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Segura AVC, da Silva SIO, Santiago KM, Brianese RC, Carraro DM, Torrezan GT. Misclassification of a frequent variant from PMS2CL pseudogene as a PMS2 loss of function variant in Brazilian patients. Fam Cancer 2024; 23:653-657. [PMID: 38900223 DOI: 10.1007/s10689-024-00411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
PMS2, a Lynch Syndrome gene, presents challenges in genetic testing due to the existence of multiple pseudogenes. This study aims to describe a series of cases harboring a variant in the PMS2CL pseudogene that has been incorrectly assigned to PMS2 with different nomenclatures. We reviewed data from 647 Brazilian patients who underwent multigene genetic testing at a single center to identify those harboring the PMS2 V1:c.2186_2187delTC or V2:c.2182_2184delACTinsG variants, allegedly located at PMS2 exon 13. Gene-specific PCR and transcript sequencing was performed. Among the 647 individuals, 1.8% (12) carried the investigated variants, with variant allele frequencies ranging from 15 to 34%. By visually inspecting the alignments, we confirmed that both V1 and V2 represented the same variant and through gene-specific PCR and PMS2 transcript analysis, we demonstrated that V1/V2 is actually located in the PMS2CL pseudogene. Genomic databases (ExAC and gnomAD) report an incidence of 2.5 - 5.3% of this variant in the African population. Currently, V1 is classified as "uncertain significance" and V2 as "conflicting" in ClinVar, with several laboratories classifying them as "pathogenic". We identified a frequent African PMS2CL variant in the Brazilian population that is misclassified as a PMS2 variant. It is likely that V1/V2 have been erroneously assigned to PMS2 in several manuscripts and by clinical laboratories, underscoring a disparity-induced matter. Considering the limitations of short-read NGS differentiating between certain regions of PMS2 and PMS2CL, using complementary methodologies is imperative to provide an accurate diagnosis.
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Affiliation(s)
- Anthony Vladimir Campos Segura
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Sara Iolanda Oliveira da Silva
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Karina Miranda Santiago
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Rafael Canfield Brianese
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Dirce Maria Carraro
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | - Giovana Tardin Torrezan
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil.
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil.
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2
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Walker R, Mahmood K, Como J, Clendenning M, Joo JE, Georgeson P, Joseland S, Preston SG, Pope BJ, Chan JM, Austin R, Bojadzieva J, Campbell A, Edwards E, Gleeson M, Goodwin A, Harris MT, Ip E, Kirk J, Mansour J, Mar Fan H, Nichols C, Pachter N, Ragunathan A, Spigelman A, Susman R, Christie M, Jenkins MA, Pai RK, Rosty C, Macrae FA, Winship IM, Buchanan DD. DNA Mismatch Repair Gene Variant Classification: Evaluating the Utility of Somatic Mutations and Mismatch Repair Deficient Colonic Crypts and Endometrial Glands. Cancers (Basel) 2023; 15:4925. [PMID: 37894291 PMCID: PMC10605939 DOI: 10.3390/cancers15204925] [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: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the DNA mismatch repair (MMR) genes (Lynch syndrome) predispose to colorectal (CRC) and endometrial (EC) cancer. Lynch syndrome specific tumor features were evaluated for their ability to support the ACMG/InSiGHT framework in classifying variants of uncertain clinical significance (VUS) in the MMR genes. Twenty-eight CRC or EC tumors from 25 VUS carriers (6xMLH1, 9xMSH2, 6xMSH6, 4xPMS2), underwent targeted tumor sequencing for the presence of microsatellite instability/MMR-deficiency (MSI-H/dMMR) status and identification of a somatic MMR mutation (second hit). Immunohistochemical testing for the presence of dMMR crypts/glands in normal tissue was also performed. The ACMG/InSiGHT framework reclassified 7/25 (28%) VUS to likely pathogenic (LP), three (12%) to benign/likely benign, and 15 (60%) VUS remained unchanged. For the seven re-classified LP variants comprising nine tumors, tumor sequencing confirmed MSI-H/dMMR (8/9, 88.9%) and a second hit (7/9, 77.8%). Of these LP reclassified variants where normal tissue was available, the presence of a dMMR crypt/gland was found in 2/4 (50%). Furthermore, a dMMR endometrial gland in a carrier of an MSH2 exon 1-6 duplication provides further support for an upgrade of this VUS to LP. Our study confirmed that identifying these Lynch syndrome features can improve MMR variant classification, enabling optimal clinical care.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Melbourne Bioinformatics, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Susan G. Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Melbourne Bioinformatics, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - James M. Chan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Jasmina Bojadzieva
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia; (J.B.); (A.C.)
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia; (J.B.); (A.C.)
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia;
| | - Margaret Gleeson
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (A.G.); (A.S.)
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Marion T. Harris
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia;
| | - Emilia Ip
- Cancer Genetics Service, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Judy Kirk
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Julia Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia;
| | - Helen Mar Fan
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; (C.N.); (N.P.)
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; (C.N.); (N.P.)
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA 6009, Australia
- School of Medicine, Curtin University, Perth, WA 6102, Australia
| | - Abiramy Ragunathan
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Allan Spigelman
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (A.G.); (A.S.)
- St Vincent’s Cancer Genetics Unit, Sydney, NSW 2010, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW 2052, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Michael Christie
- Department of Medicine, Royal Melbourne Hospital, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rish K. Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ 85259, USA;
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Envoi Specialist Pathologists, Brisbane, QLD 4059, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
- Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
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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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Georgeson P, Harrison TA, Pope BJ, Zaidi SH, Qu C, Steinfelder RS, Lin Y, Joo JE, Mahmood K, Clendenning M, Walker R, Amitay EL, Berndt SI, Brenner H, Campbell PT, Cao Y, Chan AT, Chang-Claude J, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Giannakis M, Giles GG, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Limburg P, Manson JE, Moreno V, Nassir R, Nowak JA, Obón-Santacana M, Ogino S, Phipps AI, Potter JD, Schoen RE, Sun W, Toland AE, Trinh QM, Ugai T, Macrae FA, Rosty C, Hudson TJ, Jenkins MA, Thibodeau SN, Winship IM, Peters U, Buchanan DD. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures. Nat Commun 2022; 13:3254. [PMID: 35668106 PMCID: PMC9170691 DOI: 10.1038/s41467-022-30916-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023] Open
Abstract
Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert S Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Efrat L Amitay
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center(DKFZ), Heidelberg, Germany
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Amy J French
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Limburg
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rami Nassir
- Department of Pathology, College of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Finlay A Macrae
- Parkville Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | | | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia.
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5
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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6
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Kaushik V, Plazzer JP, Winship I, Macrae F. Genetic variant interpretation: a primer for clinicians. Intern Med J 2021; 51:1401-1406. [PMID: 34541770 DOI: 10.1111/imj.15485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/08/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
Clinicians beyond specialist genetic services are now able to order tests to interrogate the genetic basis of disease. Behind every genetic report lies a significant body of work that draws on decades of collaboration between clinicians, researchers and database curators. Understanding these advances in genetic variant interpretation may allow practising clinicians to develop a more nuanced appreciation of the role genetic variant interpretation can play in the diagnosis and management of heritable disorders. In this article, we consider genetic variant interpretation with reference to efforts to better understand variation in the mismatch repair genes and their relation to Lynch syndrome - the most common cause of hereditary colon cancer.
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Affiliation(s)
- Varun Kaushik
- The Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
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7
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Ollodart AR, Yeh CLC, Miller AW, Shirts BH, Gordon AS, Dunham MJ. Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 2021; 218:iyab058. [PMID: 33848333 PMCID: PMC8225350 DOI: 10.1093/genetics/iyab058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 01/01/2023] Open
Abstract
Despite the fundamental importance of mutation rate as a driving force in evolution and disease risk, common methods to assay mutation rate are time-consuming and tedious. Established methods such as fluctuation tests and mutation accumulation experiments are low-throughput and often require significant optimization to ensure accuracy. We established a new method to determine the mutation rate of many strains simultaneously by tracking mutation events in a chemostat continuous culture device and applying deep sequencing to link mutations to alleles of a DNA-repair gene. We applied this method to assay the mutation rate of hundreds of Saccharomyces cerevisiae strains carrying mutations in the gene encoding Msh2, a DNA repair enzyme in the mismatch repair pathway. Loss-of-function mutations in MSH2 are associated with hereditary nonpolyposis colorectal cancer, an inherited disorder that increases risk for many different cancers. However, the vast majority of MSH2 variants found in human populations have insufficient evidence to be classified as either pathogenic or benign. We first benchmarked our method against Luria-Delbrück fluctuation tests using a collection of published MSH2 missense variants. Our pooled screen successfully identified previously characterized nonfunctional alleles as high mutators. We then created an additional 185 human missense variants in the yeast ortholog, including both characterized and uncharacterized alleles curated from ClinVar and other clinical testing data. In a set of alleles of known pathogenicity, our assay recapitulated ClinVar's classification; we then estimated pathogenicity for 157 variants classified as uncertain or conflicting reports of significance. This method is capable of studying the mutation rate of many microbial species and can be applied to problems ranging from the generation of high-fidelity polymerases to measuring the frequency of antibiotic resistance emergence.
