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Bozgeyik E. Variations in genomic regions encoding long non-coding RNA genes associated with increased prostate cancer risk. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 791:108456. [PMID: 36948485 DOI: 10.1016/j.mrrev.2023.108456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/24/2023]
Abstract
From a single restriction fragment length polymorphism analysis to next generation sequencing analysis that screens the entire human genome, testing for genomic variations provides a great and robust approach to cancer testing. Non-coding RNAs have been shown to have a major impact on the development and progression of human cancers, including prostate cancer. However, the low stability of these molecules under laboratory conditions has made their clinical utility challenging, as in the case of PCA3 long non-coding RNA. Since testing for variations in genomic regions encoding non-coding RNAs offers a promising approach for cancer testing, identification and interpretation of single nucleotide polymorphisms associated with prostate cancer susceptibility is of great interest. Accordingly, here, for the first time, we review and discuss current available knowledge about genomic variation of long non-coding RNA molecules in prostate cancer.
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Affiliation(s)
- Esra Bozgeyik
- Department of Medical Services and Techniques, Vocational School of Health Services, Adiyaman University, Adiyaman, Turkey.
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2
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Abstract
Prostate Cancer is now the second biggest cause of cancer mortality in the UK. Media coverage has been rising, with some attributing to a rise in the cases diagnosed and treated in the NHS down to the “Fry and Turnbull effect”. Our understanding of prostate cancer has increased tremendously in the past decades, with advances in molecular biology and genomics driving the way to new treatments and diagnostics. This Special Edition of Translational Andrology and Urology 2019: Prostate Cancer Biology and Genomics aims to review the current state of prostate cancer genomics, proteomics, diagnostics and treatment.
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Affiliation(s)
- Hayley Whitaker
- Division of Surgical and Interventional Sciences, Faculty of Medicine, University College London, London, UK
| | - Joseph O Tam
- Imperial Prostate, Division of Surgery, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Martin J Connor
- Imperial Prostate, Division of Surgery, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Alistair Grey
- Division of Surgical and Interventional Sciences, Faculty of Medicine, University College London, London, UK.,Imperial Prostate, Division of Surgery, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.,Department of Urology, Bart's and Royal London Hospitals, London, UK
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3
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Beikzadeh B, Angaji SA, Abolhasani M. Association study between common variations in some candidate genes and prostate adenocarcinoma predisposition through multi-stage approach in Iranian population. BMC MEDICAL GENETICS 2020; 21:81. [PMID: 32295536 PMCID: PMC7161142 DOI: 10.1186/s12881-020-01014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/27/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Prostate cancer is one of the five common cancers and has the second incidence rate and the third mortality rate in Iranian population. The purpose of this study was to evaluate the association of rs16901979, rs4242382 and rs1447295 on 8q24 locus, rs2735839 (KLK3 gene) and rs721048 (EHBP1 gene) with prostate adenocarcinoma through multi-stage approach to identify the polymorphisms associated with prostate cancer and use them as screening factors. Screening tests can identify people who may have a chance of developing the disease before detection and any symptoms. METHODS The case-control study included 103 cases (prostate adenocarcinoma) and 100 controls (benign prostatic hyperplasia). Tetra-primer ARMS-PCR was used to genotyping of each participant. A Multi-stage approach was used for efficient genomic study. In this method, a smaller number of people can be used. Chi-squared, Fisher's exact test and logistic regression were used to investigate the SNPs associated with prostate cancer and Gleason score. RESULTS In the first stage (59 men), the frequency of polymorphisms rs16901979, rs4242382, rs1447295, rs2735839 and rs721048 in the prostate adenocarcinoma group was evaluated compared to the control group (P-value < 0.3) in order to select meaningful polymorphisms. There was not any significant difference between genotype frequency rs16901979 (P = 0.671) and rs721048 (P = 0.474) in the case group compared to BPH. Therefore, these polymorphisms were eliminated, and in the second step (144 men), rs4242382, rs2735839 and rs1447295 were evaluated (P-value < 0.05). According to the total population (203 men), there was significant difference between genotype frequency rs4242382 (P = 0.001), rs2735839 (P = 0.000) and rs1447295 (P = 0.005) even after using Bonferroni correction (p = 0.016). The effect of these three polymorphisms on prostate cancer was not modified by age and PSA. There was a significant difference between the allelic frequency of A vs G (rs4242382, rs2735839) at all classes of Gleason score and A vs C (rs1447295) at Gleason score ≥ 8. CONCLUSIONS The results of this study for rs2735839, rs4242382 and rs1447295 indicate the association of these polymorphisms with prostate adenocarcinoma predisposition in Iranian population. Exposure effect is homogeneous between different ages and PSA level categories. These three polymorphisms should be studied in a larger population to confirm these results.
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Affiliation(s)
- Behnaz Beikzadeh
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Seyed Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Maryam Abolhasani
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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4
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Qian Y, Zhang L, Cai M, Li H, Xu H, Yang H, Zhao Z, Rhie SK, Farnham PJ, Shi J, Lu W. The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression. SCIENCE ADVANCES 2019; 5:eaaw6710. [PMID: 31328168 PMCID: PMC6636982 DOI: 10.1126/sciadv.aaw6710] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/11/2019] [Indexed: 05/15/2023]
Abstract
Genome-wide association studies identified single-nucleotide polymorphism (SNP) rs55958994 as a significant variant associated with increased susceptibility to prostate cancer. However, the mechanisms by which this SNP mediates increased risk to cancer are still unknown. In this study, we show that this variant is located in an enhancer active in prostate cancer cells. Deletion of this enhancer from prostate tumor cells resulted in decreased tumor initiation, tumor growth, and invasive migration, as well as a loss of stem-like cells. Using a combination of capture chromosome conformation capture (Capture-C) and RNA sequencing, we identified genes on the same and different chromosomes as targets regulated by the enhancer. Furthermore, we show that expression of individual candidate target genes in an enhancer-deleted cell line rescued different aspects of tumorigenesis. Our data suggest that the rs55958994-associated enhancer affects prostate cancer progression by influencing expression of multiple genes via long-range chromatin interactions.
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Affiliation(s)
- Yuyang Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Mingyang Cai
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Hongxia Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Heming Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Hongzhen Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wange Lu
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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5
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Gao P, Xia JH, Sipeky C, Dong XM, Zhang Q, Yang Y, Zhang P, Cruz SP, Zhang K, Zhu J, Lee HM, Suleman S, Giannareas N, Liu S, Tammela TLJ, Auvinen A, Wang X, Huang Q, Wang L, Manninen A, Vaarala MH, Wang L, Schleutker J, Wei GH. Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus. Cell 2018; 174:576-589.e18. [PMID: 30033361 PMCID: PMC6091222 DOI: 10.1016/j.cell.2018.06.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/28/2018] [Accepted: 05/31/2018] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) have identified rs11672691 at 19q13 associated with aggressive prostate cancer (PCa). Here, we independently confirmed the finding in a cohort of 2,738 PCa patients and discovered the biological mechanism underlying this association. We found an association of the aggressive PCa-associated allele G of rs11672691 with elevated transcript levels of two biologically plausible candidate genes, PCAT19 and CEACAM21, implicated in PCa cell growth and tumor progression. Mechanistically, rs11672691 resides in an enhancer element and alters the binding site of HOXA2, a novel oncogenic transcription factor with prognostic potential in PCa. Remarkably, CRISPR/Cas9-mediated single-nucleotide editing showed the direct effect of rs11672691 on PCAT19 and CEACAM21 expression and PCa cellular aggressive phenotype. Clinical data demonstrated synergistic effects of rs11672691 genotype and PCAT19/CEACAM21 gene expression on PCa prognosis. These results provide a plausible mechanism for rs11672691 associated with aggressive PCa and thus lay the ground work for translating this finding to the clinic.
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Affiliation(s)
- Ping Gao
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Ji-Han Xia
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland
| | - Xiao-Ming Dong
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Yuehong Yang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sara Pereira Cruz
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Kai Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Jing Zhu
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hang-Mao Lee
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Sufyan Suleman
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Nikolaos Giannareas
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Song Liu
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, 100005 Beijing, China
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, 33521 Tampere, Finland
| | - Anssi Auvinen
- University of Tampere, School of Health Sciences, 33520 Tampere, Finland
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, 100005 Beijing, China
| | - Qilai Huang
- School of Life Science, Shandong University, 250012 Jinan, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Aki Manninen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Markku H Vaarala
- Oulu University Hospital, 90014 Oulu, Finland; Medical Research Center Oulu, University of Oulu and Oulu University Hospital, 90014 Oulu, Finland
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland; Medical Genetics, Division of Laboratory, Turku University Hospital, 20521 Turku, Finland
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
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Vaidyanathan V, Naidu V, Kao CHJ, Karunasinghe N, Bishop KS, Wang A, Pallati R, Shepherd P, Masters J, Zhu S, Goudie M, Krishnan M, Jabed A, Marlow G, Narayanan A, Ferguson LR. Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men - a genotypic approach. MOLECULAR BIOSYSTEMS 2017; 13:681-698. [PMID: 28252132 DOI: 10.1039/c6mb00873a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs. By using this method, we identified the susceptible alleles in a New Zealand population, and examined the interaction with environmental factors. We have identified a number of SNPs that have risk associations both with and without environmental interaction. The results indicate that certain SNPs are associated with disease vulnerability based on behavioral factors. The list of genes with SNPs identified as being associated with the risk of PCa in a New Zealand population is provided in the graphical abstract.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Vijay Naidu
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Chi Hsiu-Juei Kao
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | | | - Karen S Bishop
- Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Alice Wang
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Phillip Shepherd
- Sequenom Facility, Liggins Institute, University of Auckland, Auckland 1023, New Zealand.
| | - Jonathan Masters
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Shuotun Zhu
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Megan Goudie
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Mohanraj Krishnan
- Department of Obstetrics and Gynaecology, FMHS, University of Auckland, Auckland 1023, New Zealand.
| | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ajit Narayanan
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
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7
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Marzec J, Mao X, Li M, Wang M, Feng N, Gou X, Wang G, Sun Z, Xu J, Xu H, Zhang X, Zhao SC, Ren G, Yu Y, Wu Y, Wu J, Xue Y, Zhou B, Zhang Y, Xu X, Li J, He W, Benlloch S, Ross-Adams H, Chen L, Li J, Hong Y, Kote-Jarai Z, Cui X, Hou J, Guo J, Xu L, Yin C, Zhou Y, Neal DE, Oliver T, Cao G, Zhang Z, Easton DF, Chelala C, Olama AAA, Eeles RA, Zhang H, Lu YJ. A genetic study and meta-analysis of the genetic predisposition of prostate cancer in a Chinese population. Oncotarget 2016; 7:21393-403. [PMID: 26881390 PMCID: PMC5008293 DOI: 10.18632/oncotarget.7250] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Prostate cancer predisposition has been extensively investigated in European populations, but there have been few studies of other ethnic groups. To investigate prostate cancer susceptibility in the under-investigated Chinese population, we performed single-nucleotide polymorphism (SNP) array analysis on a cohort of Chinese cases and controls and then meta-analysis with data from the existing Chinese prostate cancer genome-wide association study (GWAS). Genotyping 211,155 SNPs in 495 cases and 640 controls of Chinese ancestry identified several new suggestive Chinese prostate cancer predisposition loci. However, none of them reached genome-wide significance level either by meta-analysis or replication study. The meta-analysis with the Chinese GWAS data revealed that four 8q24 loci are the main contributors to Chinese prostate cancer risk and the risk alleles from three of them exist at much higher frequencies in Chinese than European populations. We also found that several predisposition loci reported in Western populations have different effect on Chinese men. Therefore, this first extensive single-nucleotide polymorphism study of Chinese prostate cancer in comparison with European population indicates that four loci on 8q24 contribute to a great risk of prostate cancer in a considerable large proportion of Chinese men. Based on those four loci, the top 10% of the population have six- or two-fold prostate cancer risk compared with men of the bottom 10% or median risk respectively, which may facilitate the design of prostate cancer genetic risk screening and prevention in Chinese men. These findings also provide additional insights into the etiology and pathogenesis of prostate cancer.
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Affiliation(s)
- Jacek Marzec
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Meiling Li
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Meilin Wang
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Ninghan Feng
- Department of Urology, Wuxi Second People's Hospital, Nanjing Medical University, Wuxi, 214002, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Guomin Wang
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Zan Sun
- Liaoning People's Hospital and Center of Experiment and Technology, China Medical University, Shenyang, 110001, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, North Shore University Health System, Evanston, IL 60201, U.S.A
- Fudan Institute of Urology, Huashang Hospital, Fudan University, Shanghai, 200040, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Huazhong Science and Technology University, Wuhan, 430030, China
| | - Xiaoping Zhang
- Department of Urology, Xiehe Hospital, Huazhong Science and Technology University, Wuhan, 430022, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, Medical College, Zhengzhou University, Zhengzhou, 450003, China
| | - Ji Wu
- Department of Urology, North Sichuan Medical College, Nanchong, 637000, China
| | - Yao Xue
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Bo Zhou
- Department of Nutrition Science, Shenyang Medical College, Shenyang, 110034, China
| | - Yanling Zhang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Xingxing Xu
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Jie Li
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Weiyang He
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Li Chen
- Department of Urology, Xiehe Hospital, Huazhong Science and Technology University, Wuhan, 430022, China
| | - Jucong Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yingqia Hong
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Xingang Cui
- Department of Urology, Changzheng Hospital, The Second Military Medical University, Shanghai, 200003, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Lei Xu
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Changjun Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - David E. Neal
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tim Oliver
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Zhengdong Zhang
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Rosalind A. Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- The Royal Marsden NHS Foundation Trust, London and Surrey, SM2 5NG, UK
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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8
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Ahmed M, Eeles R. Germline genetic profiling in prostate cancer: latest developments and potential clinical applications. Future Sci OA 2016; 2:FSO87. [PMID: 28031937 PMCID: PMC5137984 DOI: 10.4155/fso.15.87] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 11/10/2015] [Indexed: 12/16/2022] Open
Abstract
Familial and twin studies have demonstrated a significant inherited component to prostate cancer predisposition. Genome wide association studies have shown that there are 100 single nucleotide polymorphisms which have been associated with the development of prostate cancer. This review aims to discuss the scientific methods used to identify these susceptibility loci. It will also examine the current clinical utility of these loci, which include the development of risk models as well as predicting treatment efficacy and toxicity. In order to refine the clinical utility of the susceptibility loci, international consortia have been developed to combine statistical power as well as skills and knowledge to further develop models that could be used to predict risk and treatment outcomes.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, London SM2 5NG, UK
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9
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Chen H, Yu H, Wang J, Zhang Z, Gao Z, Chen Z, Lu Y, Liu W, Jiang D, Zheng SL, Wei GH, Issacs WB, Feng J, Xu J. Systematic enrichment analysis of potentially functional regions for 103 prostate cancer risk-associated loci. Prostate 2015; 75:1264-76. [PMID: 26015065 DOI: 10.1002/pros.23008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND More than 100 prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) have been identified by genome wide association studies (GWAS). However, the molecular mechanisms are unclear for most of these SNPs. METHODS All reported PCa risk-associated SNPs reaching the genome-wide significance level of P < 1 × 10(-7) (index SNPs), as well as SNPs in linkage disequilibrium (LD, r(2) ≥ 0.5) with them were cataloged. Genomic regions with potentially functional impact were also identified, including UCSC annotated coding regions (exon and snoRNA/miRNA) and regulatory regions, as well as binding regions for transcription factors (TFs), histone modifications (HMs), DNase I hypersensitivity (DHSs), and RNA Polymerase IIA (POLR2A) defined by ChIP-Seq in prostate cell lines and tissues. Enrichment analysis was performed to test whether PCa risk-associated SNPs are located in these functional regions more than expected. RESULTS A total of 103 PCa risk-associated index SNPs and 7,244 SNPs in LD with these index SNPs were cataloged. Genomic regions with potentially functional impact, grouped in 30 different categories of functionalities, were identified. Enrichment analysis indicated that genomic regions in the following 15 categories were enriched for the PCa risk-associated SNPs: exons, CpG regions, 6 TFs (AR, ERG, FOXA1, HOXB13, CTCF, and NR3C1), 5 HMs (H3K4me1, H3K4me2, H3K4me3, H3K27AC, and H3T11P), DHSs and POLR2A. In contrast, significantly fewer PCa risk SNPs were mapped to binding regions for H3K27me3, a repressive chromatin marker. CONCLUSIONS The PCa risk-associated SNPs discovered to date may affect PCa risk through multiple different mechanisms, especially by affecting binding regions of TFs/HMs.
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Affiliation(s)
- Haitao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Center for Genomic Translational Medicine and Prevention, Fudan School of Public Health, Fudan University, Shanghai, P.R. China
| | - Hongjie Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Jianqing Wang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Zheng Zhang
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Zhengrong Gao
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Zhuo Chen
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Yulan Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Wennuan Liu
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - Deke Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - William B Issacs
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Junjie Feng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Center for Genomic Translational Medicine and Prevention, Fudan School of Public Health, Fudan University, Shanghai, P.R. China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, P.R. China
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
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10
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Abstract
PURPOSE OF REVIEW Recent advances in sequencing technologies have allowed for the identification of genetic variants within germline DNA that can explain a significant portion of the genetic underpinnings of prostate cancer. Despite evidence suggesting that these genetic variants can be used for improved risk stratification, they have not yet been routinely incorporated into routine clinical practice. This review highlights their potential utility in prostate cancer screening. RECENT FINDINGS There are now almost 100 genetic variants, called single nucleotide polymorphisms (SNPs) that have been recently found to be associated with the risk of developing prostate cancer. In addition, some of these prostate cancer risk SNPs have also been found to influence prostate specific antigen (PSA) expression levels and potentially aggressive disease. SUMMARY Incorporation of panels of prostate cancer risk SNPs into clinical practice offers potential to provide improvements in patient selection for prostate cancer screening; PSA interpretation (e.g. by correcting for the presence of SNPs that influence PSA expression levels; decision for biopsy (using prostate cancer risk SNPs); and possibly the decision for treatment. A proposed clinical algorithm incorporating these prostate cancer risk SNPs is discussed.
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11
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Helfand BT, Roehl KA, Cooper PR, McGuire BB, Fitzgerald LM, Cancel-Tassin G, Cornu JN, Bauer S, Van Blarigan EL, Chen X, Duggan D, Ostrander EA, Gwo-Shu M, Zhang ZF, Chang SC, Jeong S, Fontham ETH, Smith G, Mohler JL, Berndt SI, McDonnell SK, Kittles R, Rybicki BA, Freedman M, Kantoff PW, Pomerantz M, Breyer JP, Smith JR, Rebbeck TR, Mercola D, Isaacs WB, Wiklund F, Cussenot O, Thibodeau SN, Schaid DJ, Cannon-Albright L, Cooney KA, Chanock SJ, Stanford JL, Chan JM, Witte J, Xu J, Bensen JT, Taylor JA, Catalona WJ. Associations of prostate cancer risk variants with disease aggressiveness: results of the NCI-SPORE Genetics Working Group analysis of 18,343 cases. Hum Genet 2015; 134:439-50. [PMID: 25715684 PMCID: PMC4586077 DOI: 10.1007/s00439-015-1534-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/06/2015] [Indexed: 01/18/2023]
Abstract
Genetic studies have identified single nucleotide polymorphisms (SNPs) associated with the risk of prostate cancer (PC). It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score (Gleason ≤ 6, 7, ≥ 8) and aggressiveness (non-aggressive, intermediate, and aggressive disease). Statistical analyses were used to compare the frequency of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 (G) was significantly and inversely associated with aggressive (OR = 0.77; 95 % CI 0.69-0.87) and high-grade disease (OR = 0.77; 95 % CI 0.68-0.86) in European men. Similar associations with aggressive (OR = 0.72; 95 % CI 0.58-0.89) and high-grade disease (OR = 0.69; 95 % CI 0.54-0.87) were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels (<4.0 ng/mL) in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness.
