1
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Rath A, Radecki AA, Rahman K, Gilmore RB, Hudson JR, Cenci M, Tavtigian SV, Grady JP, Heinen CD. A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants. Hum Mutat 2022; 43:2295-2307. [PMID: 36054288 PMCID: PMC9772141 DOI: 10.1002/humu.24462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. However, previous assays are limited due to the model system employed, the manner of gene expression, or the environment in which function is assessed. Here, we developed a human cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene. Using clustered regularly interspaced short palindromic repeats gene editing, we knocked in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact on RNA and protein, including their ability to prevent microsatellite instability and instigate a DNA damage response. A statistical clustering analysis determined the range of functions associated with known pathogenic or benign variants, and linear regression was performed using existing odds in favor of pathogenicity scores for these control variants to calibrate our functional assay results. By converting the functional outputs into a single odds in favor of pathogenicity score, variant classification expert panels can use these results to readily reassess these VUS. Ultimately, this information will guide proper diagnosis and disease management for suspected Lynch syndrome patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | | | - Kaussar Rahman
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Rachel B. Gilmore
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Jonathan R. Hudson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Matthew Cenci
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - James P. Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, CT
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2
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Kaushik V, Plazzer JP, Winship I, Macrae F. Genetic variant interpretation: a primer for clinicians. Intern Med J 2021; 51:1401-1406. [PMID: 34541770 DOI: 10.1111/imj.15485] [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: 09/06/2020] [Revised: 02/08/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
Clinicians beyond specialist genetic services are now able to order tests to interrogate the genetic basis of disease. Behind every genetic report lies a significant body of work that draws on decades of collaboration between clinicians, researchers and database curators. Understanding these advances in genetic variant interpretation may allow practising clinicians to develop a more nuanced appreciation of the role genetic variant interpretation can play in the diagnosis and management of heritable disorders. In this article, we consider genetic variant interpretation with reference to efforts to better understand variation in the mismatch repair genes and their relation to Lynch syndrome - the most common cause of hereditary colon cancer.
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Affiliation(s)
- Varun Kaushik
- The Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
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3
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Abstract
The pathogenic consequences of 369 unique human HsMLH1 missense variants has been hampered by the lack of a detailed function in mismatch repair (MMR). Here single-molecule images show that HsMSH2-HsMSH6 provides a platform for HsMLH1-HsPMS2 to form a stable sliding clamp on mismatched DNA. The mechanics of sliding clamp progression solves a significant operational puzzle in MMR and provides explicit predictions for the distribution of clinically relevant HsMLH1 missense mutations.
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4
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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5
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Diagnosis of Lynch Syndrome and Strategies to Distinguish Lynch-Related Tumors from Sporadic MSI/dMMR Tumors. Cancers (Basel) 2021; 13:cancers13030467. [PMID: 33530449 PMCID: PMC7865821 DOI: 10.3390/cancers13030467] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific, as most of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Therefore, the identification of MSI/dMMR requires additional diagnostic tools to identify LS. In this review, we address the hallmarks of LS and present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with current strategies, which should be taken into account in order to improve the diagnosis of LS. Abstract Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific to it, as approximately 80% of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Methods leading to the diagnosis of LS have considerably evolved in recent years and so have tumoral tests for LS screening and for the discrimination of LS-related to MSI-sporadic tumors. In this review, we address the hallmarks of LS, including the clinical, histopathological, and molecular features. We present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with the current strategies, which should be taken into account to improve the diagnosis of LS and avoid inappropriate clinical management.
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6
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Jia X, Burugula BB, Chen V, Lemons RM, Jayakody S, Maksutova M, Kitzman JO. Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk. Am J Hum Genet 2021; 108:163-175. [PMID: 33357406 PMCID: PMC7820803 DOI: 10.1016/j.ajhg.2020.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
The lack of functional evidence for the majority of missense variants limits their clinical interpretability and poses a key barrier to the broad utility of carrier screening. In Lynch syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed “variants of uncertain significance” (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians’ interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the ∼1,300 extant missense VUSs in MSH2 and may facilitate the prospective classification of newly discovered variants in the clinic.
