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Mahdouani M, Zhuri D, Sezginer Guler H, Hmida D, Sana M, Azaza M, Ben Said M, Masmoudi S, Hmila F, Youssef S, Ben Sghaier R, Brieger A, Zeuzem S, Saad A, Gurkan H, Yalcintepe S, Gribaa M, Plotz G. Functional analysis of MMR gene VUS from potential Lynch syndrome patients. PLoS One 2024; 19:e0304141. [PMID: 38843250 PMCID: PMC11156341 DOI: 10.1371/journal.pone.0304141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Lynch syndrome is caused by inactivating variants in DNA mismatch repair genes, namely MLH1, MSH2, MSH6 and PMS2. We have investigated five MLH1 and one MSH2 variants that we have identified in Turkish and Tunisian colorectal cancer patients. These variants comprised two small deletions causing frameshifts resulting in premature stops which could be classified pathogenic (MLH1 p.(His727Profs*57) and MSH2 p.(Thr788Asnfs*11)), but also two missense variants (MLH1 p.(Asn338Ser) and p.(Gly181Ser)) and two small, in-frame deletion variants (p.(Val647-Leu650del) and p.(Lys678_Cys680del)). For such small coding genetic variants, it is unclear if they are inactivating or not. We here provide clinical description of the variant carriers and their families, and we performed biochemical laboratory testing on the variant proteins to test if their stability or their MMR activity are compromised. Subsequently, we compared the results to in-silico predictions on structure and conservation. We demonstrate that neither missense alteration affected function, while both deletion variants caused a dramatic instability of the MLH1 protein, resulting in MMR deficiency. These results were consistent with the structural analyses that were performed. The study shows that knowledge of protein function may provide molecular explanations of results obtained with functional biochemical testing and can thereby, in conjunction with clinical information, elevate the evidential value and facilitate clinical management in affected families.
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Affiliation(s)
- Marwa Mahdouani
- Laboratory of Cytogenetics, Molecular Genetics and Human Reproduction Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Drenushe Zhuri
- Department of Medical Genetics, Trakya University School of Medicine, Edirne, Turkey
| | - Hazal Sezginer Guler
- Department of Medical Genetics, Trakya University School of Medicine, Edirne, Turkey
| | - Dorra Hmida
- Laboratory of Cytogenetics, Molecular Genetics and Human Reproduction Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Mokni Sana
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
- Department of Dermatology and Venerology, Farhat Hached University Hospital, Sousse, Tunisia
| | - Mohamed Azaza
- Department of General Surgery, Sahloul University Hospital, Sousse, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax, Tunisia
| | - Fahmi Hmila
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
- Department of General and Digestive Surgery, Farhat Hached University Hospital, Sousse, Tunisia
| | - Sabri Youssef
- Department of General Surgery, Farhat Hached University Hospital, Sousse, Tunisia
| | - Rihab Ben Sghaier
- Laboratory of Cytogenetics, Molecular Genetics and Human Reproduction Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Angela Brieger
- Biomedical Research Laboratory, Medical Clinic 1, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Biomedical Research Laboratory, Medical Clinic 1, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ali Saad
- Laboratory of Cytogenetics, Molecular Genetics and Human Reproduction Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Hakan Gurkan
- Department of Medical Genetics, Trakya University School of Medicine, Edirne, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, Trakya University School of Medicine, Edirne, Turkey
| | - Moez Gribaa
- Laboratory of Cytogenetics, Molecular Genetics and Human Reproduction Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Guido Plotz
- Biomedical Research Laboratory, Medical Clinic 1, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
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2
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Gallon R, Brekelmans C, Martin M, Bours V, Schamschula E, Amberger A, Muleris M, Colas C, Dekervel J, De Hertogh G, Coupier J, Colleye O, Sepulchre E, Burn J, Brems H, Legius E, Wimmer K. Constitutional mismatch repair deficiency mimicking Lynch syndrome is associated with hypomorphic mismatch repair gene variants. NPJ Precis Oncol 2024; 8:119. [PMID: 38789506 PMCID: PMC11126593 DOI: 10.1038/s41698-024-00603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are distinct cancer syndromes caused, respectively, by mono- and bi-allelic germline mismatch repair (MMR) variants. LS predisposes to mainly gastrointestinal and genitourinary cancers in adulthood. CMMRD predisposes to brain, haematological, and LS-spectrum cancers from childhood. Two suspected LS patients with first cancer diagnosis aged 27 or 38 years were found to be homozygous for an MMR (likely) pathogenic variant, MSH6 c.3226C>T (p.(Arg1076Cys)), or variant of uncertain significance (VUS), MLH1 c.306G>A (p.(Glu102=)). MLH1 c.306G>A was shown to cause leaky exon 3 skipping. The apparent genotype-phenotype conflict was resolved by detection of constitutional microsatellite instability in both patients, a hallmark feature of CMMRD. A hypomorphic effect of these and other variants found in additional late onset CMMRD cases, identified by literature review, likely explains a LS-like phenotype. CMMRD testing in carriers of compound heterozygous or homozygous MMR VUS may find similar cases and novel hypomorphic variants. Individualised management of mono- and bi-allelic carriers of hypomorphic MMR variants is needed until we better characterise the associated phenotypes.
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Affiliation(s)
- Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | | | | | | | - Esther Schamschula
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Albert Amberger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martine Muleris
- Département de Génétique, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMRS_938, Sorbonne Université, Centre de Recherche Saint Antoine, Paris, France
| | - Chrystelle Colas
- Département de Génétique, Institut Curie, Paris, France
- INSERM U830, Université de Paris, Paris, France
| | - Jeroen Dekervel
- Department of Digestive Oncology, University Hospital Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | | | | | | | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hilde Brems
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.
