnarep.2014.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/11/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023]
Abstract
Base-pair mismatches that occur during DNA replication or recombination can reduce genetic stability or conversely increase genetic diversity. The genetics and biophysical mechanism of mismatch repair (MMR) has been extensively studied since its discovery nearly 50 years ago. MMR is a strand-specific excision-resynthesis reaction that is initiated by MutS homolog (MSH) binding to the mismatched nucleotides. The MSH mismatch-binding signal is then transmitted to the immediate downstream MutL homolog (MLH/PMS) MMR components and ultimately to a distant strand scission site where excision begins. The mechanism of signal transmission has been controversial for decades. We have utilized single molecule Forster Resonance Energy Transfer (smFRET), Fluorescence Tracking (smFT) and Polarization Total Internal Reflection Fluorescence (smP-TIRF) to examine the interactions and dynamic behaviors of single Thermus aquaticus MutS (TaqMutS) particles on mismatched DNA. We determined that TaqMutS forms an incipient clamp to search for a mismatch in ~1 s intervals by 1-dimensional (1D) thermal fluctuation-driven rotational diffusion while in continuous contact with the helical duplex DNA. When MutS encounters a mismatch it lingers for ~3 s to exchange bound ADP for ATP (ADP→ATP exchange). ATP binding by TaqMutS induces an extremely stable clamp conformation (~10 min) that slides off the mismatch and moves along the adjacent duplex DNA driven simply by 1D thermal diffusion. The ATP-bound sliding clamps rotate freely while in discontinuous contact with the DNA. The visualization of a train of MSH proteins suggests that dissociation of ATP-bound sliding clamps from the mismatch permits multiple mismatch-dependent loading events. These direct observations have provided critical clues into understanding the molecular mechanism of MSH proteins during MMR.
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Affiliation(s)
- Jong-Bong Lee
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea; School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea.
| | - Won-Ki Cho
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Jonghyun Park
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Yongmoon Jeon
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Daehyung Kim
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Seung Hwan Lee
- School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, United States; Physics Department, The Ohio State University, Columbus, OH 43210, United States.
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13
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Martín-López JV, Fishel R. The mechanism of mismatch repair and the functional analysis of mismatch repair defects in Lynch syndrome. Fam Cancer 2014; 12:159-68. [PMID: 23572416 DOI: 10.1007/s10689-013-9635-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of Lynch syndrome (LS), also known as hereditary non-polyposis colorectal cancer (HNPCC), has been linked to heterozygous defects in DNA mismatch repair (MMR). MMR is a highly conserved pathway that recognizes and repairs polymerase misincorporation errors and nucleotide damage as well as functioning as a damage sensor that signals apoptosis. Loss-of-heterozygosity (LOH) that retains the mutant MMR allele and epigenetic silencing of MMR genes are associated with an increased mutation rate that drives carcinogenesis as well as microsatellite instability that is a hallmark of LS/HNPCC. Understanding the biophysical functions of the MMR components is crucial to elucidating the role of MMR in human tumorigenesis and determining the pathogenetic consequences of patients that present in the clinic with an uncharacterized variant of the MMR genes. We summarize the historical association between LS/HNPCC and MMR, discuss the mechanism of the MMR and finally examine the functional analysis of MMR defects found in LS/HNPCC patients and their relationship with the severity of the disease.
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Affiliation(s)
- Juana V Martín-López
- Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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14
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Silverstein TD, Gibb B, Greene EC. Visualizing protein movement on DNA at the single-molecule level using DNA curtains. DNA Repair (Amst) 2014; 20:94-109. [PMID: 24598576 DOI: 10.1016/j.dnarep.2014.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/18/2022]
Abstract
A fundamental feature of many nucleic-acid binding proteins is their ability to move along DNA either by diffusion-based mechanisms or by ATP-hydrolysis driven translocation. For example, most site-specific DNA-binding proteins must diffuse to some extent along DNA to either find their target sites, or to otherwise fulfill their biological roles. Similarly, nucleic-acid translocases such as helicases and polymerases must move along DNA to fulfill their functions. In both instances, the proteins must also be capable of moving in crowded environments while navigating through DNA-bound obstacles. These types of behaviors can be challenging to analyze by bulk biochemical methods because of the transient nature of the interactions, and/or heterogeneity of the reaction intermediates. The advent of single-molecule methodologies has overcome some of these problems, and has led to many new insights into the mechanisms that contribute to protein motion along DNA. We have developed DNA curtains as a tool to facilitate single molecule observations of protein-nucleic acid interactions, and we have applied these new research tools to systems involving both diffusive-based motion as well as ATP directed translocation. Here we highlight these studies by first discussing how diffusion contributes to target searches by proteins involved in post-replicative mismatch repair. We then discuss DNA curtain assays of two different DNA translocases, RecBCD and FtsK, which participate in homologous DNA recombination and site-specific DNA recombination, respectively.
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Affiliation(s)
- Timothy D Silverstein
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, USA.
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15
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De Lellis L, Aceto GM, Curia MC, Catalano T, Mammarella S, Veschi S, Fantini F, Battista P, Stigliano V, Messerini L, Mareni C, Sala P, Bertario L, Radice P, Cama A. Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms. PLoS One 2013; 8:e81194. [PMID: 24278394 PMCID: PMC3835792 DOI: 10.1371/journal.pone.0081194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/09/2013] [Indexed: 01/27/2023] Open
Abstract
The identification of germline variants predisposing to hereditary nonpolyposis colorectal cancer (HNPCC) is crucial for clinical management of carriers, but several probands remain negative for such variants or bear variants of uncertain significance (VUS). Here we describe the results of integrative molecular analyses in 132 HNPCC patients providing evidences for improved genetic testing of HNPCC with traditional or next generation methods. Patients were screened for: germline allele-specific expression (ASE), nucleotide variants, rearrangements and promoter methylation of mismatch repair (MMR) genes; germline EPCAM rearrangements; tumor microsatellite instability (MSI) and immunohistochemical (IHC) MMR protein expression. Probands negative for pathogenic variants of MMR genes were screened for germline APC and MUTYH sequence variants. Most germline defects identified were sequence variants and rearrangements of MMR genes. Remarkably, altered germline ASE of MMR genes was detected in 8/22 (36.5%) probands analyzed, including 3 cases negative at other screenings. Moreover, ASE provided evidence for the pathogenic role and guided the characterization of a VUS shared by 2 additional probands. No germline MMR gene promoter methylation was observed and only one EPCAM rearrangement was detected. In several cases, tumor IHC and MSI diverged from germline screening results. Notably, APC or biallelic MUTYH germline defects were identified in 2/19 probands negative for pathogenic variants of MMR genes. Our results show that ASE complements gDNA-based analyses in the identification of MMR defects and in the characterization of VUS affecting gene expression, increasing the number of germline alterations detected. An appreciable fraction of probands negative for MMR gene variants harbors APC or MUTYH variants. These results indicate that germline ASE analysis and screening for APC and MUTYH defects should be included in HNPCC diagnostic algorithms.
