1
|
Tan X, Fang Y, Fan X, Deng W, Huang J, Cai Y, Zou J, Chen Z, Lin H, Xu L, Wang G, Zhan H, Huang S, Fu X. Testing region selection and prognostic analysis of MLH1 promoter methylation in colorectal cancer in China. Gastroenterol Rep (Oxf) 2024; 12:goae011. [PMID: 38566849 PMCID: PMC10985700 DOI: 10.1093/gastro/goae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
Background MLH1 promoter methylation analysis is recommended in screening for Lynch syndrome (LS) in patients with MLH1-deficient colorectal cancer (CRC). The study aims to identify specific methylation regions in the MLH1 promoter and to evaluate the clinicopathologic characteristics of and prognosis for patients with MLH1 methylation. Methods A total of 580 CRC cases were included. The DNA mismatch repair (MMR) protein expression was assessed by using immunohistochemistry (IHC). The methylation status of the Regions A, B, C, D, and E in the MLH1 promoter was tested by using bisulfite sequencing PCR. The specificities of the five regions were calculated. Associations between MLH1 methylation and clinicopathologic characteristics were evaluated. Kaplan-Meier analyses for overall survival (OS) were carried out. Results In 580 CRC cases, the specificities of the methylation test in Regions D and E were both 97.8%. In the MLH1-deficient CRCs, the frequencies of MLH1 methylation and BRAFV600E mutation were 52.6% and 14.6%, respectively; BRAFV600E mutation occurred in 27.7% of patients with MLH1-methylated CRC. In the MMR-deficient patients, compared with MLH1 unmethylation, MLH1 methylation was more common in patients who were aged ≥50 years, female, had no family history of LS-related tumors, and had tumors located at the right colon. In the MMR-deficient patients, the MLH1-methylated cases had lower OS rates than the unmethylated cases with a family history of LS-related tumors (P = 0.047). Conclusions Regions D and E in the MLH1 promoter are recommended for determining the MLH1 methylation status in screening for LS in MLH1-deficient CRC. In MMR-deficient patients, the MLH1-methylated cases had a worse OS than the unmethylated cases with a family history of LS-related cancer.
Collapse
Affiliation(s)
- Xiaoli Tan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Yongzhen Fang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Xinjuan Fan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Weihao Deng
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Jinglin Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Yacheng Cai
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Jiaxin Zou
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Zhiting Chen
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Hanjie Lin
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Liang Xu
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Guannan Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Huanmiao Zhan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Shuhui Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Xinhui Fu
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| |
Collapse
|
2
|
Abstract
AbstractLynch syndrome was formerly known as Hereditary Nonpolyposis Colorectal Cancer. Currently, these two nomenclatures each have their unique definitions and are no longer used interchangeably. The history of hereditary nonpolyposis colorectal cancer was first recognized formally in the literature by Henry Lynch in 1967. With advances of molecular genetics, there has been a transformation from clinical phenotype to genotype diagnostics. This has led to the ability to diagnose affected patients before they manifest with cancer, and therefore allow preventative surveillance strategies. Genotype diagnostics has shown a difference in penetrance of different cancer risks dependent on the gene containing the mutation. Surgery is recommended as prevention for some cancers; for others they are reserved for once cancer is noted. Various surveillance strategies are recommended dependent on the relative risk of cancer and the ability to intervene with surgery to impact on survival. Risk reduction through aspirin has shown some recent promise, and continues to be studied.
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Vakiani E. GI Including GIST. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
5
|
Dabir PD, Bruggeling CE, van der Post RS, Dutilh BE, Hoogerbrugge N, Ligtenberg MJL, Boleij A, Nagtegaal ID. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients? A systematic review and meta-analysis. Eur J Hum Genet 2019; 28:277-286. [PMID: 31695176 DOI: 10.1038/s41431-019-0538-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 11/09/2022] Open
Abstract
The colorectal cancer spectrum has changed due to population screening programs, with a shift toward adenomas and early cancers. Whether it would be a feasible option to test these adenomas for detection of Lynch syndrome (LS) patients is unclear. Through meta-analysis and systematic review, risk factors for DNA mismatch repair deficiency (dMMR) and microsatellite instability (MSI) in adenomas were identified in LS and unselected patient cohorts. Data were extracted for patient age and MMR variant together with adenoma type, grade, size, and location. A total of 41 studies were included, and contained more than 519 LS patients and 1698 unselected patients with 1142 and 2213 adenomas respectively. dMMR/MSI was present in 69.5% of conventional adenomas in LS patients, compared with 2.8% in unselected patients. In the LS cohort, dMMR/MSI was more frequently present in patients older than 60 years (82% versus 54%). dMMR/MSI was also more common in villous adenomas (84%), adenomas over 1 cm (81%), and adenomas with high grade dysplasia (88%). No significant differences were observed for dMMR/MSI in relation to MMR variants and location of adenomas. In the context of screening, we conclude that detection of dMMR/MSI in conventional adenomas of unselected patients is uncommon and might be considered as indication for LS testing. Within the LS cohort, 69.5% of LS patients could have been detected through dMMR/MSI screening of their conventional adenomas.