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3
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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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4
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Mahdouani M, Ben Ahmed S, Hmila F, Rais H, Ben Sghaier R, Saad H, Ben Said M, Masmoudi S, Hmida D, Brieger A, Zeuzem S, Saad A, Gribaa M, Plotz G. Functional characterization of MLH1 missense variants unveils mechanisms of pathogenicity and clarifies role in cancer. PLoS One 2022; 17:e0278283. [PMID: 36454741 PMCID: PMC9714755 DOI: 10.1371/journal.pone.0278283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/28/2022] [Indexed: 12/05/2022] Open
Abstract
Lynch syndrome is a heritable condition caused by a heterozygous germline inactivating mutation of the DNA mismatch repair (MMR) genes, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants, for which the clinical significance is unclear in many cases. We have identified three MLH1 missense alterations (p.(Glu736Lys), p.(Pro640Thr) and p.(Leu73Pro)) in six individuals from large Tunisian families. For none of these alterations, a classification of pathogenicity was available, consequently diagnosis, predictive testing and targeted surveillance in affected families was impossible. We therefore performed functional laboratory testing using a system testing stability as well as catalytic activity that includes clinically validated reference variants. Both p.(Leu73Pro) and p.(Pro640Thr) were found to be non-functional due to severe defects in protein stability and catalytic activity. In contrast, p.(Glu736Lys) was comparable to the wildtype protein and therefore considered a neutral substitution. Analysis of residue conservation and of the structural roles of the substituted residues corroborated these findings. In conjunction with the available clinical data, two variants fulfil classification criteria for class 4 "likely pathogenic". The findings of this work clarify the mechanism of pathogenicity of two unclear MLH1 variants and enables predictive testing and targeted surveillance in members of carrier families worldwide.
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Affiliation(s)
- Marwa Mahdouani
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Slim Ben Ahmed
- Department of Oncology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Fahmi Hmila
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
- Department of General and Digestive Surgery, Farhat Hached University Hospital, Sousse, Tunisia
| | - Henda Rais
- Medical Service, Salah Azaiez Institute, Tunis, Tunisia
| | - Rihab Ben Sghaier
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Hanene Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Dorra Hmida
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Angela Brieger
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Ali Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Moez Gribaa
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
- * E-mail:
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5
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Morak M, Pineda M, Martins A, Gaildrat P, Tubeuf H, Drouet A, Gómez C, Dámaso E, Schaefer K, Steinke-Lange V, Koehler U, Laner A, Hauchard J, Chauris K, Holinski-Feder E, Capellá G. Splicing analyses for variants in MMR genes: best practice recommendations from the European Mismatch Repair Working Group. Eur J Hum Genet 2022; 30:1051-1059. [PMID: 35676339 PMCID: PMC9437034 DOI: 10.1038/s41431-022-01106-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Over 20% of the DNA mismatch repair (MMR) germline variants in suspected Lynch syndrome patients are classified as variants of uncertain significance (VUS). Well-established functional assays are pivotal for assessing the biological impact of these variants and provide relevant evidence for clinical classification. In our collaborative European Mismatch Repair Working Group (EMMR-WG) we compared three different experimental approaches for evaluating the effect of seven variants on mRNA splicing in MMR genes: (i) RT-PCR of full-length transcripts (FLT), (ii) RT-PCR of targeted transcript sections (TTS), both from patient biological samples and (iii) minigene splicing assays. An overall good concordance was observed between splicing patterns in TTS, FLT and minigene analyses for all variants. The FLT analysis depicted a higher number of different isoforms and mitigated PCR-bias towards shorter isoforms. TTS analyses may miss aberrant isoforms and minigene assays may under/overestimate the severity of certain splicing defects. The interpretation of the experimental findings must be cautious to adequately discriminate abnormal events from physiological complex alternative splicing patterns. A consensus strategy for investigating the impact of MMR variants on splicing was defined. First, RNA should be obtained from patient's cell cultures (such as fresh lymphocyte cultures) incubated with/without a nonsense-mediated decay inhibitor. Second, FLT RT-PCR analysis is recommended to oversee all generated isoforms. Third, TTS analysis and minigene assays are useful independent approaches for verifying and clarifying FLT results. The use of several methodologies is likely to increase the strength of the experimental evidence which contributes to improve variant interpretation.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | | | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Karine Chauris
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany. .,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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6
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Yang C, Sheehan M, Borras E, Cadoo K, Offit K, Zhang L. Characterization of a germline splice site variant MLH1 c.678-3T>A in a Lynch syndrome family. Fam Cancer 2021; 19:315-322. [PMID: 32356167 DOI: 10.1007/s10689-020-00180-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Germline mutations in the DNA mismatch repair (MMR) genes cause Lynch syndrome. Classification and interpretation of intronic variants, especially those outside the consensus ± 1 ~ 2 splice sites are challenging as it is uncertain whether such variants would affect splicing accuracy and efficiency. The assessment of the pathogenicity of splice site variants in MLH1 is further complicated by the various isoforms due to alternative splicing. In this report, we describe a 42-year-old female with Lynch syndrome who carries a germline variant, MLH1 c.678-3T>A, in the splice acceptor site of intron 8. Functional studies and semiquantitative analysis demonstrated that this variant causes a significant increase in the transcripts with exon 9 or exon 9 and 10 deletions, which presumably leads to premature protein truncation or abnormal protein. In addition, we also observed MSI-H and loss of MLH1 by IHC in patient's tumor tissue. This variant also segregated with Lynch Syndrome related cancers in three affected family members. Based on these evidence, the MLH1 c.678-3T>A variant is considered pathogenic.
