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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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2
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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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3
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada
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Brandes N, Linial N, Linial M. Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition. Sci Rep 2021; 11:14901. [PMID: 34290314 PMCID: PMC8295298 DOI: 10.1038/s41598-021-94252-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Studies of genetic cancer predisposition typically identify significant genomic regions based on family-based cohorts or genome-wide association studies (GWAS). However, the results of such studies rarely provide biological insight or functional interpretation. In this study, we conducted a comprehensive analysis of cancer predisposition in the UK Biobank cohort using a new gene-based method for detecting protein-coding genes that are functionally interpretable. Specifically, we conducted proteome-wide association studies (PWAS) to identify genetic associations mediated by alterations to protein function. With PWAS, we identified 110 significant gene-cancer associations in 70 unique genomic regions across nine cancer types and pan-cancer. In 48 of the 110 PWAS associations (44%), estimated gene damage is associated with reduced rather than elevated cancer risk, suggesting a protective effect. Together with standard GWAS, we implicated 145 unique genomic loci with cancer risk. While most of these genomic regions are supported by external evidence, our results also highlight many novel loci. Based on the capacity of PWAS to detect non-additive genetic effects, we found that 46% of the PWAS-significant cancer regions exhibited exclusive recessive inheritance. These results highlight the importance of recessive genetic effects, without relying on familial studies. Finally, we show that many of the detected genes exert substantial cancer risk in the studied cohort determined by a quantitative functional description, suggesting their relevance for diagnosis and genetic consulting.
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Affiliation(s)
- Nadav Brandes
- grid.9619.70000 0004 1937 0538The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nathan Linial
- grid.9619.70000 0004 1937 0538The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Milhem A, Abu Toamih‐Atamni HJ, Karkar L, Houri‐Haddad Y, Iraqi FA. Studying host genetic background effects on multimorbidity of intestinal cancer development, type 2 diabetes and obesity in response to oral bacterial infection and high-fat diet using the collaborative cross (CC) lines. Animal Model Exp Med 2021; 4:27-39. [PMID: 33738434 PMCID: PMC7954829 DOI: 10.1002/ame2.12151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/07/2021] [Indexed: 01/07/2023] Open
Abstract
Background Multimorbidity of intestinal cancer (IC), type 2 diabetes (T2D) and obesity is a complex set of diseases, affected by environmental and genetic risk factors. High-fat diet (HFD) and oral bacterial infection play important roles in the etiology of these diseases through inflammation and various biological mechanisms. Methods To study the complexity of this multimorbidity, we used the collaborative cross (CC) mouse genetics reference population. We aimed to study the multimorbidity of IC, T2D, and obesity using CC lines, measuring their responses to HFD and oral bacterial infection. The study used 63 mice of both sexes generated from two CC lines (IL557 and IL711). For 12 weeks, experimental mice were maintained on specific dietary regimes combined with co-infection with oral bacteria Porphyromonas gingivalis and Fusobacterium nucleatum, while control groups were not infected. Body weight (BW) and results of a intraperitoneal glucose tolerance test (IPGTT) were recorded at the end of 12 weeks, after which length and size of the intestines were assessed for polyp counts. Results Polyp counts ranged between 2 and 10 per CC line. The combination of HFD and infection significantly reduced (P < .01) the colon polyp size of IL557 females to 2.5 cm2, compared to the other groups. Comparing BW gain, IL557 males on HFD gained 18 g, while the females gained 10 g under the same conditions and showed the highest area under curve (AUC) values of 40 000-45 000 (min mg/dL) in the IPGTT. Conclusion The results show that mice from different genetic backgrounds respond differently to a high fat diet and oral infection in terms of polyp development and glucose tolerance, and this effect is gender related.
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Affiliation(s)
- Asal Milhem
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
| | - Hanifa J. Abu Toamih‐Atamni
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
| | - Luna Karkar
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
| | - Yael Houri‐Haddad
- Department of ProsthodonticsDental SchoolThe Hebrew UniversityHadassah JerusalemIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
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6
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Zhang L, Han L, Huang Y, Feng Z, Wang X, Li H, Song F, Liu L, Li J, Zheng H, Wang P, Song F, Chen K. SNPs within microRNA binding sites and the prognosis of breast cancer. Aging (Albany NY) 2021; 13:7465-7480. [PMID: 33658398 PMCID: PMC7993692 DOI: 10.18632/aging.202612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/29/2020] [Indexed: 12/25/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within microRNA binding sites can affect the binding of microRNA to mRNA and regulate gene expression, thereby contributing to cancer prognosis. Here we performed a two-stage study of 2647 breast cancer patients to explore the association between SNPs within microRNA binding sites and breast cancer prognosis. In stage I, we genotyped 192 SNPs within microRNA binding sites using the Illumina Goldengate platform. In stage II, we validated SNPs associated with breast cancer prognosis in another dataset using the TaqMan platform. We identified 8 SNPs significantly associated with breast cancer prognosis in stage I (P<0.05), and only rs10878441 was statistically significant in stage II (AA vs CC, HR=2.21, 95% CI: 1.11-4.42, P=0.024). We combined the data from stage I and stage II, and found that, compared with rs10878441 AA genotype, CC genotype was associated with poor survival of breast cancer (HR=2.19, 95% CI: 1.30-3.70, P=0.003). Stratified analyses demonstrated that rs10878441 was related to breast cancer prognosis in grade II and lymph node-negative patients (P<0.05). The Leucine-rich repeat kinase 2 (LRRK2) rs10878441 CC genotype is associated with poor prognosis of breast cancer in a Chinese population and may be used as a potential prognostic biomarker for breast cancer. • The LRRK2 rs10878441 CC genotype is associated with poor prognosis of breast cancer in a Chinese population. • Stratified analyses demonstrated that rs10878441 was related to breast cancer prognosis in grade II patients and lymph node-negative patients.
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Affiliation(s)
- Liwen Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Lu Han
- Department of Infection Control, Tianjin Huanhu Hospital, Tianjin 300350, People's Republic of China
| | - Yubei Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Ziwei Feng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Xin Wang
- Department of Epidemiology and Biostatistics, West China School of Public Health, Sichuan University, Sichuan 610041, People's Republic of China
| | - Haixin Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China.,Department of Cancer Biobank, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Centre of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Luyang Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Junxian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Peishan Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
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7
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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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8
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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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9
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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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10
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Theodoratou E, Farrington SM, Timofeeva M, Din FV, Svinti V, Tenesa A, Liu T, Lindblom A, Gallinger S, Campbell H, Dunlop MG. Genome-wide scan of the effect of common nsSNPs on colorectal cancer survival outcome. Br J Cancer 2018; 119:988-993. [PMID: 30135471 PMCID: PMC6203849 DOI: 10.1038/s41416-018-0117-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We conducted a genome-wide scan to identify non-synonymous SNPs (nsSNPs) that might influence survival after a diagnosis of colorectal cancer (CRC). METHODS We genotyped 7679 nsSNPs in 1939 Scottish patients from the Scottish Colorectal Cancer Study recruited soon after a CRC diagnosis and prospectively followed for survival outcomes. All-cause and CRC-specific survival analyses were conducted using Cox proportional hazard models adjusted for stage, age and sex for all cancer cases, after cancer type stratification and assuming additive and recessive models of inheritance. For all the SNPs that had a p-value < 0.10 a meta-analysis was performed combining the results of the discovery set and a replication set of 899 Scottish CRC patients. The p-value threshold of significance was set as at p < 10-8. RESULTS 897 and 894 nsSNPs were associated with all-cause and CRC-specific mortality, respectively, at a p-value level < 0.10 in the discovery set. Meta-analysis of the results from the discovery and replication sets was performed overall and for cancers of colon and rectum separately and none of the variants reached a p-value < 10-8. CONCLUSIONS This large scale well-powered analysis demonstrates that common nsSNPs are not associated with CRC prognosis overall.