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Affiliation(s)
- Laura De Lellis
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
| | - Gitana Maria Aceto
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Teresa Catalano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Serena Veschi
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Fabiana Fantini
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Pasquale Battista
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Vittoria Stigliano
- Department of Gastroenterology, Unit of Hereditary Colorectal Cancer, National Cancer Institute, Regina Elena (IRE), Rome, Italy
| | - Luca Messerini
- Section of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Cristina Mareni
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Paola Sala
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucio Bertario
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular bases of genetic risk and genetic testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandro Cama
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
- * E-mail:
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16
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Distinct requirements within the Msh3 nucleotide binding pocket for mismatch and double-strand break repair. J Mol Biol 2013; 425:1881-1898. [PMID: 23458407 DOI: 10.1016/j.jmb.2013.02.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, repair of insertion/deletion loops is carried out by Msh2-Msh3-mediated mismatch repair (MMR). Msh2-Msh3 is also required for 3' non-homologous tail removal (3' NHTR) in double-strand break repair. In both pathways, Msh2-Msh3 binds double-strand/single-strand junctions and initiates repair in an ATP-dependent manner. However, the kinetics of the two processes appear different; MMR is likely rapid in order to coordinate with the replication fork, whereas 3' NHTR has been shown to be a slower process. To understand the molecular requirements in both repair pathways, we performed an in vivo analysis of well-conserved residues in Msh3 that are hypothesized to be required for MMR and/or 3' NHTR. These residues are predicted to be involved in either communication between the DNA-binding and ATPase domains within the complex or nucleotide binding and/or exchange within Msh2-Msh3. We identified a set of aromatic residues within the FLY motif of the predicted Msh3 nucleotide binding pocket that are essential for Msh2-Msh3-mediated MMR but are largely dispensable for 3' NHTR. In contrast, mutations in other regions gave similar phenotypes in both assays. Based on these results, we suggest that the two pathways have distinct requirements with respect to the position of the bound ATP within Msh3. We propose that the differences are related, at least in part, to the kinetics of each pathway. Proper binding and positioning of ATP is required to induce rapid conformational changes at the replication fork, but is less important when more time is available for repair, as in 3' NHTR.
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17
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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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18
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Belvederesi L, Bianchi F, Loretelli C, Bracci R, Cascinu S, Cellerino R. Sub-cellular localization analysis of MSH6 missense mutations does not reveal an overt MSH6 nuclear transport impairment. Fam Cancer 2012; 11:675-80. [PMID: 22851212 DOI: 10.1007/s10689-012-9558-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nearly one-third of the identified MSH6 germline mutations deal with single amino acid substitutions. For an effective genetic counselling it is necessary to clearly elucidate by functional tools the specific sub-processes underlying the mismatch repair (MMR) misfunctioning in MSH6 non-truncating mutants. Since the MMR repair pathway occurs in the nucleus, we suppose the impairment of MutSα nuclear trafficking to be a possible Lynch syndrome susceptibility causative mechanism. In the present study the MMR status of the tumour, the main clinical features of mutation carriers and population data associated to the MSH6 missense variants, were complemented with computational data about tolerability predictions and amino acid substitution conservation. The selected panel of ten potentially pathogenic MSH6 mutations was analyzed in a homologous expression system for possible deleterious effects on nucleo-cytoplasmic shuttling through the assessment of the sub-cellular localization of the corresponding mutated proteins. Localization analysis results do not reveal an apparent role of MSH6 missense mutations in nuclear import impairment and provide the first hint to exclude the MSH6 nuclear translocation sub-process as a possible causative mechanisms of MMR misfunctioning.
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19
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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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20
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Martín-López JV, Barrios Y, Medina-Arana V, Andújar M, Lee S, Gu L, Li GM, Rüschoff J, Salido E, Fishel R. The hMSH2(M688R) Lynch syndrome mutation may function as a dominant negative. Carcinogenesis 2012; 33:1647-54. [PMID: 22739024 DOI: 10.1093/carcin/bgs199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The hMSH2(M688R) mismatch repair (MMR) gene mutation has been found in five large families from Tenerife, Spain, suggesting it is a Lynch syndrome or hereditary non-polyposis colorectal cancer (LS/HNPCC) founder mutation. In addition to classical LS/HNPCC tumors, these families present with a high incidence of central nervous system (CNS) tumors normally associated with Turcot or constitutional mismatch repair deficiency (CMMR-D) syndromes. Turcot and CMMR-D mutations may be biallelic, knocking out both copies of the MMR gene. The hMSH2(M688R) mutation is located in the ATP hydrolysis (ATPase) domain. We show that the hMSH2(M688R)-hMSH6 heterodimer binds to mismatched nucleotides but lacks normal ATP functions and inhibits MMR in vitro when mixed with the wild-type (WT) heterodimer. Another alteration that has been associated with LS/HNPCC, hMSH2(M688I)-hMSH6, displays no identifiable differences with the WT heterodimer. Interestingly, some extracolonic tumors from hMSH2(M688R) carriers may express hMSH2-hMSH6, yet display microsatellite instability (MSI). The functional analysis along with variability in tumor expression and the high incidence of CNS tumors suggests that hMSH2(M688R) may act as a dominant negative in some tissues, while the hMSH2(M688I) is most likely a benign polymorphism.