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Affiliation(s)
- Ciyu Yang
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Margaret Sheehan
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ester Borras
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Karen Cadoo
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kenneth Offit
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), 10833 Le Conte Ave, Los Angeles, CA, 90095, USA.
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7
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Bhai P, Kulshrestha S, Puri RD, Bijarnia Mahay S, Saxena R, Verma IC. Spectrum of mutations in genes associated with familial colorectal cancer syndrome (MLH1, MSH2, PMS2, MSH6, and APC): A not so common hereditary cancer syndrome in Indian population. Indian J Gastroenterol 2020; 39:599-607. [PMID: 33191490 DOI: 10.1007/s12664-020-01096-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/14/2020] [Indexed: 02/04/2023]
Abstract
Incidence of colorectal cancer (CRC) is lower in India than in other parts of the world. Approximately 5% to 10% of CRC is inherited. Hereditary non-polyposis colorectal cancer (HNPCC) syndrome and familial adenomatous polyposis (FAP) syndrome are the two known familial cancer syndromes of gastrointestinal tract, which occur due to inherited genetic predisposition. Not much is known about the molecular profile of families with inherited CRC syndromes seen in Indian population. At our institute, we have been providing genetic testing and counseling service to all the families referred to us with suspicion of inherited cancer predisposition syndrome. We analyzed 36 suspected families at our clinic. Personal and family history of cancer was obtained from the proband and appropriate genetic testing was performed in 19 patients (13 with HNPCC, 5 with FAP, and 1 with Cowden syndrome). We present here our experience and spectrum of pathogenic variants observed in this patient cohort and review on published studies describing molecular profile of Indian patients with CRC syndromes.
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Affiliation(s)
- Pratibha Bhai
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India.
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110 060, India
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8
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Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals. Cancers (Basel) 2020; 12:cancers12071799. [PMID: 32635641 PMCID: PMC7408773 DOI: 10.3390/cancers12071799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
The causal mechanism for cancer predisposition in Lynch-like syndrome (LLS) remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive (epi)genetic analysis. One hundred and fifteen LLS patients harboring MMR-deficient tumors and no germline MMR mutations were included. Mutational analysis of 26 colorectal cancer (CRC)-associated genes was performed. Pathogenicity of MMR variants was assessed by splicing and multifactorial likelihood analyses. Genome-wide methylome analysis was performed by the Infinium Human Methylation 450K Bead Chip. The multigene panel analysis revealed the presence of two MMR gene truncating mutations not previously found. Of a total of 15 additional MMR variants identified, five -present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation, but no additional differentially methylated regions were identified in LLS compared to LS patients or cancer-free individuals. In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allowed the identification of deleterious MMR mutations as well as new LLS candidate causal genes. Constitutional epimutations in non-LS-associated genes are not responsible for LLS.
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9
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Landrith T, Li B, Cass AA, Conner BR, LaDuca H, McKenna DB, Maxwell KN, Domchek S, Morman NA, Heinlen C, Wham D, Koptiuch C, Vagher J, Rivera R, Bunnell A, Patel G, Geurts JL, Depas MM, Gaonkar S, Pirzadeh-Miller S, Krukenberg R, Seidel M, Pilarski R, Farmer M, Pyrtel K, Milliron K, Lee J, Hoodfar E, Nathan D, Ganzak AC, Wu S, Vuong H, Xu D, Arulmoli A, Parra M, Hoang L, Molparia B, Fennessy M, Fox S, Charpentier S, Burdette J, Pesaran T, Profato J, Smith B, Haynes G, Dalton E, Crandall JRR, Baxter R, Lu HM, Tippin-Davis B, Elliott A, Chao E, Karam R. Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes. NPJ Precis Oncol 2020; 4:4. [PMID: 32133419 PMCID: PMC7039900 DOI: 10.1038/s41698-020-0109-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.
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Affiliation(s)
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | - Deborah Wham
- Aurora St. Luke’s Medical Center, Milwaukee, WI USA
| | | | | | - Ragene Rivera
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Ann Bunnell
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Gayle Patel
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | | | | | | | | | | | | | - Robert Pilarski
- Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH USA
| | - Meagan Farmer
- University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - John Lee
- Cedars-Sinai Medical Center, Los Angeles, CA USA
| | | | | | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | - Dong Xu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA USA
- University of California at Irvine, Irvine, CA USA
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10
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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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11
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Morak M, Schaefer K, Steinke-Lange V, Koehler U, Keinath S, Massdorf T, Mauracher B, Rahner N, Bailey J, Kling C, Haeusser T, Laner A, Holinski-Feder E. Full-length transcript amplification and sequencing as universal method to test mRNA integrity and biallelic expression in mismatch repair genes. Eur J Hum Genet 2019; 27:1808-1820. [PMID: 31332305 DOI: 10.1038/s41431-019-0472-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/13/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
In pathogenicity assessment, RNA-based analyses are important for the correct classification of variants, and require gene-specific cut-offs for allelic representation and alternative/aberrant splicing. Beside this, the diagnostic yield of RNA-based techniques capable to detect aberrant splicing or allelic loss due to intronic/regulatory variants has to be elaborated. We established a cDNA analysis for full-length transcripts (FLT) of the four DNA mismatch repair (MMR) genes to investigate the splicing pattern and transcript integrity with active/inhibited nonsense-mediated mRNA-decay (NMD). Validation was based on results from normal controls, samples with premature termination codons (PTC), samples with splice-site defects (SSD), and samples with pathogenic putative missense variants. The method was applied to patients with variants of uncertain significance (VUS) or unexplained immunohistochemical MMR deficiency. We categorized the allelic representation into biallelic (50 ± 10%) or allelic loss (≤10%), and >10% and <40% as unclear. We defined isoforms up to 10% and exon-specific exceptions as alternative splicing, set the cut-off for SSD in cDNA + P to 30-50%, and regard >10% and <30% as unclear. FLT cDNA analyses designated 16% of all putative missense variants and 12% of VUS as SSD, detected MMR-defects in 19% of the unsolved patients, and re-classified >30% of VUS. Our method allows a standardized, systematic cDNA analysis of the MMR FLTs to assess the pathogenicity mechanism of VUS on RNA level, which will gain relevance for precision medicine and gene therapy. Diagnostic accuracy will be enhanced by detecting MMR defects in hitherto unsolved patients. The data generated will help to calibrate a high-throughput NGS-based mRNA-analysis and optimize prediction programs.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany. .,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany.