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Affiliation(s)
- Evropi Theodoratou
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Farhat Vn Din
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Harry Campbell
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK.
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11
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Impact of Occupational Exposures and Genetic Polymorphisms on Recurrence and Progression of Non-Muscle-Invasive Bladder Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081563. [PMID: 30042310 PMCID: PMC6121504 DOI: 10.3390/ijerph15081563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/10/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022]
Abstract
Introduction: Additional or better markers are needed to guide the clinical monitoring of patients with non-muscle-invasive bladder cancer (NMIBC). Aim: To investigate the influence of occupational exposures and genetic polymorphisms on recurrence and progression of NMIBC. Methods: The study includes 160 NMIBC patients. We collected on questionnaire information on demographic variables, lifetime smoking history, lifetime history of occupational exposure to aromatic amines and polycyclic aromatic hydrocarbons. Genetic polymorphism (glutathione S-transferase M1; T1; P1 (GSTM1; GSTT1; GSTP1); N-acetyltransferase 1; 2 (NAT1; NAT2); cytochrome P450 1B1 (CYP1B1); sulfotransferase 1A1 (SULT1A1); myeloperoxidase (MPO); catechol-O-methyltransferase (COMT); manganese superoxide dismutase (MnSOD); NAD(P)H:quinone oxidoreductase (NQO1); X-ray repair cross-complementing group 1; 3 (XRCC1; XRCC3) and xeroderma pigmentosum complementation group (XPD)) was assessed in peripheral blood lymphocytes. DNA adducts were evaluated by 32P-postlabeling. Predictors of recurrence (histological confirmation of a newly found bladder tumor) and progression (transition of tumor from low-grade to high-grade and/or increase in TNM stage) were identified by multivariate Cox proportional hazard regression with stepwise backward selection of independent variables. Hazard ratios (HR) with 95% confidence interval (95%CI) and two-tail probability of error (p-value) were estimated. Results: The risk of BC progression decreased with the homozygous genotype “ValVal” of both COMT and MnSOD (HR = 0.195; 95%CI = 0.060 to 0.623; p = 0.006). The results on BC recurrence were of borderline significance. No occupational exposure influenced recurrence or progression. Conclusion: Our results are supported by experimental evidence of a plausible mechanism between cause (ValVal genotype of both MnSOD and COMT) and effect (decreased progression of tumor in NMIBC patients). The genetic polymorphisms associated with better prognosis may be used in clinic to guide selection of treatment for patients initially diagnosed with NMIBC. However, external validation studies are required.
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12
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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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13
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Risk of eighteen genome-wide association study-identified genetic variants for colorectal cancer and colorectal adenoma in Han Chinese. Oncotarget 2018; 7:77651-77663. [PMID: 27769063 PMCID: PMC5363611 DOI: 10.18632/oncotarget.12750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 10/01/2016] [Indexed: 01/20/2023] Open
Abstract
Background Recent genome-wide association studies (GWAS) identified eighteen single-nucleotide polymorphisms (SNPs) to be significantly associated with the risk of colorectal cancer (CRC). However, overall results of the following replications are inconsistent and little is known about whether these associations also exit in colorectal adenomas (CRA). Methods The SNP genotyping was performed using a Sequenom MassARRAY to investigate the association of these eighteen SNPs with colorectal neoplasm in a case-control study consisted of 1049 colorectal cancers, 283 adenomas, and 1030 controls. Results Two of these SNPs, rs10505477 and rs719725, showed evidence of an association in both CRC and CRA in our study population. Besides, seven SNPs (rs10808555, rs7014346, rs7837328, rs704017, rs11196172, rs4779584, and rs7229639) were significantly associated with CRC, and another one SNP rs11903757 was over-represented in CRA compared with controls. The strongest association was provided by rs11196172 (OR = 2.02, 95% CI = 1.66 - 2.46, P < 0.0001) and rs11903757 (OR = 1.96, 95% CI = 1.28 - 3.00, P = 0.0026). Conclusion These results suggest that some previously reported SNP associations also have impact on CRC and CRA predispositions in the Han Chinese population. A part of genetic risk to CRC is possibly mediated by susceptibility to adenomas.
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14
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Abstract
Germ cell tumors (GCTs) arising in infants, children, and adolescents present a set of special challenges. GCTs make up about 3% of malignancies in children aged 0–18 and nearly 15% of cancers in adolescents. Epidemiologic and molecular evidence suggests that GCTs in young children likely represent a distinct biologic group as compared to GCTs of older adolescents and adults. Despite this difference, pediatric GCTs are typically treated with cisplatin-based multiagent regimens similar to those used in adults. There is evidence that children are particularly vulnerable to late effects of conventional therapy, including ototoxicity, pulmonary abnormalities, and secondary malignancies, motivating the search for molecular targets for novel therapies. Evidence is accumulating that the genes and mechanisms controlling normal germ cell development are particularly relevant to the understanding of germ cell tumorigenesis. Perturbations in the epigenetic program of germ cell differentiation, with resulting effects on the regulation of pluripotency, may contribute to the marked histologic variability of GCTs. Perturbations in the KIT receptor signaling pathway have been identified via next-generation sequencing studies and in genome-wide association studies of testicular cancer susceptibility. Here, we review these and other biological insights that may fuel further translational and clinical research in childhood GCTs.