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Affiliation(s)
- Anja R Ollodart
- Molecular Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Chiann-Ling C Yeh
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Aaron W Miller
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Adam S Gordon
- Department of Pharmacology, Northwestern University, Chicago, IL 60208, USA
| | - Maitreya J Dunham
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
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8
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Cini G, Carnevali I, Sahnane N, Chiaravalli AM, Dell'Elice A, Maestro R, Pin E, Bestetti I, Radovic S, Armelao F, Viel A, Tibiletti MG. Lynch syndrome and Muir-Torre phenotype associated with a recurrent variant in the 3'UTR of the MSH6 gene. Cancer Genet 2021; 254-255:1-10. [PMID: 33516942 DOI: 10.1016/j.cancergen.2021.01.005] [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] [Received: 08/07/2020] [Revised: 12/18/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
A MSH6 3'UTR variant (c.*23_26dup) was found in 13 unrelated families consulted for Lynch/Muir-Torre Syndrome. This variant, which is very rare in the genomic databases, was absent in healthy controls and strongly segregated with the disease in the studied pedigrees. All tumors were defective for MSH2/MSH6/MSH3 proteins expression, but only MSH2 somatic pathogenic mutations were found in 5 of the 12 sequenced tumors. Moreover, we had no evidence of MSH6 transcript decrease in carriers, whereas MSH2 transcript was downregulated. Additional evaluations performed in representative carriers, including karyotype, arrayCGH and Linked-Reads whole genome sequencing, failed to evidence any MSH2 germline pathogenic variant. Posterior probability of pathogenicity for MSH6 c.*23_26dup was obtained from a multifactorial analysis incorporating segregation and phenotypic data and resulted >0.999, allowing to classify the variant as pathogenic (InSiGHT Class 5). Carriers shared a common haplotype involving MSH2/MSH6 loci, then a cryptic disease-associated variant, linked with MSH6 c.*23_26dup, cannot be completely excluded. Even if it is not clear whether the MSH6 variant is pathogenic per se or simply a marker of a disease-associated MSH2/MSH6 haplotype, all data collected on patients and pedigrees prompted us to manage the variant as pathogenic and to offer predictive testing within these families.
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Affiliation(s)
- Giulia Cini
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Ileana Carnevali
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Nora Sahnane
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Anna Maria Chiaravalli
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Anastasia Dell'Elice
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Roberta Maestro
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, The Royal Institute of Technology KTH, Tomtebodavägen 23B, 171 65 Solna, Stockholm, Sweden
| | - Ilaria Bestetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Via Zucchi, 18 - 20095 Cusano Milanino (MI); Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20133 Milan, Italy
| | | | - Franco Armelao
- U.O. Gastroenterologia ed Endoscopia Digestiva, Ospedale S. Chiara, APSS, Via A. de Gasperi 79 - 38123, Trento, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Maria Grazia Tibiletti
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
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9
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Bläker H, Haupt S, Morak M, Holinski-Feder E, Arnold A, Horst D, Sieber-Frank J, Seidler F, von Winterfeld M, Alwers E, Chang-Claude J, Brenner H, Roth W, Engel C, Löffler M, Möslein G, Schackert HK, Weitz J, Perne C, Aretz S, Hüneburg R, Schmiegel W, Vangala D, Rahner N, Steinke-Lange V, Heuveline V, von Knebel Doeberitz M, Ahadova A, Hoffmeister M, Kloor M. Age-dependent performance of BRAF mutation testing in Lynch syndrome diagnostics. Int J Cancer 2020; 147:2801-2810. [PMID: 32875553 DOI: 10.1002/ijc.33273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/17/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022]
Abstract
BRAF V600E mutations have been reported as a marker of sporadic microsatellite instability (MSI) colorectal cancer (CRC). Current international diagnostic guidelines recommend BRAF mutation testing in MSI CRC patients to predict low risk of Lynch syndrome (LS). We evaluated the age-specific performance of BRAF testing in LS diagnostics. We systematically compared the prevalence of BRAF mutations in LS-associated CRCs and unselected MSI CRCs in different age groups as available from published studies, databases and population-based patient cohorts. Sensitivity/specificity analysis of BRAF testing for exclusion of LS and cost calculations were performed. Among 969 MSI CRCs from LS carriers in the literature and German HNPCC Consortium, 15 (1.6%) harbored BRAF mutations. Six of seven LS patients with BRAF-mutant CRC and reported age were <50 years. Among 339 of 756 (44.8%) of BRAF mutations detected in unselected MSI CRC, only 2 of 339 (0.6%) BRAF mutations were detected in patients <50 years. The inclusion of BRAF testing led to high risk of missing LS patients and increased costs at age <50 years. BRAF testing in patients <50 years carries a high risk of missing a hereditary cancer predisposition and is cost-inefficient. We suggest direct referral of MSI CRC patients <50 years to genetic counseling without BRAF testing.
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Affiliation(s)
- Hendrik Bläker
- Department of General Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Saskia Haupt
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center, Munich, Germany
| | - Alexander Arnold
- Department of General Pathology, Institute of Pathology, Charite Berlin, Berlin, Germany
| | - David Horst
- Department of General Pathology, Institute of Pathology, Charite Berlin, Berlin, Germany
| | - Julia Sieber-Frank
- Department of Applied Tumor Biology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer research Center (DKFZ), and Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Florian Seidler
- Department of Applied Tumor Biology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer research Center (DKFZ), and Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Moritz von Winterfeld
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Hiedelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ) Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wilfried Roth
- Institute of Pathology, University Hospital Mainz, Mainz, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Markus Löffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Gabriela Möslein
- Center for Hereditary Tumors, Helios University Hospital Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
| | - Hans-Konrad Schackert
- Department of Surgery, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Jürgen Weitz
- Department of Surgery, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Claudia Perne
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Wolff Schmiegel
- Department of Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Deepak Vangala
- Department of Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Nils Rahner
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center, Munich, Germany
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer research Center (DKFZ), and Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer research Center (DKFZ), and Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer research Center (DKFZ), and Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
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10
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Thompson BA, Walters R, Parsons MT, Dumenil T, Drost M, Tiersma Y, Lindor NM, Tavtigian SV, de Wind N, Spurdle AB. Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation. Front Genet 2020; 11:798. [PMID: 32849802 PMCID: PMC7398121 DOI: 10.3389/fgene.2020.00798] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/03/2020] [Indexed: 12/25/2022] Open
Abstract
Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected: 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants.
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Affiliation(s)
- Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rhiannon Walters
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael T Parsons
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Troy Dumenil
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, United States
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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11
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Dámaso E, González-Acosta M, Vargas-Parra G, Navarro M, Balmaña J, Ramon y Cajal T, Tuset N, Thompson BA, Marín F, Fernández A, Gómez C, Velasco À, Solanes A, Iglesias S, Urgel G, López C, del Valle J, Campos O, Santacana M, Matias-Guiu X, Lázaro C, Valle L, Brunet J, Pineda M, Capellá G. Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals. Cancers (Basel) 2020; 12:E1799. [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] [Grants] [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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Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d’Hebron Institute of Oncology (VHIO), Carrer de Natzaret 115-117, 08035 Barcelona, Spain;
| | - Teresa Ramon y Cajal
- Medical Oncology Department, Hospital de Santa Creu i Sant Pau, Carrer de Sant Quintí 89, 08041 Barcelona, Spain; (T.R.y.C.); (C.L.)
| | - Noemí Tuset
- Genetic Counseling Unit, Hospital Arnau de Vilanova, Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain; (N.T.); (G.U.)
| | - Bryony A. Thompson
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Building 181 Grattan St, VIC 3010 Melbourne, Australia;
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Àngela Velasco
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Girona (IDIBGI), Carrer del Dr. Castany s/n, 17190 Salt, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gisela Urgel
- Genetic Counseling Unit, Hospital Arnau de Vilanova, Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain; (N.T.); (G.U.)
| | - Consol López
- Medical Oncology Department, Hospital de Santa Creu i Sant Pau, Carrer de Sant Quintí 89, 08041 Barcelona, Spain; (T.R.y.C.); (C.L.)
| | - Jesús del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Maria Santacana
- Pathology Department, Hospital Arnau de Vilanova, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain;
| | - Xavier Matias-Guiu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Pathology Department, Hospital Arnau de Vilanova, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain;
- Pathology Department, Bellvitge University Hospital, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), Carrer de la Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Girona (IDIBGI), Carrer del Dr. Castany s/n, 17190 Salt, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Carrer Emili Grahit 77, 17003 Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
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12
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Li F, Xia Y, Wang G, Tang C, Zhan T, Shen J, Zhang J. Identification of a novel pathogenic MLH1 mutation and recommended genetic screening strategy: An investigation of three Chinese Lynch syndrome pedigrees. Mol Genet Genomic Med 2020; 8:e1295. [PMID: 32490589 PMCID: PMC7434735 DOI: 10.1002/mgg3.1295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/07/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
Background Lynch syndrome (LS) is an autosomal‐dominant disorder that increases the risk of many cancers. The genetic basis of LS is germline mutations in DNA mismatch repair genes. Methods We performed next‐generation sequencing on blood cells obtained from the members of three unrelated LS pedigrees. Immunohistochemistry staining was performed to analyze protein expression. Results Multigene panel screening revealed three mutL homolog 1 (MLH1) pathogenic mutations (c.199G>A, c.790 + 1G>A, and c.1557_1558 + 8delGGGTACGTAA, unreported) confirmed by Sanger sequencing. Immunohistochemistry showed a loss of MLH1 protein expression. We also confirmed that the unreported mutant allele was inherited for at least three generations. Conclusion These results provide new insights into the molecular mechanisms underlying the pathogenicity of MLH1 mutations and reaffirm the importance of genetic screening for the early diagnosis of LS.