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany.,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Udo Koehler
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Susanne Keinath
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Trisari Massdorf
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany.,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Brigitte Mauracher
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Nils Rahner
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Jessica Bailey
- Clinical Genetics, St. George's University Hospital NHS Foundation Trust, London, UK
| | | | - Tanja Haeusser
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Andreas Laner
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany. .,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany.
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12
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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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13
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Belhadj S, Moutinho C, Mur P, Setien F, Llinàs-Arias P, Pérez-Salvia M, Pons T, Pineda M, Brunet J, Navarro M, Capellá G, Esteller M, Valle L. Germline variation in O 6-methylguanine-DNA methyltransferase (MGMT) as cause of hereditary colorectal cancer. Cancer Lett 2019; 447:86-92. [PMID: 30677446 DOI: 10.1016/j.canlet.2019.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023]
Abstract
Somatic epigenetic inactivation of the DNA repair protein O6-methylguanine DNA methyltransferase (MGMT) is frequent in colorectal cancer (CRC); however, its involvement in CRC predisposition remains unexplored. We assessed the role and relevance of MGMT germline mutations and epimutations in familial and early-onset CRC. Mutation and promoter methylation screenings were performed in 473 familial and/or early-onset mismatch repair-proficient nonpolyposis CRC cases. No constitutional MGMT inactivation by promoter methylation was observed. Of six rare heterozygous germline variants identified, c.346C > T (p.H116Y) and c.476G > A (p.R159Q), detected in three and one families respectively, affected highly conserved residues and showed segregation with cancer in available family members. In vitro, neither p.H116Y nor p.R159Q caused statistically significant reduction of MGMT repair activity. No evidence of somatic second hits was found in the studied tumors. Case-control data showed over-representation of c.346C > T (p.H116Y) in familial CRC compared to controls, but no overall association of MGMT mutations with CRC predisposition. In conclusion, germline mutations and constitutional epimutations in MGMT are not major players in hereditary CRC. Nevertheless, the over-representation of c.346C > T (p.H116Y) in our familial CRC cohort warrants further research.
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Affiliation(s)
- Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Cátia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Fernando Setien
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Pérez-Salvia
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Tirso Pons
- Department of Immunology and Oncology, National Center for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain.
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.
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14
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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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15
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Köger N, Paulsen L, López-Kostner F, Della Valle A, Vaccaro CA, Palmero EI, Alvarez K, Sarroca C, Neffa F, Kalfayan PG, Gonzalez ML, Rossi BM, Reis RM, Brieger A, Zeuzem S, Hinrichsen I, Dominguez-Valentin M, Plotz G. Evaluation of MLH1 variants of unclear significance. Genes Chromosomes Cancer 2018. [PMID: 29520894 DOI: 10.1002/gcc.22536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in silico predictions on structure and conservation. Additionally, we collected all available clinical information of the families to come to a conclusion concerning their pathogenic potential and facilitate clinical diagnosis in the affected families. We provide evidence that four of the alterations are causative for Lynch syndrome, four are likely neutral and one shows compromised activity which can currently not be classified with respect to its pathogenic potential. The work demonstrates that biochemical testing, corroborated by congruent evolutionary and structural information, can serve to reliably classify uncertain variants when other data are insufficient.
