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Wills C, Houseman A, Watts K, Maughan TS, Fisher D, Houlston RS, West HD, Escott-Price V, Cheadle JP. Relationship between 233 colorectal cancer risk loci and survival in 1926 patients with advanced disease. BJC REPORTS 2023; 1:2. [PMID: 38665548 PMCID: PMC11041780 DOI: 10.1038/s44276-023-00003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 04/28/2024]
Abstract
Background Genome, transcriptome and methylome-wide association studies have identified single-nucleotide polymorphisms (SNPs) or genes at 258 loci associated with colorectal cancer (CRC) risk. We studied the relationship between these and patient outcome. Methods We studied 1926 unrelated patients with advanced CRC from COIN and COIN-B. Of 205 CRC-risk SNPs, 19 were directly genotyped and 162 were imputed, and of 53 risk genes, 52 were tested. An additive Cox model for overall survival was adjusted for known prognostic factors. For nominally significant SNPs or genes, we considered a recessive model with a Bonferroni corrected threshold of P = 2.1 × 10-4. We examined SNPs as expression quantitative trait loci (eQTL) and the relationship between gene expression in colorectal tumours and survival in 597 unrelated patients. Results Eleven SNPs or genes were nominally associated with survival under an additive model. Only rs117079142 mapping to UTP23 and EIF3H (Hazard Ratio [HR] = 2.79, 95% Confidence Intervals [CI] = 1.70-4.58, P = 4.7 × 10-5) and rs9924886 mapping to CDH1 and CDH3 (HR = 1.24, 95% CI = 1.12-1.38, P = 5.2 × 10-5) passed the multiple testing threshold under a recessive model. rs117079142 was an eQTL for UTP23 and rs9924886 for CDH1, CDH3 and ZFP90. Decreased CDH1 expression in CRCs was associated with worse survival (HR = 2.18, 95% CI = 1.3-3.5, P = 1.8 × 10-3). Conclusion rs117079142 and rs9924886 may represent potential prognostic biomarkers for CRC.
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Affiliation(s)
- Christopher Wills
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Amy Houseman
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Katie Watts
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Timothy S. Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - David Fisher
- MRC Clinical Trials Unit, University College of London, 125 Kingsway, London, WC2B 6NH UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP UK
| | - Hannah D. West
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Jeremy P. Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
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Wills C, He Y, Summers MG, Lin Y, Phipps AI, Watts K, Law PJ, Al-Tassan NA, Maughan TS, Kaplan R, Houlston RS, Peters U, Newcomb PA, Chan AT, Buchanan DD, Gallinger S, Marchand LL, Pai RK, Shi Q, Alberts SR, Gray V, West HD, Escott-Price V, Dunlop MG, Cheadle JP. A genome-wide search for determinants of survival in 1926 patients with advanced colorectal cancer with follow-up in over 22,000 patients. Eur J Cancer 2021; 159:247-258. [PMID: 34794066 PMCID: PMC9132154 DOI: 10.1016/j.ejca.2021.09.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND While genome-wide association studies (GWAS) have identified germline variants influencing the risk of developing colorectal cancer (CRC), there has been limited examination of the possible role of inherited variation as a determinant of patient outcome. PATIENTS AND METHODS We performed a GWAS for overall survival (OS) in 1926 patients with advanced CRC from the COIN and COIN-B clinical trials. For single nucleotide polymorphisms (SNPs) showing an association with OS (P < 1.0 × 10-5), we conducted sensitivity analyses based on the time from diagnosis to death and sought independent replications in 5675 patients from the Study of Colorectal Cancer in Scotland (SOCCS) and 16,964 patients from the International Survival Analysis in Colorectal cancer Consortium (ISACC). We analysed the Human Protein Atlas to determine if ERBB4 expression was associated with survival in 438 patients with colon adenocarcinomas. RESULTS The most significant SNP associated with OS was rs79612564 in ERBB4 (hazard ratio [HR] = 1.24, 95% confidence interval [CI] = 1.16-1.32, P = 1.9 × 10-7). SNPs at 17 loci had suggestive associations for OS and all had similar effects on the time from diagnosis to death. No lead SNPs were independently replicated in the meta-analysis of all patients from SOCCS and ISACC. However, rs79612564 was significant in stage-IV patients from SOCCS (P = 2.1 × 10-2) but not ISACC (P = 0.89) and SOCCS combined with COIN and COIN-B attained genome-wide significance (P = 1.7 × 10-8). Patients with high ERBB4 expression in their colon adenocarcinomas had worse survival (HR = 1.50, 95% CI = 1.1-1.9, P = 4.6 × 10-2). CONCLUSIONS Genetic and expression data support a potential role for rs79612564 in the receptor tyrosine kinase ERBB4 as a predictive biomarker of survival.