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Affiliation(s)
- Fan Li
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yunwei Xia
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guoguang Wang
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Chaoyang Tang
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Tian Zhan
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jian Shen
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jianping Zhang
- Department of General Surgery, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
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13
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Li S, Qian D, Thompson BA, Gutierrez S, Wu S, Pesaran T, LaDuca H, Lu HM, Chao EC, Black MH. Tumour characteristics provide evidence for germline mismatch repair missense variant pathogenicity. J Med Genet 2019; 57:62-69. [PMID: 31391288 DOI: 10.1136/jmedgenet-2019-106096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Pathogenic variants in mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2) increase risk for Lynch syndrome and related cancers. We quantified tumour characteristics to assess variant pathogenicity for germline MMR genes. METHODS Among 4740 patients with cancer with microsatellite instability (MSI) and immunohistochemical (IHC) results, we tested MMR pathogenic variant association with MSI/IHC status, and estimated likelihood ratios which we used to compute a tumour characteristic likelihood ratio (TCLR) for each variant. Predictive performance of TCLR in combination with in silico predictors, and a multifactorial variant prediction (MVP) model that included allele frequency, co-occurrence, co-segregation, and clinical and family history information was assessed. RESULTS Compared with non-carriers, carriers of germline pathogenic/likely pathogenic (P/LP) variants were more likely to have abnormal MSI/IHC status (p<0.0001). Among 150 classified missense variants, 73.3% were accurately predicted with TCLR alone. Models leveraging in silico scores as prior probabilities accurately classified >76.7% variants. Adding TCLR as quantitative evidence in an MVP model (MVP +TCLR Pred) increased the proportion of accurately classified variants from 88.0% (MVP alone) to 98.0% and generated optimal performance statistics among all models tested. Importantly, MVP +TCLR Pred resulted in the high yield of predicted classifications for missense variants of unknown significance (VUS); among 193 VUS, 62.7% were predicted as P/PL or benign/likely benign (B/LB) when assessed according to American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. CONCLUSION Our study demonstrates that when used separately or in conjunction with other evidence, tumour characteristics provide evidence for germline MMR missense variant assessment, which may have important implications for genetic testing and clinical management.
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Affiliation(s)
- Shuwei Li
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Dajun Qian
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Bryony A Thompson
- Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Sitao Wu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Tina Pesaran
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Holly LaDuca
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Mary Helen Black
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
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14
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Vaisfeld A, Calicchia M, Pomponi MG, Lucci-Cordisco E, Reggiani-Bonetti L, Genuardi M. Lynch syndrome with exclusive skin involvement: time to consider a molecular definition? Fam Cancer 2019; 18:421-427. [PMID: 31292797 DOI: 10.1007/s10689-019-00139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Muir-Torre syndrome (MTS) is clinically characterized by the occurrence of skin, usually sebaceous, and visceral tumors in the same individual. The most common underlying mechanism is a constitutional defect of the mismatch repair (MMR) genes that cause Lynch syndrome (LS). Herewithin we report on a 76 years-old male patient heterozygous for a pathogenic MSH2 missense substitution who presented with a striking cutaneous phenotype in the absence of typical LS visceral tumors. The patient developed 20 skin tumors, including sebaceous adenomas/carcinomas and keratoacanthomas. Two skin tumors showed immunohistochemical loss of MSH2 and MSH6 expression. There was no apparent family history of neoplasia. Based on the variable involvement of the skin and internal organs, we suggest that the definition of tumor associations that are often observed as variants of inherited tumor syndromes, such as MTS, should be guided by the underlying molecular bases. In addition, the presence of multiple sebaceous tumors, especially if showing MMR deficiency, appears to be a very strong indicator of a constitutional MMR gene defect. The reasons underlying the high phenotypic variability of cutaneous phenotypes associated with constitutional MMR defects are yet to be determined.
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Affiliation(s)
- Alessandro Vaisfeld
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Genetica Medica, Rome, Italy.,Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Martina Calicchia
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria Grazia Pomponi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Genetica Medica, Rome, Italy
| | - Emanuela Lucci-Cordisco
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Genetica Medica, Rome, Italy.,Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luca Reggiani-Bonetti
- Dipartimento di Medicina di Laboratorio e Anatomia Patologica, Università di Modena e Reggio Emilia, Modena, Italy
| | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Genetica Medica, Rome, Italy. .,Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy.
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15
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Lessons learned from two decades of BRCA1 and BRCA2 genetic testing: the evolution of data sharing and variant classification. Genet Med 2019; 21:1476-1480. [PMID: 30474649 PMCID: PMC9936330 DOI: 10.1038/s41436-018-0370-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/06/2018] [Indexed: 02/02/2023] Open
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Abstract
Radiomic features based classifiers and neural networks have shown promising results in tumor classification. The classification performance can be further improved greatly by exploring and incorporating the discriminative features towards cancer into mathematical models. In this research work, we have developed two radiomics driven likelihood models in Computed Tomography(CT) images to classify lung, colon, head and neck cancer. Initially, two diagnostic radiomic signatures were derived by extracting 105 3-D features from 200 lung nodules and by selecting the features with higher average scores from several supervised as well as unsupervised feature ranking algorithms. The signatures obtained from both the ranking approaches were integrated into two mathematical likelihood functions for tumor classification. Validation of the likelihood functions was performed on 265 public data sets of lung, colon, head and neck cancer with high classification rate. The achieved results show robustness of the models and suggest that diagnostic mathematical functions using general tumor phenotype can be successfully developed for cancer diagnosis.
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17
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Valle L, Vilar E, Tavtigian SV, Stoffel EM. Genetic predisposition to colorectal cancer: syndromes, genes, classification of genetic variants and implications for precision medicine. J Pathol 2019; 247:574-588. [PMID: 30584801 PMCID: PMC6747691 DOI: 10.1002/path.5229] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Abstract
This article reviews genes and syndromes associated with predisposition to colorectal cancer (CRC), with an overview of gene variant classification. We include updates on the application of preventive and therapeutic measures, focusing on the use of non-steroidal anti-inflammatory drugs (NSAIDs) and immunotherapy. Germline pathogenic variants in genes conferring high or moderate risk to cancer are detected in 6-10% of all CRCs and 20% of those diagnosed before age 50. CRC syndromes can be subdivided into nonpolyposis and polyposis entities, the most common of which are Lynch syndrome and familial adenomatous polyposis, respectively. In addition to known and novel genes associated with highly penetrant CRC risk, identification of pathogenic germline variants in genes associated with moderate-penetrance cancer risk and/or hereditary cancer syndromes not traditionally linked to CRC may have an impact on genetic testing, counseling, and surveillance. The use of multigene panels in genetic testing has exposed challenges in the classification of variants of uncertain significance. We provide an overview of the main classification systems and strategies for improving these. Finally, we highlight approaches for integrating chemoprevention in the care of individuals with genetic predisposition to CRC and use of targeted agents and immunotherapy for treatment of mismatch repair-deficient and hypermutant tumors. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Eduardo Vilar
- Departments of Clinical Cancer Prevention, GI Medical Oncology and Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Elena M. Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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18
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Rañola JMO, Liu Q, Rosenthal EA, Shirts BH. A comparison of cosegregation analysis methods for the clinical setting. Fam Cancer 2019; 17:295-302. [PMID: 28695303 DOI: 10.1007/s10689-017-0017-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative cosegregation analysis can help evaluate the pathogenicity of genetic variants. However, genetics professionals without statistical training often use simple methods, reporting only qualitative findings. We evaluate the potential utility of quantitative cosegregation in the clinical setting by comparing three methods. One thousand pedigrees each were simulated for benign and pathogenic variants in BRCA1 and MLH1 using United States historical demographic data to produce pedigrees similar to those seen in the clinic. These pedigrees were analyzed using two robust methods, full likelihood Bayes factors (FLB) and cosegregation likelihood ratios (CSLR), and a simpler method, counting meioses. Both FLB and CSLR outperform counting meioses when dealing with pathogenic variants, though counting meioses is not far behind. For benign variants, FLB and CSLR greatly outperform as counting meioses is unable to generate evidence for benign variants. Comparing FLB and CSLR, we find that the two methods perform similarly, indicating that quantitative results from either of these methods could be combined in multifactorial calculations. Combining quantitative information will be important as isolated use of cosegregation in single families will yield classification for less than 1% of variants. To encourage wider use of robust cosegregation analysis, we present a website ( http://www.analyze.myvariant.org ) which implements the CSLR, FLB, and Counting Meioses methods for ATM, BRCA1, BRCA2, CHEK2, MEN1, MLH1, MSH2, MSH6, and PMS2. We also present an R package, CoSeg, which performs the CSLR analysis on any gene with user supplied parameters. Future variant classification guidelines should allow nuanced inclusion of cosegregation evidence against pathogenicity.