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Affiliation(s)
- Juana V Martín-López
- Unidad de Investigación Mixta HUC-ULL, Facultad de Medicina, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, 38002, Spain
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21
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Heinen CD, Cyr JL, Cook C, Punja N, Sakato M, Forties RA, Lopez JM, Hingorani MM, Fishel R. Human MSH2 (hMSH2) protein controls ATP processing by hMSH2-hMSH6. J Biol Chem 2011; 286:40287-95. [PMID: 21937421 DOI: 10.1074/jbc.m111.297523] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanics of hMSH2-hMSH6 ATP binding and hydrolysis are critical to several proposed mechanisms for mismatch repair (MMR), which in turn rely on the detailed coordination of ATP processing between the individual hMSH2 and hMSH6 subunits. Here we show that hMSH2-hMSH6 is strictly controlled by hMSH2 and magnesium in a complex with ADP (hMSH2(magnesium-ADP)-hMSH6). Destabilization of magnesium results in ADP release from hMSH2 that allows high affinity ATP binding by hMSH6, which then enhances ATP binding by hMSH2. Both subunits must be ATP-bound to efficiently form a stable hMSH2-hMSH6 hydrolysis-independent sliding clamp required for MMR. In the presence of magnesium, the ATP-bound sliding clamps remain on the DNA for ∼8 min. These results suggest a precise stepwise kinetic mechanism for hMSH2-hMSH6 functions that appears to mimic G protein switches, severely constrains models for MMR, and may partially explain the MSH2 allele frequency in Lynch syndrome or hereditary nonpolyposis colorectal cancer.
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Affiliation(s)
- Christopher D Heinen
- University of Connecticut Health Center, Farmington, Connecticut 06030-3101, USA.
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22
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Cyr JL, Brown GD, Stroop J, Heinen CD. The predicted truncation from a cancer-associated variant of the MSH2 initiation codon alters activity of the MSH2-MSH6 mismatch repair complex. Mol Carcinog 2011; 51:647-58. [PMID: 21837758 DOI: 10.1002/mc.20838] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 06/24/2011] [Accepted: 07/11/2011] [Indexed: 12/15/2022]
Abstract
Lynch syndrome (LS) is caused by germline mutations in DNA mismatch repair (MMR) genes. MMR recognizes and repairs DNA mismatches and small insertion/deletion loops. Carriers of MMR gene variants have a high risk of developing colorectal, endometrial, ovarian, and other extracolonic carcinomas. We report on an ovarian cancer patient who carries a germline MSH2 c.1A>C variant which alters the translation initiation codon. Mutations affecting the MSH2 start codon have been described previously for LS-related malignancies. However, the patients often lack a clear family history indicative of LS and their tumors often fail to display microsatellite instability, a hallmark feature of LS. Therefore, the pathogenicity of start codon variants remains undefined. Loss of the MSH2 start codon has been predicted to result in a truncated protein translated from a downstream in-frame AUG that would lack the first 25 amino acids. We therefore purified recombinant MSH2(NΔ25)-MSH6 and MSH2(NΔ25)-MSH3 to examine their DNA lesion recognition and adenosine nucleotide processing functions in vitro. We found that the MSH2(NΔ25) mutant confers distinct biochemical defects on MSH2-MSH6, but does not have a significant effect on MSH2-MSH3. We confirmed that expression of the MSH2 c.1A>C cDNA results in the production of multiple protein products in human cells that may include the truncated and full-length forms of MSH2. An in vivo MMR assay revealed a slight reduction in MMR efficiency in these cells. These data suggest that mutation of the MSH2 initiation codon, while not a strong, high-risk disease allele, may have a moderate impact on disease phenotype.
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Affiliation(s)
- Jennifer L Cyr
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030-3101, USA
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Mastrocola AS, Heinen CD. Lynch syndrome-associated mutations in MSH2 alter DNA repair and checkpoint response functions in vivo. Hum Mutat 2011; 31:E1699-708. [PMID: 20672385 PMCID: PMC2947597 DOI: 10.1002/humu.21333] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The DNA mismatch repair (MMR) pathway is essential in maintaining genomic stability through its role in DNA repair and the checkpoint response. Loss of DNA MMR underlies the hereditary cancer disease Lynch Syndrome (LS). Germline mutations in MSH2 account for approximately 40% of LS patients and of these, 18% are missense variants. One important clinical challenge has been discriminating between missense variants that are pathogenic and those that are not. Current analysis of missense mutations in MSH2 is performed using a combination of clinical, biochemical, and functional data; however, suitable cell culture models to test the various functions of the DNA MMR proteins are lacking. Here, we have generated human cell lines stably expressing a subset of MSH2 missense mutants and tested their effect on DNA repair and checkpoint response functions. We have expanded on previous biochemical and functional analyses performed in non-human systems to further understand defects conferred by this subset of single amino acid alterations. The functional characterization of MSH2 missense mutants combined with clinical and biochemical data is essential for appropriate patient management and genetic counseling decisions.
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Affiliation(s)
- Adam S Mastrocola
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030-3101, USA
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24
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Functional analysis of human mismatch repair gene mutations identifies weak alleles and polymorphisms capable of polygenic interactions. Proc Natl Acad Sci U S A 2010; 107:5070-5. [PMID: 20176959 DOI: 10.1073/pnas.1000798107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many of the mutations reported as potentially causing Lynch syndrome are missense mutations in human mismatch repair (MMR) genes. Here, we used a Saccharomyces cerevisiae-based system to study polymorphisms and suspected missense mutations in human MMR genes by modeling them at the appropriate S. cerevisiae chromosomal locus and determining their effect on mutation rates. We identified a number of weak alleles of MMR genes and MMR gene polymorphisms that are capable of interacting with other weak alleles of MMR genes to produce strong polygenic MMR defects. We also identified a number of alleles of MSH2 that act as if they inactivate the Msh2-Msh3 mispair recognition complex thus causing weak MMR defects that interact with an msh6Delta mutation to result in complete MMR defects. These results indicate that weak MMR gene alleles capable of polygenic interactions with other MMR gene alleles may be relatively common.