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7
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Cerretelli G, Ager A, Arends MJ, Frayling IM. Molecular pathology of Lynch syndrome. J Pathol 2020; 250:518-531. [PMID: 32141610 DOI: 10.1002/path.5422] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) is characterised by predisposition to colorectal, endometrial, and other cancers and is caused by inherited pathogenic variants affecting the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. It is probably the most common predisposition to cancer, having an estimated prevalence of between 1/100 and 1/180. Resources such as the International Society for Gastrointestinal Hereditary Cancer's MMR gene variant database, the Prospective Lynch Syndrome Database (PLSD), and the Colon Cancer Family Register (CCFR), as well as pathological and immunological studies, are enabling advances in the understanding of LS. These include defined criteria by which to interpret gene variants, the function of MMR in the normal control of apoptosis, definition of the risks of the various cancers, and the mechanisms and pathways by which the colorectal and endometrial tumours develop, including the critical role of the immune system. Colorectal cancers in LS can develop along three pathways, including flat intramucosal lesions, which depend on the underlying affected MMR gene. This gives insights into the limitations of colonoscopic surveillance and highlights the need for other forms of anti-cancer prophylaxis in LS. Finally, it shows that the processes of autoimmunisation and immunoediting fundamentally constrain the development of tumours in LS and explain the efficacy of immune checkpoint blockade therapy in MMR-deficient tumours. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Guia Cerretelli
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ann Ager
- Division of Infection and Immunity, School of Medicine and Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Mark J Arends
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ian M Frayling
- Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, UK
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8
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González-Acosta M, Hinrichsen I, Fernández A, Lázaro C, Pineda M, Plotz G, Capellá G. Validation of an in Vitro Mismatch Repair Assay Used in the Functional Characterization of Mismatch Repair Variants. J Mol Diagn 2019; 22:376-385. [PMID: 31881334 DOI: 10.1016/j.jmoldx.2019.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/27/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022] Open
Abstract
A significant proportion of DNA-mismatch repair (MMR) variants are classified as of unknown significance, precluding diagnosis. The in vitro MMR assay is used to assess their MMR capability, likely the most important function of an MMR protein. However, the robustness of the assay, crucial for its use in the clinical setting, has been rarely evaluated. The aim of the present work was to validate an in vitro MMR assay approach to the functional characterization of MMR variants, as a first step to meeting quality standards of diagnostic laboratories. The MMR assay was optimized by testing a variety of reagents and experimental conditions. Reference materials and standard operating procedures were established. To determine the intra- and interexperimental variability of the assay and its reproducibility among centers, independent transfections of six previously characterized MLH1 variants were performed in two independent laboratories. Reagents and conditions optimal for performing the in vitro MMR assay were determined. The validated assay demonstrated no significant intra- or interexperimental variability and good reproducibility between centers. We set up a robust in vitro MMR assay that can provide relevant in vitro functional evidence for MMR variant pathogenicity assessment, eventually improving the molecular diagnosis of hereditary cancer syndromes associated with MMR deficiency.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inga Hinrichsen
- Biomedical Research Laboratory, Department of Internal Medicine 1, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Anna Fernández
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Gabriel Capellá
- Hereditary Cancer Program, the Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Ciber Oncología (CIBERONC) Instituto Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.
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9
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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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10
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DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis. Genetics 2019; 212:445-460. [PMID: 31028114 PMCID: PMC6553831 DOI: 10.1534/genetics.119.302194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The initiation of eukaryotic DNA replication at replication origins is tightly regulated to prevent re-initiation and re-replication within each cell cycle. This regulation is critical for genome stability as re-replication is an extremely potent inducer... The sources of genome instability, a hallmark of cancer, remain incompletely understood. One potential source is DNA rereplication, which arises when the mechanisms that prevent the reinitiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA rereplication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of rereplication forks to break. Here, we examine the ability of DNA rereplication to induce nucleotide-level mutations. During normal replication these mutations are restricted by three overlapping error-avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14, a frameshift reporter that is poorly proofread, we show that rereplication induces up to a 30× higher rate of frameshift mutations and that this mutagenesis is due to passage of the rereplication fork, not secondary to rereplication fork breakage. Rereplication can also induce comparable rates of frameshift and base-substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated. Finally, we show that the rereplication-induced mutagenesis of both lys2InsEA14 and CAN1 disappears in the absence of mismatch repair. These results suggest that mismatch repair is attenuated during rereplication, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, rereplication can facilitate nucleotide-level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability.
