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Garcia FADO, de Andrade ES, de Campos Reis Galvão H, da Silva Sábato C, Campacci N, de Paula AE, Evangelista AF, Santana IVV, Melendez ME, Reis RM, Palmero EI. New insights on familial colorectal cancer type X syndrome. Sci Rep 2022; 12:2846. [PMID: 35181726 PMCID: PMC8857274 DOI: 10.1038/s41598-022-06782-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is a heterogeneous colorectal cancer predisposition syndrome that, although displays a cancer pattern similar to Lynch syndrome, is mismatch repair proficient and does not exhibit microsatellite instability. Besides, its genetic etiology remains to be elucidated. In this study we performed germline exome sequencing of 39 cancer-affected patients from 34 families at risk for FCCTX. Variant classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. Pathogenic/likely pathogenic variants were identified in 17.65% of the families. Rare and potentially pathogenic alterations were identified in known hereditary cancer genes (CHEK2), in putative FCCTX candidate genes (OGG1 and FAN1) and in other cancer-related genes such as ATR, ASXL1, PARK2, SLX4 and TREX1. This study provides novel important clues that can contribute to the understanding of FCCTX genetic basis.
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Affiliation(s)
- Felipe Antonio de Oliveira Garcia
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | | | - Natália Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil. .,Department of Genetics, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
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Abdollahi Z, Tabatabaiefar MA, Noruzi M, Miar P, Kazemi M, Naimi A, Emami MH, Zeinalian M. A Simplified Protocol for Microsatellite Instability Evaluation in Iranian Patients at Risk for Lynch Syndrome. Lab Med 2021; 53:235-241. [PMID: 34611695 DOI: 10.1093/labmed/lmab064] [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: 11/13/2022] Open
Abstract
OBJECTIVE The most important tumor characteristic of Lynch syndrome (LS) is microsatellite instability (MSI). In the current study, BAT34c4 and BAT26 mononucleotide markers were evaluated as part of efforts to test a cost-effective panel for MSI testing in Iranian patients, comparing it with the Promega kit. METHODS Amsterdam II clinical criteria were used to identify patients at risk for LS. The MSI status of these patients was determined using BAT34c4 and BAT26 markers, as well as the Promega kit. The results of both methods were compared, and the sensitivity and specificity of new short tandem repeat (STR) markers were estimated using statistical formulas. RESULTS Of the 37 patients we studied who were at risk for LS, 27% showed MSI-high results, via the Promega kit. The same results were achieved for BAT34c4 and BAT26 separately. CONCLUSIONS The novel 2-marker kit for MSI testing has similar accuracy as the Promega kit at a lower cost, due to fewer markers and a more economical labeling method.
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Affiliation(s)
- Zeinab Abdollahi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Disease Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahnaz Noruzi
- Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran
| | - Paniz Miar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azar Naimi
- Department of Pathology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Mehrdad Zeinalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Disease Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.,Ala Cancer Prevention and Control Center, Isfahan, Iran
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3
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Martín-Morales L, Garre P, Lorca V, Cazorla M, Llovet P, Bando I, García-Barberan V, González-Morales ML, Esteban-Jurado C, de la Hoya M, Castellví-Bel S, Caldés T. BRIP1, a Gene Potentially Implicated in Familial Colorectal Cancer Type X. Cancer Prev Res (Phila) 2020; 14:185-194. [PMID: 33115781 DOI: 10.1158/1940-6207.capr-20-0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/17/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Familial colorectal cancer Type X (FCCTX) comprises a heterogeneous group of families with an increased risk of developing colorectal cancer and other related tumors, but with mismatch repair-proficient, microsatellite-stable (MSS) tumors. Unfortunately, the genetic basis underlying their cancer predisposition remains unknown. Although pathogenic germline variants in BRIP1 increase the risk of developing hereditary ovarian cancer, the involvement of BRIP1 in hereditary colorectal cancer is still not well known. In order to identify new BRIP1 variants associated with inherited colorectal cancer, affected and nonaffected individuals from 18 FCCTX or high-risk MSS colorectal cancer families were evaluated by whole-exome sequencing, and another 62 colorectal cancer patients from FCCTX or high-risk MSS colorectal cancer families were screened by a next-generation sequencing (NGS) multigene panel. The families were recruited at the Genetic Counseling Unit of Hospital Clínico San Carlos of Madrid. A total of three different BRIP1 mutations in three unrelated families were identified. Among them, there were two frameshift variants [c.1702_1703del, p.(Asn568TrpfsTer9) and c.903del, p.(Leu301PhefsTer2)] that result in the truncation of the protein and are thus classified as pathogenic (class 5). The remaining was a missense variant [c.2220G>T, p.(Gln740His)] considered a variant of uncertain significance (class 3). The segregation and loss-of-heterozygosity studies provide evidence linking the two BRIP1 frameshift variants to colorectal cancer risk, with suggestive but not definitive evidence that the third variant may be benign. The results here presented suggest that germline BRIP1 pathogenic variants could be associated with hereditary colorectal cancer predisposition.Prevention Relevance: We suggest that BRIP1 pathogenic germline variants may have a causal role in CRC as moderate cancer susceptibility alleles and be associated with hereditary CRC predisposition. A better understanding of hereditary CRC may provide important clues to disease predisposition and could contribute to molecular diagnostics, improved risk stratification, and targeted therapeutic strategies.