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Affiliation(s)
- John Michael O Rañola
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA.
| | - Quanhui Liu
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98105, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA
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Gong H, Cheng W, Wang Y. Tumor necrosis factor-related apoptosis-inducing ligand inhibits the growth and aggressiveness of colon carcinoma via the exogenous apoptosis signaling pathway. Exp Ther Med 2019; 17:41-50. [PMID: 30651763 PMCID: PMC6307519 DOI: 10.3892/etm.2018.6901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/15/2018] [Indexed: 12/26/2022] Open
Abstract
Colon cancer is one of the most common types of gastrointestinal tumor. Previous studies have demonstrated that tumor necrosis factor-(TNF)-related apoptosis-inducing ligand (TRAIL) reduces the aggressiveness of colon cancer tumors and promotes the apoptosis of colon carcinoma cells. In the present study, the inhibitory effects of TRAIL were investigated and the potential mechanism of TRAIL-mediated apoptosis was explored in colon cancer cells. Reverse transcription-quantitative polymerase chain reaction, western blotting, immunofluorescence, immunohistochemistry, TUNEL and flow cytometry assays were used to analyze the effects of TRAIL on the growth, migration, invasion and apoptosis of colon tumor cells. In vivo experiments were performed in mice to analyze the therapeutic effects of TRAIL. The results demonstrated that TRAIL significantly suppressed the growth of colorectal tumor cells in a dose-dependent manner (0.5–2.5 mg/ml) and also promoted colon tumor cell death. The migration and invasion of colon tumor cells were inhibited by the downregulation of fibronectin, Vimentin and E-cadherin. The apoptotic rate revealed that TRAIL (2.0 mg/ml) significantly promoted the apoptosis of colon tumor cells by regulating apoptosis-related gene expression. TRAIL administration promoted the apoptosis of colon tumor cells via the exogenous apoptosis signaling pathway due to the upregulation of caspase-3, caspase-8 and nuclear factor-κB protein expression. In vivo assays revealed that TRAIL administration significantly inhibited tumor growth and promoted apoptotic body and lymphocyte infiltration, which led to increased survival in tumor-bearing mice compared with the control group. Immunohistochemistry revealed that P53 and B-cell lymphoma-2 were downregulated in TRAIL-treated tumors. In conclusion, TRAIL treatment significantly inhibited the growth and aggressiveness of colon tumors by inducing apoptosis via the exogenous apoptosis pathway, which suggests that TRAIL may be a potential anticancer agent for colon carcinoma therapy.
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Affiliation(s)
- Hongyan Gong
- Department of General Surgery, Yantaishan Hospital, Yantai, Shandong 264000, P.R. China
| | - Weicai Cheng
- Department of General Surgery, Yantaishan Hospital, Yantai, Shandong 264000, P.R. China
| | - Yong Wang
- Department of General Surgery, Yantaishan Hospital, Yantai, Shandong 264000, P.R. China
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20
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Makhnoon S, Shirts BH, Bowen DJ. Patients' perspectives of variants of uncertain significance and strategies for uncertainty management. J Genet Couns 2019; 28:313-325. [PMID: 30636062 DOI: 10.1002/jgc4.1075] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 12/24/2022]
Abstract
Variants of uncertain significance (VUS) are a well-recognized source of uncertainty in genomic medicine. Despite the existence of straightforward clinical management recommendations, patients report feeling anxiety, worry, and uncertainty in response to VUS. We report the first structured analysis of patient perspectives of VUS-related uncertainty in genome sequencing using Han's taxonomy of genomic uncertainty. We conducted in-depth semi-structured interviews with 11 patients to elicit their thoughts regarding implications of the result for themselves and their family members. Patients' primary concern with VUS-related uncertainty involved personal and practical issues as they directly inform health-care decisions. Patients demonstrated good understanding of the epistemic nature of VUS uncertainty-that information about such variant is currently unknown. However, between-provider discordance in explanations of the implication of this uncertainty for patients' diagnosis, prognosis, and therapy was a major contributor to the overall experience of uncertainty. Strategies for uncertainty reduction involved periodically checking back for reclassification and receiving concordant and clear recommendation from providers. Other proactive strategies of uncertainty reduction-such as information seeking and reading the genetic test report-were not helpful. Collectively, these findings offer previously unreported insight into uncertainty management strategies used by patients which have the potential to guide clinical management practices.
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Affiliation(s)
- Sukh Makhnoon
- Institute of Public Health Genetics, University of Washington, Seattle, Washington
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Deborah J Bowen
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington
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21
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A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome. Genet Med 2018; 21:1486-1496. [PMID: 30504929 DOI: 10.1038/s41436-018-0372-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/07/2018] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data. METHODS Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay. The assay was calibrated by regression analysis followed by symmetric cross-validation and Bayesian integration with in silico predictions of pathogenicity. CIMRA assay reproducibility was assessed in four laboratories. RESULTS Concordance between the training runs met our prespecified validation criterion. The CIMRA assay alone correctly classified 65% of variants, with only 3% discordant classification. Bayesian integration with in silico predictions of pathogenicity increased the proportion of correctly classified variants to 87%, without changing the discordance rate. Interlaboratory results were highly reproducible. CONCLUSION The CIMRA assay accurately predicts pathogenic and benign MMR gene variants. Quantitative combination of assay results with in silico analysis correctly classified the majority of variants. Using this calibration, CIMRA assay results can be integrated into the diagnostic algorithm for MMR gene variants.
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22
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Outcomes of 92 patient-driven family studies for reclassification of variants of uncertain significance. Genet Med 2018; 21:1435-1442. [PMID: 30374176 DOI: 10.1038/s41436-018-0335-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/28/2018] [Indexed: 01/30/2023] Open
Abstract
PURPOSE Family studies are an important but underreported source of information for reclassification of variants of uncertain significance (VUS). We evaluated outcomes of a patient-driven framework that offered familial VUS reclassification analysis to any adult with any clinically ascertained VUS from any laboratory in the United States. METHODS With guidance from FindMyVariant.org, participants recruited their own relatives for study participation. We genotyped relatives, calculated quantitative cosegregation likelihood ratios, and evaluated variant classifications using Tavtigian's unified framework for Bayesian analysis with American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria. We report participation and VUS reclassification rates from the 50 families enrolled for at least one year and reclassification results for 112 variants from the larger 92-family cohort. RESULTS For the 50-family cohort, 6.7 relatives per family were invited to participate and 67% of relatives returned samples for genotyping. Sixty-one percent of VUS were reclassified, 84% of which were classified as benign or likely benign. Genotyping relatives identified a de novo variant, phase variants, and relatives with phenotypes highly specific for or incompatible with specific classifications. CONCLUSIONS Motivated families can contribute to successful VUS reclassification at substantially higher rates than those previously published. Clinical laboratories could consider offering family studies to all patients with VUS.
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23
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A Bayesian framework for efficient and accurate variant prediction. PLoS One 2018; 13:e0203553. [PMID: 30212499 PMCID: PMC6136750 DOI: 10.1371/journal.pone.0203553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
There is a growing need to develop variant prediction tools capable of assessing a wide spectrum of evidence. We present a Bayesian framework that involves aggregating pathogenicity data across multiple in silico scores on a gene-by-gene basis and multiple evidence statistics in both quantitative and qualitative forms, and performs 5-tiered variant classification based on the resulting probability credible interval. When evaluated in 1,161 missense variants, our gene-specific in silico model-based meta-predictor yielded an area under the curve (AUC) of 96.0% and outperformed all other in silico predictors. Multifactorial model analysis incorporating all available evidence yielded 99.7% AUC, with 22.8% predicted as variants of uncertain significance (VUS). Use of only 3 auto-computed evidence statistics yielded 98.6% AUC with 56.0% predicted as VUS, which represented sufficient accuracy to rapidly assign a significant portion of VUS to clinically meaningful classifications. Collectively, our findings support the use of this framework to conduct large-scale variant prioritization using in silico predictors followed by variant prediction and classification with a high degree of predictive accuracy.
