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Meulemans L, Baert Desurmont S, Waill MC, Castelain G, Killian A, Hauchard J, Frebourg T, Coulet F, Martins A, Muleris M, Gaildrat P. Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in-frame splicing alterations. J Med Genet 2022; 60:450-459. [PMID: 36113988 DOI: 10.1136/jmg-2022-108576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
BackgroundSpliceogenic variants in disease-causing genes are often presumed pathogenic since most induce frameshifts resulting in loss of function. However, it was recently shown in cancer predisposition genes that some may trigger in-frame anomalies that preserve function. Here, we addressed this question by using MSH2, a DNA mismatch repair gene implicated in Lynch syndrome, as a model system.MethodsEighteen MSH2 variants, mostly localised within canonical splice sites, were analysed by using minigene splicing assays. The impact of the resulting protein alterations was assessed in a methylation tolerance-based assay. Clinicopathological characteristics of variant carriers were collected.ResultsThree in-frame RNA biotypes were identified based on variant-induced spliceogenic outcomes: exon skipping (E3, E4, E5 and E12), segmental exonic deletions (E7 and E15) and intronic retentions (I3, I6, I12 and I13). The 10 corresponding protein isoforms exhibit either large deletions (49–93 amino acids (aa)), small deletions (12 or 16 aa) or insertions (3–10 aa) within different functional domains. We showed that all these modifications abrogate MSH2 function, in agreement with the clinicopathological features of variant carriers.ConclusionAltogether, these data demonstrate that MSH2 function is intolerant to in-frame indels caused by the spliceogenic variants analysed in this study, supporting their pathogenic nature. This work stresses the importance of combining complementary RNA and protein approaches to ensure accurate clinical interpretation of in-frame spliceogenic variants.
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Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Stéphanie Baert Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Marie-Christine Waill
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Gaia Castelain
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Audrey Killian
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Julie Hauchard
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Florence Coulet
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Martine Muleris
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
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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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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: 54] [Impact Index Per Article: 18.0] [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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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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5
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Rosenthal E, Bowles K, Pruss D, van Kan A, Vail P, McElroy H, Wenstrup R. Exceptions to the rule: Case studies in the prediction of pathogenicity for genetic variants in hereditary cancer genes. Clin Genet 2015; 88:533-41. [DOI: 10.1111/cge.12560] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | - K.R. Bowles
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - D. Pruss
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - A. van Kan
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - P.J. Vail
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - H. McElroy
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - R.J. Wenstrup
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
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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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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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8
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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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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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DNA mismatch repair proteins are required for efficient herpes simplex virus 1 replication. J Virol 2011; 85:12241-53. [PMID: 21957315 DOI: 10.1128/jvi.05487-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a double-stranded DNA virus that replicates in the nucleus of its human host cell and is known to interact with many cellular DNA repair proteins. In this study, we examined the role of cellular mismatch repair (MMR) proteins in the virus life cycle. Both MSH2 and MLH1 are required for efficient replication of HSV-1 in normal human cells and are localized to viral replication compartments. In addition, a previously reported interaction between MSH6 and ICP8 was confirmed by coimmunoprecipitation and extended to show that UL12 is also present in this complex. We also report for the first time that MLH1 associates with ND10 nuclear bodies and that like other ND10 proteins, MLH1 is recruited to the incoming genome. Knockdown of MLH1 inhibits immediate-early viral gene expression. MSH2, on the other hand, which is generally thought to play a role in mismatch repair at a step prior to that of MLH1, is not recruited to incoming genomes and appears to act at a later step in the viral life cycle. Silencing of MSH2 appears to inhibit early gene expression. Thus, both MLH1 and MSH2 are required but appear to participate in distinct events in the virus life cycle. The observation that MLH1 plays an earlier role in HSV-1 infection than does MSH2 is surprising and may indicate a novel function for MLH1 distinct from its known MSH2-dependent role in mismatch repair.
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