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Affiliation(s)
- Lorena Martín-Morales
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Marta Cazorla
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Patricia Llovet
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Inmaculada Bando
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Vanesa García-Barberan
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | | | - Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain.
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Xu Y, Li C, Zhang Y, Guo T, Zhu C, Xu Y, Liu F. Comparison Between Familial Colorectal Cancer Type X and Lynch Syndrome: Molecular, Clinical, and Pathological Characteristics and Pedigrees. Front Oncol 2020; 10:1603. [PMID: 32984025 PMCID: PMC7493642 DOI: 10.3389/fonc.2020.01603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Objective This study aimed to compare the molecular, clinical, and pathological characteristics and pedigrees of familial colorectal cancer type X (FCCTX) with those of Lynch syndrome (LS) to provide a theoretical basis for the management of FCCTX. Methods Overall, 46 cases of FCCTX and 47 LS probands and affected families were enrolled between June 2008 and September 2018 for this study. Multigene cancer panel tests that included 139 genes were performed for all patients, and variants in each group were described. The clinical, pathological, and pedigree characteristics were also compared between the two groups. Results In total, 42 variants were detected in 27 (58.7%) cases in the FCCTX group, with BRCA1, BRCA2, POLE, POLD1, ATR, and ATM being the most frequently mutated genes. The mean onset age of colorectal cancer (CRC) was significantly older in the FCCTX group than in the LS group (53.57 ± 12.88 years vs. 44.36 ± 11.26 years, t = −9.204, p < 0.001). The proportion of patients with rectal cancer was also higher in the FCCTX group than in the LS group [43.5% (20/46) vs. 10.6% (5/47), χ2 = 12.823, p = 0.005]. Within a median follow-up time of 53.9 ± 37.0 months, the proportion of patients who developed metachronous CRC was significantly higher in the LS group than in the FCCTX group [34.0% (16/47) vs. 13.0% (6/46), χ2 = 5.676, p = 0.017]. When comparing pedigrees, older age at cancer onset and rectal cancer clustering were observed in the FCCTX families. A higher prevalence in male patients was also observed in the FCCTX families. Conclusion FCCTX is an entity distinct from LS, but its genetic etiology remains unknown. A larger multigene panel would be recommended for determining the underlying pathogenic variants. Considering the pathology and moderate penetrance of the CRC link to FCCTX, less stringent surgical treatments and colonoscopy surveillance would be preferable. Rectum preference is a typical feature of FCCTX. Colonoscopy surveillance in FCCTX families could be less intensive, and more attention should be given to male members.
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Affiliation(s)
- Yun Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cong Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuqin Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian'an Guo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangqi Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
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Peltomäki P, Olkinuora A, Nieminen TT. Updates in the field of hereditary nonpolyposis colorectal cancer. Expert Rev Gastroenterol Hepatol 2020; 14:707-720. [PMID: 32755332 DOI: 10.1080/17474124.2020.1782187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Up to one third of colorectal cancers show familial clustering and 5% are hereditary single-gene disorders. Hereditary non-polyposis colorectal cancer comprises DNA mismatch repair-deficient and -proficient subsets, represented by Lynch syndrome (LS) and familial colorectal cancer type X (FCCTX), respectively. Accurate knowledge of molecular etiology and genotype-phenotype correlations are critical for tailored cancer prevention and treatment. AREAS COVERED The authors highlight advances in the molecular dissection of hereditary non-polyposis colorectal cancer, based on recent literature retrieved from PubMed. Future possibilities for novel gene discoveries are discussed. EXPERT COMMENTARY LS is molecularly well established, but new information is accumulating of the associated clinical and tumor phenotypes. FCCTX remains poorly defined, but several promising candidate genes have been discovered and share some preferential biological pathways. Multi-level characterization of specimens from large patient cohorts representing multiple populations, combined with proper bioinformatic and functional analyses, will be necessary to resolve the outstanding questions.