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Affiliation(s)
- Christopher Wills
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Yazhou He
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Department of Oncology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610000, China
| | - Matthew G Summers
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Yi Lin
- Epidemiology Department, University of Washington, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda I Phipps
- Epidemiology Department, University of Washington, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katie Watts
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nada A Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, University College of London, 125 Kingsway, London, WC2B 6NH, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ulrike Peters
- Epidemiology Department, University of Washington, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Polly A Newcomb
- Epidemiology Department, University of Washington, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Loic L Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Rish K Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Qian Shi
- Department of Quantitative Science, Mayo Clinic, Rochester, MN, USA
| | | | - Victoria Gray
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Hannah D West
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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Summers MG, Maughan TS, Kaplan R, Law PJ, Houlston RS, Escott-Price V, Cheadle JP. Comprehensive analysis of colorectal cancer-risk loci and survival outcome: A prognostic role for CDH1 variants. Eur J Cancer 2020; 124:56-63. [PMID: 31734605 DOI: 10.1016/j.ejca.2019.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/29/2022]
Abstract
PURPOSE Genome-wide association studies have identified common single nucleotide polymorphisms (SNPs) at 83 loci associated with colorectal cancer (CRC) risk in European populations. Because germline variation can also influence patient outcome, we studied the relationship between these SNPs and CRC survivorship. EXPERIMENTAL DESIGN For the 83 risk loci, 10 lead SNPs were directly genotyped, 72 were imputed and 1 was not genotyped nor imputed, in 1948 unrelated patients with advanced CRC from the clinical trials COIN and COIN-B (oxaliplatin and fluoropyrimidine chemotherapy ± cetuximab). A Cox survival model was used for each variant, and variants classified by pathway, adjusting for known prognostic factors. We imposed a Bonferroni threshold of P = 6.6 × 10-4 for multiple testing. We carried out meta-analyses of published risk SNPs associated with survival. RESULTS Univariate analysis identified six SNPs associated with overall survival (OS) (P < 0.05); however, only rs9939049 in CDH1 remained significant beyond the Bonferroni threshold (Hazard Ratio [HR] 1.44, 95% Confidence Intervals [CI]: 1.21-1.71, P = 5.0 × 10-5). Fine mapping showed that rs12597188 was the most significant SNP at this locus and remained significant after adjustment for known prognostic factors beyond multiple testing thresholds (HR 1.23, 95% CI: 1.13-1.34, P = 1.9 × 10-6). rs12597188 was also associated with poor response to therapy (OR 0.61, 95% CI: 0.42-0.87, P = 6.6 × 10-3). No combinations of SNPs within pathways were more significantly associated with survival compared with single variants alone, and no other risk SNPs were associated with survival in meta-analyses. CONCLUSIONS The CRC susceptibility SNP rs9939049 in CDH1 influences patient survival and warrants further evaluation as a prognostic biomarker.
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Affiliation(s)
- Matthew G Summers
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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He Y, Theodoratou E, Li X, Din FV, Vaughan‐Shaw P, Svinti V, Farrington SM, Campbell H, Dunlop MG, Timofeeva M. Effects of common genetic variants associated with colorectal cancer risk on survival outcomes after diagnosis: A large population-based cohort study. Int J Cancer 2019; 145:2427-2432. [PMID: 31271446 PMCID: PMC6771941 DOI: 10.1002/ijc.32550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/06/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
Genome-wide association studies have thus far identified 130 genetic variants linked to colorectal cancer (CRC) risk (r2 < 0.2). Given their implication in disease causation, and thus plausible biologically effects on cancer-relevant biological pathways, we investigated whether these variants are associated with CRC prognosis and also whether they might provide predictive value for survival outcome. We conducted the analysis in a well-characterized population-based study of 5,675 patients after CRC diagnosis in Scotland. None of the genetic risk variants were associated with either overall survival (OS) or CRC-specific survival. Next, we combined the variants in a polygenic risk score, but again we observed no association between survival outcome and overall genetic susceptibility to CRC risk-as defined by common genetic variants (OS: hazard ratio = 1.00, 95% confidence interval = 0.96-1.05). Furthermore, we found no incremental increase in the discriminative performance when adding these genetic variants to the baseline CRC-survival predictive model of age, sex and stage at diagnosis. Given that our study is well-powered (>0.88) to detect effects on survival for 74% of the variants, we conclude that effects of common variants associated with CRC risk which have been identified to date are unlikely to have clinically relevant effect on survival outcomes for patients diagnosed with CRC.