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11
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D'Arcy BM, Blount J, Prakash A. Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene. Hum Mutat 2019; 40:458-471. [PMID: 30653781 DOI: 10.1002/humu.23708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/28/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited disorder that is associated with an increased predisposition to certain cancers caused by loss-of-function mutations in one of four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, or PMS2). The diagnosis of LS is often challenged by the identification of missense mutations where the functional effects are not known. These are termed variants of uncertain significance (VUSs) and account for 20%-30% of noncoding and missense mutations. VUSs cause ambiguity during clinical diagnosis and hinder implementation of appropriate medical management. In the current study, we focus on the functional and biological consequences of two nonsynonymous VUSs in PMS2. These variants, c.620G>A and c.123_131delGTTAGTAGA, result in the alteration of glycine 207 to glutamate (p.Gly207Glu) and the deletion of amino acid residues 42-44 (p.Leu42_Glu44del), respectively. While the PMS2 p.Gly207Glu variant retains in vitro MMR and ATPase activities, PMS2 p.Leu42_Glu44del appears to lack such capabilities. Structural and biophysical characterization using circular dichroism, small-angle X-ray scattering, and X-ray crystallography of the N-terminal domain of the PMS2 variants indicate that the p.Gly207Glu variant is properly folded similar to the wild-type enzyme, whereas p.Leu42_Glu44del is disordered and prone to aggregation.
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Affiliation(s)
- Brandon M D'Arcy
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
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12
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Blount J, Prakash A. The changing landscape of Lynch syndrome due to PMS2 mutations. Clin Genet 2018; 94:61-69. [PMID: 29286535 PMCID: PMC5995637 DOI: 10.1111/cge.13205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations.
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Affiliation(s)
- Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
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13
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Arora S, Huwe PJ, Sikder R, Shah M, Browne AJ, Lesh R, Nicolas E, Deshpande S, Hall MJ, Dunbrack RL, Golemis EA. Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods. Cancer Biol Ther 2017; 18:519-533. [PMID: 28494185 DOI: 10.1080/15384047.2017.1326439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS.
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Affiliation(s)
- Sanjeevani Arora
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Peter J Huwe
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Rahmat Sikder
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Manali Shah
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Amanda J Browne
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Randy Lesh
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Emmanuelle Nicolas
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Sanat Deshpande
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Michael J Hall
- c Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Roland L Dunbrack
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Erica A Golemis
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
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14
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Enhanced gene targeting to evaluate Lynch syndrome alterations. Proc Natl Acad Sci U S A 2016; 113:3918-20. [PMID: 27035997 DOI: 10.1073/pnas.1602650113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Oligonucleotide-directed mutagenesis screen to identify pathogenic Lynch syndrome-associated MSH2 DNA mismatch repair gene variants. Proc Natl Acad Sci U S A 2016; 113:4128-33. [PMID: 26951660 DOI: 10.1073/pnas.1520813113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA oligonucleotides can achieve targeted base-pair substitution with modest efficiency but high precision. We show that "oligo targeting" can be used effectively to study missense mutations in DNA mismatch repair (MMR) genes. Inherited inactivating mutations in DNA MMR genes are causative for the cancer predisposition Lynch syndrome (LS). Although overtly deleterious mutations in MMR genes can clearly be ascribed as the cause of LS, the functional implications of missense mutations are often unclear. We developed a genetic screen to determine the pathogenicity of these variants of uncertain significance (VUS), focusing on mutator S homolog 2 (MSH2). VUS were introduced into the endogenous Msh2 gene of mouse embryonic stem cells by oligo targeting. Subsequent selection for MMR-deficient cells using the guanine analog 6-thioguanine allowed the detection of MMR-abrogating VUS. The screen was able to distinguish weak and strong pathogenic variants from polymorphisms and was used to investigate 59 Msh2 VUS. Nineteen of the 59 VUS were identified as pathogenic. Functional assays revealed that 14 of the 19 detected variants fully abrogated MMR activity and that five of the detected variants attenuated MMR activity. Implementation of the screen in clinical practice allows proper counseling of mutation carriers and treatment of their tumors.