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Affiliation(s)
- Paivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
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6
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Choi YH, Lakhal-Chaieb L, Kröl A, Yu B, Buchanan D, Ahnen D, Le Marchand L, Newcomb PA, Win AK, Jenkins M, Lindor NM, Briollais L. Risks of Colorectal Cancer and Cancer-Related Mortality in Familial Colorectal Cancer Type X and Lynch Syndrome Families. J Natl Cancer Inst 2020; 111:675-683. [PMID: 30380125 DOI: 10.1093/jnci/djy159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/15/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The risk of cancers is well characterized in Lynch syndrome (LS) families but has been less studied in familial colorectal cancer type X (FCCTX) families. METHODS In this article, we compare the risk estimates of first and second colorectal cancers (CRCs) in 168 FCTTX and 780 LS families recruited through the Colon Cancer Family Registry as well as the risk of cancer-related deaths and disease-free survival (DFS) after a first CRC. Our methodology is based on a survival analysis approach, developed specifically to model the occurrence of successive cancers (ie, first and second CRCs) in the presence of competing risk events (ie, death from any causes). RESULTS We found an excess risk of first and second CRC in individuals with LS compared to FCCTX family members. However, for an average age at first CRC of 60 years in FCCTX families and 50 years in LS families, the DFS rates were comparable in men but lower in women from FCCTX vs LS families, eg , 75.1% (95% confidence interval [CI] = 69.0% to 80.9%) vs 78.9% (95% CI = 76.3% to 81.3%) for the 10-year DFS. The 10-year risk of cancer-related death was higher in FCCTX families vs LS families, eg, 15.4% in men (95% CI = 10.9% to 19.8%) and 19.3% in women (95% CI = 13.6% to 24.7%) vs 8.9% (95% CI = 7.5% to 11.4%) and 8.7% (95% CI = 7.1% to 10.8%), respectively. CONCLUSIONS Individuals with CRCs arising in the context of FCCTX do not experience the same improved DFS and overall survival of those with LS, and that difference may be relevant in management decisions.
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Affiliation(s)
- Yun-Hee Choi
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
| | - Lajmi Lakhal-Chaieb
- Department of Mathematics and Statistics, Laval University, Québec, QC, Canada
| | - Agnieszka Kröl
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bing Yu
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
| | - Daniel Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Dennis Ahnen
- Division of Gastroenterology, Faculty of Medicine, University of Colorado, Aurora, CO
| | - Loic Le Marchand
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, Honolulu, HI
| | - Polly A Newcomb
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | | | - Laurent Briollais
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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You YN, Lee LD, Deschner BW, Shibata D. Colorectal Cancer in the Adolescent and Young Adult Population. JCO Oncol Pract 2020; 16:19-27. [PMID: 32039664 PMCID: PMC7351341 DOI: 10.1200/jop.19.00153] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 01/22/2023] Open
Abstract
Colorectal cancer in the young adult population is of increasing incidence and concern. Genetic predisposition and heritable syndromes contribute to this trend, but perhaps more concerning is the majority of new diagnoses that involve no traceable genetic risk factors. Prevention and early recognition, with a high suspicion in the symptomatic young adult, are critical in attenuating recent trends. Clinical management requires coordinated multidisciplinary care from diagnosis to surveillance in order to ensure appropriate management. This review provides a summary of key aspects related to colorectal cancer in adolescents and young adults, including epidemiology, biology, genetics, clinical management, and prevention.