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24
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Tavtigian SV, Greenblatt MS, Harrison SM, Nussbaum RL, Prabhu SA, Boucher KM, Biesecker LG. Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework. Genet Med 2018; 20:1054-1060. [PMID: 29300386 PMCID: PMC6336098 DOI: 10.1038/gim.2017.210] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/13/2017] [Indexed: 02/05/2023] Open
Abstract
PURPOSE We evaluated the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines for internal consistency and compatibility with Bayesian statistical reasoning. METHODS The ACMG/AMP criteria were translated into a naive Bayesian classifier, assuming four levels of evidence and exponentially scaled odds of pathogenicity. We tested this framework with a range of prior probabilities and odds of pathogenicity. RESULTS We modeled the ACMG/AMP guidelines using biologically plausible assumptions. Most ACMG/AMP combining criteria were compatible. One ACMG/AMP likely pathogenic combination was mathematically equivalent to pathogenic and one ACMG/AMP pathogenic combination was actually likely pathogenic. We modeled combinations that include evidence for and against pathogenicity, showing that our approach scored some combinations as pathogenic or likely pathogenic that ACMG/AMP would designate as variant of uncertain significance (VUS). CONCLUSION By transforming the ACMG/AMP guidelines into a Bayesian framework, we provide a mathematical foundation for what was a qualitative heuristic. Only 2 of the 18 existing ACMG/AMP evidence combinations were mathematically inconsistent with the overall framework. Mixed combinations of pathogenic and benign evidence could yield a likely pathogenic, likely benign, or VUS result. This quantitative framework validates the approach adopted by the ACMG/AMP, provides opportunities to further refine evidence categories and combining rules, and supports efforts to automate components of variant pathogenicity assessments.
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Affiliation(s)
- Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont Robert Larner, MD, College of Medicine, Burlington, Vermont, USA
| | - Steven M Harrison
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Snehit A Prabhu
- Department of Genetics and Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Kenneth M Boucher
- Division of Epidemiology and Huntsman Cancer Institute, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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25
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Shirts BH, Konnick EQ, Upham S, Walsh T, Ranola JMO, Jacobson AL, King MC, Pearlman R, Hampel H, Pritchard CC. Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes. Am J Hum Genet 2018; 103:19-29. [PMID: 29887214 DOI: 10.1016/j.ajhg.2018.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023] Open
Abstract
Present guidelines for classification of constitutional variants do not incorporate inferences from mutations seen in tumors, even when these are associated with a specific molecular phenotype. When somatic mutations and constitutional mutations lead to the same molecular phenotype, as for the mismatch repair genes, information from somatic mutations may enable interpretation of previously unclassified variants. To test this idea, we first estimated likelihoods that somatic variants in MLH1, MSH2, MSH6, and PMS2 drive microsatellite instability and characteristic IHC staining patterns by calculating likelihoods of high versus low normalized variant read fractions of 153 mutations known to be pathogenic versus those of 760 intronic passenger mutations from 174 paired tumor-normal samples. Mutations that explained the tumor mismatch repair phenotype had likelihood ratio for high variant read fraction of 1.56 (95% CI 1.42-1.71) at sites with no loss of heterozygosity and of 26.5 (95% CI 13.2-53.0) at sites with loss of heterozygosity. Next, we applied these ratios to 165 missense, synonymous, and splice variants observed in tumors, combining in a Bayesian analysis the likelihood ratio corresponding with the adjusted variant read fraction with pretest probabilities derived from published analyses and public databases. We suggest classifications for 86 of 165 variants: 7 benign, 31 likely benign, 22 likely pathogenic, and 26 pathogenic. These results illustrate that for mismatch repair genes, characterization of tumor mutations permits tumor mutation data to inform constitutional variant classification. We suggest modifications to incorporate molecular phenotype in future variant classification guidelines.
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Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah Upham
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Angela L Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Pearlman
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Heather Hampel
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
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26
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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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27
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RNA analysis of cancer predisposing genes in formalin-fixed paraffin-embedded tissue determines aberrant splicing. Eur J Hum Genet 2018; 26:1143-1150. [PMID: 29706640 DOI: 10.1038/s41431-018-0153-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 03/20/2018] [Accepted: 03/30/2018] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing efforts in molecular tumour diagnostics detect increasing numbers of novel variants, including variants predicted to affect splicing. In silico prediction tools can reliably predict the effect of variant disrupting canonical splice sites; however, experimental validation is required to confirm aberrant splicing. Here, we present RNA analysis performed for 13 canonical splice site variants predicted or known to result in splicing in the cancer predisposition genes MLH1, MSH2, MSH6, APC and BRCA1. Total nucleic acid was successfully isolated for 10 variants from eight formalin-fixed paraffin-embedded (FFPE) tumour tissues and two B-cell lines. Aberrant splicing was confirmed in all six variants known to result in splicing. Of one known variant in the B-cell line, aberrant splicing could only be detected after formalin fixation, which indicated that formalin fixation could possibly inhibit RNA degradation. Aberrant splicing was concluded in three of four predicted splice variants of uncertain significance, supporting their pathogenic effect. With this assay, somatic splice variants can be easily and rapidly analysed, enabling retrospective analysis to support the pathogenicity of variants predicted to result in splicing when only FFPE material is available.
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28
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Jenkins MA, Win AK, Templeton AS, Angelakos MS, Buchanan DD, Cotterchio M, Figueiredo JC, Thibodeau SN, Baron JA, Potter JD, Hopper JL, Casey G, Gallinger S, Le Marchand L, Lindor NM, Newcomb PA, Haile RW. Cohort Profile: The Colon Cancer Family Registry Cohort (CCFRC). Int J Epidemiol 2018; 47:387-388i. [PMID: 29490034 PMCID: PMC5913593 DOI: 10.1093/ije/dyy006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 01/02/2023] Open
Affiliation(s)
- Mark A Jenkins
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Allyson S Templeton
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maggie S Angelakos
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Oncogenomics Group, University of Melbourne, Parkville, VIC, Australia
| | | | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, and Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Robert W Haile
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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29
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You S, Li W, Guan Y. Tunicamycin inhibits colon carcinoma growth and aggressiveness via modulation of the ERK-JNK-mediated AKT/mTOR signaling pathway. Mol Med Rep 2018; 17:4203-4212. [PMID: 29344654 PMCID: PMC5802191 DOI: 10.3892/mmr.2018.8444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 07/05/2017] [Indexed: 12/21/2022] Open
Abstract
Epidemiology and evidence have demonstrated that colon carcinoma is one of the most common gastrointestinal tumors in the clinic. Reports have suggested that Tunicamycin significantly inhibits aggressiveness of colon carcinoma cells by promotion of apoptosis. In the present study, the inhibitory effect of tunicamycin on colon cancer cells and the potential underlying molecular mechanism was investigated. Western blotting, immunohistochemistry, apoptotic assays and immunofluorescence were used to analyze the therapeutic effects of tunicamycin on apoptosis, growth, aggressiveness and cell cycle of colon tumor cells, by downregulation of fibronectin, vimentin and E‑cadherin expression levels. In vitro experiments demonstrated that tunicamycin significantly inhibited growth, migration and invasion of colon carcinoma cells. In addition, tunicamycin administration promoted apoptosis of colon carcinoma cells via upregulation of apoptotic protease activating factor 1 and cytochrome c expression levels, which are proteins that have a role in mitochondrial apoptosis signaling. Cell cycle assays revealed that tunicamycin suppressed proliferation and arrested S phase entry of colon carcinoma cells. Mechanistic analysis demonstrated that tunicamycin reduced expression and phosphorylation levels of extracellular signal‑regulated kinase (ERK), c‑JUN N‑terminal kinase (JNK) and protein kinase B (AKT), and inhibited mammalian target of rapamycin (mTOR) expression levels in colon carcinoma cells. Endogenous overexpression of ERK inhibited tunicamycin‑mediated downregulation of JNK, AKT and mTOR expression, which further blocked tunicamycin‑mediated inhibition of growth and aggressiveness of colon carcinoma. In vivo assays revealed that tunicamycin treatment significantly inhibited tumor growth and promoted apoptosis, which led to long‑term survival of tumor‑bearing mice compared with the control group. In conclusion, these results suggested that tunicamycin may inhibit growth and aggressiveness of colon cancer via the ERK‑JNK‑mediated AKT/mTOR signaling pathway, and suggested that tunicamycin may be a potential anti‑cancer agent for colon carcinoma therapy.