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15
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Sung H, Hu N, Yang HH, Giffen CA, Zhu B, Song L, Su H, Wang C, Parisi DM, Goldstein AM, Taylor PR, Hyland PL. Association of high-evidence gastric cancer susceptibility loci and somatic gene expression levels with survival. Carcinogenesis 2017; 38:1119-1128. [PMID: 29028942 DOI: 10.1093/carcin/bgx090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/17/2017] [Indexed: 12/17/2022] Open
Abstract
Eleven high-evidence single-nucleotide polymorphisms (SNPs) at nine loci for gastric cancer (GC) risk were reported, but their associations with survival remain unknown. In this study, we examined associations between SNP and GC survival by anatomic location and histology among 1147 incident cases from the Shanxi Upper Gastrointestinal Genetics Project. We further examined whether SNPs were expression quantitative trait loci in normal and tumor gastric tissues, and whether tumor versus normal somatic mRNA differences in 126 cases were associated with survival. No SNPs were associated with GC survival overall. However, subtype-specific associations were observed for gastric cardia adenocarcinomas at MUC1/TRIM46/1q22 rs2070803 [HRAA versus GA+GG = 2.16; 95% confidence interval (CI) = 1.24-3.78; P = 0.0068] and LTA/TNF/6p21.33 rs1799724 (HRTT+CT versus CC = 1.30; 95% CI = 1.07-1.57; P = 0.0077), and for diffuse-type GC at PSCA/8q24.3 rs2294008 (HRTT versus CT+CC = 1.99; 95% CI = 1.33-2.97; P = 7.8E-04). Rs2294008T was a cis-expression quantitative trait loci for PSCA, upregulating mRNA in normal gastric (β = 0.60; P = 5.7E-21) and GC (β = 0.30; P = 0.0089) tissues. Cases in the highest quartile (the smallest downregulation of tumor PSCA) had shortest survival than cases with the most downregulated PSCA (median survival of 0.47 years in the highest quartile versus 3.73 years in the lowest quartile; hazard ratio = 9.70; 95% CI = 2.46-38.4; P = 0.0012). Less striking effects for mRNA levels were observed for MTX1 at 1q22 in gastric cardia adenocarcinoma and for JRK at 8q24.3 in diffuse GC. Our results suggest three high-evidence GC risk loci have prognostic importance in GC subtypes. Future studies in well-characterized independent populations are warranted to validate our findings and further investigate the clinical utility of these variants in predicting GC prognosis.
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Affiliation(s)
- Hyuna Sung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Howard H Yang
- High-dimension Data Analysis Group, Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Carol A Giffen
- Information Management Services, Inc, Calverton, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
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16
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Wang N, Lu Y, Khankari NK, Long J, Li HL, Gao J, Gao YT, Xiang YB, Shu XO, Zheng W. Evaluation of genetic variants in association with colorectal cancer risk and survival in Asians. Int J Cancer 2017; 141:1130-1139. [PMID: 28567967 PMCID: PMC5524202 DOI: 10.1002/ijc.30812] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have identified over 40 genetic loci associated with colorectal cancer (CRC) risk. The association of single nucleotide polymorphisms (SNPs) at these loci with CRC risk and survival has not been adequately evaluated in East Asians. GWAS-identified CRC risk variants were used to construct weighted genetic risk scores (GRSs). We evaluated these GRSs in association with CRC risk in 3,303 CRC cases and 3,553 controls using logistic regression models. Associations with overall and CRC-specific survival were assessed in 731 CRC patients using Cox regression models. The association between the GRSs (overall and Asian-specific) and CRC risk was approximately twofold (highest vs. lowest quintile), and the shape of the dose-response was linear (ptrend = 1.24 × 10-13 and 3.02 × 10-14 for overall GRS and Asian-specific GRS, respectively). The association of the GRS with CRC risk was stronger among those with a family history of CRC (pinteraction = 0.007). Asian-specific GRS using previously reported survival SNPs increased risk for mortality and the shape of the dose-response was linear for CRC-specific and all-cause mortality (ptrend = 0.01 and 0.006, respectively). Furthermore, the minor alleles of rs6983267 and rs1957636 were associated with worse CRC-specific and overall survival. We show that GRSs constructed using GWAS-identified common variants are strongly associated with CRC risk in Asians. We confirm previous findings for the possible association between some SNPs with survival, and provide evidence for two additional CRC risk variants that may be related to CRC survival.
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Affiliation(s)
- Nan Wang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nikhil K. Khankari
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hong-Lan Li
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jing Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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17
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Li J, Zou L, Zhou Y, Li L, Zhu Y, Yang Y, Gong Y, Lou J, Ke J, Zhang Y, Tian J, Zou D, Peng X, Chang J, Gong J, Zhong R, Zhou X, Miao X. A low-frequency variant in SMAD7 modulates TGF-β signaling and confers risk for colorectal cancer in Chinese population. Mol Carcinog 2017; 56:1798-1807. [PMID: 28218435 DOI: 10.1002/mc.22637] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/08/2017] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
The TGF-β pathway plays an essential role in regulating cell proliferation and differentiation. GWASs and candidate approaches have identified a battery of genetic variants in the TGF-β pathway contributing to colorectal cancer (CRC). However, most of the significant variants are common variants and their functions remain ambiguous. To identify causal variants with low-frequency in the TGF-β pathway contributing to CRC susceptibility in Chinese population, we performed targeted sequencing of 12 key genes in TGF-β signaling in CRC patients followed by a two-stage case-control study with a total of 5109 cases and 5169 controls. Bioinformatic annotations and biochemical experiments were applied to reveal the potential functions of significant variants. Seven low-frequency genetic variants were captured through targeted sequencing. The two stage association studies showed that missense variant rs3764482 (c. 83C>T; p. S28F) in the gene SMAD7 was consistently and significantly associated with CRC risk. Compared with the wild type, the ORs for variant allele were 1.37 (95%CI: 1.10-1.70, P = 0.005), 1.55 (95%CI: 1.30-1.86, P = 1.15 × 106 ), and 1.48 (1.29-1.70, P = 2.44 × 10;8 ) in stage 1, stage 2, and the combined analyses, respectively. Functional annotations revealed that the minor allele T of rs3764482 was more effective than the major allele C in blocking the TGF-β signaling and inhibiting the phosphorylation of receptor-regulated SMADs (R-SMADs). In conclusion, low-frequency coding variant rs3764482 in SMAD7 is associated with CRC risk in Chinese population. The rs3764482 variant may block the TGF-β signaling via impeding the activation of downstream genes, leading to cancer cell proliferation, thus contributing to CRC pathogenesis.