Collapse
Affiliation(s)
- Parag D Dabir
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Randers Regional Hospital, Randers, Denmark
| | - Carlijn E Bruggeling
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.
| |
Collapse
|
6
|
Vakiani E. Molecular Testing of Colorectal Cancer in the Modern Era: What Are We Doing and Why? Surg Pathol Clin 2017; 10:1009-1020. [PMID: 29103530 DOI: 10.1016/j.path.2017.07.013] [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] [Indexed: 01/05/2023]
Abstract
A plethora of tests are routinely ordered and interpreted by pathologists to assist the management of colorectal cancer patients. Many of these tests are immunohistochemistry assays using antibodies against prognostically relevant proteins, some of which predict therapeutic response. This review focuses on tissue DNA-based tests. It presents novel methodologies for assessing well-established biomarkers, updates the expanding spectrum of genetic alterations that are associated with resistance to inhibition of epidermal growth factor receptor signaling, and briefly discusses emerging actionable alterations that may translate into new therapeutic options for colorectal cancer patients. The utility of next-generation sequencing is emphasized.
Collapse
Affiliation(s)
- Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
7
|
Bartley AN, Hamilton SR. Select biomarkers for tumors of the gastrointestinal tract: present and future. Arch Pathol Lab Med 2014; 139:457-68. [PMID: 25333834 DOI: 10.5858/arpa.2014-0189-ra] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Advances in molecular biomarkers of the gastrointestinal tract have contributed to a decline in the incidence of and mortality from diseases of the gastrointestinal tract. The discovery and clinical validation of new biomarkers are important to personalized cancer therapy, and numerous clinical trials are currently ongoing to help identify individualized therapy affecting these biomarkers and molecular mechanisms they represent. Distinct molecular pathways leading to cancers of the colorectum, esophagus, stomach, small bowel, and pancreas have been identified. Using biomarkers in these pathways to direct patient care, including selection of proper molecular testing for identification of actionable mutations and reporting the results of these biomarkers to guide clinicians and genetic counselors, is paramount. OBJECTIVE To examine and review select clinically actionable biomarkers of the colon, esophagus, stomach, small bowel, and pancreas, including present and future biomarkers with relevant clinical trials. DATA SOURCES Extensive literature review and practical and consultation experience of the authors. CONCLUSIONS Although numerous biomarkers have been identified and are currently guiding patient therapy, few have shown evidence of clinical utility in the management of patients with gastrointestinal cancers. Inconsistent results and discordant proposed algorithms for testing were identified throughout the literature; however, the potential for biomarkers to improve outcomes for patients with gastrointestinal cancer remains high. Continued advances through high-quality studies are needed.