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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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17
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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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19
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Abstract
Lynch syndrome, which is now recognized as the most common hereditary colorectal cancer condition, is characterized by the predisposition to a spectrum of cancers, primarily colorectal cancer and endometrial cancer. We chronicle over a century of discoveries that revolutionized the diagnosis and clinical management of Lynch syndrome, beginning in 1895 with Warthin's observations of familial cancer clusters, through the clinical era led by Lynch and the genetic era heralded by the discovery of causative mutations in mismatch repair (MMR) genes, to ongoing challenges.
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Affiliation(s)
- Henry T Lynch
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Carrie L Snyder
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Trudy G Shaw
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3101, USA
| | - Megan P Hitchins
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Grant Building S169, 1291 Welch Road, Stanford, California 94305, USA
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20
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Valle L. Genetic predisposition to colorectal cancer: Where we stand and future perspectives. World J Gastroenterol 2014; 20:9828-9849. [PMID: 25110415 PMCID: PMC4123366 DOI: 10.3748/wjg.v20.i29.9828] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/10/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
The development of colorectal cancer (CRC) can be influenced by genetic factors in both familial cases and sporadic cases. Familial CRC has been associated with genetic changes in high-, moderate- and low-penetrance susceptibility genes. However, despite the availability of current gene-identification techniques, the genetic causes of a considerable proportion of hereditary cases remain unknown. Genome-wide association studies of CRC have identified a number of common low-penetrance alleles associated with a slightly increased or decreased risk of CRC. The accumulation of low-risk variants may partly explain the familial risk of CRC, and some of these variants may modify the risk of cancer in patients with mutations in high-penetrance genes. Understanding the predisposition to develop CRC will require investigators to address the following challenges: the identification of genes that cause uncharacterized hereditary cases of CRC such as familial CRC type X and serrated polyposis; the classification of variants of unknown significance in known CRC-predisposing genes; and the identification of additional cancer risk modifiers that can be used to perform risk assessments for individual mutation carriers. We performed a comprehensive review of the genetically characterized and uncharacterized hereditary CRC syndromes and of low- and moderate-penetrance loci and variants identified through genome-wide association studies and candidate-gene approaches. Current challenges and future perspectives in the field of CRC predisposition are also discussed.
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21
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Dominguez-Valentin M, Drost M, Therkildsen C, Rambech E, Ehrencrona H, Angleys M, Lau Hansen T, de Wind N, Nilbert M, Juel Rasmussen L. Functional implications of the p.Cys680Arg mutation in the MLH1 mismatch repair protein. Mol Genet Genomic Med 2014; 2:352-5. [PMID: 25077178 PMCID: PMC4113276 DOI: 10.1002/mgg3.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 12/15/2022] Open
Abstract
In clinical genetic diagnostics, it is difficult to predict whether genetic mutations that do not greatly alter the primary sequence of the encoded protein causing unknown functional effects on cognate proteins lead to development of disease. Here, we report the clinical identification of c.2038 T>C missense mutation in exon 18 of the human MLH1 gene and biochemically characterization of the p.Cys680Arg mutant MLH1 protein to implicate it in the pathogenicity of the Lynch syndrome (LS). We show that the mutation is deficient in DNA mismatch repair and, therefore, contributing to LS in the carriers.
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Affiliation(s)
- Mev Dominguez-Valentin
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden ; The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center Leiden, The Netherlands
| | - Christina Therkildsen
- The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Eva Rambech
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University Lund, Sweden
| | - Maria Angleys
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
| | - Thomas Lau Hansen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
| | - Niels de Wind
- Department of Toxicogenetics, Leiden University Medical Center Leiden, The Netherlands
| | - Mef Nilbert
- Department of Oncology, Institute for Clinical Sciences, Lund University 22185, Lund, Sweden ; The Danish HNPCC-register, Clinical Research Centre, Hvidovre University Hospital, Copenhagen University Hvidovre, Denmark
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen DK-2200, Copenhagen N, Denmark
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22
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Sijmons RH, Greenblatt MS, Genuardi M. Gene variants of unknown clinical significance in Lynch syndrome. An introduction for clinicians. Fam Cancer 2014; 12:181-7. [PMID: 23525798 DOI: 10.1007/s10689-013-9629-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clinicians referring patients for genetic testing for Lynch syndrome will sooner or later receive results for DNA Mismatch Repair (MMR) genes reporting DNA changes that are unclear from a clinical point of view. These changes are referred to as variants of unknown, or unclear, clinical significance (VUS). In contrast to clearly pathogenic mutations, VUS do not firmly diagnose Lynch syndrome at the molecular level and cannot be used to identify with certainty any of the patients' asymptomatic relatives as Lynch syndrome mutation carriers. The International database that collects MMR gene variants ( www.insight-group.org/mutations ) already lists more than 1,000 different VUSs and these variants are likely the tip of the iceberg. This paper aims at introducing non-geneticist clinicians to the topic of clinical MMR gene variant interpretation. Many lines of evidence are being used to classify VUS. Some are already familiar to clinicians and others may be less familiar but are expected to become important in clinical genetics in the coming years. Clinicians can play an important role in collecting the data needed to interpret the MMR variants detected in their patients.