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Affiliation(s)
- Brian T Helfand
- Department of Surgery, Division of Urology, John and Carol Walter Center for Urological Health, NorthShore University Health System, Evanston, IL, USA
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12
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Grill S, Fallah M, Leach RJ, Thompson IM, Hemminki K, Ankerst DP. A simple-to-use method incorporating genomic markers into prostate cancer risk prediction tools facilitated future validation. J Clin Epidemiol 2015; 68:563-73. [PMID: 25684153 DOI: 10.1016/j.jclinepi.2015.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 01/23/2023]
Abstract
OBJECTIVES To incorporate single-nucleotide polymorphisms (SNPs) into the Prostate Cancer Prevention Trial Risk Calculator (PCPTRC). STUDY DESIGN AND SETTING A multivariate random-effects meta-analysis of likelihood ratios (LRs) for 30 validated SNPs was performed, allowing the incorporation of linkage disequilibrium. LRs for an SNP were defined as the ratio of the probability of observing the SNP in prostate cancer cases relative to controls and estimated by published allele or genotype frequencies. LRs were multiplied by the PCPTRC prior odds of prostate cancer to provide updated posterior odds. RESULTS In the meta-analysis (prostate cancer cases/controls = 386,538/985,968), all but two of the SNPs had at least one statistically significant allele LR (P < 0.05). The two SNPs with the largest LRs were rs16901979 [LR = 1.575 for one risk allele, 2.552 for two risk alleles (homozygous)] and rs1447295 (LR = 1.307 and 1.887, respectively). CONCLUSION The substantial investment in genome-wide association studies to discover SNPs associated with prostate cancer risk and the ability to integrate these findings into the PCPTRC allows investigators to validate these observations, to determine the clinical impact, and to ultimately improve clinical practice in the early detection of the most common cancer in men.
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Affiliation(s)
- Sonja Grill
- Department of Life Sciences of the Technical University Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany.
| | - Mahdi Fallah
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Im Neuenheimer Feld 580, Im Technologiepark, 69120 Heidelberg, Germany
| | - Robin J Leach
- Department of Urology of the University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA; Department of Cellular and Structural Biology of the University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Ian M Thompson
- Department of Urology of the University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Im Neuenheimer Feld 580, Im Technologiepark, 69120 Heidelberg, Germany; Center for Primary Health Care Research, Lund University, Box 117, 221 00 LUND, Sweden
| | - Donna P Ankerst
- Department of Life Sciences of the Technical University Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; Department of Urology of the University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA; Department of Mathematics of the Technical University Munich, Boltzmannstr. 3, 85748 Garching b. München, Germany; Department of Epidemiology and Biostatistics of the University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
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13
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Mikropoulos C, Goh C, Leongamornlert D, Kote-Jarai Z, Eeles R. Translating genetic risk factors for prostate cancer to the clinic: 2013 and beyond. Future Oncol 2014; 10:1679-94. [PMID: 25145435 DOI: 10.2217/fon.14.72] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PrCa) is the most commonly diagnosed cancer in the male UK population, with over 40,000 new cases per year. PrCa has a complex, polygenic predisposition, due to rare variants such as BRCA and common variants such as single nucleotide polymorphisms (SNPs). With the introduction of genome-wide association studies, 78 susceptibility loci (SNPs) associated with PrCa risk have been identified. Genetic profiling could risk-stratify a population, leading to the discovery of a higher proportion of clinically significant disease and a reduction in the morbidity related to age-based prostate-specific antigen screening. Based on the combined risk of the 78 SNPs identified so far, the top 1% of the risk distribution has a 4.7-times higher risk of developing PrCa compared with the average of the general population.
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14
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Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014; 10:e1004102. [PMID: 24497837 PMCID: PMC3907334 DOI: 10.1371/journal.pgen.1004102] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations--we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r(2) ≥ 0.88%. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r(2) = 0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
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Affiliation(s)
- Dennis J. Hazelett
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Suhn Kyong Rhie
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Malaina Gaddis
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chunli Yan
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Daniel L. Lakeland
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Simon G. Coetzee
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Ellipse/GAME-ON consortium
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Houtan Noushmehr
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Wendy Cozen
- USC Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | | | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gerhard A. Coetzee
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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15
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Ren S, Xu J, Zhou T, Jiang H, Chen H, Liu F, Na R, Zhang L, Wu Y, Sun J, Yang B, Gao X, Zheng SL, Xu C, Ding Q, Sun Y. Plateau effect of prostate cancer risk-associated SNPs in discriminating prostate biopsy outcomes. Prostate 2013; 73:1824-35. [PMID: 24037738 PMCID: PMC3910089 DOI: 10.1002/pros.22721] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022]
Abstract
BACKGROUND Additional prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) continue to be identified. It is unclear whether addition of newly identified SNPs improves the discriminative performance of biopsy outcomes over previously established SNPs. METHODS A total of 667 consecutive patients that underwent prostate biopsy for detection of PCa at Huashan Hospital and Changhai Hospital, Shanghai, China were recruited. Genetic scores were calculated for each patient using various combinations of 29 PCa risk-associated SNPs. Performance of these genetic scores for discriminating prostate biopsy outcomes were compared using the area under a receiver operating characteristic curve (AUC). RESULTS The discriminative performance of genetic score derived from a panel of all 29 SNPs (24 previous and 5 new) was similar to that derived from the 24 previously established SNPs, the AUC of which were 0.60 and 0.61, respectively (P = 0.72). When SNPs with the strongest effect on PCa risk (ranked based on contribution to the total genetic variance from an external study) were sequentially added to the models for calculating genetic score, the AUC gradually increased and peaked at 0.62 with the top 13 strongest SNPs. Under the 13-SNP model, the PCa detection rate was 21.52%, 36.74%, and 51.98%, respectively for men with low (<0.5), intermediate (0.5-1.5), and high (>1.5) genetic score, P-trend = 9.91 × 10(-6). CONCLUSION Genetic score based on PCa risk-associated SNPs implicated to date is a significant predictor of biopsy outcome. Additional small-effect PCa risk-associated SNPs to be discovered in the future are unlikely to further improve predictive performance.
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Affiliation(s)
- Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Tie Zhou
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Haowen Jiang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haitao Chen
- State Key Laboratory of Genetic Engineering, Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Fang Liu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Rong Na
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Limin Zhang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yishuo Wu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Bo Yang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xu Gao
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Chuanliang Xu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qiang Ding
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Correspondence to: Qiang Ding, Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
- Correspondence to: Yinghao Sun, Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.
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16
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Na R, Liu F, Zhang P, Ye D, Xu C, Shao Q, Qi J, Wang X, Chen Z, Wang M, He D, Wang Z, Zhou F, Yuan J, Gao X, Wei Q, Yang J, Jiao Y, Ou-Yang J, Zhu Y, Wu Q, Chen H, Lu D, Shi R, Lin X, Jiang H, Wang Z, Jiang D, Sun J, Zheng SL, Ding Q, Mo Z, Sun Y, Xu J. Evaluation of reported prostate cancer risk-associated SNPs from genome-wide association studies of various racial populations in Chinese men. Prostate 2013; 73:1623-35. [PMID: 24038036 PMCID: PMC3928594 DOI: 10.1002/pros.22629] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 11/16/2012] [Indexed: 11/06/2022]
Abstract
BACKGROUND Several genome-wide association studies (GWAS) of prostate cancer (PCa) have identified many single nucleotide polymorphisms (SNPs) that are significantly associated with PCa risk in various racial groups. The objective of this study is to evaluate which of these SNPs are associated with PCa risk in Chinese men and estimate their strength of association. METHODS All SNPs that were reported to be associated with PCa risk in GWAS from populations of European, African American, Japanese, and Chinese descent were evaluated in 1,922 PCa cases and 2,175 controls selected from the Chinese Consortium for Prostate Cancer Genetics (ChinaPCa). A logistic regression analysis was used to estimate allelic odds ratios (ORs) of these SNPs for PCa. RESULTS Among the 53 SNPs, 50 were polymorphic in the Chinese population. Of which, 10 and 24 SNPs were significantly associated with PCa risk in Chinese men at P < 0.001 and <0.05, respectively. These 24 significant SNPs included 17, 5, and 2 SNPs that were originally discovered in European, Japanese, and Chinese descent, respectively. The estimated ORs ranged from 1.10 to 1.49 and the direction of association was consistent with previous studies. When ORs were estimated separately for PCa with Gleason score ≤7 and ≥8, a marginally significant difference in ORs was found only for two of the 24 SNPs (P = 0.02 and 0.04). CONCLUSION About half of PCa risk-associated SNPs identified in GWAS of various populations are associated with PCa risk in Chinese men. Information on PCa risk-associated SNPs and their ORs may facilitate risk assessment of PCa risk in Chinese men.