Collapse
Affiliation(s)
- Angela N Bartley
- From Molecular Diagnostics, Department of Pathology, St. Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); and the Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas (Dr Hamilton)
| | | |
Collapse
|
8
|
Newton K, Jorgensen NM, Wallace AJ, Buchanan DD, Lalloo F, McMahon RFT, Hill J, Evans DG. Tumour MLH1 promoter region methylation testing is an effective prescreen for Lynch Syndrome (HNPCC). J Med Genet 2014; 51:789-96. [PMID: 25280751 DOI: 10.1136/jmedgenet-2014-102552] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Lynch syndrome (LS) patients have DNA mismatch repair deficiency and up to 80% lifetime risk of colorectal cancer (CRC). Screening of mutation carriers reduces CRC incidence and mortality. Selection for constitutional mutation testing relies on family history (Amsterdam and Bethesda Guidelines) and tumour-derived biomarkers. Initial biomarker analysis uses mismatch repair protein immunohistochemistry and microsatellite instability. Abnormalities in either identify mismatch repair deficiency but do not differentiate sporadic epigenetic defects, due to MLH1 promoter region methylation (13% of CRCs) from LS (4% of CRCs). A diagnostic biomarker capable of making this distinction would be valuable. This study compared two biomarkers in tumours with mismatch repair deficiency; quantification of methylation of the MLH1 promoter region using a novel assay and BRAF c.1799T>A, p.(Val600Glu) mutation status in the identification of constitutional mutations. METHODS Tumour DNA was extracted (formalin fixed, paraffin embedded, FFPE tissue) and pyrosequencing used to test for MLH1 promoter methylation and presence of the BRAF c.1799T>A, p.(Val600Glu) mutation 71 CRCs from individuals with pathogenic MLH1 mutations and 73 CRCs with sporadic MLH1 loss. Specificity and sensitivity was compared. FINDINGSS Unmethylated MLH1 promoter: sensitivity 94.4% (95% CI 86.2% to 98.4%), specificity 87.7% (95% CI 77.9% to 94.2%), Wild-type BRAF (codon 600): sensitivity 65.8% (95% CI 53.7% to 76.5%), specificity 98.6% (95% CI 92.4% to 100.0%) for the identification of those with pathogenic MLH1 mutations. CONCLUSIONS Quantitative MLH1 promoter region methylation using pyrosequencing is superior to BRAF codon 600 mutation status in identifying constitutional mutations in mismatch repair deficient tumours.
Collapse
Affiliation(s)
- K Newton
- Department of General Surgery, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK
| | - N M Jorgensen
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - A J Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - D D Buchanan
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, Queensland, Australia Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - F Lalloo
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - R F T McMahon
- Department of Histopathology, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK Manchester Medical School, University of Manchester, Manchester, UK
| | - J Hill
- Department of General Surgery, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK
| | - D G Evans
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| |
Collapse
|
9
|
Bellizzi AM. Contributions of molecular analysis to the diagnosis and treatment of gastrointestinal neoplasms. Semin Diagn Pathol 2013; 30:329-61. [DOI: 10.1053/j.semdp.2013.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
10
|
Clendenning M, Young JP, Walsh MD, Woodall S, Arnold J, Jenkins M, Win AK, Hopper JL, Sweet K, Gallinger S, Rosty C, Parry S, Buchanan DD. Germline Mutations in the Polyposis-Associated Genes BMPR1A, SMAD4, PTEN, MUTYH and GREM1 Are Not Common in Individuals with Serrated Polyposis Syndrome. PLoS One 2013; 8:e66705. [PMID: 23805267 PMCID: PMC3689730 DOI: 10.1371/journal.pone.0066705] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/08/2013] [Indexed: 12/28/2022] Open
Abstract
Background Recent reports have observed that individuals with serrated polyps, some of whom meet the clinical diagnostic criteria for Serrated Polyposis Syndrome (SPS), are among those who carry germline mutations in genes associated with polyposis syndromes including; (1) genes known to underlie hamartomatous polyposes (SMAD4, BMPR1A, and PTEN), (2) MUTYH-associated polyposis and (3) GREM1 in Hereditary Mixed Polyposis Syndrome (HMPS). The aim of this study was to characterise individuals fulfilling the current WHO criteria for SPS for germline mutations in these polyposis-associated genes. Methods A total of 65 individuals with SPS (fulfilling WHO criteria 1 or 3), were recruited to the Genetics of Serrated Neoplasia study between 2000 and 2012, through multiple Genetics or Family Cancer Clinics within Australia, or from the New Zealand Familial Gastrointestinal Cancer Service. Individuals with SPS were tested for coding mutations and large deletions in the PTEN, SMAD4, and BMPR1A genes, for the MUTYH variants in exons 7 (Y179C) and 13 (G396D), and for the duplication upstream of GREM1. Results We found no variants that were likely to be deleterious germline mutations in the SPS cases in the PTEN, SMAD4, and BMPR1A genes. A novel variant in intron 2 (c.164+223T>C) of PTEN was identified in one individual and was predicted by in silico analysis to have no functional consequences. One further individual with SPS was found to be mono-allelic for the MUTYH G396D mutation. No individuals carried the recently reported duplication within GREM1. Conclusions Genes involved in the gastrointestinal hamartomatous polyposis, Hereditary Mixed Polyposis Syndrome and MUTYH-associated polyposis syndromes are not commonly altered in individuals with SPS.