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25
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Mastrocola AS, Heinen CD. Nuclear reorganization of DNA mismatch repair proteins in response to DNA damage. DNA Repair (Amst) 2010; 9:120-33. [PMID: 20004149 PMCID: PMC2819642 DOI: 10.1016/j.dnarep.2009.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 10/16/2009] [Accepted: 11/04/2009] [Indexed: 12/16/2022]
Abstract
The DNA mismatch repair (MMR) system is highly conserved and vital for preserving genomic integrity. Current mechanistic models for MMR are mainly derived from in vitro assays including reconstitution of strand-specific MMR and DNA binding assays using short oligonucleotides. However, fundamental questions regarding the mechanism and regulation in the context of cellular DNA replication remain. Using synchronized populations of HeLa cells we demonstrated that hMSH2, hMLH1 and PCNA localize to the chromatin during S-phase, and accumulate to a greater extent in cells treated with a DNA alkylating agent. In addition, using small interfering RNA to deplete hMSH2, we demonstrated that hMLH1 localization to the chromatin is hMSH2-dependent. hMSH2/hMLH1/PCNA proteins, when associated with the chromatin, form a complex that is greatly enhanced by DNA damage. The DNA damage caused by high doses of alkylating agents leads to a G(2) arrest after only one round of replication. In these G(2)-arrested cells, an hMSH2/hMLH1 complex persists on chromatin, however, PCNA is no longer in the complex. Cells treated with a lower dose of alkylating agent require two rounds of replication before cells arrest in G(2). In the first S-phase, the MMR proteins form a complex with PCNA, however, during the second S-phase PCNA is missing from that complex. The distinction between these complexes may suggest separate functions for the MMR proteins in damage repair and signaling. Additionally, using confocal immunofluorescence, we observed a population of hMSH6 that localized to the nucleolus. This population is significantly reduced after DNA damage suggesting that the protein is shuttled out of the nucleolus in response to damage. In contrast, hMLH1 is excluded from the nucleolus at all times. Thus, the nucleolus may act to segregate a population of hMSH2-hMSH6 from hMLH1-hPMS2 such that, in the absence of DNA damage, an inappropriate response is not invoked.
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Affiliation(s)
- Adam S. Mastrocola
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Christopher D. Heinen
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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26
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Mutations in the conserved glycine and serine of the MutS ABC signature motif affect nucleotide exchange, kinetics of sliding clamp release of mismatch and mismatch repair. Mutat Res 2009; 684:56-65. [PMID: 19954745 DOI: 10.1016/j.mrfmmm.2009.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 11/13/2009] [Accepted: 11/24/2009] [Indexed: 12/19/2022]
Abstract
The MutS protein controls genomic stability by coordinating recognition and repair of DNA mismatches with ATP utilization. The nature of this coordination is unclear. This study demonstrates the importance of a highly conserved flexible loop found in Escherichia coli MutS (residues 658-670) in DNA mismatch repair. This loop is speculated to be analogous to the ABC signature motif of drug transporters based on its proximity to the ATP catalytic site in crystal structures. Our studies show that amino acid residues G666 and S668 control MutS functions subsequent to mismatch recognition by MutS, i.e., nucleotide-mediated exchange and ATP-dependent dissociation from mismatch. G666V mutation affects mismatch-provoked ADP-ATP exchange and results in slower dissociation kinetics of MutS from the mismatch while S668A mutation affects stable clamp formation and dissociation kinetics but does not affect nucleotide exchange. Both mutants harbor defects in ATP hydrolysis and cause a significant mutator phenotype in vivo. The mutator effect of S668A is indistinguishable from that of a MutS-deficient background and is similar to that seen with G658A. Neither mutations affect protein stability or cause a dominant mutator effect. Together with our studies on G658, D661 and F670 [1], this study implicates the signature motif as a primary regulator of MutS function and suggests concerted action of the individual amino acid residues within this motif in mediating communication between the Walker and mismatch recognition domains.
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27
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Li LS, Morales JC, Veigl M, Sedwick D, Greer S, Meyers M, Wagner M, Fishel R, Boothman DA. DNA mismatch repair (MMR)-dependent 5-fluorouracil cytotoxicity and the potential for new therapeutic targets. Br J Pharmacol 2009; 158:679-92. [PMID: 19775280 DOI: 10.1111/j.1476-5381.2009.00423.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The metabolism and efficacy of 5-fluorouracil (FUra) and other fluorinated pyrimidine (FP) derivatives have been intensively investigated for over fifty years. FUra and its antimetabolites can be incorporated at RNA- and DNA-levels, with RNA level incorporation provoking toxic responses in human normal tissue, and DNA-level antimetabolite formation and incorporation believed primarily responsible for tumour-selective responses. Attempts to direct FUra into DNA-level antimetabolites, based on mechanism-of-action studies, have led to gradual improvements in tumour therapy. These include the use of leukovorin to stabilize the inhibitory thymidylate synthase-5-fluoro-2'-deoxyuridine 5' monophoshate (FdUMP)-5,10-methylene tetrahydrofolate (5,10-CH(2)FH(4)) trimeric complex. FUra incorporated into DNA also contributes to antitumour activity in preclinical and clinical studies. This review examines our current state of knowledge regarding the mechanistic aspects of FUra:Gua lesion detection by DNA mismatch repair (MMR) machinery that ultimately results in lethality. MMR-dependent direct cell death signalling or futile cycle responses will be discussed. As 10-30% of sporadic colon and endometrial tumours display MMR defects as a result of human MutL homologue-1 (hMLH1) promoter hypermethylation, we discuss the use and manipulation of the hypomethylating agent, 5-fluorodeoxycytidine (FdCyd), and our ability to manipulate its metabolism using the cytidine or deoxycytidylate (dCMP) deaminase inhibitors, tetrahydrouridine or deoxytetrahydrouridine, respectively, as a method for re-expression of hMLH1 and re-sensitization of tumours to FP therapy.
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Affiliation(s)
- Long Shan Li
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
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28
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Clyne M, Offman J, Shanley S, Virgo JD, Radulovic M, Wang Y, Ardern-Jones A, Eeles R, Hoffmann E, Yu VPCC. The G67E mutation in hMLH1 is associated with an unusual presentation of Lynch syndrome. Br J Cancer 2009; 100:376-80. [PMID: 19142183 PMCID: PMC2634701 DOI: 10.1038/sj.bjc.6604860] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Germline mutations in the mismatch repair (MMR) genes are associated with Lynch syndrome, also known as hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Here, we characterise a variant of hMLH1 that confers a loss-of-function MMR phenotype. The mutation changes the highly conserved Gly67 residue to a glutamate (G67E) and is reminiscent of the hMLH1-p.Gly67Arg mutation, which is present in several Lynch syndrome cohorts. hMLH1-Gly67Arg has previously been shown to confer loss-of-function (Shimodaira et al, 1998), and two functional assays suggest that the hMLH1-Gly67Glu protein fails to sustain normal MMR functions. In the first assay, hMLH1-Gly67Glu abolishes the protein's ability to interfere with MMR in yeast. In the second assay, mutation of the analogous residue in yMLH1 (yMLH1-Gly64Glu) causes a loss-of-function mutator phenotype similar to yMLH1-Gly64Arg. Despite these molecular similarities, an unusual spectrum of tumours is associated with hMLH1-Gly67Glu, which is not typical of those associated with Lynch syndrome and differs from those found in families carrying the hMLH1-Gly67Arg allele. This suggests that hMLH1 may have different functions in certain tissues and/or that additional factors may modify the influence of hMLH1 mutations in causing Lynch syndrome.