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Affiliation(s)
- Jiaoyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Li Zou
- Department of Health Care, Bao'an Maternal and Child Health Hospital, Shenzhen, China
| | - Ying Zhou
- Institute of Orthopaedics, the First Affiliated Hospital of Chinese PLA General Hospial, Beijing, China
| | - Lu Li
- Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yi Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jiang Chang
- Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jing Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Xiaobo Zhou
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, Massachusetts
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
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Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
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Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
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Hu L, Chen SH, Lv QL, Sun B, Qu Q, Qin CZ, Fan L, Guo Y, Cheng L, Zhou HH. Clinical Significance of Long Non-Coding RNA CASC8 rs10505477 Polymorphism in Lung Cancer Susceptibility, Platinum-Based Chemotherapy Response, and Toxicity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13060545. [PMID: 27249003 PMCID: PMC4924002 DOI: 10.3390/ijerph13060545] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/13/2016] [Accepted: 05/20/2016] [Indexed: 12/24/2022]
Abstract
Long non-coding RNA (lncRNA) CASC8 rs10505477 polymorphism has been identified to be related to risk of many kinds of cancers, such as colorectal cancer, gastric cancer, and invasive ovarian cancer, and it may be involved in the prognosis of gastric cancer patients who have received platinum-based chemotherapy after surgical treatment. So far, there is no study investigating the clinical significance of lncRNA CASC8 rs10505477 in lung cancer susceptibility and treatment. In this study, we genotyped 498 lung cancer patients and 213 healthy control subjects to explore the correlation between the rs10505477 polymorphism and lung cancer risk in a Chinese population. Among the 498 patients, 467 were selected for the chemotherapy response and toxicity study. We found that the single nucleotide polymorphisms (SNP) rs10505477 was greatly related to lung cancer risk in male and adenocarcinoma subgroups in recessive model (adjusted OR = 0.51, 95%CI = 0.29–0.90, p = 0.02; adjusted OR = 0.52, 95%CI = 0.30–0.89, p = 0.02, respectively). It was also closely correlated with platinum-based chemotherapy response in dominant model (adjusted OR = 1.58, 95%CI = 1.05–2.39, p = 0.03). Additionally, we observed that CASC8 rs10505477 polymorphism was significantly relevant to severe hematologic toxicity in non-small-cell lung cancer (NSCLC) subgroup in dominant model (adjusted OR = 0.59, 95%CI = 0.35–0.98, p = 0.04) and in additive model (adjusted OR = 0.62, 95%CI = 0.43–0.90, p = 0.01). Furthermore, it was found that rs10505477 polymorphism was greatly associated with gastrointestinal toxicity in SCLC and cisplatin subgroups in dominant model (adjusted OR = 7.82, 95%CI = 1.36–45.07, p = 0.02; adjusted OR = 1.94, 95%CI = 1.07–3.53, p = 0.03, respectively). Thus, lncRNA CASC8 rs10505477 could serve as a possible risk marker for diagnosing lung cancer, and could be used to forecast the response and toxicity of platinum-based treatment in lung cancer patients.
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Affiliation(s)
- Lei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Shu-Hui Chen
- Department of Oncology, Changsha Central Hospital, Changsha 410006, China.
| | - Qiao-Li Lv
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Chong-Zhen Qin
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Central South University, Zhengzhou 450052, China.
| | - Lan Fan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Ying Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Lin Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
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20
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Azad AK, Bairati I, Qiu X, Girgis H, Cheng L, Waggott D, Cheng D, Mirshams M, Ho J, Fortin A, Vigneault E, Huang SH, O'Sullivan B, Waldron J, Boutros PC, Goldstein D, Meyer F, Xu W, Liu G. A genome-wide association study of non-HPV-related head and neck squamous cell carcinoma identifies prognostic genetic sequence variants in the MAP-kinase and hormone pathways. Cancer Epidemiol 2016; 42:173-80. [PMID: 27173062 DOI: 10.1016/j.canep.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Carcinomas of the oral cavity, pharynx and larynx are referred to as head and neck cancers (HNC); together they account for 2-3% of all newly diagnosed cancers in North America. Between 40-50% of HNC are early diagnosed at stages I-II. The 5-year and 10-year relative survival rates are 61% and 50%, respectively. Germline genetic sequence variants (GSV) have become increasingly found to have prognostic implications in a variety of cancers. Identifying these variants may have important clinical and biological implications. METHODS We conducted a genome-wide association study (GWAS) in 531 Stage I-II radiation-treated HNC patients (originally recruited for α-tocopherol/β-carotene placebo-controlled secondary prevention study) and used a replication cohort of 566 HNC patients of all stages, of mostly non-HPV-related cancers. Survival rates were estimated by the Kaplan-Meier method. Cox proportional hazards models adjusted for potential clinical factors and principal components were used to test for associations between the GSV and overall survival (OS) in these tumors. RESULTS The median follow-up time for OS was 9.21 years (GWAS cohort) and 2.37 years (replication cohort). In both cohorts, CACNA2D1:rs2299187, ESRRG:rs946465 and ESRRG:rs1416612 were each individually significantly associated with survival. In silico analysis of ESRRG:rs946465 identifies that it produces a splice variant in ESRRG. Variant alleles of CACNA2D1:rs2299187 and ESRRG:rs946465 were associated with higher expression of the corresponding protein. CONCLUSIONS Putatively functional polymorphisms in the MAP-Kinase and estrogen pathways, identified through GWAS and replicated in an independent dataset were associated with the survival of HNC patients.
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Affiliation(s)
- Abul Kalam Azad
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Isabelle Bairati
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Xin Qiu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hala Girgis
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lu Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daryl Waggott
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dangxiao Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maryam Mirshams
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James Ho
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - André Fortin
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eric Vigneault
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Shao-Hui Huang
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Brian O'Sullivan
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John Waldron
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada,; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,; Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Francois Meyer
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Wei Xu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Geoffrey Liu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada,; Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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21
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Yao K, Hua L, Wei L, Meng J, Hu J. Correlation Between CASC8, SMAD7 Polymorphisms and the Susceptibility to Colorectal Cancer: An Updated Meta-Analysis Based on GWAS Results. Medicine (Baltimore) 2015; 94:e1884. [PMID: 26579801 PMCID: PMC4652810 DOI: 10.1097/md.0000000000001884] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWASs) and a number of case-control studies have suggested that several single nucleotide polymorphisms (SNPs), rs7837328, rs7014346, rs6983267, rs10505477 on CASC8 gene and rs4939827, rs4464148, rs12953717 on SMAD7 gene are significantly correlated with the susceptibility to colorectal cancer (CRC). For the sake of clarifying the association, a meta-analysis was conducted and population heterogeneity was considered in the study.A total of 34 articles including 90 studies (168,471 cases and 163,223 controls) that evaluated the relationship between the CASC8, SMAD7 genes and the risk of CRC under the allelic model were reviewed. Also subgroup analysis was performed by ethnicity (Caucasian, Asian, and African) and all of the analyses were implemented in R 3.2.1 software.Pooled data from the meta-analysis revealed that the A allele of rs7837328, the A allele of rs7014346, the G allele of rs6983267, the A allele of rs10505477, the T allele of rs4939827, the T of rs4464148, and the T of rs12953717 were significantly associated with an increased risk of CRC under the allelic model. Additionally, subgroup analyses of 6 SNPs by ethnicity (rs4464148 excepted) witnessed that the A allele of rs7837328, the G allele of rs6983267, and the T of rs12953717 were notably associated with an increased risk of CRC among Caucasian and Asian. Furthermore, the A allele of rs7014346, the A allele of rs10505477, and the T allele of rs4939827 were significantly related with an elevated risk of CRC only among Caucasian.Our study suggested that for CASC8 gene, SNP of rs7837328 and rs6983267 are risk factors for CRC among both Caucasian and Asian whereas rs7014346 and rs10505477 are risky gene polymorphisms only among Caucasian. For SMAD7 gene, rs4939827 and rs4464148 are risk factors for CRC among Caucasian whereas rs12953717 could elevate the susceptibility to CRC in both Caucasian and Asian.