Collapse
Affiliation(s)
- Mark Clendenning
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Joanne P. Young
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Michael D. Walsh
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- Department of Histopathology, Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia
| | - Sonja Woodall
- New Zealand Familial Gastrointestinal Cancer Service, Auckland Hospital, Auckland, New Zealand
| | - Julie Arnold
- New Zealand Familial Gastrointestinal Cancer Service, Auckland Hospital, Auckland, New Zealand
| | - Mark Jenkins
- Centre for MEGA Epidemiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for MEGA Epidemiology, University of Melbourne, Melbourne, Victoria, Australia
| | - John L. Hopper
- Centre for MEGA Epidemiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Sweet
- Division of Human Genetics, The Ohio State University Medical Centre, Columbus, Ohio, United States of America
| | - Steven Gallinger
- Cancer Care Ontario, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Christophe Rosty
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- Department of Molecular and Cellular Pathology, University of Queensland, Brisbane, Queensland, Australia
- Envoi Specialist Pathologists, Brisbane, Queensland, Australia
| | - Susan Parry
- New Zealand Familial Gastrointestinal Cancer Service, Auckland Hospital, Auckland, New Zealand
- Department of Gastroenterology and Hepatology, Middlemore Hospital, Auckland, New Zealand
| | - Daniel D. Buchanan
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- * E-mail:
| |
Collapse
|
11
|
Serrated lesions and hyperplastic (serrated) polyposis relationship with colorectal cancer: classification and surveillance recommendations. Gastrointest Endosc 2013; 77:858-71. [PMID: 23684091 DOI: 10.1016/j.gie.2013.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/11/2013] [Indexed: 02/08/2023]
|
12
|
Thompson BA, Goldgar DE, Paterson C, Clendenning M, Walters R, Arnold S, Parsons MT, Walsh MD, Gallinger S, Haile RW, Hopper JL, Jenkins MA, LeMarchand L, Lindor NM, Newcomb PA, Thibodeau SN, Young JP, Buchanan DD, Tavtigian SV, Spurdle AB. A multifactorial likelihood model for MMR gene variant classification incorporating probabilities based on sequence bioinformatics and tumor characteristics: a report from the Colon Cancer Family Registry. Hum Mutat 2013; 34:200-9. [PMID: 22949379 PMCID: PMC3538359 DOI: 10.1002/humu.22213] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 08/22/2012] [Indexed: 01/04/2023]
Abstract
Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ~12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing.
Collapse
Affiliation(s)
- Bryony A. Thompson
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Carol Paterson
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Mark Clendenning
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Rhiannon Walters
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Sven Arnold
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Michael T. Parsons
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Michael D. Walsh
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Steven Gallinger
- Cancer Care Ontario, Department of Surgery, Familial Gastrointestinal Cancer Registry, University of Toronto, Toronto, Ontario, Canada
| | - Robert W. Haile
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - John L. Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Mark A. Jenkins
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Loic LeMarchand
- Cancer Research Center of Hawaii, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Noralane M. Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Polly A. Newcomb
- Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Joanne P. Young
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Daniel D. Buchanan
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Amanda B. Spurdle
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia
| |
Collapse
|
13
|