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Affiliation(s)
- Nicole Köger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Lea Paulsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | | | - Adriana Della Valle
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Edenir Inêz Palmero
- Barretos Cancer Hospital, Molecular Oncology Research Center, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, São Paulo, Brazil
| | - Karin Alvarez
- Laboratorio de Oncología y Genética Molecular, Clínica Los Condes, Santiago, Chile
| | - Carlos Sarroca
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | - Florencia Neffa
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Maria Laura Gonzalez
- Hereditary Cancer Program (PROCANHE), Hospital Italiano, Buenos Aires, Argentina
| | | | - Rui Manuel Reis
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany.,Life and Health Sciences Q5 753 Research Institute (ICVS), Health Sciences School, University of Minho, Braga, 754, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, 755, Portugal
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Inga Hinrichsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
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16
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Bellido F, Sowada N, Mur P, Lázaro C, Pons T, Valdés-Mas R, Pineda M, Aiza G, Iglesias S, Soto JL, Urioste M, Caldés T, Balbín M, Blay P, Rueda D, Durán M, Valencia A, Moreno V, Brunet J, Blanco I, Navarro M, Calin GA, Borck G, Puente XS, Capellá G, Valle L. Association Between Germline Mutations in BRF1, a Subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer. Gastroenterology 2018; 154:181-194.e20. [PMID: 28912018 DOI: 10.1053/j.gastro.2017.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/21/2017] [Accepted: 09/03/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Although there is a genetic predisposition to colorectal cancer (CRC), few of the genes that affect risk have been identified. We performed whole-exome sequence analysis of individuals in a high-risk family without mutations in genes previously associated with CRC risk to identify variants associated with inherited CRC. METHODS We collected blood samples from 3 relatives with CRC in Spain (65, 62, and 40 years old at diagnosis) and performed whole-exome sequence analyses. Rare missense, truncating or splice-site variants shared by the 3 relatives were selected. We used targeted pooled DNA amplification followed by next generation sequencing to screen for mutations in candidate genes in 547 additional hereditary and/or early-onset CRC cases (502 additional families). We carried out protein-dependent yeast growth assays and transfection studies in the HT29 human CRC cell line to test the effects of the identified variants. RESULTS A total of 42 unique or rare (population minor allele frequency below 1%) nonsynonymous genetic variants in 38 genes were shared by all 3 relatives. We selected the BRF1 gene, which encodes an RNA polymerase III transcription initiation factor subunit for further analysis, based on the predicted effect of the identified variant and previous association of BRF1 with cancer. Previously unreported or rare germline variants in BRF1 were identified in 11 of 503 CRC families, a significantly greater proportion than in the control population (34 of 4300). Seven of the identified variants (1 detected in 2 families) affected BRF1 mRNA splicing, protein stability, or expression and/or function. CONCLUSIONS In an analysis of families with a history of CRC, we associated germline mutations in BRF1 with predisposition to CRC. We associated deleterious BRF1 variants with 1.4% of familial CRC cases, in individuals without mutations in high-penetrance genes previously associated with CRC. Our findings add additional evidence to the link between defects in genes that regulate ribosome synthesis and risk of CRC.
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Affiliation(s)
- Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Nadine Sowada
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Rafael Valdés-Mas
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - José Luís Soto
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain; Alicante Institute for Health and Biomedical Research (ISABIAL-FISABIO Foundation), Alicante, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO) and Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Trinidad Caldés
- Laboratorio de Oncología Molecular, Servicio de Oncología Médica, Hospital Clínico San Carlos, Madrid, Spain
| | - Milagros Balbín
- Laboratorio de Oncología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Pilar Blay
- Familial Cancer Unit, Department of Medical Oncology, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Daniel Rueda
- Molecular Biology Laboratory, 12 de Octubre University Hospital, Madrid, Spain
| | - Mercedes Durán
- Instituto de Biología y Genética Molecular, IBGM-UVA-CSIC, Valladolid, Spain
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Life Science Department, Barcelona; Supercomputing Centre (BSC-CNS), Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Spain; Department of Clinical Sciences, School of Medicine, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain; Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Hospitalet de Llobregat, Barcelona, Spain.
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17
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Borras E, Chang K, Pande M, Cuddy A, Bosch JL, Bannon SA, Mork ME, Rodriguez-Bigas MA, Taggart MW, Lynch PM, You YN, Vilar E. In Silico Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation. Cancer Prev Res (Phila) 2017; 10:580-587. [PMID: 28765196 DOI: 10.1158/1940-6207.capr-17-0058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/09/2017] [Accepted: 07/26/2017] [Indexed: 01/23/2023]
Abstract
Lynch syndrome (LS) is a genetic condition secondary to germline alterations in the DNA mismatch repair (MMR) genes with 30% of changes being variants of uncertain significance (VUS). Our aim was to perform an in silico reclassification of VUS from a large single institutional cohort that will help prioritizing functional validation. A total of 54 VUS were detected with 33 (61%) novel variants. We integrated family history, pathology, and genetic information along with supporting evidence from eight different in silico tools at the RNA and protein level. Our assessment allowed us to reclassify 54% (29/54) of the VUS as probably damaging, 13% (7/54) as possibly damaging, and 28% (15/54) as probably neutral. There are more than 1,000 VUS reported in MMR genes and our approach facilitates the prioritization of further functional efforts to assess the pathogenicity to those classified as probably damaging. Cancer Prev Res; 10(10); 580-7. ©2017 AACR.