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Affiliation(s)
- Rong Na
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
| | - Fang Liu
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Penyin Zhang
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer
Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan
University, Shanghai, PR China
| | - Chuanliang Xu
- Department of Urology, Shanghai Changhai Hospital, Second
Military Medical University, Shanghai, PR China
| | - Qiang Shao
- Department of Urology, Suzhou Municipal Hospital, Suzhou,
PR China
| | - Jun Qi
- Department of Urology, Xinhua Hospital, School of Medicine,
Shanghai Jiaotong University, Shanghai, PR China
| | - Xiang Wang
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
| | - Zhiwen Chen
- Urology Institute of PLA, Southwest Hospital, Third
Military Medical University, Chongqing, PR China
| | - Meilin Wang
- Department of Molecular and Genetic Toxicology, The Key
Laboratory of Modern Toxicology of Ministry of Education, School of Public Health,
Nanjing Medical University, Nanjing, PR China
- State Key Laboratory of Reproductive Medicine, Nanjing
Medical University, Nanjing, PR China
| | - Dalin He
- Department of Urology, The First Affiliated Hospital of
Medical College of Xi’an Jiaotong University, Xi’an, PR China
| | - Zhong Wang
- Department of Urology, Ninth People’s Hospital,
School of Medicine, Shanghai Jiaotong University, Shanghai, PR China
| | - Fangjian Zhou
- State Key Laboratory of Oncology in Southern China,
Guangzhou, PR China
- Department of Urology, Cancer Center, Sun Yat-Sen
University, Guangzhou, PR China
| | - Jianlin Yuan
- Department of Urology, Xijing Hospital, The Fourth
Military Medical University, Xi’an, PR China
| | - Xin Gao
- Department of Urology, The Third Affiliated Hospital, Sun
Yat-sen University, Guangzhou, PR China
| | - Qiang Wei
- Department of Urology, West China Hospital, Sichuan
University, Chengdu, Sichuan, PR China
| | - Jin Yang
- Department of Cell Biology, Third Military Medical
University, Chongqing, PR China
| | - Yang Jiao
- Department of Urology, Xinhua Hospital, School of Medicine,
Shanghai Jiaotong University, Shanghai, PR China
| | - Jun Ou-Yang
- Department of Urology, First People’s Hospital,
Suzhou University, Suzhou, PR China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer
Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan
University, Shanghai, PR China
| | - Qijun Wu
- State Key Laboratory of Oncogene and Related Genes,
Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of
Medicine, Shanghai, PR China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Rong Shi
- School of Public Health, Shanghai Jiaotong University,
Shanghai, PR China
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Haowen Jiang
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
| | - Zhong Wang
- Center for Cancer Genomics, Wake Forest School of
Medicine, Winston-Salem, North Carolina
| | - Deke Jiang
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest School of
Medicine, Winston-Salem, North Carolina
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of
Medicine, Winston-Salem, North Carolina
| | - Qing Ding
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi
Medical University, Nanning, Guangxi, PR China
- Department of Urology and Nephrology, The First
Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second
Military Medical University, Shanghai, PR China
- Correspondence to: Yinghao Sun, Department of
Urology, Shanghai Changhai Hospital, Second Military Medical University, 168
Changhai Road, Shanghai, PR China.
| | - Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan
University, Shanghai, PR China
- State Key Laboratory of Genetic Engineering, School of Life
Sciences, Fudan University, Shanghai, PR China
- Center for Genetic Epidemiology, School of Life Sciences,
Fudan University, Shanghai, PR China
- Center for Cancer Genomics, Wake Forest School of
Medicine, Winston-Salem, North Carolina
- Correspondence to: Jianfeng Xu, Fudan Institute
of Urology, Huashan Hospital, Fudan University, 12 Mid-Wulumuqi Road, Shanghai,
PR China.
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17
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Xu J, Sun J, Zheng SL. Prostate cancer risk-associated genetic markers and their potential clinical utility. Asian J Androl 2013; 15:314-22. [PMID: 23564047 PMCID: PMC3739659 DOI: 10.1038/aja.2013.42] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/16/2013] [Accepted: 03/18/2013] [Indexed: 02/02/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common cancers among men in Western developed countries and its incidence has increased considerably in many other parts of the world, including China. The etiology of PCa is largely unknown but is thought to be multifactorial, where inherited genetics plays an important role. In this article, we first briefly review results from studies of familial aggregation and genetic susceptibility to PCa. We then recap key findings of rare and high-penetrance PCa susceptibility genes from linkage studies in PCa families. We devote a significant portion of this article to summarizing discoveries of common and low-penetrance PCa risk-associated single-nucleotide polymorphisms (SNPs) from genetic association studies in PCa cases and controls, especially those from genome-wide association studies (GWASs). A strong focus of this article is to review the literature on the potential clinical utility of these implicated genetic markers. Most of these published studies described PCa risk estimation using a genetic score derived from multiple risk-associated SNPs and its utility in determining the need for prostate biopsy. Finally, we comment on the newly proposed concept of genetic score; the notion is to treat it as a marker for genetic predisposition, similar to family history, rather than a diagnostic marker to discriminate PCa patients from non-cancer patients. Available evidence to date suggests that genetic score is an objective and better measurement of inherited risk of PCa than family history. Another unique feature of this article is the inclusion of genetic association studies of PCa in Chinese and Japanese populations.
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Affiliation(s)
- Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan UniversityFudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China.
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18
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Agalliu I, Wang Z, Wang T, Dunn A, Parikh H, Myers T, Burk RD, Amundadottir L. Characterization of SNPs associated with prostate cancer in men of Ashkenazic descent from the set of GWAS identified SNPs: impact of cancer family history and cumulative SNP risk prediction. PLoS One 2013; 8:e60083. [PMID: 23573233 PMCID: PMC3616024 DOI: 10.1371/journal.pone.0060083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 02/24/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified multiple SNPs associated with prostate cancer (PrCa). Population isolates may have different sets of risk alleles for PrCa constituting unique population and individual risk profiles. METHODS To test this hypothesis, associations between 31 GWAS SNPs of PrCa were examined among 979 PrCa cases and 1,251 controls of Ashkenazic descent using logistic regression. We also investigated risks by age at diagnosis, pathological features of PrCa, and family history of cancer. Moreover, we examined associations between cumulative number of risk alleles and PrCa and assessed the utility of risk alleles in PrCa risk prediction by comparing the area under the curve (AUC) for different logistic models. RESULTS Of the 31 genotyped SNPs, 8 were associated with PrCa at p ≤ 0.002 (corrected p-value threshold) with odds ratios (ORs) ranging from 1.22 to 1.42 per risk allele. Four SNPs were associated with aggressive PrCa, while three other SNPs showed potential interactions for PrCa by family history of PrCa (rs8102476; 19q13), lung cancer (rs17021918; 4q22), and breast cancer (rs10896449; 11q13). Men in the highest vs. lowest quartile of cumulative number of risk alleles had ORs of 3.70 (95% CI 2.76-4.97); 3.76 (95% CI 2.57-5.50), and 5.20 (95% CI 2.94-9.19) for overall PrCa, aggressive cancer and younger age at diagnosis, respectively. The addition of cumulative risk alleles to the model containing age at diagnosis and family history of PrCa yielded a slightly higher AUC (0.69 vs. 0.64). CONCLUSION These data define a set of risk alleles associated with PrCa in men of Ashkenazic descent and indicate possible genetic differences for PrCa between populations of European and Ashkenazic ancestry. Use of genetic markers might provide an opportunity to identify men at highest risk for younger age of onset PrCa; however, their clinical utility in identifying men at highest risk for aggressive cancer remains limited.
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Affiliation(s)
- Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America.
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19
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Amin Al Olama A, Kote-Jarai Z, Schumacher FR, Wiklund F, Berndt SI, Benlloch S, Giles GG, Severi G, Neal DE, Hamdy FC, Donovan JL, Hunter DJ, Henderson BE, Thun MJ, Gaziano M, Giovannucci EL, Siddiq A, Travis RC, Cox DG, Canzian F, Riboli E, Key TJ, Andriole G, Albanes D, Hayes RB, Schleutker J, Auvinen A, Tammela TL, Weischer M, Stanford JL, Ostrander EA, Cybulski C, Lubinski J, Thibodeau SN, Schaid DJ, Sorensen KD, Batra J, Clements JA, Chambers S, Aitken J, Gardiner RA, Maier C, Vogel W, Dörk T, Brenner H, Habuchi T, Ingles S, John EM, Dickinson JL, Cannon-Albright L, Teixeira MR, Kaneva R, Zhang HW, Lu YJ, Park JY, Cooney KA, Muir KR, Leongamornlert DA, Saunders E, Tymrakiewicz M, Mahmud N, Guy M, Govindasami K, O'Brien LT, Wilkinson RA, Hall AL, Sawyer EJ, Dadaev T, Morrison J, Dearnaley DP, Horwich A, Huddart RA, Khoo VS, Parker CC, Van As N, Woodhouse CJ, Thompson A, Dudderidge T, Ogden C, Cooper CS, Lophatonanon A, Southey MC, Hopper JL, English D, Virtamo J, Le Marchand L, Campa D, Kaaks R, Lindstrom S, Diver WR, Gapstur S, Yeager M, Cox A, Stern MC, Corral R, Aly M, Isaacs W, Adolfsson J, Xu J, Zheng SL, Wahlfors T, Taari K, Kujala P, Klarskov P, Nordestgaard BG, Røder MA, Frikke-Schmidt R, Bojesen SE, FitzGerald LM, Kolb S, Kwon EM, Karyadi DM, Orntoft TF, Borre M, Rinckleb A, Luedeke M, Herkommer K, Meyer A, Serth J, Marthick JR, Patterson B, Wokolorczyk D, Spurdle A, Lose F, McDonnell SK, Joshi AD, Shahabi A, Pinto P, Santos J, Ray A, Sellers TA, Lin HY, Stephenson RA, Teerlink C, Muller H, Rothenbacher D, Tsuchiya N, Narita S, Cao GW, Slavov C, Mitev V, Chanock S, Gronberg H, Haiman CA, Kraft P, Easton DF, Eeles RA. A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease. Hum Mol Genet 2013; 22:408-15. [PMID: 23065704 PMCID: PMC3526158 DOI: 10.1093/hmg/dds425] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/04/2012] [Indexed: 01/14/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple common genetic variants associated with an increased risk of prostate cancer (PrCa), but these explain less than one-third of the heritability. To identify further susceptibility alleles, we conducted a meta-analysis of four GWAS including 5953 cases of aggressive PrCa and 11 463 controls (men without PrCa). We computed association tests for approximately 2.6 million SNPs and followed up the most significant SNPs by genotyping 49 121 samples in 29 studies through the international PRACTICAL and BPC3 consortia. We not only confirmed the association of a PrCa susceptibility locus, rs11672691 on chromosome 19, but also showed an association with aggressive PrCa [odds ratio = 1.12 (95% confidence interval 1.03-1.21), P = 1.4 × 10(-8)]. This report describes a genetic variant which is associated with aggressive PrCa, which is a type of PrCa associated with a poorer prognosis.