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Affiliation(s)
- Y Nancy You
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lucas D Lee
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - David Shibata
- University of Tennessee Health Science Center, Memphis, TN
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Rashid MU, Naeemi H, Muhammad N, Loya A, Lubiński J, Jakubowska A, Yusuf MA. Prevalence and spectrum of MLH1, MSH2, and MSH6 pathogenic germline variants in Pakistani colorectal cancer patients. Hered Cancer Clin Pract 2019; 17:29. [PMID: 31660093 PMCID: PMC6806584 DOI: 10.1186/s13053-019-0128-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/25/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pathogenic germline variants in MLH1, MSH2 and MSH6 genes account for the majority of Lynch syndrome (LS). In this first report from Pakistan, we investigated the prevalence of pathogenic MLH1/MSH2/MSH6 variants in colorectal cancer (CRC) patients. METHODS Consecutive cases (n = 212) were recruited at the Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), between November 2007 to March 2011. Patients with a family history of > 3 or 2 HNPCC-associated cancers were classified as HNPCC (n = 9) or suspected-HNPCC (n = 20), respectively (group 1; n = 29). Cases with no family history were designated as non-HNPCC (group 2; n = 183). MLH1/MSH2/MSH6 genes were comprehensively screened in group 1. Pathogenic/likely pathogenic variants identified in group 1 were subsequently evaluated in group 2. RESULTS Eight distinct pathogenic/likely pathogenic MLH1/MSH2 variants were found in group 1 (10/29; 34.5%), belonging to HNPCC (5/9; 55.6%) and suspected-HNPCC (5/20; 25%) families and in group 2 (2/183; 1.1%) belonging to non-HNPCC. Overall, three recurrent variants (MSH2 c.943-1G > C, MLH1 c.1358dup and c.2041G > A) accounted for 58.3% (7/12) of all families harboring pathogenic/likely pathogenic MLH1/MSH2 variants. Pathogenic MSH6 variants were not detected. CONCLUSION Pathogenic/likely pathogenic MLH1/MSH2 variants account for a substantial proportion of CRC patients with HNPCC/suspected-HNPCC in Pakistan. Our findings suggest that HNPCC/suspected-HNPCC families should be tested for these recurrent variants prior to comprehensive gene screening in this population.
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Affiliation(s)
- Muhammad Usman Rashid
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, Punjab 54000 Pakistan
| | - Humaira Naeemi
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, Punjab 54000 Pakistan
| | - Noor Muhammad
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, Punjab 54000 Pakistan
| | - Asif Loya
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
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Walkowska J, Kallemose T, Jönsson G, Jönsson M, Andersen O, Andersen MH, Svane IM, Langkilde A, Nilbert M, Therkildsen C. Immunoprofiles of colorectal cancer from Lynch syndrome. Oncoimmunology 2018; 8:e1515612. [PMID: 30546958 PMCID: PMC6287783 DOI: 10.1080/2162402x.2018.1515612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 02/09/2023] Open
Abstract
Colorectal cancers associated with Lynch syndrome are characterized by defective mismatch repair, microsatellite instability, high mutation rates, and a highly immunogenic environment. These features define a subset of cancer with a favorable prognosis and high likelihood to respond to treatment with anti-programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) drugs. With the aim to define immune-evasive mechanisms and a potential impact hereof in colorectal cancers from Lynch syndrome versus hereditary cases with retained mismatch repair function, we immunohistochemically and transcriptionally profiled 270 tumors. Lynch syndrome-associated tumors showed an overrepresentation of tumor-infiltrating CD3, CD8 and CD68 positive cells, loss of beta-2-microglobulin (B2M) and up-regulation of PD-L1 on tumor cells. The gene expression signature of Lynch syndrome tumors was characterized by upregulation of genes related to antigen processing and presentation, apoptosis, natural killer cell-mediated cytotoxicity, and T cell activation. Tumors with loss of B2M and up-regulation of PD-L1 showed distinctive immunogenic profiles. In summary, our data demonstrate a complex tumor-host interplay where B2M loss and PD-L1 up-regulation influence immunological pathways and clinical outcome in Lynch syndrome tumors. Immunological classification may thus aid in the preselection of colorectal cancers relevant for treatment with anti-PD-1/PD-L1 therapies.
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Affiliation(s)
- Joanna Walkowska
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Thomas Kallemose
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Göran Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Mats Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Ove Andersen
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Mads Hald Andersen
- Center for Cancer Immune Therapy, Department of Hematology and Oncology, Copenhagen University Hospital, Herlev Hospital, Herlev, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Department of Hematology and Oncology, Copenhagen University Hospital, Herlev Hospital, Herlev, Denmark
| | - Anne Langkilde
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Mef Nilbert
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark.,Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina Therkildsen
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
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10
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Lee LD, You YN. Young-onset colorectal cancer: Diagnosis and management. SEMINARS IN COLON AND RECTAL SURGERY 2018. [DOI: 10.1053/j.scrs.2018.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Tanakaya K. Current clinical topics of Lynch syndrome. Int J Clin Oncol 2018; 24:1013-1019. [DOI: 10.1007/s10147-018-1282-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 01/02/2023]
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12
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Martín-Morales L, Feldman M, Vershinin Z, Garre P, Caldés T, Levy D. SETD6 dominant negative mutation in familial colorectal cancer type X. Hum Mol Genet 2018; 26:4481-4493. [PMID: 28973356 DOI: 10.1093/hmg/ddx336] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 08/15/2017] [Indexed: 01/01/2023] Open
Abstract
Familiar colorectal cancer type X (FCCTX) comprises families that fulfill the Amsterdam criteria for hereditary non-polyposis colorectal cancer, but that lack the mismatch repair deficiency that defines the Lynch syndrome. Thus, the genetic cause that increases the predisposition to colorectal and other related cancers in families with FCCTX remains to be elucidated. Using whole-exome sequencing, we have identified a truncating mutation in the SETD6 gene (c.791_792insA, p.Met264IlefsTer3) in all the affected members of a FCCTX family. SETD6 is a mono-methyltransferase previously shown to modulate the NF-κB and Wnt signaling pathways, among other. In the present study, we characterized the truncated version of SETD6, providing evidence that this SETD6 mutation may play a role in the cancer inheritance in this family. Here we demonstrate that the truncated SETD6 lacks its enzymatic activity as a methyltransferase, while maintaining other properties such as its expression, localization and substrate-binding ability. In addition, we show that the mutant allele is expressed and that the resulting protein competes with the wild type for their substrates, pointing to a dominant negative nature. These findings suggest that the identified mutation impairs the normal function of SETD6, which may result in the deregulation of the different pathways in which it is involved, contributing to the increased susceptibility to cancer in this FCCTX family.