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Affiliation(s)
- Ester Borras
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mala Pande
- Department of Gastroenterology, Hepatology, and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amanda Cuddy
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L Bosch
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Bannon
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maureen E Mork
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miguel A Rodriguez-Bigas
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Lynch
- Department of Gastroenterology, Hepatology, and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y Nancy You
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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18
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Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dámaso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, Valencia A, Holinski-Feder E, Brunet J, Feliubadaló L, Lázaro C, Navarro M, Pineda M, Capellá G. Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis. Int J Cancer 2017; 141:1365-1380. [PMID: 28577310 DOI: 10.1002/ijc.30820] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/06/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022]
Abstract
In a proportion of patients presenting mismatch repair (MMR)-deficient tumors, no germline MMR mutations are identified, the so-called Lynch-like syndrome (LLS). Recently, MMR-deficient tumors have been associated with germline mutations in POLE and MUTYH or double somatic MMR events. Our aim was to elucidate the molecular basis of MSH2-deficient LS-suspected cases using a comprehensive analysis of colorectal cancer (CRC)-associated genes at germline and somatic level. Fifty-eight probands harboring MSH2-deficient tumors were included. Germline mutational analysis of MSH2 (including EPCAM deletions) and MSH6 was performed. Pathogenicity of MSH2 variants was assessed by RNA analysis and multifactorial likelihood calculations. MSH2 cDNA and methylation of MSH2 and MSH6 promoters were studied. Matched blood and tumor DNA were analyzed using a customized next generation sequencing panel. Thirty-five individuals were carriers of pathogenic or probably pathogenic variants in MSH2 and EPCAM. Five patients harbored 4 different MSH2 variants of unknown significance (VUS) and one had 2 novel MSH6 promoter VUS. Pathogenicity assessment allowed the reclassification of the 4 MSH2 VUS and 6 probably pathogenic variants as pathogenic mutations, enabling a total of 40 LS diagnostics. Predicted pathogenic germline variants in BUB1, SETD2, FAN1 and MUTYH were identified in 5 cases. Three patients had double somatic hits in MSH2 or MSH6, and another 2 had somatic alterations in other MMR genes and/or proofreading polymerases. In conclusion, our comprehensive strategy combining germline and somatic mutational status of CRC-associated genes by means of a subexome panel allows the elucidation of up to 86% of MSH2-deficient suspected LS tumors.
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Affiliation(s)
- Gardenia M Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Àngela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
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19
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Mur P, Sánchez-Cuartielles E, Aussó S, Aiza G, Valdés-Mas R, Pineda M, Navarro M, Brunet J, Urioste M, Lázaro C, Moreno V, Capellá G, Puente XS, Valle L. Scarce evidence of the causal role of germline mutations in UNC5C in hereditary colorectal cancer and polyposis. Sci Rep 2016; 6:20697. [PMID: 26852919 PMCID: PMC4745060 DOI: 10.1038/srep20697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/23/2015] [Indexed: 01/17/2023] Open
Abstract
Germline mutations in UNC5C have been suggested to increase colorectal cancer (CRC) risk, thus causing hereditary CRC. However, the evidence gathered thus far is insufficient to include the study of the UNC5C gene in the routine genetic testing of familial CRC. Here we aim at providing a more conclusive answer about the contribution of germline UNC5C mutations to genetically unexplained hereditary CRC and/or polyposis cases. To achieve this goal we sequenced the coding region and exon-intron boundaries of UNC5C in 544 familial CRC or polyposis patients (529 families), using a technique that combines pooled DNA amplification and massively parallel sequencing. A total of eight novel or rare variants, all missense, were identified in eight families. Co-segregation data in the families and association results in case-control series are not consistent with a causal effect for 7 of the 8 identified variants, including c.1882_1883delinsAA (p.A628K), previously described as a disease-causing mutation. One variant, c.2210G > A (p.S737N), remained unclassified. In conclusion, our results suggest that the contribution of germline mutations in UNC5C to hereditary colorectal cancer and to polyposis cases is negligible.
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Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Elena Sánchez-Cuartielles
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology, IDIBELL and CIBERESP, 08908 Hospitalet de Llobregat, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Rafael Valdés-Mas
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, 17007 Girona, Spain.,Department of Medical Sciences, School of Medicine, University of Girona, 17071 Girona, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO) and Center for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology, IDIBELL and CIBERESP, 08908 Hospitalet de Llobregat, Spain.,Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Hospitalet de Llobregat, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
| | - Xose S Puente
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 Hospitalet de Llobregat, Spain
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20
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Clinical and Molecular Characterization of Brazilian Patients Suspected to Have Lynch Syndrome. PLoS One 2015; 10:e0139753. [PMID: 26437257 PMCID: PMC4593564 DOI: 10.1371/journal.pone.0139753] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/15/2015] [Indexed: 12/30/2022] Open
Abstract
Lynch syndrome (LS) accounts for 3–5% of all colorectal cancers (CRC) and is inherited in an autosomal dominant fashion. This syndrome is characterized by early CRC onset, high incidence of tumors in the ascending colon, excess of synchronous/metachronous tumors and extra-colonic tumors. Nowadays, LS is regarded of patients who carry deleterious germline mutations in one of the five mismatch repair genes (MMR), mostly in MLH1 and MSH2, but also in MSH6, PMS1 and PMS2. To comprehensively characterize 116 Brazilian patients suspected for LS, we assessed the frequency of germline mutations in the three minor genes MSH6, PMS1 and PMS2 in 82 patients negative for point mutations in MLH1 and MSH2. We also assessed large genomic rearrangements by MLPA for detecting copy number variations (CNVs) in MLH1, MSH2 and MSH6 generating a broad characterization of MMR genes. The complete analysis of the five MMR genes revealed 45 carriers of pathogenic mutations, including 25 in MSH2, 15 in MLH1, four in MSH6 and one in PMS2. Eleven novel pathogenic mutations (6 in MSH2, 4 in MSH6 and one in PMS2), and 11 variants of unknown significance (VUS) were found. Mutations in the MLH1 and MSH2 genes represented 89% of all mutations (40/45), whereas the three MMR genes (MSH6, PMS1 and PMS2) accounted for 11% (5/45). We also investigated the MLH1 p.Leu676Pro VUS located in the PMS2 interaction domain and our results revealed that this variant displayed no defective function in terms of cellular location and heterodimer interaction. Additionally, we assessed the tumor phenotype of a subset of patients and also the frequency of CRC and extra-colonic tumors in 2,365 individuals of the 116 families, generating the first comprehensive portrait of the genetic and clinical aspects of patients suspected of LS in a Brazilian cohort.