Walsh MD, Buchanan DD, Pearson SA, Clendenning M, Jenkins MA, Win AK, Walters RJ, Spring K, Nagler B, Pavluk E, Arnold ST, Goldblatt J, George J, Suthers G, Phillips K, Hopper JL, Jass JR, Baron JA, Ahnen D, Thibodeau S, Lindor N, Parry S, Walker N, Rosty C, Young JP. Immunohistochemical testing of conventional adenomas for loss of expression of mismatch repair proteins in Lynch syndrome mutation carriers: a case series from the Australasian site of the colon cancer family registry. Mod Pathol 2012; 25:722-30. [PMID: 22322191 PMCID: PMC3477239 DOI: 10.1038/modpathol.2011.209] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Debate continues as to the usefulness of assessing adenomas for loss of mismatch repair protein expression to identify individuals with suspected Lynch syndrome. We tested 109 polyps from 69 proven mutation carriers (35 females and 34 males) belonging to 49 Lynch syndrome families. All polyps were tested by immunohistochemistry for four mismatch repair proteins MLH1, MSH2, MSH6 and PMS2. Detailed pathology review was performed by specialist gastrointestinal pathologists. The majority of polyps (86%) were conventional adenomas (n=94), with 65 tubular and 28 tubulovillous adenomas and a single villous adenoma. The remaining 15 lesions (14%) were serrated polyps. Overall, loss of mismatch repair expression was noted for 78/109 (72%) of polyps. Loss of mismatch repair expression was seen in 74 of 94 (79%) conventional adenomas, and 4 of 15 (27%) serrated polyps from mismatch repair gene mutation carriers. In all instances, loss of expression was consistent with the underlying germline mutation. Mismatch repair protein expression was lost in 27 of 29 adenomas with a villous component compared with 47 of 65 adenomas without this feature (93 vs 73%; P=0.028). A strong trend was observed for high-grade dysplasia. Mismatch repair deficiency was observed in 12 of 12 conventional adenomas with high-grade dysplasia compared with 60 of 79 with low-grade dysplasia (100 vs 76%; P=0.065). We were unable to demonstrate a significant association between conventional adenoma size or site and mismatch repair deficiency. All (4/4 or 100%) of the serrated polyps demonstrating mismatch repair deficiency were traditional serrated adenomas from a single family. Diagnostic testing of adenomas in suspected Lynch syndrome families is a useful alternative in cases where cancers are unavailable. The overwhelming majority of conventional adenomas from mutation carriers show loss of mismatch repair protein expression concordant with the underlying germline mutation.
Collapse
Affiliation(s)
- Michael D Walsh
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia,School of Medicine, University of Queensland, Herston QLD 4006, Australia
| | | | | | | | - Mark A Jenkins
- Centre for MEGA, School of Population Health, University of Melbourne, Carlton, VIC 3053, Australia
| | - Aung Ko Win
- Centre for MEGA, School of Population Health, University of Melbourne, Carlton, VIC 3053, Australia
| | | | - Kevin Spring
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia
| | - Belinda Nagler
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia
| | - Erika Pavluk
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia
| | - Sven T Arnold
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia
| | - Jack Goldblatt
- School of Paediatrics and Child Health, University of Western Australia, Nedlands, WA 6009, Australia,Genetic Services of Western Australia, Subiaco, WA 6008, Australia
| | - Jill George
- Genetic Services of Western Australia, Subiaco, WA 6008, Australia
| | - Graeme Suthers
- Department of Paediatrics, University of Adelaide, SA 5005, Australia,South Australian Clinical Genetics Service, North Adelaide, SA 5009, Australia
| | - Kerry Phillips
- South Australian Clinical Genetics Service, North Adelaide, SA 5009, Australia
| | - John L Hopper
- Centre for MEGA, School of Population Health, University of Melbourne, Carlton, VIC 3053, Australia
| | - Jeremy R Jass
- Department of Cellular Pathology, St Mark’s Hospital, Harrow, HA1 3UJ, UK
| | - John A Baron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dennis Ahnen
- Denver Department of Veterans Affairs Medical Center and University of Colorado School of Medicine, Denver Colorado 80220 USA
| | - Stephen Thibodeau
- Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota USA
| | - Noralane Lindor
- Departments of Laboratory Medicine and Pathology and Medical Genetics, Mayo Clinic, Rochester, Minnesota USA
| | - Susan Parry
- New Zealand Familial Gastrointestinal Cancer Registry, Auckland City Hospital, Auckland, New Zealand
| | | | - Christophe Rosty
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia,School of Medicine, University of Queensland, Herston QLD 4006, Australia,Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston QLD 4006, Australia
| | - Joanne P Young
- Familial Cancer Laboratory, QIMR, Herston QLD 4006, Australia,School of Medicine, University of Queensland, Herston QLD 4006, Australia
| |
Collapse
|
14
|