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Affiliation(s)
- Lorena Martín-Morales
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Pilar Garre
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
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13
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Dominguez-Valentin M, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Martins A, Møller P, Hovig E. Identification of genetic variants for clinical management of familial colorectal tumors. BMC MEDICAL GENETICS 2018; 19:26. [PMID: 29458332 PMCID: PMC5819082 DOI: 10.1186/s12881-018-0533-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/24/2018] [Indexed: 12/22/2022]
Abstract
Background The genetic mechanisms for families who meet the clinical criteria for Lynch syndrome (LS) but do not carry pathogenic variants in the mismatch repair (MMR) genes are still undetermined. We aimed to study the potential contribution of genes other than MMR genes to the biological and clinical characteristics of Norwegian families fulfilling Amsterdam (AMS) criteria or revised Bethesda guidelines. Methods The Hereditary Cancer Biobank of the Norwegian Radium Hospital was interrogated to identify individuals with a high risk of developing colorectal cancer (CRC) for whom no pathogenic variants in MMR genes had been found in routine diagnostic DNA sequencing. Forty-four cancer susceptibility genes were selected and analyzed by using our in-house designed TruSeq amplicon-based assay for targeted sequencing. RNA splicing- and protein-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as likely to affect splicing were experimentally analyzed by resorting to minigene assays. Results We identified a patient who met the revised Bethesda guidelines and carried a likely pathogenic variant in CHEK2 (c.470 T > C, p.I157T). In addition, 25 unique VUS were identified in 18 individuals, of which 2 exonic variants (MAP3K1 c.764A > G and NOTCH3 c.5854G >A) were analyzed in the minigene splicing assay and found not to have an effect on RNA splicing. Conclusions Among high-risk CRC patients that fulfill the AMS criteria or revised Bethesda guidelines, targeted gene sequencing identified likely pathogenic variant and VUS in other genes than the MMR genes (CHEK2, NOTCH3 and MAP3K1). Our study suggests that the analysis of genes currently excluded from routine molecular diagnostic screens may confer cancer susceptibility. Electronic supplementary material The online version of this article (10.1186/s12881-018-0533-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hélène Tubeuf
- Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Daniel Vodak
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anke M Nissen
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alexandra Martins
- Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Human Medicine, Universität Witten, Herdecke, Germany.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway.,Institute of Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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14
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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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15
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Nejadtaghi M, Jafari H, Farrokhi E, Samani KG. Familial Colorectal Cancer Type X (FCCTX) and the correlation with various genes-A systematic review. Curr Probl Cancer 2017; 41:388-397. [PMID: 29096939 DOI: 10.1016/j.currproblcancer.2017.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 05/10/2017] [Accepted: 10/12/2017] [Indexed: 02/09/2023]
Abstract
Familial Colorectal Cancer Type X (FCCTX) is a type of hereditary nonpolyposis colorectal cancer in accordance to Amsterdam criteria-1 for Lynch syndrome, with no related mutation in mismatch repair gene. FCCTX is microsatellite stable and is accounted for 40% of families with Amsterdam criteria-1 with a high age of onset. Thus, the carcinogenesis of FCCTX is different compared to Lynch syndrome. In addition to the microsatellite stability and the presence of less predominant tumors in proximal colon, various clinical features have also been associated with FCCTX in comparison with Lynch syndrome such as no increased risk of extra-colonic cancers, older age of diagnosis and higher adenoma/carcinoma rate. Genetic etiology of this type of cancer which is autosomal dominant is unknown. In this review, we focus on the genes and their variants identified in this type of CRC. In order to find out the correlation between FCCTX and various genes database such as PubMed and PMC, search engine such as Google scholar and portals such as Springer and Elsevier have been searched. Based on our literature search, several studies suggest that FCCTX is a heterogeneous type of disease with different genetic variants. Recent studies describe the correlation between FCCTX and genes such as BRCA2, SEMA4, NTS, RASSF9, GALNT12, KRAS, BRAF, APC, BMPR1A, and RPS20. Considering the fact that BRCA2 has the highest mutation rate (60%) and is one of the most crucial DNA repair genes, it will be considered as a big role player in this type of cancer in comparison with other genes.