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Affiliation(s)
- Yazhou He
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Xue Li
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Farhat V.N. Din
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Peter Vaughan‐Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Susan M. Farrington
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Harry Campbell
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Malcolm G. Dunlop
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Maria Timofeeva
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
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Wang SQ, Cui SX, Qu XJ. Metformin inhibited colitis and colitis-associated cancer (CAC) through protecting mitochondrial structures of colorectal epithelial cells in mice. Cancer Biol Ther 2018; 20:338-348. [PMID: 30359174 DOI: 10.1080/15384047.2018.1529108] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although a mountain of papers have showed that metformin plays a role in inhibiting cancers, but the mechanism underpinning this has not yet fully elucidated. Herein, we used AOM/DSS model, the clinicopathological features are similar to those found in humans, to investigate the effects of metformin as well as combination with 5-FU in the prevention of colitis and colitis associated cancer (CAC). Oral metformin significantly inhibited DSS-induced ulcerative colitis and AOM/DSS-induced CAC. Metformin also ameliorated 5-FU-induced colorectal gastrointestinal symptoms in mice. Metformin combination with 5-FU strongly inhibited colorectal cancer. Metformin reduced levels of the NFκB signaling components p-IKKα/β, p-NFκB, p-IκBα in colorectal mucosal cells. Transmission electron microscopy analysis suggested that the inhibition of metformin on colitis and CAC might associate with its biological activity of protecting mitochondrial structures of colorectal epithelial cells. Further analysis by Mito Tracker Red staining assay indicated that metformin prevented H2O2-induced mitochondrial fission correlated with a decrease of mitochondrial perimeter. In addition, metformin increased the level of NDUFA9, a Q-module subunit required for complex I assembly, in colorectal epithelial cells. These observations of metformin in the inhibition of colitis and CAC might associate with its activity of activating the LKB1/AMPK pathway in colorectal epithelial cells. In conclusion, metformin inhibited colitis and CAC through protecting the mitochondrial structures of colorectal epithelial cells.
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Affiliation(s)
- Shu-Qing Wang
- a Department of Pharmacology , School of Basic Medical Sciences, Capital Medical University , Beijing , China
| | - Shu-Xiang Cui
- b Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry , School of Public Health, Capital Medical University , Beijing , China
| | - Xian-Jun Qu
- a Department of Pharmacology , School of Basic Medical Sciences, Capital Medical University , Beijing , China
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Song N, Kim K, Shin A, Park JW, Chang HJ, Shi J, Cai Q, Kim DY, Zheng W, Oh JH. Colorectal cancer susceptibility loci and influence on survival. Genes Chromosomes Cancer 2018; 57:630-637. [DOI: 10.1002/gcc.22674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Nan Song
- Cancer Research Institute; Seoul National University College of Medicine; Seoul South Korea
| | - Kyeezu Kim
- Division of Epidemiology and Biostatistics; University of Illinois at Chicago School of Public Health; Chicago Illinois
| | - Aesun Shin
- Cancer Research Institute; Seoul National University College of Medicine; Seoul South Korea
- Department of Preventive Medicine; Seoul National University College of Medicine; Seoul South Korea
- Molecular Epidemiology Branch, National Cancer Center; Goyang South Korea
| | - Ji Won Park
- Department of Surgery; Seoul National University College of Medicine and Hospital; Seoul South Korea
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Hee Jin Chang
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Dae Yong Kim
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
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Li D, Zhang R, Jin T, He N, Ren L, Zhang Z, Zhang Q, Xu R, Tao H, Zeng G, Gao J. ADH1B and CDH1 polymorphisms predict prognosis in male patients with non-metastatic laryngeal cancer. Oncotarget 2018; 7:73216-73228. [PMID: 27689323 PMCID: PMC5341974 DOI: 10.18632/oncotarget.12301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/20/2016] [Indexed: 01/10/2023] Open
Abstract
In this study, we assessed the association between single nucleotide polymorphisms (SNPs) in candidate genes and the prognosis of laryngeal cancer (LC) patients. Thirty-seven SNPs in 26 genes were genotyped in 170 male Han Chinese patients with LC. The effects of the candidate genes on the prognosis of LC patients were evaluated using Kaplan-Meier curves and Cox proportional hazards regression models. The GA genotype of rs1229984 (hazard ratio [HR], 0.537; 95% confidence interval [CI], 0.340-0.848; p = 0.008) in alcohol dehydrogenase 1B (ADH1B), and the AA genotype of rs9929218 (HR, 6.074; 95% CI, 1.426-25.870; p = 0.015) in CDH1 were associated with overall survival. Our data suggest that polymorphisms in ADH1B and CDH1 may be prognostic indicators in LC.