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Affiliation(s)
- Ali Amin Al Olama
- Strangeways Laboratory, Centre for Cancer Genetic Epidemiology, Worts Causeway, Cambridge CB1 8RN, UK
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Fredrick R. Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Sara Benlloch
- Strangeways Laboratory, Centre for Cancer Genetic Epidemiology, Worts Causeway, Cambridge CB1 8RN, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, 1 Rathdowne Street, Carlton, VIC 3053, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, 723 Swanston Street, Carlton, VIC 3053, Australia
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, 1 Rathdowne Street, Carlton, VIC 3053, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, 723 Swanston Street, Carlton, VIC 3053, Australia
| | - David E. Neal
- Surgical Oncology (Uro-Oncology: S4), Addenbrooke's Hospital, University of Cambridge, Box 279, Hills Road, Cambridge, UK
- Li Ka Shing Centre, Cancer Research UK Cambridge Research Institute, Cambridge CB2 2QQ, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgery and
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology and
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Michael J. Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Michael Gaziano
- Massachusetts Veterans Epidemiology and Research Information Center (MAVERIC) and Geriatric Research, Education, and Clinical Center (GRECC), Boston Veterans Affairs Healthcare System, Boston, MA 02114, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | | | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College, London SW7 2AZ, UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - David G. Cox
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
- Lyon Cancer Research Center, INSERM U1052, Lyon, France
| | | | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
| | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Gerald Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Richard B. Hayes
- Division of Epidemiology, Department of Environmental Medicine, NYU Langone Medical Centre, NYU Cancer Institute, New York, NY 10016, USA
| | - Johanna Schleutker
- Institute of Biomedical Technology/BioMediTech, University of Tampere and
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences and
| | - Teuvo L.J. Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Centre, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Room 5351, Bethesda, MD, USA
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | | | | | | | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Suzanne Chambers
- Griffith Health Institute, Griffith University, Gold Coast, QLD, Australia
- Viertel Centre for Research in Cancer Control, Cancer Council Queensland, Brisbane, QLD, Australia
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Joanne Aitken
- Viertel Centre for Research in Cancer Control, Cancer Council Queensland, Brisbane, QLD, Australia
| | - Robert A. Gardiner
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Christiane Maier
- Department of Urology and
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Walther Vogel
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Thilo Dörk
- Hannover Medical School, Hannover, Germany
| | | | - Tomonori Habuchi
- Department of Urology,Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Sue Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA, USA
- Division of Epidemiology, Department of Health Research and Policy and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanne L. Dickinson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, TAS, Australia
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Centre, Salt Lake City, UT, USA
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Radka Kaneva
- Molecular Medicine Centre, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, 2 Zdrave St, Sofia 1431, Bulgaria
| | - Hong-Wei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yong-Jie Lu
- Centre for Molecular Oncology and Imaging, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Jong Y. Park
- Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Centre, 12902 Magnolia Drive, Tampa, FL, USA
| | - Kathleen A. Cooney
- Department of Internal Medicine and
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | | | - Edward Saunders
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | | | - Nadiya Mahmud
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Michelle Guy
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Koveela Govindasami
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Lynne T. O'Brien
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | | | - Amanda L. Hall
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Emma J. Sawyer
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Tokhir Dadaev
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Jonathan Morrison
- Strangeways Laboratory, Centre for Cancer Genetic Epidemiology, Worts Causeway, Cambridge CB1 8RN, UK
| | - David P. Dearnaley
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Alan Horwich
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Robert A. Huddart
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Vincent S. Khoo
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Christopher C. Parker
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Nicholas Van As
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | | | - Alan Thompson
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Chris Ogden
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
| | - Colin S. Cooper
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | | | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Grattan street, Parkville, VIC, Australia
| | - John L. Hopper
- Cancer Epidemiology Centre, Cancer Council Victoria, 1 Rathdowne Street, Carlton, VIC, Australia
| | - Dallas English
- Cancer Epidemiology Centre, Cancer Council Victoria, 1 Rathdowne Street, Carlton, VIC, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, 723 Swanston Street, Carlton, VIC, Australia
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Centre, Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Daniele Campa
- Lyon Cancer Research Center, INSERM U1052, Lyon, France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sara Lindstrom
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology and
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Susan Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Angela Cox
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Mariana C. Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Roman Corral
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm SE-171 77, Sweden
- Division of Urology, Department of Clinical Sciences, Danderyd Hospital and
| | - William Isaacs
- School of Medicine, Johns Hopkins University, 115 Marburg Building, 600 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jan Adolfsson
- Oncological Centre, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Tiina Wahlfors
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Kimmo Taari
- Department of Urology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Paula Kujala
- Department of Pathology, Centre for Laboratory Medicine, Tampere University Hospital, Tampere, Finland
| | - Peter Klarskov
- Department of Urology, Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 75, Herlev DK-2730, Denmark
| | | | | | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | | | - Liesel M. FitzGerald
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Centre, Seattle, WA, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Centre, Seattle, WA, USA
| | - Erika M. Kwon
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Room 5351, Bethesda, MD, USA
| | - Danielle M. Karyadi
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Room 5351, Bethesda, MD, USA
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Skejby, Denmark
| | | | - Manuel Luedeke
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Rechts der Isar Medical Centre, Technical University of Munich, Munich, Germany
| | | | | | - James R. Marthick
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, TAS, Australia
| | - Briony Patterson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, TAS, Australia
| | - Dominika Wokolorczyk
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | | | - Felicity Lose
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | | | - Amit D. Joshi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Ahva Shahabi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Pedro Pinto
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Joana Santos
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Ana Ray
- Department of Internal Medicine and
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Thomas A. Sellers
- Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Centre, 12902 Magnolia Drive, Tampa, FL, USA
| | - Hui-Yi Lin
- Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Centre, 12902 Magnolia Drive, Tampa, FL, USA
| | | | - Craig Teerlink
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heiko Muller
- Division of Clinical Epidemiology and Aging Research and
| | | | - Norihiko Tsuchiya
- Department of Urology,Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Shintaro Narita
- Department of Urology,Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Guang-Wen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital,Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Centre, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, 2 Zdrave St, Sofia 1431, Bulgaria
| | | | | | | | | | - Stephen Chanock
- Core Genotyping Facility, SAIC-Frederick, Inc., National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, CA, USA
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology and
| | - Douglas F. Easton
- Strangeways Laboratory, Centre for Cancer Genetic Epidemiology, Worts Causeway, Cambridge CB1 8RN, UK
| | - Rosalind A. Eeles
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham and Sutton, London and Surrey, UK
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20
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Chen SH, Ip EH, Xu J, Sun J, Hsu FC. Using graded response model for the prediction of prostate cancer risk. Hum Genet 2012; 131:1327-36. [PMID: 22461065 DOI: 10.1007/s00439-012-1160-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/21/2012] [Indexed: 12/16/2022]
Abstract
Disease risk-associated single nucleotide polymorphisms (SNPs) identified from genome-wide association studies (GWAS) have the potential to be used for disease risk prediction. An important feature of these risk-associated SNPs is their weak individual effect but stronger cumulative effect on disease risk. To date, a stable summary estimate of the joint effect of genetic variants on disease risk prediction is not available. In this study, we propose to use the graded response model (GRM), which is based on the item response theory, for estimating the individual risk that is associated with a set of SNPs. We compare the GRM with a recently proposed risk prediction model called cumulative relative risk (CRR). Thirty-three prostate cancer risk-associated SNPs were originally discovered in GWAS by December 2009. These SNPs were used to evaluate the performance of GRM and CRR for predicting prostate cancer risk in three GWAS populations, including populations from Sweden, Johns Hopkins Hospital, and the National Cancer Institute Cancer Genetic Markers of Susceptibility study. Computational results show that the risk prediction estimates of GRM, compared to CRR, are less biased and more stable.
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Affiliation(s)
- Shyh-Huei Chen
- Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Wells Fargo Center 23rd floor, Medical Center Blvd, Winston-Salem, NC 27157, USA.
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21
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Lu Y, Sun J, Kader AK, Kim ST, Kim JW, Liu W, Sun J, Lu D, Feng J, Zhu Y, Jin T, Zhang Z, Dimitrov L, Lowey J, Campbell K, Suh E, Duggan D, Carpten J, Trent JM, Gronberg H, Zheng SL, Isaacs WB, Xu J. Association of prostate cancer risk with SNPs in regions containing androgen receptor binding sites captured by ChIP-On-chip analyses. Prostate 2012; 72:376-85. [PMID: 21671247 PMCID: PMC3366362 DOI: 10.1002/pros.21439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/16/2011] [Indexed: 12/30/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified approximately three dozen single nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. Despite the reproducibility of these associations, the molecular mechanism for most of these SNPs has not been well elaborated as most lie within non-coding regions of the genome. Androgens play a key role in prostate carcinogenesis. Recently, using ChIP-on-chip technology, 22,447 androgen receptor (AR) binding sites have been mapped throughout the genome, greatly expanding the genomic regions potentially involved in androgen-mediated activity. METHODOLOGY/PRINCIPAL FINDINGS To test the hypothesis that sequence variants in AR binding sites are associated with PCa risk, we performed a systematic evaluation among two existing PCa GWAS cohorts; the Johns Hopkins Hospital and the Cancer Genetic Markers of Susceptibility (CGEMS) study population. We demonstrate that regions containing AR binding sites are significantly enriched for PCa risk-associated SNPs, that is, more than expected by chance alone. In addition, compared with the entire genome, these newly observed risk-associated SNPs in these regions are significantly more likely to overlap with established PCa risk-associated SNPs from previous GWAS. These results are consistent with our previous finding from a bioinformatics analysis that one-third of the 33 known PCa risk-associated SNPs discovered by GWAS are located in regions of the genome containing AR binding sites. CONCLUSIONS/SIGNIFICANCE The results to date provide novel statistical evidence suggesting an androgen-mediated mechanism by which some PCa associated SNPs act to influence PCa risk. However, these results are hypothesis generating and ultimately warrant testing through in-depth molecular analyses.