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Affiliation(s)
- M Clyne
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, UK
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29
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Couch FJ, Rasmussen LJ, Hofstra R, Monteiro ANA, Greenblatt MS, de Wind N. Assessment of functional effects of unclassified genetic variants. Hum Mutat 2008; 29:1314-26. [PMID: 18951449 PMCID: PMC2771414 DOI: 10.1002/humu.20899] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been extensively characterized at the functional level, few assays based on functional properties of the encoded proteins have been established for the purpose of predicting the contribution of rare inherited variants to disease. Much of the difficulty in establishing predictive functional assays stems from the technical complexity of the assays. However, perhaps the most challenging aspect of functional assay development for clinical testing purposes is the absolute requirement for validation of the sensitivity and specificity of the assays and the determination of positive predictive values (PPVs) and negative predictive values (NPVs) of the assays relative to a "gold standard" measure of disease predisposition. In this commentary, we provide examples of some of the functional assays under development for several cancer predisposition genes (BRCA1, BRCA2, CDKN2A, and mismatch repair [MMR] genes MLH1, MSH2, MSH6, and PMS2) and present a detailed review of the issues associated with functional assay development. We conclude that validation is paramount for all assays that will be used for clinical interpretation of inherited variants of any gene, but note that in certain circumstances information derived from incompletely validated assays may be valuable for classification of variants for clinical purposes when used to supplement data derived from other sources.
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Affiliation(s)
- Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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30
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Cyr JL, Heinen CD. Hereditary cancer-associated missense mutations in hMSH6 uncouple ATP hydrolysis from DNA mismatch binding. J Biol Chem 2008; 283:31641-8. [PMID: 18790734 DOI: 10.1074/jbc.m806018200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hereditary nonpolyposis colorectal cancer is caused by germline mutations in DNA mismatch repair genes. The majority of cases are associated with mutations in hMSH2 or hMLH1; however, about 12% of cases are associated with alterations in hMSH6. The hMSH6 protein forms a heterodimer with hMSH2 that is capable of recognizing a DNA mismatch. The heterodimer then utilizes its adenosine nucleotide processing ability in an, as of yet, unclear mechanism to facilitate communication between the mismatch and a distant strand discrimination site. The majority of reported mutations in hMSH6 are deletions or truncations that entirely eliminate the function of the protein; however, nearly a third of the reported variations are missense mutations whose functional significance is unclear. We analyzed seven cancer-associated single amino acid alterations in hMSH6 distributed throughout the functional domains of the protein to determine their effect on the biochemical activity of the hMSH2-hMSH6 heterodimer. Five alterations affect mismatch-stimulated ATP hydrolysis activity providing functional evidence that missense variants of hMSH6 can disrupt mismatch repair function and may contribute to disease. Of the five mutants that affect mismatch-stimulated ATP hydrolysis, only two (R976H and H1248D) affect mismatch recognition. Thus, three of the mutants (G566R, V878A, and D803G) appear to uncouple the mismatch binding and ATP hydrolysis activities of the heterodimer. We also demonstrate that these three mutations alter ATP-dependent conformation changes of hMSH2-hMSH6, suggesting that cancer-associated mutations in hMSH6 can disrupt the intramolecular signaling that coordinates mismatch binding with adenosine nucleotide processing.
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Affiliation(s)
- Jennifer L Cyr
- Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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31
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Lützen A, de Wind N, Georgijevic D, Nielsen FC, Rasmussen LJ. Functional analysis of HNPCC-related missense mutations in MSH2. Mutat Res 2008; 645:44-55. [PMID: 18822302 DOI: 10.1016/j.mrfmmm.2008.08.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 07/25/2008] [Accepted: 08/26/2008] [Indexed: 12/28/2022]
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) is associated with germline mutations in the human DNA mismatch repair (MMR) genes, most frequently MSH2 and MLH1. The majority of HNPCC mutations cause truncations and thus loss of function of the affected polypeptide. However, a significant proportion of MMR mutations found in HNPCC patients are single amino acid substitutions and the functional consequences of many of these mutations in DNA repair are unclear. We have examined the consequences of seven MSH2 missense mutations found in HNPCC families by testing the MSH2 mutant proteins in functional assays as well as by generating equivalent missense mutations in Escherichia coli MutS and analyzing the phenotypes of these mutants. Here we show that two mutant proteins, MSH2-P622L and MSH2-C697F confer multiple biochemical defects, namely in mismatch binding, in vivo interaction with MSH6 and EXO1, and in nuclear localization in the cell. Mutation G674R, located in the ATP-binding region of MSH2, appears to confer resistance to ATP-dependent mismatch release. Mutations D167H and H639R show reduced mismatch binding. Results of in vivo experiments in E. coli with MutS mutants show that one additional mutant, equivalent of MSH2-A834T that do not show any defects in MSH2 assays, is repair deficient. In conclusion, all mutant proteins (except for MSH2-A305T) have defects; either in mismatch binding, ATP-release, mismatch repair activity, subcellular localization or protein-protein interactions.
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Affiliation(s)
- Anne Lützen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
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32
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Ou J, Niessen RC, Lützen A, Sijmons RH, Kleibeuker JH, de Wind N, Rasmussen LJ, Hofstra RMW. Functional analysis helps to clarify the clinical importance of unclassified variants in DNA mismatch repair genes. Hum Mutat 2007; 28:1047-54. [PMID: 17594722 DOI: 10.1002/humu.20580] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is caused by DNA variations in the DNA mismatch repair (MMR) genes MSH2, MLH1, MSH6, and PMS2. Many of the mutations identified result in premature termination of translation and thus in loss-of-function of the encoded mutated protein. These DNA variations are thought to be pathogenic mutations. However, some patients carry other DNA mutations, referred to as unclassified variants (UVs), which do not lead to such a premature termination of translation; it is not known whether these contribute to the disease phenotype or merely represent rare polymorphisms. This is a major problem which has direct clinical consequences. Several criteria can be used to classify these UVs, such as: whether they segregate with the disease within pedigrees, are absent in control individuals, show a change of amino acid polarity or size, provoke an amino acid change in a domain that is evolutionary conserved and/or shared between proteins belonging to the same protein family, or show altered function in an in vitro assay. In this review we discuss the various functional assays reported for the HNPCC-associated MMR proteins and the outcomes of these tests on UVs identified in patients diagnosed with or suspected of having HNPCC. We conclude that a large proportion of MMR UVs are likely to be pathogenic, suggesting that missense variants of MMR proteins do indeed play a role in HNPCC.