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Affiliation(s)
- Daxu Li
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Ruizhi Zhang
- Department of Stomatology, Ankang Central Hospital, Ankang 725000, Shaanxi
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Na He
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Le Ren
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Zhe Zhang
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Qingna Zhang
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Ran Xu
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Hong Tao
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Guang Zeng
- Department of Plastic and Burn Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Jing Gao
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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8
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Hong Y, Wu G, Li W, Liu D, He K. A comprehensive meta-analysis of genetic associations between five key SNPs and colorectal cancer risk. Oncotarget 2018; 7:73945-73959. [PMID: 27661122 PMCID: PMC5342026 DOI: 10.18632/oncotarget.12154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) on colorectal cancer (CRC) have identified dozens of single nucleotide polymorphisms (SNPs) in more than 19 independent loci associated with CRC. Due to the heterogeneity of the studied subjects and the contrary results, it is challenging to verify the certainty of the association between these loci and CRC.We conducted a critical review of the published studies of SNPs associated with CRC. Five most frequently reported SNPs, which are rs6983267/8q24.21, rs4939827/18q21.1, rs10795668/10p14, rs4444235/14q22.2 and rs4779584/ 15q13.3, were selected for the current study from the qualified studies. Then meta-analyses based on larger sample sizes with average of 33,000 CRC cases and 34,000 controls were performed to assess the association between SNPs and CRC risk. Heterogeneity among studies and publication bias were assessed by the χ2-based Q statistic test Begg's funnel plot or Egger's test, respectively.Our meta-analysis confirmed significant associations of the five SNPs with CRC risk under different genetic models. Two risk variants at rs6983267 {Odds Ratio (OR) 1.388, 95% Confidence Interval (CI) 1.180-1.8633} and rs10795668 (OR 1.323, 95% CI 1.062-1.648) had the highest ORs in homogeneous model. While ORs of the other three variants at rs4939827 {OR 1.298, 95% CI 1.135-1.483}, rs4779584 (OR 1.261, 95% CI 1.146-1.386) and rs4444235 (OR 1.160, 95% CI 1.106-1.216) were also statistically significant. Sensitivity analyses and publication bias assessment indicated the robust stability and reliability of the results.
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Affiliation(s)
- Yi Hong
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Guoying Wu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Wei Li
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Kan He
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China.,Department of Biostatistics, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
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9
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Spanou E, Kalisperati P, Pateras IS, Papalampros A, Barbouti A, Tzioufas AG, Kotsinas A, Sougioultzis S. Genetic Variability as a Regulator of TLR4 and NOD Signaling in Response to Bacterial Driven DNA Damage Response (DDR) and Inflammation: Focus on the Gastrointestinal (GI) Tract. Front Genet 2017; 8:65. [PMID: 28611823 PMCID: PMC5447025 DOI: 10.3389/fgene.2017.00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
The fundamental role of human Toll-like receptors (TLRs) and NOD-like receptors (NLRs), the two most studied pathogen recognition receptors (PRRs), is the protection against pathogens and excessive tissue injury. Recent evidence supports the association between TLR/NLR gene mutations and susceptibility to inflammatory, autoimmune, and malignant diseases. PRRs also interfere with several cellular processes, such as cell growth, apoptosis, cell proliferation, differentiation, autophagy, angiogenesis, cell motility and migration, and DNA repair mechanisms. We briefly review the impact of TLR4 and NOD1/NOD2 and their genetic variability in the process of inflammation, tumorigenesis and DNA repair, focusing in the gastrointestinal tract. We also review the available data on new therapeutic strategies utilizing TLR/NLR agonists and antagonists for cancer, allergic diseases, viral infections and vaccine development against both infectious diseases and cancer.
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Affiliation(s)
- Evagelia Spanou
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Polyxeni Kalisperati
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Ioannis S. Pateras
- Department of Histology and Embryology, University of AthensAthens, Greece
| | - Alexandros Papalampros
- 1st Department of Surgery, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Alexandra Barbouti
- Department of Anatomy-Histology-Embryology, University of IoanninaIoannina, Greece
| | - Athanasios G. Tzioufas
- Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | | | - Stavros Sougioultzis
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
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10