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Affiliation(s)
- Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, The Netherlands.
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23
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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Parsons MT, Whiley PJ, Beesley J, Drost M, de Wind N, Thompson BA, Marquart L, Hopper JL, Jenkins MA, Brown MA, Tucker K, Warwick L, Buchanan DD, Spurdle AB. Consequences of germline variation disrupting the constitutional translational initiation codon start sites of MLH1 and BRCA2: Use of potential alternative start sites and implications for predicting variant pathogenicity. Mol Carcinog 2013; 54:513-22. [PMID: 24302565 DOI: 10.1002/mc.22116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/03/2013] [Accepted: 11/07/2013] [Indexed: 12/21/2022]
Abstract
Variants that disrupt the translation initiation sequences in cancer predisposition genes are generally assumed to be deleterious. However, few studies have validated these assumptions with functional and clinical data. Two cancer syndrome gene variants likely to affect native translation initiation were identified by clinical genetic testing: MLH1:c.1A>G p.(Met1?) and BRCA2:c.67+3A>G. In vitro GFP-reporter assays were conducted to assess the consequences of translation initiation disruption on alternative downstream initiation codon usage. Analysis of MLH1:c.1A>G p.(Met1?) showed that translation was mostly initiated at an in-frame position 103 nucleotides downstream, but also at two ATG sequences downstream. The protein product encoded by the in-frame transcript initiating from position c.103 showed loss of in vitro mismatch repair activity comparable to known pathogenic mutations. BRCA2:c.67+3A>G was shown by mRNA analysis to result in an aberrantly spliced transcript deleting exon 2 and the consensus ATG site. In the absence of exon 2, translation initiated mostly at an out-of-frame ATG 323 nucleotides downstream, and to a lesser extent at an in-frame ATG 370 nucleotides downstream. Initiation from any of the downstream alternative sites tested in both genes would lead to loss of protein function, but further clinical data is required to confirm if these variants are associated with a high cancer risk. Importantly, our results highlight the need for caution in interpreting the functional and clinical consequences of variation that leads to disruption of the initiation codon, since translation may not necessarily occur from the first downstream alternative start site, or from a single alternative start site.
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Affiliation(s)
- Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Phillip J Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Niels de Wind
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Louise Marquart
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - John L Hopper
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia.,School of Public Health, Seoul National University, Seoul, Korea
| | - Mark A Jenkins
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | | | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, Sydney, Australia
| | - Linda Warwick
- ACT Genetics Service, The Canberra Hospital, Canberra, Australia
| | - Daniel D Buchanan
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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25
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Ku CS, Cooper DN, Iacopetta B, Roukos DH. Integrating next-generation sequencing into the diagnostic testing of inherited cancer predisposition. Clin Genet 2012; 83:2-6. [PMID: 23020236 DOI: 10.1111/cge.12028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/25/2012] [Accepted: 09/25/2012] [Indexed: 12/18/2022]
Abstract
The clinical application of next-generation sequencing (NGS) as a diagnostic tool has become increasingly evident. The coupling of NGS technologies with new genomic sequence enrichment methods has made the sequencing of panels of target genes technically feasible, at the same time as making such an approach cost-effective for diagnostic applications. In this article, we discuss recent studies that have applied NGS in the diagnostic setting in relation to hereditary cancer.
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Affiliation(s)
- C S Ku
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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