MLH1 promoter hypermethylation in the analytical algorithm of Lynch syndrome: a cost-effectiveness study. Eur J Hum Genet 2012; 20:762-8. [PMID: 22274583 DOI: 10.1038/ejhg.2011.277] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The analytical algorithm of Lynch syndrome (LS) is increasingly complex. BRAF V600E mutation and MLH1 promoter hypermethylation have been proposed as a screening tool for the identification of LS. The aim of this study was to assess the clinical usefulness and cost-effectiveness of both somatic alterations to improve the yield of the diagnostic algorithm of LS. A total of 122 colorectal tumors from individuals with family history of colorectal cancer that showed microsatellite instability and/or loss of mismatch repair (MMR) protein expression were studied. MMR germline mutations were detected in 57 cases (40 MLH1, 15 MSH2 and 2 MSH6). BRAF V600E mutation was assessed by single-nucleotide primer extension. MLH1 promoter hypermethylation was assessed by methylation-specific multiplex ligation-dependent probe amplification in a subset of 71 cases with loss of MLH1 protein. A decision model was developed to estimate the incremental costs of alternative case-finding methods for detecting MLH1 mutation carriers. One-way sensitivity analysis was performed to assess robustness of estimations. Sensitivity of the absence of BRAF mutations for depiction of LS patients was 96% (23/24) and specificity was 28% (13/47). Specificity of MLH1 promoter hypermethylation for depiction of sporadic tumors was 66% (31/47) and sensitivity of 96% (23/24). The cost per additional mutation detected when using hypermethylation analysis was lower when compared with BRAF study and germinal MLH1 mutation study. Somatic hypermethylation of MLH1 is an accurate and cost-effective pre-screening method in the selection of patients that are candidates for MLH1 germline analysis when LS is suspected and MLH1 protein expression is absent.
Collapse
|
15
|
Buchanan DD, Roberts A, Walsh MD, Parry S, Young JP. Lessons from Lynch syndrome: a tumor biology-based approach to familial colorectal cancer. Future Oncol 2010; 6:539-49. [PMID: 20373868 DOI: 10.2217/fon.10.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) develops within precursor lesions in the single-celled epithelial lining of the gut. The two most common epithelial lesions are the adenoma and the serrated polyp. CRC is also one of the most familial of the common cancers, and just as there are syndromes associated with increased risk of CRC arising in adenomas, there are also syndromes with increased CRC risk associated with serrated polyps. In this article, we describe the features of such a syndrome, familial serrated neoplasia, which distinguish it from the well-characterized condition Lynch syndrome (or hereditary nonpolyposis CRC), and show that the molecular pathology of tumors forms the basis for this distinction. Lynch syndrome CRC arises almost exclusively within adenomatous precursor lesions, in contrast with familial serrated neoplasia where at least half of the cancers develop in serrated polyps. Finally, rare families exist in which both conditions segregate independently, producing a difficult diagnostic picture.
Collapse
|
16
|
Abstract
OBJECTIVE Hyperplastic polyposis is a colonic polyposis condition of unknown aetiology. The purpose of this study was to examine the spectrum of phenotypic variation in patients with multiple serrated polyps as a basis for gene discovery. METHODS One hundred and twenty-six patients with multiple (> or = 5) serrated polyps were recruited to the study. Polyp counts were extracted from histology and colonoscopy reports. Ethnicity was self-reported. Family history of cancer data were derived from pedigrees. Ascertainment status was classified as either index case or identified by screening. RESULTS The average reported polyp count was 39. Patients with highest polyp numbers were more likely to be male (P = 0.02). Colorectal cancer (CRC) was identified in 49 of 119 patients (41%) and 28% of these patients had multiple CRC. Young onset patients had higher polyp numbers (P = 0.03) and were more likely to have their CRC in the distal colon (P = 0.02). CRC was significantly associated with the presence of adenomas (P = 0.03). Patients were divided into moderate polyposis (5-79 serrated polyps) and dense polyposis (80 or more) categories. The dense polyposis category was associated with a lack of family history for CRC (P = 0.034) and male gender (P = 0.014), independent of ascertainment status and recruitment site. CONCLUSION Multiple serrated polyps were associated with an increased personal risk of CRC. A subset of patients with the highest polyp numbers was more likely to be male and to have no family history of CRC. This result suggests heterogeneous modes of inheritance and has implications for studies investigating the genetic basis of multiple serrated polyps.
Collapse
|