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Domingo E, Freeman-Mills L, Rayner E, Glaire M, Briggs S, Vermeulen L, Fessler E, Medema JP, Boot A, Morreau H, van Wezel T, Liefers GJ, Lothe RA, Danielsen SA, Sveen A, Nesbakken A, Zlobec I, Lugli A, Koelzer VH, Berger MD, Castellví-Bel S, Muñoz J, de Bruyn M, Nijman HW, Novelli M, Lawson K, Oukrif D, Frangou E, Dutton P, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church DN. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study. Lancet Gastroenterol Hepatol 2016; 1:207-216. [PMID: 28404093 DOI: 10.1016/s2468-1253(16)30014-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Precision cancer medicine depends on defining distinct tumour subgroups using biomarkers that may occur at very modest frequencies. One such subgroup comprises patients with exceptionally mutated (ultramutated) cancers caused by mutations that impair DNA polymerase epsilon (POLE) proofreading. METHODS We examined the association of POLE proofreading domain mutation with clinicopathological variables and immune response in colorectal cancers from clinical trials (VICTOR, QUASAR2, and PETACC-3) and colorectal cancer cohorts (Leiden University Medical Centre 1 and 2, Oslo 1 and 2, Bern, AMC-AJCC-II, and Epicolon-1). We subsequently investigated its association with prognosis in stage II/III colorectal cancer by Cox regression of pooled individual patient data from more than 4500 cases from these studies. FINDINGS Pathogenic somatic POLE mutations were detected in 66 (1·0%) of 6517 colorectal cancers, and were mutually exclusive with mismatch repair deficiency (MMR-D) in the 6277 cases for whom both markers were determined (none of 66 vs 833 [13·4%] of 6211; p<0·0001). Compared with cases with wild-type POLE, cases with POLE mutations were younger at diagnosis (median 54·5 years vs 67·2 years; p<0·0001), were more frequently male (50 [75·8%] of 66 vs 3577 [55·5%] of 6445; p=0·0010), more frequently had right-sided tumour location (44 [68·8%] of 64 vs 2463 [39·8%] of 6193; p<0·0001), and were diagnosed at an earlier disease stage (p=0·006, χ2 test for trend). Compared with mismatch repair proficient (MMR-P) POLE wild-type tumours, POLE-mutant colorectal cancers displayed increased CD8+ lymphocyte infiltration and expression of cytotoxic T-cell markers and effector cytokines, similar in extent to that observed in immunogenic MMR-D cancers. Both POLE mutation and MMR-D were associated with significantly reduced risk of recurrence compared with MMR-P colorectal cancers in multivariable analysis (HR 0·34 [95% CI 0·11-0·76]; p=0·0060 and 0·72 [0·60-0·87]; p=0·00035), although the difference between the groups was not significant. INTERPRETATION POLE proofreading domain mutations identify a subset of immunogenic colorectal cancers with excellent prognosis. This association underscores the importance of rare biomarkers in precision cancer medicine, but also raises important questions about how to identify and implement them in practice. FUNDING Cancer Research UK, Academy of Medical Sciences, Health Foundation, EU, ERC, NIHR, Wellcome Trust, Dutch Cancer Society, Dutch Digestive Foundation.
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Affiliation(s)
- Enric Domingo
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Emily Rayner
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Mark Glaire
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK
| | - Sarah Briggs
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Louis Vermeulen
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Evelyn Fessler
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Jan Paul Medema
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden, Netherlands
| | | | | | | | - Ragnhild A Lothe
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Stine A Danielsen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Gastrointestinal Surgery, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Institute of Pathology, University of Bern, Bern, Switzerland
| | - Martin D Berger
- Department of Medical Oncology, University Hospital of Bern, Bern, Switzerland
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Kay Lawson
- Department of Histopathology, UCL, London, UK
| | | | - Eleni Frangou
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Peter Dutton
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sabine Tejpar
- Department of Molecular Digestive Oncology, University of Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute Bioinformatics, Lausanne, Switzerland
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK
| | - David Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David N Church
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK.
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11
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Sheng WY, Yong Z, Yun Z, Hong H, Hai LL. Toll-like receptor 4 gene polymorphisms and susceptibility to colorectal cancer: a meta-analysis and review. Arch Med Sci 2015; 11:699-707. [PMID: 26322080 PMCID: PMC4548027 DOI: 10.5114/aoms.2015.53288] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/11/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Many case-control studies have investigated the association between toll-like receptor 4 (TLR4) Asp299Gly and Thr399Ile polymorphisms and risk of colorectal cancer (CRC). However, published data are still conflicting. MATERIAL AND METHODS A systematic search was conducted in the electronic databases of PubMed, MEDLINE, EMBASE, Web of Science and CNKI between 2000 and 2014. The associations between TLR4 polymorphisms and CRC susceptibility were assessed by pooled odds ratios (ORs) and 95% confidence intervals (95% CI) in fixed or random effects models. RESULTS In total nine case-control studies were identified in this meta-analysis. For TLR4 Asp299Gly polymorphism, 9 studies included 1198 cases and 1290 controls. The GG genotype carriers had higher risk for developing CRC than AA + GA genotype carriers (OR = 1.95, 95% CI: 1.00-3.77, p = 0.05). No association was found in other genetic models (p > 0.05). Analysis stratified by ethnicity showed no association in any genetic models among the Asian or Caucasian population. For TLR4 Thr399Ile polymorphism, 6 studies contained 619 cases and 632 controls. The overall analysis showed significantly increased risk in TT homozygote carriers compared to CC homozygote (OR = 4.99, 95% CI: 1.41-17.65, p = 0.01) and C carriers (TC + CC) (OR = 4.50, 95% CI: 1.27-15.87, p = 0.02). In terms of analyses stratified by race, a significant association was found in each genetic model among the Asian population, rather than the Caucasian group. CONCLUSIONS The GG homozygote carriers of TLR4 Asp299Gly and TT homozygote carriers of TLR4 Thr399Ile polymorphisms might be correlated with an increased risk of CRC, suggesting they may serve as genetic risk factors for CRC.