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Affiliation(s)
- Jianghua Ou
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
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33
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Bianchi F, Galizia E, Bracci R, Belvederesi L, Catalani R, Loretelli C, Giorgetti G, Ferretti C, Bearzi I, Porfiri E, Cellerino R. Effectiveness of the CRCAPRO program in identifying patients suspected for HNPCC. Clin Genet 2007; 71:158-64. [PMID: 17250665 DOI: 10.1111/j.1399-0004.2007.00746.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subjects affected by hereditary non-polyposis colorectal cancer exhibit a high susceptibility to colon and extracolonic tumours, due to MMR gene defects. Revised Bethesda criteria are used to select patients as candidates for genetic tests. Recently, the CRCAPRO model has been developed, based on family history of colorectal and endometrial cancers. Our study aims to evaluate the reliability of CRCAPRO in identifying mutation carriers. We used the CRCAPRO program to evaluate carrier probability risk in 99 patients fulfilling Amsterdam or Bethesda guidelines. MLH1 and MSH2 were studied by direct sequencing in all the 99 patients, and the study of microsatellite instability and of MMR proteins expression was performed. Nine MLH1 and nine MSH2 germline mutations were identified. Five out of the nine patients with MLH1 mutation showed a CRCAPRO risk evaluation of less than 20%. The same happened for four out of nine patients with MSH2 mutation. Of the 17 patients with an estimated risk of more than 80%, only four harboured a mutation, all in the MSH2 gene. The highest risk calculated by the CRCAPRO system in the nine carriers of a MLH1 mutation has been 31.7%. In our experience, the CRCAPRO program sensitivity and specificity appears to be low but needs to be further evaluated in larger samples.
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Affiliation(s)
- F Bianchi
- Centro Regionale di Genetica Oncologica, Oncologia Medica, Università Politecnica delle Marche, Ancona, Italy.
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Abstract
Significant advances in the treatment of colorectal cancer have been observed over the past several years. With the introduction of oxaliplatin combined with infusional 5-fluorouracil and leucovorin, survival for patients with metastatic colorectal cancer has nearly doubled. The incorporation of biologic agents that target angiogenesis (bevacizumab) and tumor growth pathways (cetuximab, panitumimab) extends survival even further, in addition to increasing response rates in patients with metastatic disease. The benefit of these newer drugs is also being realized in the adjuvant setting, where the addition of oxaliplatin to infusional 5-fluorouracil and leucovorin has led to improvements in 3-year disease-free survival. Future challenges with the use of oxaliplatin include defining strategies to optimize its use while avoiding treatment-limiting neurotoxicity and identification of markers predictive of response.
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Affiliation(s)
- George P Kim
- Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32082, USA.
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35
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Ollila S, Sarantaus L, Kariola R, Chan P, Hampel H, Holinski-Feder E, Macrae F, Kohonen-Corish M, Gerdes AM, Peltomäki P, Mangold E, de la Chapelle A, Greenblatt M, Nyström M. Pathogenicity of MSH2 missense mutations is typically associated with impaired repair capability of the mutated protein. Gastroenterology 2006; 131:1408-17. [PMID: 17101317 DOI: 10.1053/j.gastro.2006.08.044] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 07/12/2006] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Inherited deleterious mutations in mismatch repair genes MLH1, MSH2, and MSH6 predispose to hereditary nonpolyposis colorectal cancer. A major diagnostic challenge is the difficulty in evaluating the pathogenicity of missense mutations. Previously we showed that most missense variants in MSH6 do not impair MMR capability and are associated with no or low cancer susceptibility, whereas in MLH1, functional studies distinguished nontruncating mutations with severe defects from those not or slightly impaired in protein expression or function. The present study was undertaken to evaluate the pathogenicity of inherited missense mutations in MSH2. METHODS Fifteen mutated MSH2 proteins including 14 amino acid substitutions and one in-frame deletion were tested for expression/stability, MSH2/MSH6 interaction, and repair efficiency. The genetic and biochemical data were correlated with the clinical data. Comparative sequence analysis was performed to assess the value of sequence homology as a tool for predicting functional results. RESULTS None of the studied MSH2 mutations destroyed the protein or abolished MSH2/MSH6 interaction, whereas 12 mutations impaired the repair capability of the protein. Comparative sequence analysis correctly predicted functional studies for 13 of 14 amino acid substitutions. CONCLUSIONS Interpretation was pathogenic for 12, nonpathogenic for 2, and contradictory for 1 mutation. The pathogenicity could not be distinguished unambiguously by phenotypic characteristics, although correlation between the absence of staining for MSH2 and pathogenicity of the missense mutation was notable. Unlike in MSH6 and MLH1, the pathogenicity of missense mutations in MSH2 was always associated with impaired repair capability of the mutated protein.
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Affiliation(s)
- Saara Ollila
- Department of Biological and Environmental Sciences, Genetics, University of Helsinki, Helsinki, Finland
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36
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Jascur T, Boland CR. Structure and function of the components of the human DNA mismatch repair system. Int J Cancer 2006; 119:2030-5. [PMID: 16804905 DOI: 10.1002/ijc.22023] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA mismatch repair (MMR) is one of the several enzyme systems involved in DNA homeostasis. DNA MMR is involved in the repair of specific types of errors that occur during new DNA synthesis; loss of this system leads to an accelerated accumulation of potential mutations, and predisposes to certain types of cancers. Germline mutations in some of the DNA MMR genes cause the hereditary cancer predisposition, Lynch syndrome. This review addresses advances in the biochemistry of DNA MMR and its relationship to carcinogenesis.
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Affiliation(s)
- Thomas Jascur
- Department of Internal Medicine, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA.