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Affiliation(s)
- Yizhen Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Andrew K. Kader
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Seong-Tae Kim
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Jin-Woo Kim
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Wennuan Liu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Jishan Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Junjie Feng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Yi Zhu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Tao Jin
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Zheng Zhang
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Latchezar Dimitrov
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - James Lowey
- Translational Genomics Research Institute, Phoenix, AZ
| | | | - Edward Suh
- Translational Genomics Research Institute, Phoenix, AZ
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, AZ
| | - John Carpten
- Translational Genomics Research Institute, Phoenix, AZ
| | - Jeffrey M. Trent
- Translational Genomics Research Institute, Phoenix, AZ
- Van Andel Research Institute, Grand Rapids, MI
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Siqun L. Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - William B. Isaacs
- Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD
- Address for correspondence: Dr. William B. Isaacs, Ph.D., Marburg 115, Johns Hopkins Hospital, 600 N. Wolfe Street, Baltimore, MD 21287, Phone: (410) 955-2518, Fax: (410) 955-0833, ; & Dr. Jianfeng Xu, Center for Cancer Genomics, Medical Center Blvd, Winston-Salem, NC 27157, Phone: (336) 713-7500, Fax: (336) 713-7566,
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, NC
- Van Andel Research Institute, Grand Rapids, MI
- Address for correspondence: Dr. William B. Isaacs, Ph.D., Marburg 115, Johns Hopkins Hospital, 600 N. Wolfe Street, Baltimore, MD 21287, Phone: (410) 955-2518, Fax: (410) 955-0833, ; & Dr. Jianfeng Xu, Center for Cancer Genomics, Medical Center Blvd, Winston-Salem, NC 27157, Phone: (336) 713-7500, Fax: (336) 713-7566,
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Tao S, Feng J, Webster T, Jin G, Hsu FC, Chen SH, Kim ST, Wang Z, Zhang Z, Zheng SL, Isaacs WB, Xu J, Sun J. Genome-wide two-locus epistasis scans in prostate cancer using two European populations. Hum Genet 2012; 131:1225-34. [PMID: 22367438 DOI: 10.1007/s00439-012-1148-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 02/12/2012] [Indexed: 12/22/2022]
Abstract
Approximately 40 single nucleotide polymorphisms (SNPs) that are associated with prostate cancer (PCa) risk have been identified through genome-wide association studies (GWAS). However, these GWAS-identified PCa risk-associated SNPs can explain only a small proportion of heritability (~13%) of PCa risk. Gene-gene interaction is speculated to be one of the major factors contributing to the so-called missing heritability. To evaluate the gene-gene interaction and PCa risk, we performed a two-stage genome-wide gene-gene interaction scan using a novel statistical approach named "Boolean Operation-based Screening and Testing". In the first stage, we exhaustively evaluated all pairs of SNP-SNP interactions for ~500,000 SNPs in 1,176 PCa cases and 1,101 control subjects from the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) study. No SNP-SNP interaction reached a genome-wide significant level of 4.4E-13. The second stage of the study involved evaluation of the top 1,325 pairs of SNP-SNP interactions (P(interaction) <1.0E-08) implicated in CGEMS in another GWAS population of 1,964 PCa cases from the Johns Hopkins Hospital (JHH) and 3,172 control subjects from the Illumina iControl database. Sixteen pairs of SNP-SNP interactions were significant in the JHH population at a P(interaction) cutoff of 0.01. However, none of the 16 pairs of SNP-SNP interactions were significant after adjusting for multiple tests. The current study represents one of the first attempts to explore the high-dimensional etiology of PCa on a genome-wide scale. Our results suggested a list of SNP-SNP interactions that can be followed in other replication studies.
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Affiliation(s)
- Sha Tao
- Center for Genetic Epidemiology and Prevention, Van Andel Research Institute, Grand Rapids, MI, USA
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23
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Tao S, Wang Z, Feng J, Hsu FC, Jin G, Kim ST, Zhang Z, Gronberg H, Zheng LS, Isaacs WB, Xu J, Sun J. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. Carcinogenesis 2012; 33:598-603. [PMID: 22219177 DOI: 10.1093/carcin/bgr316] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified ∼30 single-nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. To test the hypothesis that other sequence variants in the genome may interact with those 32 known PCa risk-associated SNPs identified from GWAS to affect PCa risk, we performed a systematic evaluation among three existing PCa GWAS populations: CAncer of the Prostate in Sweden population, a Johns Hopkins Hospital population, and the Cancer Genetic Markers of Susceptibility population, with a total sample size of 4723 PCa cases and 4792 control subjects. Meta-analysis of the interaction term between each of those 32 SNPs and SNPs in the genome was performed in three PCa GWAS populations. The most significant interaction detected was between rs12418451 in MYEOV and rs784411 in CEP152, with a P(interaction) of 1.15 × 10(-7) in the meta-analysis. In addition, we emphasized two pairs of interactions with potential biological implication, including an interaction between rs7127900 near insulin-like growth factor-2 (IGF2)/IGF2AS and rs12628051 in TNRC6B, with a P(interaction) of 3.39 × 10(-6) and an interaction between rs7679763 near TET2 and rs290258 in SYK, with a P(interaction) of 1.49 × 10(-6). Those results show statistical evidence for novel loci interacting with known risk-associated SNPs to modify PCa risk. The interacting loci identified provide hints on the underlying molecular mechanism of the associations with PCa risk for the known risk-associated SNPs. Additional studies are warranted to further confirm the interaction effects detected in this study.
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Affiliation(s)
- Sha Tao
- Center for Genetic Epidemiology and Prevention, Van Andel Research Institute, Grand Rapids, MI, USA
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24
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Base excision repair pathway genes polymorphism in prostate and bladder cancer risk in North Indian population. Mech Ageing Dev 2011; 133:127-32. [PMID: 22019847 DOI: 10.1016/j.mad.2011.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 09/24/2011] [Accepted: 10/06/2011] [Indexed: 12/30/2022]
Abstract
PURPOSE Carcinogens causes DNA damage, including oxidative lesions that are removed efficiently by the base excision repair (BER) pathway. Variations in BER genes may reduce DNA repair capacity, leading to development of urological cancers. METHODS This study included 195 prostate cancer (PCa) and 212 bladder cancer (BC) patients and 250 controls who had been frequency matched by age, sex, and ethnicity. We genotyped XRCC1 Exon 6 (C>T), 9 (G>A), 10 (G>A), OGG1 Exon 7 (C>G) and APE1 Exon 5 (T>G) genes polymorphism using PCR-RFLP and ARMS. RESULTS GA of XRCC1 Exon 9 demonstrated increased risk with PCa as well as in BC (p=0.001; p=0.006). Similarly variant containing genotype revealed association with PCa (p=0.031). Haplotype of XRCC1 also associated with significant risk for PCa and BC. The APE1 GG genotype showed a decreased risk of BC (OR=0.25; p=0.017). Variant genotype GG of OGG1 demonstrated significant risk with BC (p=0.028). CONCLUSIONS Our observations suggested increased risk for PCa and BC in case of GA genotype for XRCC1, and variant GG in case of OGG1. However APE1 GG genotype conferred a protective association with BC susceptibility. Larger studies and the more SNPs in the same pathway are needed to verify these findings.
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25
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Schumacher FR, Berndt SI, Siddiq A, Jacobs KB, Wang Z, Lindstrom S, Stevens VL, Chen C, Mondul AM, Travis RC, Stram DO, Eeles RA, Easton DF, Giles G, Hopper JL, Neal DE, Hamdy FC, Donovan JL, Muir K, Al Olama AA, Kote-Jarai Z, Guy M, Severi G, Grönberg H, Isaacs WB, Karlsson R, Wiklund F, Xu J, Allen NE, Andriole GL, Barricarte A, Boeing H, Bas Bueno-de-Mesquita H, Crawford ED, Diver WR, Gonzalez CA, Gaziano JM, Giovannucci EL, Johansson M, Le Marchand L, Ma J, Sieri S, Stattin P, Stampfer MJ, Tjonneland A, Vineis P, Virtamo J, Vogel U, Weinstein SJ, Yeager M, Thun MJ, Kolonel LN, Henderson BE, Albanes D, Hayes RB, Spencer Feigelson H, Riboli E, Hunter DJ, Chanock SJ, Haiman CA, Kraft P. Genome-wide association study identifies new prostate cancer susceptibility loci. Hum Mol Genet 2011; 20:3867-75. [PMID: 21743057 PMCID: PMC3168287 DOI: 10.1093/hmg/ddr295] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 06/18/2011] [Accepted: 06/27/2011] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer (PrCa) is the most common non-skin cancer diagnosed among males in developed countries and the second leading cause of cancer mortality, yet little is known regarding its etiology and factors that influence clinical outcome. Genome-wide association studies (GWAS) of PrCa have identified at least 30 distinct loci associated with small differences in risk. We conducted a GWAS in 2782 advanced PrCa cases (Gleason grade ≥ 8 or tumor stage C/D) and 4458 controls with 571 243 single nucleotide polymorphisms (SNPs). Based on in silico replication of 4679 SNPs (Stage 1, P < 0.02) in two published GWAS with 7358 PrCa cases and 6732 controls, we identified a new susceptibility locus associated with overall PrCa risk at 2q37.3 (rs2292884, P= 4.3 × 10(-8)). We also confirmed a locus suggested by an earlier GWAS at 12q13 (rs902774, P= 8.6 × 10(-9)). The estimated per-allele odds ratios for these loci (1.14 for rs2292884 and 1.17 for rs902774) did not differ between advanced and non-advanced PrCa (case-only test for heterogeneity P= 0.72 and P= 0.61, respectively). Further studies will be needed to assess whether these or other loci are differentially associated with PrCa subtypes.