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Affiliation(s)
| | - Zhang Yong
- The People's Hospital of Yuxi, Yuxi, China
| | - Zhu Yun
- The People's Hospital of Yuxi, Yuxi, China
| | - Hu Hong
- The People's Hospital of Yuxi, Yuxi, China
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12
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Wang C, Jia Z, Cao D, You L, Jin M, Wu X, Wen S, Cao X, Jiang J. Polymorphism of DNA Methyltransferase 3b and Association with Development and Prognosis in Gastric Cancer. PLoS One 2015; 10:e0134059. [PMID: 26262893 PMCID: PMC4532499 DOI: 10.1371/journal.pone.0134059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/03/2015] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE DNA methyltransferase 3b (DNMT3b) plays an important role in abnormal methylation during tumorigenesis. Polymorphism of the DNMT3b gene may influence DNMT3b activity and be associated with cancer risk. This study aimed to investigate the association between single nucleotide polymorphisms (SNPs) of the DNMT3b gene and susceptibility and prognosis of gastric cancer. METHODS Four hundred and forty-seven histologically-confirmed gastric cancer cases, 111 gastric atrophy cases and 961 tumor-free controls were enrolled into the study. Five tag SNPs (rs6119954, rs1569686, rs4911107, rs4911259 and rs8118663) of the DNMT3b gene were genotyped by TaqMan assay. DNMT3b expression was evaluated in 104 cancer tissues by immunohistochemistry method. RESULTS The median follow-up time for 422 gastric patients with prognosis information was 55.1 (51.8-58.5) month. We found that individuals with the rs1569686 variant genotype (TG/GG) were significantly associated with poor prognosis in gastric cancer compared to those carrying the TT genotype (HR = 1.43, 95%CI: 1.02-1.99). This trend was more evident in the long-term survival of gastric cancer. Similar results were observed for the G allele carriers of rs4911107 and T allele carriers of rs4911259 as these two sites were in complete linkage disequilibrium with rs1569686. The rs8118663 GG carriers tended to live shorter than AA/AG genotype (HR = 2.72, 95%CI: 1.45-5.12) in patients living longer than 2.0 years. None of the five SNPs was associated with the risks of gastric cancer or gastric atrophy. And no relationship was found between each of the five SNPs and DNMT3b expression. CONCLUSIONS This study provides evidence that DNMT3b polymorphisms may predict long-term survival of gastric cancer. However, further studies are needed to reveal the underlying biological roles of DNMT3b polymorphism.
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Affiliation(s)
- Chuan Wang
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Zhifang Jia
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Donghui Cao
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Lili You
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Meishan Jin
- Division of Pathology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xing Wu
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Simin Wen
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Jing Jiang
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
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13
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Smith CG, Fisher D, Harris R, Maughan TS, Phipps AI, Richman S, Seymour M, Tomlinson I, Rosmarin D, Kerr D, Chan AT, Peters U, Newcomb PA, Idziaszczyk S, West H, Meade A, Kaplan R, Cheadle JP. Analyses of 7,635 Patients with Colorectal Cancer Using Independent Training and Validation Cohorts Show That rs9929218 in CDH1 Is a Prognostic Marker of Survival. Clin Cancer Res 2015; 21:3453-61. [PMID: 25873087 PMCID: PMC4526710 DOI: 10.1158/1078-0432.ccr-14-3136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/06/2015] [Indexed: 01/05/2023]
Abstract
PURPOSE Genome-wide association studies have identified numerous loci associated with colorectal cancer risk. Several of these have also been associated with patient survival, although none have been validated. Here, we used large independent training and validation cohorts to identify robust prognostic biomarkers for colorectal cancer. EXPERIMENTAL DESIGN In our training phase, we analyzed 20 colorectal cancer-risk SNPs from 14 genome-wide associated loci, for their effects on survival in 2,083 patients with advanced colorectal cancer. A Cox survival model was used, stratified for treatment, adjusted for known prognostic factors, and corrected for multiple testing. Three SNPs were subsequently analyzed in an independent validation cohort of 5,552 colorectal cancer patients. A validated SNP was analyzed by disease stage and response to treatment. RESULTS Three variants associated with survival in the training phase; however, only rs9929218 at 16q22 (intron 2 of CDH1, encoding E-cadherin) was significant in the validation phase. Patients homozygous for the minor allele (AA genotype) had worse survival (training phase HR, 1.43; 95% confidence intervals; CI, 1.20-1.71, P = 5.8 × 10(-5); validation phase HR, 1.18; 95% CI, 1.01-1.37, P = 3.2 × 10(-2); combined HR, 1.28; 95% CI, 1.14-1.43, P = 2.2 × 10(-5)). This effect was independent of known prognostic factors, and was significant amongst patients with stage IV disease (P = 2.7 × 10(-5)). rs9929218 was also associated with poor response to chemotherapy (P = 3.9 × 10(-4)). CONCLUSIONS We demonstrate the potential of common inherited genetic variants to inform patient outcome and show that rs9929218 identifies approximately 8% of colorectal cancer patients with poor prognosis. rs9929218 may affect CDH1 expression and E-cadherin plays a role in epithelial-to-mesenchymal transition providing a mechanism underlying its prognostic potential. Clin Cancer Res; 21(15); 3453-61. ©2015 AACR.