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Affiliation(s)
- Kunhou Yao
- From the Department of General Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China (KY, LH, JM, JH); and Department of Digestive Medicine, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China (LW)
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22
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Damavand B, Derakhshani S, Saeedi N, Mohebbi SR, Milanizadeh S, Azimzadeh P, Aghdaie HA, Zali MR. Intronic polymorphisms of the SMAD7 gene in association with colorectal cancer. Asian Pac J Cancer Prev 2015; 16:41-4. [PMID: 25640388 DOI: 10.7314/apjcp.2015.16.1.41] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Based on genome-wide association studies (GWAS) a linkage between several variants such as single nucleotide polymorphisms (SNPs) in intron 3 of SMAD7 (mothers against decapentaplegic homolog7) were, rs12953717, rs4464148 and rs4939827 has been noted for susceptibility to colorectal cancer (CRC). In this study we investigated the relationship of rs12953717 and rs4464148 with risk of CRC among 487 Iranian individuals based on a case- control study. Genotyping of SNPs was performed by PCR-RFLP and for confirming the outcomes, 10% of genotyping cases were sequenced with RFLP. Comparing the case and control group, we have found significant association between the rs4464148 SNP and lower risk of CRC. The AG genotype showed decreased risk with and odds ratio of 0.635 (adjusted OR=0.635, 95% CI: 0.417-0.967, p=0.034). There was no significant difference in the distribution of SMAD7 gene rs12953717 TT genotype between two groups of the population evaluated (adjusted OR=1.604, 95% CI: 0.978-2.633, p=0.061). On the other hand, rs12953717 T allele showed a statistically significant association with CRC risk (adjusted OR=1.339, 95% CI: 1.017-1.764, p=0.037). In conclusion, we found a significant association between CRC risk and the rs4464148 AG genotype. Furthermore, the rs12953717 T allele may act as a risk factor. This association may be caused by alternative splicing of pre mRNA. Although we observed a strong association with rs4464148 GG genotype in affected women, we did not detect the same association in CRC male patients.
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Affiliation(s)
- Behzad Damavand
- Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran E-mail :
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23
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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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Clinical validation study of genetic markers for capecitabine efficacy in metastatic colorectal cancer patients. Pharmacogenet Genomics 2015; 25:279-88. [DOI: 10.1097/fpc.0000000000000119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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A Survival Association Study of 102 Polymorphisms Previously Associated with Survival Outcomes in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:968743. [PMID: 26064972 PMCID: PMC4443940 DOI: 10.1155/2015/968743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/06/2015] [Indexed: 12/31/2022]
Abstract
Several published studies identified associations of a number of polymorphisms with a variety of survival outcomes in colorectal cancer. In this study, we aimed to explore 102 previously reported common genetic polymorphisms and their associations with overall survival (OS) and disease-free survival (DFS) in a colorectal cancer patient cohort from Newfoundland (n = 505). Genotypes were obtained using a genomewide SNP genotyping platform. For each polymorphism, the best possible genetic model was estimated for both overall survival and disease-free survival using a previously published approach. These SNPs were then analyzed under their genetic models by Cox regression method. Correction for multiple comparisons was performed by the False Discovery Rate (FDR) method. Univariate analysis results showed that RRM1-rs12806698, IFNGR1-rs1327474, DDX20-rs197412, and PTGS2-rs5275 polymorphisms were nominally associated with OS or DFS (p < 0.01). In stage-adjusted analysis, the nominal associations of DDX20-rs197412, PTGS2-rs5275, and HSPA5-rs391957 with DFS were detected. However, after FDR correction none of these polymorphisms remained significantly associated with the survival outcomes. We conclude that polymorphisms investigated in this study are not associated with OS or DFS in our colorectal cancer patient cohort.
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27
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Kang BW, Jeon HS, Chae YS, Lee SJ, Park JY, Choi JE, Park JS, Choi GS, Kim JG. Association between GWAS-identified genetic variations and disease prognosis for patients with colorectal cancer. PLoS One 2015; 10:e0119649. [PMID: 25799222 PMCID: PMC4370892 DOI: 10.1371/journal.pone.0119649] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/01/2015] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies (GWASs) have already identified at least 22 common susceptibility loci associated with an increased risk of colorectal cancer (CRC). This study examined the relationship between these single nucleotide polymorphisms (SNPs) and the clinical outcomes of patients with colorectal cancer. Seven hundred seventy-six patients with surgically resected colorectal adenocarcinoma were enrolled in the present study. Twenty-two of the GWAS-identified SNPs were genotyped using a Sequenom MassARRAY. Among the 22 SNPs, two (rs1321311G>T in CDKN1A and rs10411210C>T in RHPN2) were significantly associated with the survival outcomes of CRC in a multivariate survival analysis. In a recessive model, the rs1321311 TT genotype (vs. GG + GT) and rs10411210 TT genotype (vs. CC + CT) were associated with a worse prognosis for disease-free survival (adjusted HR = 1.90; 95% confidence interval = 1.00-3.60; P = 0.050, adjusted HR = 1.94; 95% confidence interval = 1.05-3.57; P = 0.034, respectively) and overall survival (adjusted HR = 2.05; 95% confidence interval = 1.00-4.20; P = 0.049, adjusted HR = 2.06; 95% confidence interval = 1.05-4.05; P = 0.036, respectively). None of the other SNPs was significantly associated with any clinicopathologic features or survival. The present results suggest that the genetic variants of the CDKN1A (rs1321311) and RHPN2 (rs10411210) genes can be used as prognostic biomarkers for patients with surgically resected colorectal cancer.
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Affiliation(s)
- Byung Woog Kang
- Department of Oncology/Hematology, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Hyo-Sung Jeon
- Department of Molecular diagnostics and Imaging research institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Yee Soo Chae
- Department of Oncology/Hematology, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Soo Jung Lee
- Department of Oncology/Hematology, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jae Yong Park
- Department of Biochemistry and Cell biology, Kyungpook National University School of Medicine, Daegu, Republic of Korea
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell biology, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jun Seok Park
- Colorectal Cancer Center, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Gyu Seog Choi
- Colorectal Cancer Center, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jong Gwang Kim
- Department of Oncology/Hematology, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
- * E-mail:
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28
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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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Verma M. Molecular profiling and companion diagnostics: where is personalized medicine in cancer heading? Per Med 2014; 11:761-771. [PMID: 29764045 DOI: 10.2217/pme.14.41] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The goal of personalized medicine is to use the right drug at the right dose - with minimal or no toxicity - for the right patient at the right time. Recent advances in understanding cell biology and pathways, and in using molecular 'omics' technologies to diagnose cancer, offer a strategic bridge to personalized medicine in cancer. Modern personalized medicine takes into account an individual's genetic makeup and disease history before developing a treatment regimen. The future of clinical oncology will be based on the use of predictive and prognostic biomarkers in patient management. Once implemented widely, personalized medicine will benefit patients and the healthcare system greatly.