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Affiliation(s)
- Shuping You
- Department of Anus and Bowel Surgery, Jingmen No. 2 People's Hospital, Jingmen, Hubei 448000, P.R. China
| | - Weihong Li
- Department of Anus and Bowel Surgery, Jingmen No. 2 People's Hospital, Jingmen, Hubei 448000, P.R. China
| | - Yun Guan
- Department of Anus and Bowel Surgery, Jingmen No. 2 People's Hospital, Jingmen, Hubei 448000, P.R. China
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30
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Wang Q, Wang P, Xiao Z. Resistant starch prevents tumorigenesis of dimethylhydrazine-induced colon tumors via regulation of an ER stress-mediated mitochondrial apoptosis pathway. Int J Mol Med 2018; 41:1887-1898. [PMID: 29393371 PMCID: PMC5810243 DOI: 10.3892/ijmm.2018.3423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/12/2018] [Indexed: 12/11/2022] Open
Abstract
Resistant starch is as common soluble fiber that escapes digestion in the small intestine and can regulate intestinal function, metabolism of blood glucose and lipids, and may prevent tumorigenesis of gastrointestinal cancer. Epidemiology and other evidence have suggested that resistant starch may prevent colon cancer development. The aim of the current study was to explore the ameliorative effects and potential mechanisms of resistant starch in the tumorigenesis of colon tumors induced by dimethylhydrazine in C57BL/6 mice. Western blot analysis, ELISA, microscopy, immunofluorescence and immunohistochemistry were used to analyze the efficacy of resistant starch on the metabolic balance in the colon and tumorigenesis of colon tumors. The results demonstrated that a diet containing resistant starch decreased the animal body weight and reduced free ammonia, pH and short chain fatty acids in feces compared with mice that received a standard diet. Resistant starch reduced the incidence of colon tumors and suppressed the expression of carcinogenesis-associated proteins, including heat shock protein 25, protein kinase C-d and gastrointestinal glutathione peroxidase in colon epithelial cells compared with standard starch and control groups. Colon tumor cells proliferation and dedifferentiation were significantly decreased by a resistant starch diet. The results also demonstrated that resistant starch increased the apoptosis of colon tumor cells through regulation of apoptosis-associated gene expression levels in colon tumor cells. Oxidative stress and endoplasmic reticulum stress were upregulated, and elevation eukaryotic translation initiation factor 2α (eIF2α), activating transcription factor-4 and secretase-β expression levels were increased in the resistant starch diet group. Additionally, the activity of eIF2α and PERK were increased in colon tumor cells from mice that had received resistant starch. Increasing DNA damage-inducible transcript 3 protein (CHOP), binding immunoglobulin protein (BIP) and caspase-12 expression levels upregulated by resistant starch diet may contribute to the resistant starch-induced apoptosis of colon tumor cells induced by 1,2-dimethylhydrazine. In vitro assays demonstrated that knockdown of eIF2α inhibited apoptosis of colon tumor cells isolated from mice fed with resistant starch, which also downregulated CHOP, BIP and caspase-3 expression levels compared with controls. Furthermore, long-term survival of experimental mice was prolonged by the resistant starch diet compared with the standard diet group. In conclusion, the results indicate that resistant starch in the diet may prevent carcinogenesis of colon epithelial cells, mediated by enhancing apoptosis through an endoplasmic reticulum stress-mediated mitochondrial apoptosis pathway.
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Affiliation(s)
- Qiuyu Wang
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, P.R. China
| | - Peng Wang
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, P.R. China
| | - Zhigang Xiao
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, P.R. China
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31
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Lorans M, Dow E, Macrae FA, Winship IM, Buchanan DD. Update on Hereditary Colorectal Cancer: Improving the Clinical Utility of Multigene Panel Testing. Clin Colorectal Cancer 2018; 17:e293-e305. [PMID: 29454559 DOI: 10.1016/j.clcc.2018.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the most common cancers, is a major public health issue globally, especially in Westernized countries. Up to 35% of CRCs are thought to be due to heritable factors, but currently only 5% to 10% of CRCs are attributable to high-risk mutations in known CRC susceptibility genes, predominantly the mismatch repair genes (Lynch syndrome) and adenomatous polyposis coli gene (APC; familial adenomatous polyposis). In this era of precision medicine, high-risk mutation carriers, when identified, can be offered various risk management options that prevent cancers and improve survival, including risk-reducing medication, screening for early detection, and surgery. The practice of clinical genetics is currently transitioning from phenotype-directed single gene testing to multigene panels, now offered by numerous providers. For CRC, the genes included across these panels vary, ranging from well established, clinically actionable susceptibility genes with quantified magnitude of risk, to genes that lack extensive validation or have less evidence of association with CRC and, therefore, have minimal clinical utility. The current lack of consensus regarding inclusion of genes in CRC panels presents challenges in patient counseling and management, particularly when a variant in a less validated gene is identified. Furthermore, there remain considerable challenges regarding variant interpretation even for the well established CRC susceptibility genes. Ironically though, only through more widespread testing and the accumulation of large international data sets will sufficient information be generated to (i) enable well powered studies to determine if a gene is associated with CRC susceptibility, (ii) to develop better models for variant interpretation and (iii) to facilitate clinical translation.
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Affiliation(s)
- Marie Lorans
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eryn Dow
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Finlay A Macrae
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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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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33
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Niroula A, Vihinen M. PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat 2017; 38:1085-1091. [PMID: 28224672 DOI: 10.1002/humu.23199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/25/2017] [Accepted: 02/17/2017] [Indexed: 01/14/2023]
Abstract
Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed toward the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools. These areas include collection and distribution of benchmark datasets, their use for systematic large-scale method assessment, and the development of guidelines for reporting methods and their performance. For us, CAGI has provided a chance to experiment with new ideas, test the application areas of our methods, and network with other prediction method developers. In this article, we discuss our experiences and lessons learned from the various CAGI challenges. We describe our approaches, their performance, and impact of CAGI on our research. Finally, we discuss some of the possibilities that CAGI experiments have opened up and make some suggestions for future experiments.
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Affiliation(s)
- Abhishek Niroula
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mauno Vihinen
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
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González-Acosta M, Del Valle J, Navarro M, Thompson BA, Iglesias S, Sanjuan X, Paúles MJ, Padilla N, Fernández A, Cuesta R, Teulé À, Plotz G, Cadiñanos J, de la Cruz X, Balaguer F, Lázaro C, Pineda M, Capellá G. Elucidating the clinical significance of two PMS2 missense variants coexisting in a family fulfilling hereditary cancer criteria. Fam Cancer 2017; 16:501-507. [PMID: 28365877 DOI: 10.1007/s10689-017-9981-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The clinical spectrum of germline mismatch repair (MMR) gene variants continues increasing, encompassing Lynch syndrome, Constitutional MMR Deficiency (CMMRD), and the recently reported MSH3-associated polyposis. Genetic diagnosis of these hereditary cancer syndromes is often hampered by the presence of variants of unknown significance (VUS) and overlapping phenotypes. Two PMS2 VUS, c.2149G>A (p.V717M) and c.2444C>T (p.S815L), were identified in trans in one individual diagnosed with early-onset colorectal cancer (CRC) who belonged to a family fulfilling clinical criteria for hereditary cancer. Clinico-pathological data, multifactorial likelihood calculations and functional analyses were used to refine their clinical significance. Likelihood analysis based on cosegregation and tumor data classified the c.2444C>T variant as pathogenic, which was supported by impaired MMR activity associated with diminished protein expression in functional assays. Conversely, the c.2149G>A variant displayed MMR proficiency and protein stability. These results, in addition to the conserved PMS2 expression in normal tissues and the absence of germline microsatellite instability (gMSI) in the biallelic carrier ruled out a CMMRD diagnosis. The use of comprehensive strategies, including functional and clinico-pathological information, is mandatory to improve the clinical interpretation of naturally occurring MMR variants. This is critical for appropriate clinical management of cancer syndromes associated to MMR gene mutations.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - María José Paúles
- 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
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Raquel Cuesta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Guido Plotz
- Medical Clinic 1, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain.
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35
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Tricarico R, Kasela M, Mareni C, Thompson BA, Drouet A, Staderini L, Gorelli G, Crucianelli F, Ingrosso V, Kantelinen J, Papi L, De Angioletti M, Berardi M, Gaildrat P, Soukarieh O, Turchetti D, Martins A, Spurdle AB, Nyström M, Genuardi M. Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants. Hum Mutat 2016; 38:64-77. [PMID: 27629256 DOI: 10.1002/humu.23117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/04/2016] [Accepted: 09/09/2016] [Indexed: 01/15/2023]
Abstract
Pathogenicity assessment of DNA variants in disease genes to explain their clinical consequences is an integral component of diagnostic molecular testing. The International Society for Gastrointestinal Hereditary Tumors (InSiGHT) has developed specific criteria for the interpretation of mismatch repair (MMR) gene variants. Here, we performed a systematic investigation of 24 MLH1 and MSH2 variants. The assessments were done by analyzing population frequency, segregation, tumor molecular characteristics, RNA effects, protein expression levels, and in vitro MMR activity. Classifications were confirmed for 15 variants and changed for three, and for the first time determined for six novel variants. Overall, based on our results, we propose the introduction of some refinements to the InSiGHT classification rules. The proposed changes have the advantage of homogenizing the InSIGHT interpretation criteria with those set out by the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium for the BRCA1/BRCA2 genes. We also observed that the addition of only few clinical data was sufficient to obtain a more stable classification for variants considered as "likely pathogenic" or "likely nonpathogenic." This shows the importance of obtaining as many as possible points of evidence for variant interpretation, especially from the clinical setting.