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Affiliation(s)
- Christopher G Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David Fisher
- MRC Clinical Trials Unit, Aviation House, London, United Kingdom
| | - Rebecca Harris
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Amanda I Phipps
- Epidemiology Department, University of Washington, Seattle, Washington. Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Susan Richman
- Wellcome Trust Brenner Building, St James' University Hospital, University of Leeds, Leeds, United Kingdom
| | - Matthew Seymour
- Wellcome Trust Brenner Building, St James' University Hospital, University of Leeds, Leeds, United Kingdom
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dan Rosmarin
- Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ulrike Peters
- Epidemiology Department, University of Washington, Seattle, Washington. Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Polly A Newcomb
- Epidemiology Department, University of Washington, Seattle, Washington. Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shelley Idziaszczyk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Hannah West
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Angela Meade
- MRC Clinical Trials Unit, Aviation House, London, United Kingdom
| | - Richard Kaplan
- MRC Clinical Trials Unit, Aviation House, London, United Kingdom
| | - Jeremy P Cheadle
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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14
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Nucleotide variants of the cancer predisposing gene CDH1 and the risk of non-syndromic cleft lip with or without cleft palate. Fam Cancer 2015; 13:415-21. [PMID: 24838934 PMCID: PMC4164844 DOI: 10.1007/s10689-014-9727-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The CDH1 gene plays an important role during carcinogenesis and craniofacial morphogenesis. Germline mutations in this gene have been described in families presenting syndromic diffuse gastric cancer and orofacial clefts. The aim of this study was to evaluate the association between nucleotide variants of CDH1 and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). Six single nucleotide polymorphisms (SNPs) of the CDH1 gene (rs16260, rs9929218, rs7186053, rs4783573, rs16958383, and rs1801552) were genotyped using the TaqMan SNP genotyping assays in 250 patients with NSCL/P and 540 controls from the Polish population. Comparison between patient and control groups showed that the CDH1 rs1801552 variant, under the assumption of recessive model, was associated with a two-fold decrease in the risk of NSCL/P (ORTT vs CT + CC = 0.481, 95 % CI 0.281–0.824, p = 0.007). This association remained statistically significant even after the multiple testing correction. No significant associations with NSCL/P risk were found for the other five tested SNPs. We found a strong association between the cancer predisposing gene CDH1 and the risk of NSCL/P in the Polish population. This result, together with previous observations of co-occurrence of orofacial clefts and a variety of cancer types, suggests the need for replication studies testing rs1801552 in NSCL/P cohorts with a known cancer history.
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15
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A subset of genetic susceptibility variants for colorectal cancer also has prognostic value. THE PHARMACOGENOMICS JOURNAL 2015; 16:173-9. [PMID: 25963333 DOI: 10.1038/tpj.2015.35] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 02/03/2015] [Accepted: 03/24/2015] [Indexed: 01/25/2023]
Abstract
We investigated the possible influence of 86 single-nucleotide polymorphisms (SNPs), known to associate with the risk of colorectal cancer (CRC), on overall survival and time to recurrence (TTR) in 733 Italian CRC patients followed up for up to 84 months after surgery. In the Cox multivariate analysis, adjusted for gender, age, pathological stage and adjuvant chemotherapy (yes/no), the risk of death significantly increased by rare allele count (P<0.05) for rs1801133 (MTHFR), rs4939827 (SMAD7), rs2306283 (SLCO1B1) and rs12898159 (BMP4), whereas for rs736775 (GPX3) the opposite was observed. Two additional SNPs associated with TTR, namely rs16892766 (downstream of EIF3H) and rs10749971 (COLCA2). Our findings show that some genetic variants previously found to associate with CRC risk are also associated with survival after treatment. The identification of alleles defining subgroups of patients with worse clinical outcome may have application in developing pharmacogenetic strategies aimed at personalizing CRC treatment.
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16
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Linnekamp JF, Wang X, Medema JP, Vermeulen L. Colorectal cancer heterogeneity and targeted therapy: a case for molecular disease subtypes. Cancer Res 2015; 75:245-9. [PMID: 25593032 DOI: 10.1158/0008-5472.can-14-2240] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Personalized cancer medicine is becoming increasingly important in colorectal cancer treatment. Especially for targeted therapies, large variations between individual treatment responses exist. Predicting therapy response is of utmost significance, as it prevents overtreatment and adverse effects in patients. For EGFR-targeted therapy, many mechanisms of resistance have been uncovered, for example, mutations in KRAS and BRAF, and upregulation of alternative receptors. Currently, routine testing for all known modifiers of response is unpractical, and as a result, decision-making for anti-EGFR therapy is still largely based on assessing the mutation status of an individual gene (KRAS). Recently, comprehensive classifications of colorectal cancer have been presented that integrate many of the (epi-)genetic and microenvironmental factors that contribute to colorectal cancer heterogeneity. These classification systems are not only of prognostic value but also predict therapy efficacy, including the response to anti-EGFR agents. Therefore, molecular subtype-based stratification to guide therapeutic decisions is a promising new strategy that might overcome the shortcomings of single gene testing in colorectal cancer as well as in other malignancies. Furthermore, the development of new agents in a disease subtype-specific fashion has the potential to transform drug-discovery studies and generate novel, more effective therapies.