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Affiliation(s)
- Mahdieh Nejadtaghi
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Hamideh Jafari
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Effat Farrokhi
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran.
| | - Keihan Ghatreh Samani
- Clinical Biochemistry Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
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16
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Haraldsson S, Klarskov L, Nilbert M, Bernstein I, Bonde J, Holck S. Differential expression of CK20, β-catenin, and MUC2/5AC/6 in Lynch syndrome and familial colorectal cancer type X. BMC Clin Pathol 2017; 17:11. [PMID: 28824332 PMCID: PMC5559789 DOI: 10.1186/s12907-017-0052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Hereditary non-polyposis colorectal cancer comprises Lynch syndrome and familial colorectal cancer type X (FCCTX). Differences in genetics, demographics and histopathology have been extensively studied. The purpose of this study is to characterize their immunoprofile of markers other than MMR proteins. METHODS We compared the expression patterns of cytokeratins (CK7 and CK20), mucins (MUC2/5 AC/6), CDX2 and β-catenin in Lynch syndrome and FCCTX. RESULTS Differences were identified for CK20 and nuclear β-catenin, which were significantly more often expressed in FCCTX than in Lynch syndrome (p < 0.001), whereas MUC2, MUC5AC and MUC6 were overexpressed in Lynch syndrome tumors compared with FCCTX tumors (p = 0.001, < 0.01, and < 0.001, respectively). We observed no differences in the expression patterns of CK7 and CDX2. CONCLUSIONS In summary, we identified significant differences in the immunoprofiles of colorectal cancers linked to FCCTX and Lynch syndrome with a more sporadic-like profile in the former group and a more distinct profile with frequent MUC6 positivity in the latter group.
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Affiliation(s)
- Stefan Haraldsson
- Department of Gastroenterology, Copenhagen University Hospital, Kettegaard Alle 29, DK-2650 Hvidovre, Denmark
| | - Louise Klarskov
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
| | - Mef Nilbert
- Clinical Research Centre, HNPCC register, Copenhagen University Hospital, Hvidovre, Denmark.,Institute of Clinical Sciences, Division of Oncology, Lund University, Lund, Sweden
| | - Inge Bernstein
- HNPCC register, Copenhagen University Hospital, Hvidovre, Denmark.,Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - Jesper Bonde
- Department of Pathology and Clinical Research Center, Copenhagen University Hospital, Hvidovre, Denmark
| | - Susanne Holck
- Department of Pathology, Copenhagen University Hospital, Hvidovre, Denmark
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17
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Abstract
Four main DNA mismatch repair (MMR) genes have been identified, MLH1, MSH2, MSH6, and PMS2, which when mutated cause susceptibility to Lynch syndrome (LS). LS is one of the most prevalent hereditary cancer syndromes in man and accounts for 1–3 % of unselected colorectal carcinomas and some 15 % of those with microsatellite instability and/or absent MMR protein. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) maintains a database for LS-associated mutations since 1996. The database was recently reorganized to efficiently gather published and unpublished data and to classify the variants according to a five-tiered scheme linked to clinical recommendations. This review provides an update of germline mutations causing susceptibility to LS based on information available in the InSiGHT database and the latest literature. MMR gene mutation profiles, correlations between genotype and phenotype, and possible mechanisms leading to the characteristic spectrum of tumors in LS are discussed in light of the different functions of MMR proteins, many of which directly serve cancer avoidance.