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21
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Aguirre-Rodríguez FJ, Lucenilla MIR, Alvarez-Cubero M, Mata C, Entrala-Bernal C, Fernandez-Rosado F. Novel FA2H mutation in a girl with familial spastic paraplegia. J Neurol Sci 2015; 357:332-4. [DOI: 10.1016/j.jns.2015.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022]
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22
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A founder MLH1 mutation in Lynch syndrome families from Piedmont, Italy, is associated with an increased risk of pancreatic tumours and diverse immunohistochemical patterns. Fam Cancer 2015; 13:401-13. [PMID: 24802709 DOI: 10.1007/s10689-014-9726-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The MLH1 c.2252_2253delAA mutation was found in 11 unrelated families from a restricted area south-west of Turin among 140 families with mutations in the mismatch repair genes. The mutation is located in the highly conserved C-terminal region, responsible for dimerization with the PMS2 protein. Twenty-five tumour tissues from 61 individuals with the c.2252_2253delAA mutation were tested for microsatellite instability (MSI) and protein expression. We compared the clinical features of these families versus the rest of our cohort and screened for a founder effect. All but one tumours showed the MSI-high mutator phenotype. Normal, focal and lack of MLH1 staining were observed in 16, 36 and 48 % of tumours, respectively. PMS2 expression was always lost. The mutation co-segregated with Lynch syndrome-related cancers in all informative families. All families but one fulfilled Amsterdam criteria, a frequency higher than in other MLH1 mutants. This was even more evident for AC II (72.7 vs. 57.5 %). Moreover, all families had at least one colon cancer diagnosed before 50 years and one case with multiple Lynch syndrome-related tumours. Interestingly, a statistically significant (p = 0.0057) higher frequency of pancreatic tumours was observed compared to families with other MLH1 mutations: 8.2 % of affected individuals versus 1.6 %. Haplotype analysis demonstrated a common ancestral origin of the mutation, which originated about 1,550 years ago. The mutation is currently classified as having an uncertain clinical significance. Clinical features, tissue analysis and co-segregation with disease strongly support the hypothesis that the MLH1 c.2252_2253delAA mutation has a pathogenic effect.
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23
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Hinrichsen I, Schäfer D, Langer D, Köger N, Wittmann M, Aretz S, Steinke V, Holzapfel S, Trojan J, König R, Zeuzem S, Brieger A, Plotz G. Functional testing strategy for coding genetic variants of unclear significance in MLH1 in Lynch syndrome diagnosis. Carcinogenesis 2014; 36:202-11. [PMID: 25477341 DOI: 10.1093/carcin/bgu239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lynch syndrome is caused by inactivating mutations in the MLH1 gene, but genetic variants of unclear significance frequently preclude diagnosis. Functional testing can reveal variant-conferred defects in gene or protein function. Based on functional defect frequencies and clinical applicability of test systems, we developed a functional testing strategy aimed at efficiently detecting pathogenic defects in coding MLH1 variants. In this strategy, tests of repair activity and expression are prioritized over analyses of subcellular protein localization and messenger RNA (mRNA) formation. This strategy was used for four unclear coding MLH1 variants (p.Asp41His, p.Leu507Phe, p.Gln689Arg, p.Glu605del + p.Val716Met). Expression was analyzed using a transfection system, mismatch repair (MMR) activity by complementation in vitro, mRNA formation by reverse transcriptase-PCR in carrier lymphocyte mRNA, and subcellular localization with dye-labeled fusion constructs. All tests included clinically meaningful controls. The strategy enabled efficient identification of defects in two unclear variants: the p.Asp41His variant showed loss of MMR activity, whereas the compound variant p.Glu605del + p.Val716Met had a defect of expression. This expression defect was significantly stronger than the pathogenic expression reference variant analyzed in parallel, therefore the defect of the compound variant is also pathogenic. Interestingly, the expression defect was caused additively by both of the compound variants, at least one of which is non-pathogenic when occurring by itself. Tests were neutral for p.Leu507Phe and p.Gln689Arg, and the results were consistent with available clinical data. We finally discuss the improved sensitivity and efficiency of the applied strategy and its limitations in analyzing unclear coding MLH1 variants.
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Affiliation(s)
- Inga Hinrichsen
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Dieter Schäfer
- Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany
| | - Deborah Langer
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Nicole Köger
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Margarethe Wittmann
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Verena Steinke
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and
| | - Jörg Trojan
- Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Rainer König
- Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Angela Brieger
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1 and Department of Human Genetics, Universitätsklinikum Frankfurt, Frankfurt D-60590, Germany, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Department of Internal Medicine 1, Universitätsklinikum Frankfurt D-60590, Frankfurt, Germany
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24
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Pineda M, González-Acosta M, Thompson BA, Sánchez R, Gómez C, Martínez-López J, Perea J, Caldés T, Rodríguez Y, Landolfi S, Balmaña J, Lázaro C, Robles L, Capellá G, Rueda D. Detailed characterization of MLH1 p.D41H and p.N710D variants coexisting in a Lynch syndrome family with conserved MLH1 expression tumors. Clin Genet 2014; 87:543-8. [PMID: 25060679 DOI: 10.1111/cge.12467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 12/26/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant cancer-susceptibility disease caused by inactivating germline mutations in mismatch repair (MMR) genes. Variants of unknown significance (VUS) are often detected in mutational analysis of MMR genes. Here we describe a large family fulfilling Amsterdam I criteria carrying two rare VUS in the MLH1 gene: c.121G > C (p.D41H) and c.2128A > G (p.N710D). Collection of clinico-pathological data, multifactorial analysis, in silico predictions, and functional analyses were used to elucidate the clinical significance of the identified MLH1 VUS. Only the c.121G > C variant cosegregated with LS-associated tumors in the family. Diagnosed colorectal tumors were microsatellite unstable although immunohistochemical staining revealed no loss of MMR proteins expression. Multifactorial likelihood analysis classified c.2128A > G as a non-pathogenic variant and c.121G > C as pathogenic. In vitro functional tests revealed impaired MMR activity and diminished expression of c.121G > C. Accordingly, the N710 residue is located in the unconserved MLH1 C-terminal domain, whereas D41 is highly conserved and located in the ATPase domain. The obtained results will enable adequate genetic counseling of c.121G > C and c.2128A > G variant carriers and their families. Furthermore, they exemplify how cumulative data and comprehensive analyses are mandatory to refine the classification of MMR variants.