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Shen L, Du M, Wang C, Gu D, Wang M, Zhang Q, Zhao T, Zhang X, Tan Y, Huo X, Gong W, Xu Z, Chen J, Zhang Z. Clinical significance of POU5F1P1 rs10505477 polymorphism in Chinese gastric cancer patients receving cisplatin-based chemotherapy after surgical resection. Int J Mol Sci 2014; 15:12764-77. [PMID: 25046748 PMCID: PMC4139873 DOI: 10.3390/ijms150712764] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/30/2014] [Accepted: 07/09/2014] [Indexed: 01/06/2023] Open
Abstract
This study aimed to investigate the association between POU class5 homeobox 1 pseudogene 1 gene (POU5F1P1) rs10505477 polymorphism and the prognosis of Chinese gastric cancer patients, who received cisplatin-based chemotherapy after surgical resection. POU5F1P1 rs10505477 was genotyped using the SNaPshot method in 944 gastric cancer patients who received gastrectomy. The association of rs10505477 G > A polymorphism with the progression and prognosis in gastric cancer patients was statistically analyzed using the SPSS version 18.0 for Windows. The results reveal that rs10505477 polymorphism has a negatively effect on the overall survival of gastric cancer patients in cisplatin-based chemotherapy subgroup (HR = 1.764, 95% CI = 1.069–2.911, p = 0.023). Our preliminary study indicates for the first time that POU5F1P1 rs10505477 is correlated with survival of gastric cancer patients who receving cisplatin-based chemotherapy after gastrectomy. Further studies are warranted to investigate the mechanism and to verify our results in different populations.
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Affiliation(s)
- Lili Shen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, 818 East Tianyuan Road, Nanjing 211166, China.
| | - Chun Wang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, 818 East Tianyuan Road, Nanjing 211166, China.
| | - Qi Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Tingting Zhao
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Xunlei Zhang
- Department of Oncology, Nantong Tumor Hospital, Nantong 226000, 30 Tongyang North Road, China.
| | - Yongfei Tan
- Department of Surgery, Yixing People's Hospital, 75 Tongzhenguan Road, Yixing 214200, China.
| | - Xinying Huo
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Weida Gong
- Department of General Surgery, Yixing Tumor Hospital, 45 Dongshan East Road, Yixing 214200, China.
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, 818 East Tianyuan Road, Nanjing 211166, China.
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Li C, Bi X, Huang Y, Zhao J, Li Z, Zhou J, Zhang M, Huang Z, Zhao H, Cai J. Variants identified by hepatocellular carcinoma and chronic hepatitis B virus infection susceptibility GWAS associated with survival in HBV-related hepatocellular carcinoma. PLoS One 2014; 9:e101586. [PMID: 24987808 PMCID: PMC4079718 DOI: 10.1371/journal.pone.0101586] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/08/2014] [Indexed: 02/07/2023] Open
Abstract
Recent genome-wide association studies (GWAS) have identified several common susceptibility loci associated with the risk of hepatocellular carcinoma (HCC) or chronic hepatitis B infection (CHB). However, the relationship between these genetic variants and survival of patients with hepatitis B virus (HBV)-related HCC is still unknown. In this study, 22 single nucleotide polymorphisms (SNPs) were genotyped among 330 HBV-related HCC patients using the MassARRAY system from Sequenom. Cox proportional hazards regression was used to examine the effects of genotype on survival time under an additive model with age, sex, smoking status and clinical stage as covariates. We identified four SNPs on 6p21 (rs1419881 T>C, rs7453920 G>A,rs3997872 G>A and rs7768538 T>C), and two SNPs on 8p12 (rs2275959 C>T and rs7821974 C>T) significantly associated with survival time of HBV-related HCC patients. Our results suggest that HCC or CHB susceptibility loci might also affect the prognosis of patients with HBV-related HCC.
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Affiliation(s)
- Cong Li
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyu Bi
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Huang
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jianjun Zhao
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyu Li
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianguo Zhou
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhang
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhen Huang
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Zhao
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (HZ); (JC)
| | - Jianqiang Cai
- Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (HZ); (JC)
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Liang Y, Tang W, Huang T, Gao Y, Tan A, Yang X, Zhang H, Hu Y, Qin X, Li S, Zhang S, Mo L, Liang Z, Shi D, Huang Z, Guan Y, Zhou J, Winkler C, O'Brien SJ, Xu J, Mo Z, Peng T. Genetic variations affecting serum carcinoembryonic antigen levels and status of regional lymph nodes in patients with sporadic colorectal cancer from Southern China. PLoS One 2014; 9:e97923. [PMID: 24941225 PMCID: PMC4062418 DOI: 10.1371/journal.pone.0097923] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/27/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Serum carcinoembryonic antigen (sCEA) level might be an indicator of disease. Indeed, an elevated sCEA level is a prognostic factor in colorectal cancer (CRC) patients. However, the genetic determinants of sCEA level in healthy and CRC population remains unclear. Thus we investigated the genetic markers associated with elevated serum sCEA level in these two populations and its clinical implications. METHODS AND FINDINGS Genome-wide association study (GWAS) was conducted in a cohort study with 4,346 healthy male adults using the Illumina Omni 1 M chip. Candidate SNPs associated with elevated sCEA levels were validated in 194 CRC patients on ABI Taqman platform. Eight candidate SNPs were validated in CRC patients. The rs1047781 (chr19- FUT2) (A/T) was associated with elevated sCEA levels, and rs8176746 (chr9- ABO) was associated with the regional lymph metastasis in the CRC patients. The preoperative sCEA level was a risk factor for tumor recurrence in 5 years after operation (OR = 1.427, 95% CI: 1.005∼1.843, P = 0.006). It was also one of the risk factors for regional lymph node metastasis (OR = 2.266, 95% CI: 1.196∼4.293, P = 0.012). The sCEA level in rs1047781-T carriers was higher than that in the A carriers in CRC patients without lymph node metastasis (P = 0.006). The regional lymph node metastasis in patients with homozygote AA of rs8176746 was more common than that in the heterozygote AG carriers (P = 0.022). In addition, rs1047781-AT and TT CRC patients exhibited a worse disease-free survival than AA genotype carriers (P = 0.023). CONCLUSIONS We found candidate SNPs associated with elevated sCEA levels in both healthy males and CRC population. Rs1047781 (chr19- FUT2) may be the susceptible locus for recurrence of CRC in a population from Southern China.