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18
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Yu H, Hemminki A, Sundquist K, Hemminki K. Familial Associations of Colorectal Cancer with Other Cancers. Sci Rep 2017; 7:5243. [PMID: 28701784 PMCID: PMC5507930 DOI: 10.1038/s41598-017-05732-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/02/2017] [Indexed: 11/26/2022] Open
Abstract
Colorectal cancer (CRC) has a strong familial component which extends to discordant cancers (ie non-CRC tumors). This is best seen in cancer syndromes such as hereditary non-polyposis colorectal cancer (HNPCC) which predisposes to several tumor types. Population-based family studies have also found discordant associations for CRC but they have included cancers which manifest in HNPCC, and there is no convincing evidence of discordant associations beyond the known syndromes. We address familial associations of non-CRC tumors with CRC using the resources of the Swedish Family-Cancer Database and applying a powerful approach of assessing familial relative risks in families of increasing numbers of patients with discordant cancers. Among 1.8 million cancer patients and over 200,000 CRC cases consistent familial associations of CRC was observed for several HNPCC related cancers. However, for small intestinal, pancreatic and nervous system cancers RRs remained essentially unchanged when potential HNPCC families were excluded, suggesting involvement of genes not related to HNPCC. Two independent associations of CRC were found for melanoma, thyroid and eye cancers and these appeared not to be related to known syndromes. A number of other cancers associated with CRC in single analyses and independent studies are required to assess the relevance of such findings.
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Affiliation(s)
- Hongyao Yu
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, 205 02, Malmö, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, 205 02, Malmö, Sweden
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19
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Werdyani S, Yu Y, Skardasi G, Xu J, Shestopaloff K, Xu W, Dicks E, Green J, Parfrey P, Yilmaz YE, Savas S. Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse. Cancer Med 2017; 6:1220-1232. [PMID: 28544645 PMCID: PMC5463068 DOI: 10.1002/cam4.1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/24/2022] Open
Abstract
INDELs and CNVs are structural variations that may play roles in cancer susceptibility and patient outcomes. Our objectives were a) to computationally detect and examine the genome‐wide INDEL/CNV profiles in a cohort of colorectal cancer patients, and b) to examine the associations of frequent INDELs/CNVs with relapse‐free survival time. We also identified unique variants in 13 Familial Colorectal Cancer Type X (FCCX) cases. The study cohort consisted of 495 colorectal cancer patients. QuantiSNP and PennCNV algorithms were utilized to predict the INDELs/CNVs using genome‐wide signal intensity data. Duplex PCR was used to validate predictions for 10 variants. Multivariable Cox regression models were used to test the associations of 106 common variants with relapse‐free survival time. Score test and the multivariable Cox proportional hazards models with time‐varying coefficients were applied to identify the variants with time‐varying effects on the relapse‐free survival time. A total of 3486 distinct INDELs/CNVs were identified in the patient cohort. The majority of these variants were rare (83%) and deletion variants (81%). The results of the computational predictions and duplex PCR results were highly concordant (93–100%). We identified four promising variants significantly associated with relapse‐free survival time (P < 0.05) in the multivariable Cox proportional hazards regression models after adjustment for clinical factors. More importantly, two additional variants were identified to have time‐varying effects on the risk of relapse. Finally, 58 rare variants were identified unique to the FCCX cases; none of them were detected in more than one patient. This is one of the first genome‐wide analyses that identified the germline INDEL/CNV profiles in colorectal cancer patients. Our analyses identified novel variants and genes that can biologically affect the risk of relapse in colorectal cancer patients. Additionally, for the first time, we identified germline variants that can potentially be early‐relapse markers in colorectal cancer.
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Affiliation(s)
- Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Georgia Skardasi
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
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20
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DNA Methylation Identifies Loci Distinguishing Hereditary Nonpolyposis Colorectal Cancer Without Germ-Line MLH1/MSH2 Mutation from Sporadic Colorectal Cancer. Clin Transl Gastroenterol 2016; 7:e208. [PMID: 27977020 PMCID: PMC5288582 DOI: 10.1038/ctg.2016.59] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 10/26/2016] [Indexed: 12/26/2022] Open
Abstract
Objectives: Roughly half of hereditary nonpolyposis colorectal cancer (HNPCC) cases are Lynch syndrome and exhibit germ-line mutations in DNA mismatch repair (MMR) genes; the other half are familial colorectal cancer (CRC) type X (FCCTX) and are MMR proficient. About 70% of Lynch syndrome tumors have germ-line MLH1 or MSH2 mutations. The clinical presentation, histopathological features, and carcinogenesis of FCCTX resemble those of sporadic MMR-proficient colorectal tumors. It is of interest to obtain biomarkers that distinguish FCCTX from sporadic microsatellite stable (MSS) CRC, to develop preventive strategies. Methods: The tumors and adjacent normal tissues of 40 patients with HNPCC were assayed using the Illumina Infinium HumanMethylation27 (HM27) BeadChip to assess the DNA methylation level at about 27,000 loci. The germ-line mutation status of MLH1 and MSH2 and the microsatellite instability status in these patients were obtained. Genome-wide DNA methylation measurements of three groups of patients with general CRC were downloaded from public domain databases. Probes with DNA methylation levels that differed significantly between patients with sporadic MSS CRC and FCCTX were examined, to explore their potential as biomarkers. Results: We found that MSS HNPCC tumors were overwhelmingly hypomethylated compared with those from patient groups with other types of CRC, including germ-line MLH1/MSH2-mutated HNPCC and sporadic MSS CRC. Five gene-marker panels that exhibited a sensitivity of 100% and a specificity higher than 90% in both discovery and validation cohorts were proposed to distinguish MSS HNPCC tumors from sporadic MSS CRC. Conclusions: Our results warrant further investigation and validation. The loci identified here may become useful biomarkers for distinguishing between FCCTX and sporadic MSS CRC tumors.