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Affiliation(s)
- Rossella Tricarico
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mariann Kasela
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | | | - Bryony A Thompson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Aurélie Drouet
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Lucia Staderini
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Greta Gorelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Francesca Crucianelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Valentina Ingrosso
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Jukka Kantelinen
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Maria De Angioletti
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy.,ICCOM-CNR, Sesto Fiorentino, Italy
| | - Margherita Berardi
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy
| | - Pascaline Gaildrat
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Omar Soukarieh
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Daniela Turchetti
- Medical Genetics, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alexandra Martins
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Minna Nyström
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Institute of Genomic Medicine, A. Gemelli School of Medicine, Medical Genetics Unit, Catholic University of the Sacred Heart, Rome, Italy
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36
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Wang G, Gu J, Gao Y. MicroRNA target for MACC1 and CYR61 to inhibit tumor growth in mice with colorectal cancer. Tumour Biol 2016; 37:13983-13993. [PMID: 27492459 DOI: 10.1007/s13277-016-5252-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/15/2016] [Indexed: 12/30/2022] Open
Abstract
Cysteine-rich protein 61 (CYR61) and metastasis associated in colon cancer (MACC1) protein promoted human colorectal cancer (CRC) cell metastasis and closely related to the patient's prognosis in colorectal cancer. The purpose of this article is to investigate whether CYR61 and MACC1 can serve as dual potential targets for gene therapy of human CRC. In this study, microRNA (miRNA) targeting for both CYR61 and MACC1 was used to investigate the mechanism and therapeutic effects for CRC cells and mice with CRC. We observed that silencing miRNA for CYR61 and MACC1 inhibited the epithelial-mesenchymal transition (EMT) process, and co-treatment strengthened this effect. MTT assay showed that the growth of colorectal tumor cells was decreased due to miRNA treatment. Apoptosis assay revealed that miRNA for CYR61 and MACC1 promoted CRC cells apoptotic. The animals' study results showed that the expression levels of CYR61 and MACC1 were significantly decreased after miRNA-100 and miRNA-143 treatment, respectively. The expression levels of apoptosis-promoting protein were increased significantly after treatment with miRNA-100 and miRNA-143, which suggested that both miRNA-100 and miRNA-143 may induce apoptosis by mitochondria-dependent pathway. In addition, metastasis and invasion assays showed that miRNA-100 and miRNA-143 treatment inhibited obviously migratory and invasive abilities of CRC cells. Furthermore, our data also showed that the tumor growth was significantly inhibited and survival rate of tumor-bearing mice was greatly improved by common treatments of miRNA-100 and miRNA-143. In conclusion, the abilities of apoptosis, metastasis, and invasion in CRC tumor cells were significantly suppressed by miRNA-100 and miRNA-143 targeting CYR61 and MACC1, respectively. As a result, CYR61 and MACC1 may serve as potential targets for gene therapy in human CRC treatments.
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Affiliation(s)
- Guiqi Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Hebei Medical University, No. 89, Donggang Road, Shijiazhuang, 050031, China
| | - Jingfeng Gu
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Hebei Medical University, No. 89, Donggang Road, Shijiazhuang, 050031, China.
| | - Yingchao Gao
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Hebei Medical University, No. 89, Donggang Road, Shijiazhuang, 050031, China
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37
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Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV. Multigene testing of moderate-risk genes: be mindful of the missense. J Med Genet 2016; 53:366-76. [PMID: 26787654 PMCID: PMC4893078 DOI: 10.1136/jmedgenet-2015-103398] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.
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Affiliation(s)
- E L Young
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - B J Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A W Stark
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Damiola
- Breast Cancer Genetics Group, Cancer Research Centre of Lyon, Centre Léon Bérard, Lyon, France
| | - G Durand
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Forey
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T C Francy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - W K Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - K A Kaphingst
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - S McKay-Chopin
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T Nguyen-Dumont
- Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - J Oliver
- Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - A M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Pertesi
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Robinot
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J S Rosenthal
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Vallee
- Cancer Genomics Laboratory, CHUQ Research Center, Quebec City, Canada
| | - C Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia Department of Epidemiology (Genome Epidemiology Lab), Seoul National University School of Public Health, Seoul, Korea
| | - M C Southey
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - I L Andrulis
- Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - E M John
- Cancer Prevention Institute of California, Fremont, California, USA Department of Health Research and Policy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - M Hashibe
- Department of Family and Preventive Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - J Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - F Lesueur
- Genetic Epidemiology of Cancer Team, Inserm, U900, Institut Curie, Paris, France
| | - D E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - S V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
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Novel Mutations in MLH1 and MSH2 Genes in Mexican Patients with Lynch Syndrome. Gastroenterol Res Pract 2016; 2016:5278024. [PMID: 27247567 PMCID: PMC4877485 DOI: 10.1155/2016/5278024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background. Lynch Syndrome (LS) is characterized by germline mutations in the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. This syndrome is inherited in an autosomal dominant pattern and is characterized by early onset colorectal cancer (CRC) and extracolonic tumors. The aim of this study was to identify mutations in MMR genes in three Mexican patients with LS. Methods. Immunohistochemical analysis was performed as a prescreening method to identify absent protein expression. PCR, Denaturing High Performance Liquid Chromatography (dHPLC), and Sanger sequencing complemented the analysis. Results. Two samples showed the absence of nuclear staining for MLH1 and one sample showed loss of nuclear staining for MSH2. The mutations found in MLH1 gene were c.2103+1G>C in intron 18 and compound heterozygous mutants c.1852_1854delAAG (p.K618del) and c.1852_1853delinsGC (p.K618A) in exon 16. In the MSH2 gene, we identified mutation c.638dupT (p.L213fs) in exon 3. Conclusions. This is the first report of mutations in MMR genes in Mexican patients with LS and these appear to be novel.
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39
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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40
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Niroula A, Vihinen M. Variation Interpretation Predictors: Principles, Types, Performance, and Choice. Hum Mutat 2016; 37:579-97. [DOI: 10.1002/humu.22987] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
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41
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Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
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42
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Moghadasi S, Eccles DM, Devilee P, Vreeswijk MPG, van Asperen CJ. Classification and Clinical Management of Variants of Uncertain Significance in High Penetrance Cancer Predisposition Genes. Hum Mutat 2016; 37:331-6. [PMID: 26777316 DOI: 10.1002/humu.22956] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/13/2015] [Indexed: 11/12/2022]
Abstract
In 2008, the International Agency for Research on Cancer (IARC) proposed a system for classifying sequence variants in highly penetrant breast and colon cancer susceptibility genes, linked to clinical actions. This system uses a multifactorial likelihood model to calculate the posterior probability that an altered DNA sequence is pathogenic. Variants between 5%-94.9% (class 3) are categorized as variants of uncertain significance (VUS). This interval is wide and might include variants with a substantial difference in pathogenicity at either end of the spectrum. We think that carriers of class 3 variants would benefit from a fine-tuning of this classification. Classification of VUS to a category with a defined clinical significance is very important because for carriers of a pathogenic mutation full surveillance and risk-reducing surgery can reduce cancer incidence. Counselees who are not carriers of a pathogenic mutation can be discharged from intensive follow-up and avoid unnecessary risk-reducing surgery. By means of examples, we show how, in selected cases, additional data can lead to reclassification of some variants to a different class with different recommendations for surveillance and therapy. To improve the clinical utility of this classification system, we suggest a pragmatic adaptation to clinical practice.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2333 ZA, The Netherlands
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333 ZC, The Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333 ZC, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2333 ZA, The Netherlands
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43
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Niroula A, Vihinen M. PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations. Nucleic Acids Res 2016; 44:2020-7. [PMID: 26843426 PMCID: PMC4797295 DOI: 10.1093/nar/gkw046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.
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Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
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44
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Luo J, Xu L, Jiang Y, Zhuo D, Zhang S, Wu L, Xu H, Huang Y. Expression profile of long non-coding RNAs in colorectal cancer: A microarray analysis. Oncol Rep 2016; 35:2035-44. [PMID: 26847923 DOI: 10.3892/or.2016.4606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/16/2015] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignant tumors and the second cause of cancer-related mortality worldwide. Due to increased morbidity and mortality rates, there is an urgent need to understand the pathogenesis of CRC, discover strategies that can improve diagnosis, and ultimately identify therapies targeting this disease. Over the past several years, research into tumor progression mechanisms has been devoted to identifying and understanding various coding and non-coding regions of the genome and how these genetic variants may affect tumorigenesis and progression. Recently, long non-coding RNAs (lncRNAs), which are non‑protein coding transcripts longer than 200 nucleotides, have emerged as a key aspect in tumor pathogenesis. In the present study, we examined the lncRNA and mRNA expression profiles in 4 patients with colon adenocarcinoma, with paired adjacent normal tissues as controls. Microarray data showed that a total of 3,523 lncRNAs and 2,515 mRNAs were consistently differentially expressed in the CRC tissues compared to adjacent normal tissues. Upon comparison of the differentially expressed transcripts between the groups, we identified 22 pathways which were related to the upregulated transcripts and 24 pathways that corresponded to the downregulated transcripts. Gene ontology analysis revealed that the upregulated transcripts were predominantly enriched in DNA metabolic processes, and the downregulated transcripts were predominantly enriched in organic hydroxyl compound metabolic processes. Coding-non-coding gene co-expression analysis showed that these differentially expressed lncRNAs were closely correlated with 'Wnt signaling pathway' components, whose aberrant activation plays a central role in CRC, indicating that a functional correlation exists between them. In conclusion, the results of the microarray and informatic analysis strongly suggest that lncRNA dysregulation is involved in the complicated process of CRC development, and may represent a novel class of diagnostic markers or therapeutic targets for CRC.