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Affiliation(s)
- Fredrick R. Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Kevin B. Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Core Genotyping Facility, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD, USA
- Bioinformed Consulting Services, Gaithersburg, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Core Genotyping Facility, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD, USA
| | - Sara Lindstrom
- Program in Molecular and Genetic Epidemiology
- Department of Epidemiology and
| | | | - Constance Chen
- Program in Molecular and Genetic Epidemiology
- Department of Epidemiology and
| | - Alison M. Mondul
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ruth C. Travis
- Cancer Epidemiology Unit
- Nuffield Department of Clinical Medicine and
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology
- Department of Public Health
- Department of Primary Care and
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Graham Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Victoria, Australia
| | - John L. Hopper
- Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology, Melbourne School of Population Health, The University of Melbourne, Melbourne, Australia
| | - David E. Neal
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Kenneth Muir
- Health Sciences Research Institute, University of Warwick, Coventry, UK
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology
- Department of Public Health
- Department of Primary Care and
| | | | - Michelle Guy
- Oncogenetics Team, The Institute of Cancer Research, Sutton, UK
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, Victoria, Australia
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - William B. Isaacs
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jianfeng Xu
- Centers for Cancer Genomics and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Naomi E. Allen
- Cancer Epidemiology Unit
- Nuffield Department of Clinical Medicine and
| | - Gerald L. Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | | | - Heiner Boeing
- Department of Epidemiology, Deutsches Institut für Ernährungsforschung, Potsdam-Rehbrücke, Germany
| | | | | | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Carlos A. Gonzalez
- Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology (ICO-IDIBELL-RETICC RD06/0020), L'Hospitalet de Llobregat, Barcelona, Spain
| | - J. Michael Gaziano
- Division of Aging and
- Massachusetts Veterans Epidemiology Research and Information Center/VA Cooperative Studies Programs, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward L. Giovannucci
- Department of Epidemiology and
- Department of Nutrition, Harvard School of Public Health, Boston 02115, MA, USA
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC), Lyon, France
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Loic Le Marchand
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI, USA
| | - Jing Ma
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Channing Laboratory, Boston, MA, USA
| | - Sabina Sieri
- Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Pär Stattin
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Meir J. Stampfer
- Department of Epidemiology and
- Department of Nutrition, Harvard School of Public Health, Boston 02115, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Channing Laboratory, Boston, MA, USA
| | - Anne Tjonneland
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Paolo Vineis
- MRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
- National Food Institute, Technical University of Denmark, Soborg, Denmark
| | - Stephanie J. Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Michael J. Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Richard B. Hayes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Division of Epidemiology, Department of Environmental Medicine, New York University Langone Medical Center, NYU Cancer Institute, New York, NY, USA and
| | | | - Elio Riboli
- Department of Epidemiology and Biostatistics and
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology
- Department of Epidemiology and
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology
- Department of Epidemiology and
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Feng J, Sun J, Kim ST, Lu Y, Wang Z, Zhang Z, Gronberg H, Isaacs WB, Zheng SL, Xu J. A genome-wide survey over the ChIP-on-chip identified androgen receptor-binding genomic regions identifies a novel prostate cancer susceptibility locus at 12q13.13. Cancer Epidemiol Biomarkers Prev 2011; 20:2396-403. [PMID: 21960693 DOI: 10.1158/1055-9965.epi-11-0523] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The molecular mechanisms for the genome-wide association studies (GWAS)-identified prostate cancer (PCa) risk-associated single-nucleotide polymorphisms (SNP) remain largely unexplained. One recent finding that the PCa risk SNPs are enriched in genomic regions containing androgen receptor (AR)-binding sites has suggested altered AR signaling as a potentially important mechanism. METHODS To explore novel associations by leveraging this knowledge, we utilized a meta-analysis previously done over SNPs harbored in ChIP-on-chip identified AR-binding genomic regions using the GWAS data from the Johns Hopkins Hospital (JHH) and the Cancer Genetic Markers of Susceptibility (CGEMS) study, and subsequently evaluated the top associations in a third population from the CAncer of the Prostate in Sweden (CAPS) study. RESULTS One SNP (rs4919743: G>A), located at the KRT8 locus at 12q13.13 which encodes a keratin protein (K8) long used as a prostate epithelial malignancy marker and implicated in the tumorigenesis of several cancer types, was identified to be associated with PCa risk. The frequency of its minor "A" allele was consistently higher in PCa cases than in controls in all three study populations, with a combined OR of 1.22 (95% CI: 1.13-1.32) and an overall P value of 4.50 × 10(-7) (Bonferroni corrected, P = 0.006). CONCLUSION We have identified a novel genetic locus that is associated with PCa risk. IMPACT This study illustrated the great potential of prior biological knowledge in facilitating the search for novel disease-associated genetic loci. This finding warrants further replication in other studies.
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Affiliation(s)
- Junjie Feng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Jin G, Sun J, Isaacs SD, Wiley KE, Kim ST, Chu LW, Zhang Z, Zhao H, Zheng SL, Isaacs WB, Xu J. Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis 2011; 32:1655-9. [PMID: 21856995 DOI: 10.1093/carcin/bgr187] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), representing a large proportion of non-coding transcripts across the human genome, are evolutionally conserved and biologically functional. At least one-third of the phenotype-related loci identified by genome-wide association studies (GWAS) are mapped to non-coding intervals. However, the relationships between phenotype-related loci and lncRNAs are largely unknown. Utilizing the 1000 Genomes data, we compared single-nucleotide polymorphisms (SNPs) within the sequences of lncRNA and protein-coding genes as defined in the Ensembl database. We further annotated the phenotype-related SNPs reported by GWAS at lncRNA intervals. Because prostate cancer (PCa) risk-related loci were enriched in lncRNAs, we then performed meta-analysis of two existing GWAS for discovery and an additional sample set for replication, revealing PCa risk-related loci at lncRNA regions. The SNP density in regions of lncRNA was similar to that in protein-coding regions, but they were less polymorphic than surrounding regions. Among the 1998 phenotype-related SNPs identified by GWAS, 52 loci were located directly in lncRNA intervals with a 1.5-fold enrichment compared with the entire genome. More than a 5-fold enrichment was observed for eight PCa risk-related loci in lncRNA genes. We also identified a new PCa risk-related SNP rs3787016 in an lncRNA region at 19q13 (per allele odds ratio = 1.19; 95% confidence interval: 1.11-1.27) with P value of 7.22 × 10(-7). lncRNAs may be important for interpreting and mining GWAS data. However, the catalog of lncRNAs needs to be better characterized in order to fully evaluate the relationship of phenotype-related loci with lncRNAs.
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Affiliation(s)
- Guangfu Jin
- Center for Cancer Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
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28
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Barnholtz-Sloan JS, Raska P, Rebbeck TR, Millikan RC. Replication of GWAS "Hits" by Race for Breast and Prostate Cancers in European Americans and African Americans. Front Genet 2011; 2:37. [PMID: 22303333 PMCID: PMC3268591 DOI: 10.3389/fgene.2011.00037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/10/2011] [Indexed: 11/22/2022] Open
Abstract
In this study, we assessed association of genome-wide association studies (GWAS) “hits” by race with adjustment for potential population stratification (PS) in two large, diverse study populations; the Carolina Breast Cancer Study (CBCS; N total = 3693 individuals) and the University of Pennsylvania Study of Clinical Outcomes, Risk, and Ethnicity (SCORE; N total = 1135 individuals). In both study populations, 136 ancestry information markers and GWAS “hits” (CBCS: FGFR2, 8q24; SCORE: JAZF1, MSMB, 8q24) were genotyped. Principal component analysis was used to assess ancestral differences by race. Multivariable unconditional logistic regression was used to assess differences in cancer risk with and without adjustment for the first ancestral principal component (PC1) and for an interaction effect between PC1 and the GWAS “hit” (SNP) of interest. PC1 explained 53.7% of the variance for CBCS and 49.5% of the variance for SCORE. European Americans and African Americans were similar in their ancestral structure between CBCS and SCORE and cases and controls were well matched by ancestry. In the CBCS European Americans, 9/11 SNPs were significant after PC1 adjustment, but after adjustment for the PC1 by SNP interaction effect, only one SNP remained significant (rs1219648 in FGFR2); for CBCS African Americans, 6/11 SNPs were significant after PC1 adjustment and after adjustment for the PC1 by SNP interaction effect, all six SNPs remained significant and an additional SNP now became significant. In the SCORE European Americans, 0/9 SNPs were significant after PC1 adjustment and no changes were seen after additional adjustment for the PC1 by SNP interaction effect; for SCORE African Americans, 2/9 SNPs were significant after PC1 adjustment and after adjustment for the PC1 by SNP interaction effect, only one SNP remained significant (rs16901979 at 8q24). We show that genetic associations by race are modified by interaction between individual SNPs and PS.
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Affiliation(s)
- Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine Cleveland, OH, USA
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Barnabas N, Xu L, Savera A, Hou Z, Barrack ER. Chromosome 8 markers of metastatic prostate cancer in African American men: gain of the MIR151 gene and loss of the NKX3-1 gene. Prostate 2011; 71:857-71. [PMID: 21456068 DOI: 10.1002/pros.21302] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 10/05/2010] [Indexed: 12/19/2022]
Abstract
BACKGROUND Radical prostatectomy (RP) is not curative if patients have undetected metastatic prostate cancer. Markers that indicate the presence of metastatic disease would identify men who may benefit from systemic adjuvant therapy. Our approach was to analyze the primary tumors of men with metastatic disease versus organ-confined disease to identify molecular changes that distinguish between these groups. METHODS Patients were identified based on long-term follow-up of serum prostate specific antigen (PSA) levels following RP. We compared the tumors of African American (AA) men with undetectable serum PSA for >9 year after RP (good outcome) versus those of AA men with a rising PSA and recurrence after radiation or androgen ablation or both (poor outcome). We used real-time quantitative PCR to assay gene copy number alterations in tumor DNA relative to patient-matched non-tumor DNA isolated from paraffin-embedded tissue. We assayed several genes located in the specific regions of chromosome 8p and 8q that frequently undergo loss and/or gain, respectively, in prostate cancer, and the androgen receptor gene at Xq12. RESULTS Gain of the MIR151 gene at 8q24.3 (in 33% of poor outcome vs. 6% of good outcome tumors) and/or loss of the NKX3-1 gene at 8p21.2 (in 39% of poor outcome vs. 11% of good outcome tumors) affected 67% of poor outcome tumors, compared to only 17% of good outcome tumors. CONCLUSIONS Copy number gain of the MIR151 gene and/or loss of the NKX3-1 gene in the primary tumor may indicate the presence of metastatic disease.