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Affiliation(s)
- Janneke F Linnekamp
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Xin Wang
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Jan Paul Medema
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands.
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17
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Morris EJA, Penegar S, Whiffin N, Broderick P, Bishop DT, Northwood E, Quirke P, Finan P, Houlston RS. A retrospective observational study of the relationship between single nucleotide polymorphisms associated with the risk of developing colorectal cancer and survival. PLoS One 2015; 10:e0117816. [PMID: 25710502 PMCID: PMC4339731 DOI: 10.1371/journal.pone.0117816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/31/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND There is variability in clinical outcome for patients with apparently the same stage colorectal cancer (CRC). Single nucleotide polymorphisms (SNPs) mapping to chromosomes 1q41, 3q26.2, 6p21, 8q23.3, 8q24.21, 10p14, 11q13, 11q23.1, 12q13.13, 14q22, 14q22.2, 15q13.3, 16q22.1, 18q21.1, 19q13.11, 20p12, 20p12.3, 20q13.33 and Xp22 have robustly been shown to be associated with the risk of developing CRC. Since germline variation can also influence patient outcome the relationship between these SNPs and patient survivorship from CRC was examined. METHODS All enrolled into the National Study of Colorectal Cancer Genetics (NSCCG) were genotyped for 1q41, 3q26.2, 6p21, 8q23.3, 8q24.21, 10p14, 11q13, 11q23.1, 12q13.13, 14q22, 14q22.2, 15q13.3, 16q22.1, 18q21.1, 19q13.11, 20p12, 20p12.3, 20q13.33 and xp22 SNPs. Linking this information to the National Cancer Data Repository allowed patient genotype to be related to survival. RESULTS The linked dataset consisted of 4,327 individuals. 14q22.22 genotype defined by the SNP rs4444235 showed a significant association with overall survival. Specifically, the C allele was associated with poorer observed survival (per allele hazard ratio 1.13, 95% confidence interval 1.05-1.22, P = 0.0015). CONCLUSION The CRC susceptibility SNP rs4444235 also appears to exert an influence in modulating patient survival and warrants further evaluation as a potential prognostic marker.
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Affiliation(s)
- Eva J. A. Morris
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Steve Penegar
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, United Kingdom
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, United Kingdom
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Emma Northwood
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Philip Quirke
- Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Level 4 Wellcome Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paul Finan
- John Goligher Colorectal Unit, Leeds Teaching Hospitals, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, United Kingdom
- National Cancer Intelligence Network, 18 Floor Portland House, Bressenden Place, London, SW1E 5RS, United Kingdom
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, United Kingdom
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18
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Single nucleotide polymorphisms associated with colorectal cancer susceptibility and loss of heterozygosity in a Taiwanese population. PLoS One 2014; 9:e100060. [PMID: 24968322 PMCID: PMC4072675 DOI: 10.1371/journal.pone.0100060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/22/2014] [Indexed: 01/01/2023] Open
Abstract
Given the significant racial and ethnic diversity in genetic variation, we are intrigued to find out whether the single nucleotide polymorphisms (SNPs) identified in genome-wide association studies of colorectal cancer (CRC) susceptibility in East Asian populations are also relevant to the population of Taiwan. Moreover, loss of heterozygosity (LOH) may provide insight into how variants alter CRC risk and how regulatory elements control gene expression. To investigate the racial and ethnic diversity of CRC-susceptibility genetic variants and their relevance to the Taiwanese population, we genotyped 705 CRC cases and 1,802 healthy controls (Taiwan Biobank) for fifteen previously reported East Asian CRC-susceptibility SNPs and four novel genetic variants identified by whole-exome sequencing. We found that rs10795668 in FLJ3802842 and rs4631962 in CCND2 were significantly associated with CRC risk in the Taiwanese population. The previously unreported rs1338565 was associated with a significant increased risk of CRC. In addition, we also genotyped tumor tissue and paired adjacent normal tissues of these 705 CRC cases to search for LOH, as well as risk-associated and protective alleles. LOH analysis revealed preferential retention of three SNPs, rs12657484, rs3802842, and rs4444235, in tumor tissues. rs4444235 has been recently reported to be a cis-acting regulator of BMP4 gene; in this study, the C allele was preferentially retained in tumor tissues (p = 0.0023). rs4631962 and rs10795668 contribute to CRC risk in the Taiwanese and East Asian populations, and the newly identified rs1338565 was specifically associated with CRC, supporting the ethnic diversity of CRC-susceptibility SNPs. LOH analysis suggested that the three CRC risk variants, rs12657484, rs3802842, and rs4444235, exhibited somatic allele-specific imbalance and might be critical during neoplastic progression.
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