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Affiliation(s)
- Jia Luo
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Luning Xu
- Department of Pharmacy, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Yigui Jiang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Dexiang Zhuo
- Department of Clinical Laboratory, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Shengjun Zhang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Lianhui Wu
- Department of Endoscopy, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Huadong Xu
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Yue Huang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
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45
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Liu Q, Hesson LB, Nunez AC, Packham D, Williams R, Ward RL, Sloane MA. A cryptic paracentric inversion of MSH2 exons 2-6 causes Lynch syndrome. Carcinogenesis 2015; 37:10-17. [PMID: 26498247 DOI: 10.1093/carcin/bgv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome is an autosomal dominant disorder that predisposes carriers of DNA mismatch repair (MMR) gene mutations to early-onset cancer. Germline testing screens exons and splice sites for mutations, but does not examine introns or RNA transcripts for alterations. Pathogenic mutations have not been detected in ~30% of suspected Lynch syndrome cases with standard screening practices. We present a 38-year-old male with a clinicopathological and family history consistent with Lynch syndrome, including loss of MSH2 expression in his tumor. Germline testing revealed normal MSH2 coding sequence, splice sites and exon copy number, however, cDNA sequencing identified an aberrant MSH2 transcript lacking exons 2-6. An inversion PCR on germline DNA identified an ~18kb unbalanced, paracentric inversion within MSH2, with breakpoints in a long terminal repeat in intron 1 and an Alu repeat in intron 6. The 3' end of the inversion had a 1.2 kb deletion and an 8 bp insertion at the junction with intron 6. Screening of 55 additional Australian patients presenting with MSH2-deficient tumors who were negative in germline genetic tests for MSH2 mutations identified another inversion-positive patient. We propose an Alu-mediated recombination model to explain the origin of the inversion. Our study illustrates the potential value of cDNA screening to identify patients with cryptic MMR gene rearrangements, clarifies why standard testing may not detect some pathogenic alterations, and provides a genetic test for screening individuals with suspected Lynch syndrome that present with unexplained MSH2-deficient tumors.
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Affiliation(s)
- Qing Liu
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Luke B Hesson
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Andrea C Nunez
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Deborah Packham
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Rachel Williams
- Hereditary Cancer Clinic , Prince of Wales Hospital , Randwick, New South Wales 2031 , Australia and
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney New South Wales 2052, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mathew A Sloane
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
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46
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47
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Maresca L, Spugnesi L, Lodovichi S, Cozzani C, Naccarato AG, Tancredi M, Collavoli A, Falaschi E, Rossetti E, Aretini P, Cervelli T, Galli A, Caligo MA. MSH2 role in BRCA1-driven tumorigenesis: A preliminary study in yeast and in human tumors from BRCA1-VUS carriers. Eur J Med Genet 2015; 58:531-9. [PMID: 26381082 DOI: 10.1016/j.ejmg.2015.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 01/18/2023]
Abstract
BRCA1 interacts with several proteins implicated in homologous and non homologous recombination and in mismatch repair. The aim of this study is to determine if MSH2, a well known partner of BRCA1 involved in DNA repair, may contribute to breast and ovarian cancer development and progression. To better understand the functional interaction between BRCA1 and MSH2, we studied the effect of the deletion of MSH2 gene on BRCA1-induced genome instability in yeast. Preliminary results in yeast indicated that MSH2 and BRCA1 may interact to modulate homologous recombination (HR). We also carried out a genetic and epigenetic profiling of MSH2 gene by mutational analysis and promoter methylation evaluation in 9 breast and 2 ovarian tumors from carriers of BRCA1 unknown significance variants (VUS). 2/2 ovarian and 2/9 breast tumors carried MSH2 somatic mutations possible pathogenics (4/11, 36%): a missense mutation in exon 3 (p.G162R), a duplication of exon 1 and a deletion of exon 2. In addition, two germline synonymous variants in exon 11 were identified. None of the tumors showed promoter methylation. In conclusion, a surprisingly high frequency of MSH2 gene mutations has been found in tumor tissues from BRCA1 VUS carrier patients. This result supports the indication deriving from the yeast model that BRCA1 driven tumorigenesis may be modulated by MSH2.
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Affiliation(s)
- Luisa Maresca
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | - Laura Spugnesi
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Anita Collavoli
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Alvaro Galli
- Institute of Clinical Physiology, CNR, Pisa, Italy.
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48
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Microsatellite instability use in mismatch repair gene sequence variant classification. Genes (Basel) 2015; 6:150-62. [PMID: 25831438 PMCID: PMC4488658 DOI: 10.3390/genes6020150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/04/2015] [Accepted: 03/23/2015] [Indexed: 01/05/2023] Open
Abstract
Inherited mutations in the DNA mismatch repair genes (MMR) can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI) is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants) are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review.
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49
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Win AK, Buchanan AD, Rosty C, MacInnis RJ, Dowty JG, Dite GS, Giles GG, Southey MC, Young JP, Clendenning M, Walsh MD, Walters RJ, Boussioutas A, Smyrk TC, Thibodeau SN, Baron JA, Potter JD, Newcomb PA, Marchand LL, Haile RW, Gallinger S, Lindor NM, Hopper JL, Ahnen DJ, Jenkins MA. Role of tumour molecular and pathology features to estimate colorectal cancer risk for first-degree relatives. Gut 2015; 64:101-10. [PMID: 24615377 PMCID: PMC4180004 DOI: 10.1136/gutjnl-2013-306567] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To estimate risk of colorectal cancer (CRC) for first-degree relatives of CRC cases based on CRC molecular subtypes and tumour pathology features. DESIGN We studied a cohort of 33,496 first-degree relatives of 4853 incident invasive CRC cases (probands) who were recruited to the Colon Cancer Family Registry through population cancer registries in the USA, Canada and Australia. We categorised the first-degree relatives into four groups: 28,156 of 4095 mismatch repair (MMR)-proficient probands, 2302 of 301 MMR-deficient non-Lynch syndrome probands, 1799 of 271 suspected Lynch syndrome probands and 1239 of 186 Lynch syndrome probands. We compared CRC risk for first-degree relatives stratified by the absence or presence of specific tumour molecular pathology features in probands across each of these four groups and for all groups combined. RESULTS Compared with first-degree relatives of MMR-proficient CRC cases, a higher risk of CRC was estimated for first-degree relatives of CRC cases with suspected Lynch syndrome (HR 2.06, 95% CI 1.59 to 2.67) and with Lynch syndrome (HR 5.37, 95% CI 4.16 to 6.94), but not with MMR-deficient non-Lynch syndrome (HR 1.04, 95% CI 0.82 to 1.31). A greater risk of CRC was estimated for first-degree relatives if CRC cases were diagnosed before age 50 years, had proximal colon cancer or if their tumours had any of the following: expanding tumour margin, peritumoral lymphocytes, tumour-infiltrating lymphocytes or synchronous CRC. CONCLUSIONS Molecular pathology features are potentially useful to refine screening recommendations for first-degree relatives of CRC cases and to identify which cases are more likely to be caused by genetic or other familial factors.
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Affiliation(s)
- Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - aniel D. Buchanan
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia
| | - Christophe Rosty
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia.,Department of Molecular and Cellular Pathology, University of Queensland, Herston, Queensland, Australia.,Envoi Specialist Pathologists, Herston, Queensland, Australia
| | - Robert J. MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia.,Cancer Epidemiology Centre, Cancer Council Victoria, Carlton, Victoria, Australia
| | - James G. Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gillian S. Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G. Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia.,Cancer Epidemiology Centre, Cancer Council Victoria, Carlton, Victoria, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joanne P. Young
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia
| | - Mark Clendenning
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia
| | - Michael D. Walsh
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia
| | - Rhiannon J. Walters
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Clive Berghofer Cancer Research Centre, Herston, Queensland, Australia
| | - Alex Boussioutas
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, Australia.,Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas C. Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - John A. Baron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,School of Public Health, University of Washington, Seattle, Washington, USA.,Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,School of Public Health, University of Washington, Seattle, Washington, USA
| | | | - Robert W. Haile
- Stanford Cancer Institute, Stanford University, San Francisco, California, USA
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Cancer Care Ontario, Toronto, Ontario, Canada
| | - Noralane M. Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dennis J. Ahnen
- Department of Veterans Affairs, Eastern Colorado Health Care System, University of Colorado School of Medicine, Denver, Colorado, USA
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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50
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014; 6:32. [PMID: 25530820 PMCID: PMC4272815 DOI: 10.1186/s13148-014-0032-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Splicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries. FINDINGS Nucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy. CONCLUSION Nucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
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