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Affiliation(s)
- Yu Liang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Weizhong Tang
- Department of Anal and colorectal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Tiqiang Huang
- Department of Anal and colorectal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Yong Gao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Aihua Tan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Haiying Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Yanling Hu
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Shan Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Shijun Zhang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Linjian Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Institute of Urology and Nephrology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Zhenjia Liang
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, People's Republic of China
| | - Deyi Shi
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, People's Republic of China
| | - Zhang Huang
- Medical Examination Center, Guigang First People's Hospital, Guigang, Guangxi, People's Republic of China
| | - Yingyong Guan
- Medical Examination Center, Yulin First People's Hospital, Yulin, Guangxi, People's Republic of China
| | - Jicheng Zhou
- Department of Hematology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Cheryl Winkler
- Molecular Genetics Epidemiology Sec., Frederick Nat. Lab for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, NIH, Frederick, Maryland, United States of America
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America
| | - Jianfeng Xu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Institute of Urology and Nephrology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- * E-mail: (TP); (ZM)
| | - Tao Peng
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Laboratory of Genomic Diversity, National Cancer Institute, NIH, Frederick, Maryland, United States of America
- * E-mail: (TP); (ZM)
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Zhang K, Civan J, Mukherjee S, Patel F, Yang H. Genetic variations in colorectal cancer risk and clinical outcome. World J Gastroenterol 2014; 20:4167-4177. [PMID: 24764655 PMCID: PMC3989953 DOI: 10.3748/wjg.v20.i15.4167] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/08/2014] [Accepted: 03/06/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) has an apparent hereditary component, as evidenced by the well-characterized genetic syndromes and family history associated with the increased risk of this disease. However, in a large fraction of CRC cases, no known genetic syndrome or family history can be identified, suggesting the presence of “missing heritability” in CRC etiology. The genome-wide association study (GWAS) platform has led to the identification of multiple replicable common genetic variants associated with CRC risk. These newly discovered genetic variations might account for a portion of the missing heritability. Here, we summarize the recent GWASs related to newly identified genetic variants associated with CRC risk and clinical outcome. The findings from these studies suggest that there is a lack of understanding of the mechanism of many single nucleotide polymorphisms (SNPs) that are associated with CRC. In addition, the utility of SNPs as prognostic markers of CRC in clinical settings remains to be further assessed. Finally, the currently validated SNPs explain only a small fraction of total heritability in complex-trait diseases like CRC. Thus, the “missing heritability” still needs to be explored further. Future epidemiological and functional investigations of these variants will add to our understanding of CRC pathogenesis, and may ultimately lead to individualized strategies for prevention and treatment of CRC.
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Sanoff HK, Renfro LA, Poonnen P, Ambadwar P, Sargent DJ, Goldberg RM, McLeod H. Germline variation in colorectal risk Loci does not influence treatment effect or survival in metastatic colorectal cancer. PLoS One 2014; 9:e94727. [PMID: 24727911 PMCID: PMC3984266 DOI: 10.1371/journal.pone.0094727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/18/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) risk is partly conferred by common, low-penetrance single nucleotide polymorphisms (SNPs). We hypothesized that these SNPs are associated with outcomes in metastatic CRC. METHODS Six candidate SNPs from 8q24, 10p14, 15q13, 18q21 were investigated for their association with response rate (RR), time to progression (TTP) and overall survival (OS) among 524 patients treated on a phase III clinical trial of first-line chemotherapy for metastatic CRC. RESULTS rs10795668 was weakly associated with TTP (p = 0.02), but not RR or OS. No other SNPs carried statistically significant HRs for any of the primary outcomes (RR, TTP or OS). CONCLUSION Common low-penetrance CRC risk SNPs were not associated with outcomes among patients with metastatic CRC.
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Affiliation(s)
- Hanna K. Sanoff
- Department of Medicine, Division of Hematology/Oncology, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lindsay A. Renfro
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pradeep Poonnen
- School of Medicine, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Pratibha Ambadwar
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Daniel J. Sargent
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard M. Goldberg
- Division of Medical Oncology, The Ohio State University, Columbus, Ohio, United States of America
| | - Howard McLeod
- DeBartolo Family Personalized Medicine Institute, Division of Population Sciences, Moffitt Cancer Center, Tampa, Florida, United States of America
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Grotenhuis AJ, Dudek AM, Verhaegh GW, Witjes JA, Aben KK, van der Marel SL, Vermeulen SH, Kiemeney LA. Prognostic relevance of urinary bladder cancer susceptibility loci. PLoS One 2014; 9:e89164. [PMID: 24586564 PMCID: PMC3934869 DOI: 10.1371/journal.pone.0089164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/16/2014] [Indexed: 12/13/2022] Open
Abstract
In the last few years, susceptibility loci have been identified for urinary bladder cancer (UBC) through candidate-gene and genome-wide association studies. Prognostic relevance of most of these loci is yet unknown. In this study, we used data of the Nijmegen Bladder Cancer Study (NBCS) to perform a comprehensive evaluation of the prognostic relevance of all confirmed UBC susceptibility loci. Detailed clinical data concerning diagnosis, stage, treatment, and disease course of a population-based series of 1,602 UBC patients were collected retrospectively based on a medical file survey. Kaplan-Meier survival analyses and Cox proportional hazard regression were performed, and log-rank tests calculated, to evaluate the association between 12 confirmed UBC susceptibility variants and recurrence and progression in non-muscle invasive bladder cancer (NMIBC) patients. Among muscle-invasive or metastatic bladder cancer (MIBC) patients, association of these variants with overall survival was tested. Subgroup analyses by tumor aggressiveness and smoking status were performed in NMIBC patients. In the overall NMIBC group (n = 1,269), a statistically significant association between rs9642880 at 8q24 and risk of progression was observed (GT vs. TT: HR = 1.08 (95% CI: 0.76-1.54), GG vs. TT: HR = 1.81 (95% CI: 1.23-2.66), P for trend = 2.6 × 10(-3)). In subgroup analyses, several other variants showed suggestive, though non-significant, prognostic relevance for recurrence and progression in NMIBC and survival in MIBC. This study provides suggestive evidence that genetic loci involved in UBC etiology may influence disease prognosis. Elucidation of the causal variant(s) could further our understanding of the mechanism of disease, could point to new therapeutic targets, and might aid in improvement of prognostic tools.
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Affiliation(s)
- Anne J. Grotenhuis
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aleksandra M. Dudek
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerald W. Verhaegh
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J. Alfred Witjes
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katja K. Aben
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Comprehensive Cancer Center The Netherlands, Utrecht, The Netherlands
| | | | - Sita H. Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
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Szkandera J, Pichler M, Absenger G, Stotz M, Weissmueller M, Samonigg H, Asslaber M, Lax S, Leitner G, Winder T, Renner W, Gerger A. A functional germline variant in GLI1 implicates hedgehog signaling in clinical outcome of stage II and III colon carcinoma patients. Clin Cancer Res 2014; 20:1687-97. [PMID: 24470513 DOI: 10.1158/1078-0432.ccr-13-1517] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cumulating evidence indicates that germline variants in the Wnt, Notch, and Hedgehog pathways are involved in colon carcinoma progression and metastasis. We investigated germline polymorphisms in a comprehensive panel of Wnt, Notch, and Hedgehog pathway genes to predict time to recurrence (TTR) and overall survival in patients with stage II and III colon carcinoma. EXPERIMENTAL DESIGN A total of 742 consecutively collected patients with stage II and III colon carcinoma were included in this retrospective study. Genomic DNA was analyzed for 18 germline polymorphisms in Wnt, Notch, and Hedgehog pathway genes (SFRP, DKK 2 and 3, AXIN2, APC, MYC, TCF7L2, NOTCH2, and GLI1) by TaqMan 5'-exonuclease assays. RESULTS In univariate analysis, the homozygous mutant variant of GLI1 rs2228226 G>C was significantly associated with decreased TTR in a recessive genetic model after adjustment for multiple testing [HR = 2.35; confidence interval (95% CI), 1.48-3.74; P < 0.001] and remained significant in multivariate analysis including clinical stage, lymphovascular-, vascular-, and perineural-invasion (HR = 2.43; CI 95%, 1.52-3.87; P < 0.001). In subanalyses, the association was limited to patients with surgery alone (HR = 3.21; CI 95%, 1.59-6.49; P = 0.001), in contrast with patients with adjuvant chemotherapy (HR = 0.82; CI 95%, 0.35-1.95; P = 0.657). When the subgroup of patients with "high-risk" GLI1 rs2228226 C/C genotype was analyzed, no benefit of adjuvant 5-fluorouracil-based chemotherapy could be found. CONCLUSION This is the first study identifying GLI1 rs2228226 G>C as an independent prognostic marker in patients with stage II and III colon carcinoma. Prospective studies are warranted to validate our findings.