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21
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A Practical Approach to the Evaluation of Gastrointestinal Tract Carcinomas for Lynch Syndrome. Am J Surg Pathol 2016; 40:e17-34. [DOI: 10.1097/pas.0000000000000620] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Villacis RAR, Miranda PM, Gomy I, Santos EMM, Carraro DM, Achatz MI, Rossi BM, Rogatto SR. Contribution of rare germline copy number variations and common susceptibility loci in Lynch syndrome patients negative for mutations in the mismatch repair genes. Int J Cancer 2015; 138:1928-35. [PMID: 26620301 DOI: 10.1002/ijc.29948] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023]
Abstract
In colorectal carcinoma (CRC), 35% of cases are known to have a hereditary component, while a lower proportion (∼ 5%) can be explained by known genetic factors. In this study, copy number variations (CNVs) were evaluated in 45 unrelated patients with clinical hypothesis of Lynch syndrome (Amsterdam or Bethesda criteria); negative for MLH1, MSH2, MSH6, PMS2, CHEK2*1100delC and TP53 pathogenic mutations; aiming to reveal new predisposing genes. Analyses with two different microarray platforms (Agilent 180K and Affymetrix CytoScan HD) revealed 35 rare CNVs covering 67 known genes in 22 patients. Gains (GALNT6 and GALNT11) and losses (SEMA3C) involving the same gene families related to CRC susceptibility were found among the rare CNVs. Segregation analysis performed on four relatives from one family suggested the involvement of GALNT11 and KMT2C in those at risk of developing CRC. Notably, in silico molecular analysis revealed that 61% (41/67) of the genes covered by rare CNVs were associated with cancer, mainly colorectal (17 genes). Ten common SNPs, previously associated with CRC, were genotyped in 39 index patients and 100 sporadic CRC cases. Although no significant, an increased number of risk alleles was detected in the index cases compared with the sporadic CRC patients. None of the SNPs were covered by CNVs, suggesting an independent effect of each alteration in cancer susceptibility. In conclusion, rare germline CNVs and common SNPs may contribute to an increased risk for hereditary CRC in patients with mismatch repair proficiency.
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Affiliation(s)
- Rolando A R Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Priscila M Miranda
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Israel Gomy
- Institute of Hematology and Oncology, Faculties Little Prince, Curitiba, PR, Brazil
| | | | - Dirce M Carraro
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Silvia R Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil.,Department of Urology, Faculty of Medicine, University of São Paulo State (UNESP), Botucatu, SP, Brazil
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23
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Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X. Nat Commun 2014; 5:5191. [PMID: 25307848 PMCID: PMC4214414 DOI: 10.1038/ncomms6191] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is characterized by clinical features of hereditary non-polyposis colorectal cancer with a yet undefined genetic background. Here we identify the SEMA4A p.Val78Met germline mutation in an Austrian kindred with FCCTX, using an integrative genomics strategy. Compared with wild-type protein, SEMA4A(V78M) demonstrates significantly increased MAPK/Erk and PI3K/Akt signalling as well as cell cycle progression of SEMA4A-deficient HCT-116 colorectal cancer cells. In a cohort of 53 patients with FCCTX, we depict two further SEMA4A mutations, p.Gly484Ala and p.Ser326Phe and the single-nucleotide polymorphism (SNP) p.Pro682Ser. This SNP is highly associated with the FCCTX phenotype exhibiting increased risk for colorectal cancer (OR 6.79, 95% CI 2.63 to 17.52). Our study shows previously unidentified germline variants in SEMA4A predisposing to FCCTX, which has implications for surveillance strategies of patients and their families.
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