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Affiliation(s)
- M Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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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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Borràs E, Pineda M, Cadiñanos J, Del Valle J, Brieger A, Hinrichsen I, Cabanillas R, Navarro M, Brunet J, Sanjuan X, Musulen E, van der Klift H, Lázaro C, Plotz G, Blanco I, Capellá G. Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants. J Med Genet 2013; 50:552-63. [PMID: 23709753 DOI: 10.1136/jmedgenet-2012-101511] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM The majority of mismatch repair (MMR) gene mutations causing Lynch syndrome (LS) occur either in MLH1 or MSH2. However, the relative contribution of PMS2 is less well defined. The aim of this study was to evaluate the role of PMS2 in LS by assessing the pathogenicity of variants of unknown significance (VUS) detected in the mutational analysis of PMS2 in a series of Spanish patients. METHODS From a cohort of 202 LS suspected patients, 13 patients showing loss of PMS2 expression in tumours were screened for germline mutations in PMS2, using a long range PCR based strategy and multiplex ligation dependent probe amplification (MLPA). Pathogenicity assessment of PMS2 VUS was performed evaluating clinicopathological data, frequency in control population and in silico and in vitro analyses at the RNA and protein level. RESULTS Overall 25 different PMS2 DNA variants were detected. Fourteen were classified as polymorphisms. Nine variants were classified as pathogenic: seven alterations based on their molecular nature and two after demonstrating a functional defect (c.538-3C>G affected mRNA processing and c.137G>T impaired MMR activity). The c.1569C>G variant was classified as likely neutral while the c.384G>A remained as a VUS. We have also shown that the polymorphic variant c.59G>A is MMR proficient. CONCLUSIONS Pathogenic PMS2 mutations were detected in 69% of patients harbouring LS associated tumours with loss of PMS2 expression. In all, PMS2 mutations account for 6% of the LS cases identified. The comprehensive functional analysis shown here has been useful in the classification of PMS2 VUS and contributes to refining the role of PMS2 in LS.
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Affiliation(s)
- Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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You YN, Vilar E. Classifying MMR variants: time for revised nomenclature in Lynch syndrome. Clin Cancer Res 2013; 19:2280-2. [PMID: 23532885 DOI: 10.1158/1078-0432.ccr-13-0392] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inactivating germline mutations in DNA mismatch repair (MMR) genes are diagnostic for Lynch syndrome. However, the clinical significance of missense variants is uncertain. A threshold level of compromised MLH1 expression, correlating with greater protein instability and MMR functional defect, has been identified to help classify the pathogenicity of missense variants.
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Affiliation(s)
- Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA.
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Hinrichsen I, Brieger A, Trojan J, Zeuzem S, Nilbert M, Plotz G. Expression defect size among unclassified MLH1 variants determines pathogenicity in Lynch syndrome diagnosis. Clin Cancer Res 2013; 19:2432-41. [PMID: 23403630 DOI: 10.1158/1078-0432.ccr-12-3299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Lynch syndrome is caused by a germline mutation in a mismatch repair gene, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants with unclear clinical significance. The functionality of these variants can be tested in the laboratory, but the results cannot be used for clinical diagnosis. We therefore aimed to establish a laboratory test that can be applied clinically. EXPERIMENTAL DESIGN We assessed the expression, stability, and mismatch repair activity of 38 MLH1 missense variants and determined the pathogenicity status of recurrent variants using clinical data. RESULTS Four recurrent variants were classified as neutral (K618A, H718Y, E578G, V716M) and three as pathogenic (A681T, L622H, P654L). All seven variants were proficient in mismatch repair but showed defects in expression. Quantitative PCR, pulse-chase, and thermal stability experiments confirmed decreases in protein stability, which were stronger in the pathogenic variants. The minimal cellular MLH1 concentration for mismatch repair was determined, which corroborated that strongly destabilized variants can cause repair deficiency. Loss of MLH1 tumor immunostaining is consistently reported in carriers of the pathogenic variants, showing the impact of this protein instability on these tumors. CONCLUSIONS Expression defects are frequent among MLH1 missense variants, but only severe defects cause Lynch syndrome. The data obtained here enabled us to establish a threshold for distinguishing tolerable (clinically neutral) from pathogenic expression defects. This threshold allows the translation of laboratory results for uncertain MLH1 variants into pathogenicity statements for diagnosis, thereby improving the targeting of cancer prevention measures in affected families.
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Affiliation(s)
- Inga Hinrichsen
- Medizinische Klinik 1, Biomedical Research Laboratory, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
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