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Affiliation(s)
- Joanna Szkandera
- Authors' Affiliations: Division of Clinical Oncology, Department of Medicine; Research Unit: Genetic Epidemiology and Pharmacogenetics, Division of Clinical Oncology; Institute of Pathology; Clinical Institute of Medical and Laboratory Diagnostics, Medical University of Graz; Department of Pathology, General Hospital Graz West, Graz; Department of Pathology, General Hospital of Leoben, Leoben, Austria; and Department of Medical Oncology, University Hospital Zuerich, Zuerich, Switzerland
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Savas S, Liu G, Xu W. Special considerations in prognostic research in cancer involving genetic polymorphisms. BMC Med 2013; 11:149. [PMID: 23773794 PMCID: PMC3729672 DOI: 10.1186/1741-7015-11-149] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 05/01/2013] [Indexed: 01/08/2023] Open
Abstract
Analysis of genetic polymorphisms may help identify putative prognostic markers and determine the biological basis of variable prognosis in patients. However, in contrast to other variables commonly used in the prognostic studies, there are special considerations when studying genetic polymorphisms. For example, variable inheritance patterns (recessive, dominant, codominant, and additive genetic models) need to be explored to identify the specific genotypes associated with the outcome. In addition, several characteristics of genetic polymorphisms, such as their minor allele frequency and linkage disequilibrium among multiple polymorphisms, and the population substructure of the cohort investigated need to be accounted for in the analyses. In addition, in cancer research due to the genomic differences between the tumor and non-tumor DNA, differences in the genetic information obtained using these tissues need to be carefully assessed in prognostic studies. In this article, we review these and other considerations specific to genetic polymorphism by focusing on genetic prognostic studies in cancer.
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Affiliation(s)
- Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St, John's, Newfoundland, Canada.
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McEwan MV, Eccles MR, Horsfield JA. Cohesin is required for activation of MYC by estradiol. PLoS One 2012; 7:e49160. [PMID: 23145106 PMCID: PMC3493498 DOI: 10.1371/journal.pone.0049160] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/09/2012] [Indexed: 12/13/2022] Open
Abstract
Cohesin is best known as a multi-subunit protein complex that holds together replicated sister chromatids from S phase until G2. Cohesin also has an important role in the regulation of gene expression. We previously demonstrated that the cohesin complex positively regulates expression of the oncogene MYC. Cell proliferation driven by MYC contributes to many cancers, including breast cancer. The MYC oncogene is estrogen-responsive and a transcriptional target of estrogen receptor alpha (ERα). Estrogen-induced cohesin binding sites coincide with ERα binding at the MYC locus, raising the possibility that cohesin and ERα combine actions to regulate MYC transcription. The objective of this study was to investigate a putative role for cohesin in estrogen induction of MYC expression. We found that siRNA-targeted depletion of a cohesin subunit, RAD21, decreased MYC expression in ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231) breast cancer cell lines. In addition, RAD21 depletion blocked estradiol-mediated activation of MYC in ER-positive cell lines, and decreased ERα binding to estrogen response elements (EREs) upstream of MYC, without affecting total ERα levels. Treatment of MCF7 cells with estradiol caused enrichment of RAD21 binding at upstream enhancers and at the P2 promoter of MYC. Enriched binding at all sites, except the P2 promoter, was dependent on ERα. Since RAD21 depletion did not affect transcription driven by an exogenous reporter construct containing a naked ERE, chromatin-based mechanisms are likely to be involved in cohesin-dependent MYC transcription. This study demonstrates that ERα activation of MYC can be modulated by cohesin. Together, these results demonstrate a novel role for cohesin in estrogen-mediated regulation of MYC and the first evidence that cohesin plays a role in ERα binding.
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Affiliation(s)
- Miranda V. McEwan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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Polymorphisms on 8q24 are associated with lung cancer risk and survival in Han Chinese. PLoS One 2012; 7:e41930. [PMID: 22848662 PMCID: PMC3407045 DOI: 10.1371/journal.pone.0041930] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/29/2012] [Indexed: 11/19/2022] Open
Abstract
Chromosome 8q24 is commonly amplified in many types of cancer, particularly lung cancer. Polymorphisms in this region are associated with risk of different cancers. To investigate the relationship between three single nucleotide polymorphisms (SNPs) (rs1447295, rs16901979 and rs6983267) on 8q24 and lung cancer risk, we conducted an association study in two Han Chinese populations: one population was from Zhejiang Province (576 case patients and 576 control subjects), whereas the other was from Fujian Province (576 case patients and 576 control subjects). We found that rs6983267 was significantly associated with an increased risk of lung cancer in both populations. Compared with the TT genotype, the GG genotype was associated with a significant 1.555-fold increased risk of lung cancer [95% confidence interval (CI) 1.218-1.986, P = 4.0×10(-4)]. This effect was more pronounced in never-smokers [odds ratio (OR) = 2.366, 95% CI 1.605-3.488, P = 1.4×10(-5)]. Analyses stratified by histology revealed that rs6983267 GG genotype was most associated with patients with other histological types (OR = 3.012, 95% CI 1.675-5.417, P = 2.3×10(-4)). The AA genotype of rs1447295 was associated with increased risk for adenocarcinoma compared with the CC genotype (OR = 2.260, 95% CI 1.174-4.353, P = 0.015). Furthermore, the GG genotype of rs6983267 was associated with worse survival in the Zhejiang population (hazard ratio (HR) = 1.646, 95% CI 1.099-2.464, P = 0.016). No association was observed for rs16901979. These results suggest that genetic variations on 8q24 may play significant roles in the development and progression of lung cancer.
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Innocenti F. One SNP for both cancer risk and survival in colorectal cancer: two for the price of one? Pharmacogenomics 2012; 13:1114. [PMID: 23077730 PMCID: PMC4128334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Affiliation(s)
- Federico Innocenti
- University of North Carolina at Chapel Hill, Institute for Pharmacogenomics & Individualized Therapy, Eshelman School of Pharmacy, School of Medicine, Chapel Hill, NC 27599-7361, USA.
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