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37
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Szadkowski M, Iaccarino I, Heinimann K, Marra G, Jiricny J. Characterization of the mismatch repair defect in the human lymphoblastoid MT1 cells. Cancer Res 2005; 65:4525-9. [PMID: 15930269 DOI: 10.1158/0008-5472.can-05-0080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutations in mismatch repair (MMR) genes predispose to hereditary nonpolyposis colon cancer. Those leading to truncated proteins bring about a MMR defect, but phenotypes of missense mutations are harder to predict especially if they do not affect conserved residues. Several systems capable of predicting the phenotypes of MMR missense mutations were described. We deployed one of these to study the MMR defect in MT1 cells, which carry mutations in both alleles of the hMSH6 gene. In one, an A-->T transversion brings about an Asp(1213)Val amino acid change in the highly conserved ATP binding site, whereas the other carries a G-->A transition, which brings about a Val(1260)Ile change at a nonconserved site. The hMSH2/hMSH6 (hMutS alpha) heterodimers carrying these mutations were expressed in the baculovirus system and tested in in vitro MMR assays. As anticipated, the Asp(1213)Val mutation inactivated MMR by disabling the variant hMutS alpha from translocating along the DNA. In contrast, the recombinant Val(1260)Ile variant displayed wild-type activity. Interestingly, partial proteolytic analysis showed that this heterodimer was absent from MT1 extracts, although both hMSH6 alleles in MT1 cells could be shown to be transcribed with an efficiency similar to each other and to that seen in control cells. The MMR defect in MT1 cells is thus the compound result of one mutation that inactivates the ATPase function of hMutS alpha and a second mutation that apparently destabilizes the Val(1260)Ile hMSH6 protein in human cells in vivo.
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Affiliation(s)
- Marta Szadkowski
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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38
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Sia EA, Kirkpatrick DT. The yeast MSH1 gene is not involved in DNA repair or recombination during meiosis. DNA Repair (Amst) 2005; 4:253-61. [PMID: 15590333 DOI: 10.1016/j.dnarep.2004.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Revised: 09/24/2004] [Accepted: 10/02/2004] [Indexed: 10/26/2022]
Abstract
Six strong homologs of the bacterial MutS DNA mismatch repair (MMR) gene have been identified in the yeast Saccharomyces cerevisiae. With the exception of the MSH1 gene, the involvement of each homolog in DNA repair and recombination during meiosis has been determined previously. Five of the homologs have been demonstrated to act in meiotic DNA repair (MSH2, MSH3, MSH6 and MSH4) and/or meiotic recombination (MSH4 and MSH5). Unfortunately the loss of mitochondrial function that results from deletion of MSH1 disrupts meiotic progression, precluding an analysis of MSH1 function in meiotic DNA repair and recombination. However, the recent identification of two separation-of-function alleles of MSH1 that interfere with protein function but still maintain functional mitochondria allow the meiotic activities of MSH1 to be determined. We show that the G776D and F105A alleles of MSH1 exhibit no defects in meiotic recombination, repair base-base mismatches and large loop mismatches efficiently during meiosis, and have high levels of spore viability. These data indicate that the MSH1 protein, unlike other MutS homologs in yeast, plays no role in DNA repair or recombination during meiosis.
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Affiliation(s)
- Elaine A Sia
- Department of Biology, University of Rochester, River Campus Box 270211, Rochester, New York 14627-0211, USA
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Drotschmann K, Topping RP, Clodfelter JE, Salsbury FR. Mutations in the nucleotide-binding domain of MutS homologs uncouple cell death from cell survival. DNA Repair (Amst) 2004; 3:729-42. [PMID: 15177182 DOI: 10.1016/j.dnarep.2004.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 02/19/2004] [Accepted: 02/20/2004] [Indexed: 10/26/2022]
Abstract
After genotoxic insult, the decision to repair or undergo cell death is pivotal for undamaged cell survival, and requires a highly controlled coordination of both pathways. Disruption of this regulation results in tumorigenesis and failure of cancer therapy. Mismatch repair (MMR) proteins have a unique role by contributing to both pathways, though direct evidence for their function in the DNA damage response is ambiguous. We report separation of function mutants in the ATPase domains of yeast MutS homologous (MSH) proteins that uncouple MMR-dependent DNA repair from damage response to cisplatin. While mutations in the ATPase domain have devastating effects on the mutation rate of the cell, ATPase processing is mostly dispensable for the cell death phenotype; only limited processing by the MSH6 subunit is required in DNA damage response. Different DNA binding patterns and nucleotide sensitivity of Msh2/Msh6-DNA adduct and protein-mismatch complexes, respectively, suggest that the presence of different DNA lesions influences the requirement for ATP. Limited proteolysis of purified protein gives first indications for differences in nucleotide-induced conformational changes in the presence of platinated DNA. Structural modeling of bacterial MutS proteins reinforces nucleotide-dependent differences in structures that contribute to the distinction between DNA damage response and repair. Our results demonstrate the uncoupling of MMR-dependent damage response from repair and present first indications for the involvement of distinct conformational changes in MSH proteins in this process. These data present evidence for a mechanism of MMR-dependent damage response that differs from MMR; these results have strong implications for the chemotherapeutic treatment of MMR-defective tumors.
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Affiliation(s)
- Karin Drotschmann
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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Kim JC, Lee KH, Ka IH, Koo KH, Roh SA, Kim HC, Yu CS, Kim TW, Chang HM, Gong GY, Kim JS. Characterization of Mutator Phenotype in Familial Colorectal Cancer Patients Not Fulfilling Amsterdam Criteria. Clin Cancer Res 2004; 10:6159-68. [PMID: 15448003 DOI: 10.1158/1078-0432.ccr-04-0651] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Although the mutator phenotype, including genetic and epigenetic alterations of the mismatch repair (MMR) system, seems to be pronounced in familial colorectal cancer, there have been few integrative studies comprising the entire mutator pathway. This study was done to identify the entire mutator pathway determining risk factors in patients with familial colorectal cancer not fulfilling the Amsterdam criteria. EXPERIMENTAL DESIGN We consecutively recruited 134 colorectal cancer patients with a family history of accompanying cancers. Patients with hereditary nonpolyposis colorectal cancer meeting the Amsterdam criteria, familial adenomatous polyposis, or those receiving preoperative radiotherapy were excluded. Mutator phenotype was assessed by assaying microsatellite instability (MSI) at 24 markers, hMLH1-promoter methylation, mutations at MMR genes (hMLH1, hMSH2, hMSH6, and hPMS2), and immune staining of MMR proteins (hMLH1, hMSH2, hMSH6, hPMS1, and hPMS2). RESULTS Of the 208 cancers in first-degree and/or second-degree relatives of patients, colorectal and gastric cancers (81%) were most common. Of the 134 proband colorectal cancers, 23 (17%) were MSI in high level, and 32 (24%) were MSI in low level. MMR alterations, including known polymorphism and splicing substitution, were identified in eight patients (6%). Twenty-eight tumors with mutator phenotype were further identified by hMLH1-promoter methylation and/or loss of MMR protein expression. In 51 tumors (38%), mutator phenotype was associated with right-sided colon cancer (P < 0.001) and younger age at onset (P=0.032), but the number of patients with a mutator phenotype did not differ with respect to inheritance patterns of accompanying cancers, either successive or horizontal transmission (P=0.815). Familial impact value, which differentially associated the degree of relatives with all accompanying cancers, effectively discriminated MSI in high level from microsatellite stable/MSI in low level tumors. CONCLUSION Familial colorectal cancer may be associated with multiple occurrences of colorectal or accompanying cancers inherited by dominant or recessive transmission. MMR gene mutations, however, are less associated with mutator phenotype in familial colorectal cancer.
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Affiliation(s)
- Jin C Kim
- Department of Surgery, University of Ulsan College of Medicine, Seoul, Korea.
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Snowden T, Acharya S, Butz C, Berardini M, Fishel R. hMSH4-hMSH5 Recognizes Holliday Junctions and Forms a Meiosis-Specific Sliding Clamp that Embraces Homologous Chromosomes. Mol Cell 2004; 15:437-51. [PMID: 15304223 DOI: 10.1016/j.molcel.2004.06.040] [Citation(s) in RCA: 287] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 05/17/2004] [Accepted: 05/28/2004] [Indexed: 11/22/2022]
Abstract
Five MutS homologs (MSH), which form three heterodimeric protein complexes, have been identified in eukaryotes. While the human hMSH2-hMSH3 and hMSH2-hMSH6 heterodimers operate primarily in mitotic mismatch repair (MMR), the biochemical function(s) of the meiosis-specific hMSH4-hMSH5 heterodimer is unknown. Here, we demonstrate that purified hMSH4-hMSH5 binds uniquely to Holliday Junctions. Holliday Junctions stimulate the hMSH4-hMSH5 ATP hydrolysis (ATPase) activity, which is controlled by Holliday Junction-provoked ADP-->ATP exchange. ATP binding by hMSH4-hMSH5 induces the formation of a hydrolysis-independent sliding clamp that dissociates from the Holliday Junction crossover region, embracing two homologous duplex DNA arms. Fundamental differences between hMSH2-hMSH6 and hMSH4-hMSH5 Holliday Junction recognition are detailed. Our results support the attractive possibility that hMSH4-hMSH5 stabilizes and preserves a meiotic bimolecular double-strand break repair (DSBR) intermediate.
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Affiliation(s)
- Timothy Snowden
- Genetics and Molecular Biology Program, Kimmel Cancer Center, BLSB 933, 233 South 10th Street, Philadelphia, PA 19107, USA
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Kijas AW, Studamire B, Alani E. Msh2 separation of function mutations confer defects in the initiation steps of mismatch repair. J Mol Biol 2003; 331:123-38. [PMID: 12875840 DOI: 10.1016/s0022-2836(03)00694-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In eukaryotes the MSH2-MSH3 and MSH2-MSH6 heterodimers initiate mismatch repair (MMR) by recognizing and binding to DNA mismatches. The MLH1-PMS1 heterodimer then interacts with the MSH proteins at or near the mismatch site and is thought to act as a mediator to recruit downstream repair proteins. Here we analyzed five msh2 mutants that are functional in removing 3' non-homologous tails during double-strand break repair but are completely defective in MMR. Because non-homologous tail removal does not require MSH6, MLH1, or PMS1 functions, a characterization of the msh2 separation of function alleles should provide insights into early steps in MMR. Using the Taq MutS crystal structure as a model, three of the msh2 mutations, msh2-S561P, msh2-K564E, msh2-G566D, were found to map to a domain in MutS involved in stabilizing mismatch binding. Gel mobility shift and DNase I footprinting assays showed that two of these mutations conferred strong defects on MSH2-MSH6 mismatch binding. The other two mutations, msh2-S656P and msh2-R730W, mapped to the ATPase domain. DNase I footprinting, ATP hydrolysis, ATP binding, and MLH1-PMS1 interaction assays indicated that the msh2-S656P mutation caused defects in ATP-dependent dissociation of MSH2-MSH6 from mismatch DNA and in interactions between MSH2-MSH6 and MLH1-PMS1. In contrast, the msh2-R730W mutation disrupted MSH2-MSH6 ATPase activity but did not strongly affect ATP binding or interactions with MLH1-PMS1. These results support a model in which MMR can be dissected into discrete steps: stable mismatch binding and sensing, MLH1-PMS1 recruitment, and recycling of MMR components.
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Affiliation(s)
- Amanda Wraith Kijas
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotech Building, Ithaca, NY 14853-2703, USA
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Acharya S, Foster PL, Brooks P, Fishel R. The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol Cell 2003; 12:233-46. [PMID: 12887908 DOI: 10.1016/s1097-2765(03)00219-3] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Escherichia coli MutS and MutL proteins have been conserved throughout evolution, although their combined functions in mismatch repair (MMR) are poorly understood. We have used biochemical and genetic studies to ascertain a physiologically relevant mechanism for MMR. The MutS protein functions as a regional lesion sensor. ADP-bound MutS specifically recognizes a mismatch. Repetitive rounds of mismatch-provoked ADP-->ATP exchange results in the loading of multiple MutS hydrolysis-independent sliding clamps onto the adjoining duplex DNA. MutL can only associate with ATP-bound MutS sliding clamps. Interaction of the MutS-MutL sliding clamp complex with MutH triggers ATP binding by MutL that enhances the endonuclease activity of MutH. Additionally, MutL promotes ATP binding-independent turnover of idle MutS sliding clamps. These results support a model of MMR that relies on two dynamic and redundant ATP-regulated molecular switches.
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Affiliation(s)
- Samir Acharya
- Genetics and Molecular Biology Program, Kimmel Cancer Center - BLSB 933, 233 S. 10th Street, Philadelphia, PA 19107, USA.
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Drake AC, Campbell H, Porteous MEM, Dunlop MG. The contribution of DNA mismatch repair gene defects to the burden of gynecological cancer. Int J Gynecol Cancer 2003; 13:262-77. [PMID: 12801255 DOI: 10.1046/j.1525-1438.2003.13194.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- A C Drake
- University of Edinburgh, Edinburgh, United Kingdom.
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