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Affiliation(s)
- Nandita Barnabas
- Vattikuti Urology Institute, Henry Ford Hospital, Detroit, Michigan 48202-3450, USA
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Aly M, Wiklund F, Grönberg H. Early detection of prostate cancer with emphasis on genetic markers. Acta Oncol 2011; 50 Suppl 1:18-23. [PMID: 21604936 DOI: 10.3109/0284186x.2010.529824] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The recent advances in genomic research have made it possible to identify several new genomic-based biomarkers for prostate cancer. In this review we evaluate these new markers and speculate about future scenarios. RESULTS Today 35 single nucleotide polymorphisms (SNPs) have been identified and independently validated to associate with prostate cancer. These SNPs are common in the population (>5%) but the effect of these SNPs in these regions on prostate cancer risk is modest with odds ratios typically ranging between 1.1 and 1.3. It is estimated that these markers explain 25% of the familial risk of prostate cancer. However, it is anticipated that additional 50-75 prostate cancer SNPs will be identified in the near future. The SNPs associated with prostate cancer so far are not associated with disease stage or outcome. There are several efforts to identify germline genetic markers that can be used as prognostic markers. There are also tumor-based methods that are promising in identifying new genetic markers that can be easily measured in plasma or urine. CONCLUSION There are several new "genetic" markers that in the near future might be used in clinical routine. These markers are easy to measure and stable over time. However the challenge is not only to identify new biomarkers but the real test is to validate new biomarkers in several large well-characterized patient populations. This validation must be done together will all other known biomarkers at the same time as it not likely that one single marker is enough, but a panel of different markers. Today 2010 there are over 19 000 publications in the area of biomarkers and prostate cancer, but only one biomarker, PSA, is used in the clinic today!
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Affiliation(s)
- Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Helfand BT, Kan D, Modi P, Catalona WJ. Prostate cancer risk alleles significantly improve disease detection and are associated with aggressive features in patients with a "normal" prostate specific antigen and digital rectal examination. Prostate 2011; 71:394-402. [PMID: 20860009 PMCID: PMC3089434 DOI: 10.1002/pros.21253] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/22/2010] [Indexed: 12/28/2022]
Abstract
BACKGROUND Several reports suggest that a combination of risk alleles may be associated with prostate cancer (CaP) risk and tumor features. However, their ability to detect CaP and tumor characteristics in patients with a "normal" PSA (<4 ng/ml) and non-suspicious digital rectal examination (DRE) remains to be determined. METHODS We examined 203 men of European ancestry with clinical stage T1c CaP diagnosed at a "normal" PSA and 611 healthy volunteer controls. The genotypes for 17 different risk alleles were compared between CaP cases and controls. Additional analyses were used to compare the pathologic features between carriers and non-carriers (defined using best-fit genetic model) of these variants. RESULTS All risk alleles were present at an increased frequency in cases with "normal" PSA values and DRE compared to controls. Amongst CaP patients, carriers of an increasing number of genetic risk factors (i.e., alleles and positive family history) were at a significantly increased risk of CaP (P-trend <0.001). Specifically, men with >10 genetic risk factors had an 11.2-fold risk (95% CI 4.3-29.2) of having the disease compared to men with ≤5 variants. There also was a higher frequency of many the variants amongst men with adverse pathologic features. CONCLUSIONS A substantial proportion of biopsy-detectable CaP occurs in men with "normal" PSA levels and negative DRE. In this population, CaP risk alleles and family history are significantly associated with CaP risk and may help predict aggressive disease. Future studies are warranted to determine the utility of incorporating these variants into CaP screening programs.
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Affiliation(s)
| | | | | | - William J. Catalona
- Corresponding Author: William J. Catalona, MD 675 N. Saint Clair Street, Suite 20-150 Chicago, IL 60611 Phone: (312) 695-4471 Fax: (312) 695-1144
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Lindstrom S, Schumacher F, Siddiq A, Travis RC, Campa D, Berndt SI, Diver WR, Severi G, Allen N, Andriole G, Bueno-de-Mesquita B, Chanock SJ, Crawford D, Gaziano JM, Giles GG, Giovannucci E, Guo C, Haiman CA, Hayes RB, Halkjaer J, Hunter DJ, Johansson M, Kaaks R, Kolonel LN, Navarro C, Riboli E, Sacerdote C, Stampfer M, Stram DO, Thun MJ, Trichopoulos D, Virtamo J, Weinstein SJ, Yeager M, Henderson B, Ma J, Le Marchand L, Albanes D, Kraft P. Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3. PLoS One 2011; 6:e17142. [PMID: 21390317 PMCID: PMC3044744 DOI: 10.1371/journal.pone.0017142] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/21/2011] [Indexed: 01/12/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple single nucleotide polymorphisms (SNPs) associated with prostate cancer risk. However, whether these associations can be consistently replicated, vary with disease aggressiveness (tumor stage and grade) and/or interact with non-genetic potential risk factors or other SNPs is unknown. We therefore genotyped 39 SNPs from regions identified by several prostate cancer GWAS in 10,501 prostate cancer cases and 10,831 controls from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). We replicated 36 out of 39 SNPs (P-values ranging from 0.01 to 10⁻²⁸). Two SNPs located near KLK3 associated with PSA levels showed differential association with Gleason grade (rs2735839, P = 0.0001 and rs266849, P = 0.0004; case-only test), where the alleles associated with decreasing PSA levels were inversely associated with low-grade (as defined by Gleason grade < 8) tumors but positively associated with high-grade tumors. No other SNP showed differential associations according to disease stage or grade. We observed no effect modification by SNP for association with age at diagnosis, family history of prostate cancer, diabetes, BMI, height, smoking or alcohol intake. Moreover, we found no evidence of pair-wise SNP-SNP interactions. While these SNPs represent new independent risk factors for prostate cancer, we saw little evidence for effect modification by other SNPs or by the environmental factors examined.
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Affiliation(s)
- Sara Lindstrom
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Afshan Siddiq
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniele Campa
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - W. Ryan Diver
- Department of Epidemiology, American Cancer Society, Atlanta, Georgia, United States of America
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria and the Centre for Molecular, Genetic, Environmental, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Naomi Allen
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Gerald Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bas Bueno-de-Mesquita
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Crawford
- Urologic Oncology, University of Colorado at Denver Health Sciences Center, Denver, Colorado, United States of America
| | - J. Michael Gaziano
- Massachusetts Veterans Epidemiology and Research Information Center (MAVERIC) and Geriatric Research, Education, and Clinical Center (GRECC), Boston Veterans Affairs Healthcare System, Boston, Massachusetts, United States of America
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria and the Centre for Molecular, Genetic, Environmental, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Edward Giovannucci
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Carolyn Guo
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Richard B. Hayes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Division of Epidemiology, NYU Langone Medical Center, New York, New York, United States of America
| | - Jytte Halkjaer
- The Danish Cancer Society, Institute of Cancer Epidemiology, Copenhagen, Denmark
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Medicine, Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mattias Johansson
- International Agency for Research on Cancer, Lyon, France
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laurence N. Kolonel
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Carmen Navarro
- Department of Epidemiology, Regional Health Authority, Murcia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | | | - Meir Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Medicine, Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Michael J. Thun
- Department of Epidemiology, American Cancer Society, Atlanta, Georgia, United States of America
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Center for Food and Nutrition Policies, Athens, Greece
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie J. Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jing Ma
- Department of Medicine, Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Abstract
BACKGROUND Genome-wide and replication association studies (GWAs) have identified multiple loci at which common variants modestly influence the risk of developing prostate cancer (PCa). To enhance the power to identify loci associated with PCa, we constructed a meta-analysis of GWAs on PCa. METHODS Articles evaluating the effects of genome-wide SNPs on PCa were identified by searching the PubMed database. After extraction of relevant data, main and subgroup meta-analyses were performed to assess the effects of relevant SNPs on PCa. RESULTS 21 eligible articles containing 71 subgroups were included in this meta-analysis. Significant associations were found between 31 SNPs and PCa. They were rs445114, rs620861, rs983085, rs1016343, rs1447295, rs1859962, rs2660753, rs2710646, rs2735839, rs3760511, rs4242382, rs4430796, rs4962416, rs5945572, rs5945619, rs6470494, rs6501455, rs6983267, rs6983561, rs7000448, rs7214479, rs7501939, rs7920517, rs7931342, rs9364554, rs9623117, rs10090154, rs10486567, rs10896449, rs10993994, and rs16901979. The weighted odds ratios for above SNPs ranged between 0.64 and 1.88 (all P < 0.05). Subgroup analysis further indicated that the significant associations of some SNPs existed only in specific ancestry population (P < 10⁻⁵). CONCLUSIONS The current meta-analysis demonstrated the moderate effects of above 31 SNPs on PCa and 14 independent PCa risk loci were identified.
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Affiliation(s)
- Hong Liu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Kim ST, Cheng Y, Hsu FC, Jin T, Kader AK, Zheng SL, Isaacs WB, Xu J, Sun J. Prostate cancer risk-associated variants reported from genome-wide association studies: meta-analysis and their contribution to genetic Variation. Prostate 2010; 70:1729-38. [PMID: 20564319 PMCID: PMC3013361 DOI: 10.1002/pros.21208] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have led to the discovery of multiple single nucleotide polymorphisms (SNPs) that are associated with prostate cancer (PCa) risk. These SNPs may potentially be used for risk prediction. To date, there is not a stable estimate of their effect on PCa risk and their contribution to the genetic variation both of which are important for future risk prediction. METHODS A literature review was conducted to identify SNPs associated with PCa risk with the following criteria: (1) GWAS in the Caucasian population; (2) SNPs with P-value <1.0×10(-6); and (3) one SNP from each independent LD block. A meta-analysis was performed to estimate combined odds ratio (OR) and its 95% confidence interval (CI) for the identified SNPs. The proportion of total genetic variance that is attributable by each of these SNPs was also estimated. RESULTS Thirty PCa risk-associated SNPs were identified. These SNPs had OR estimates between 1.12 and 1.47 except for marker rs16901979 (OR=1.80). Significant heterogeneity in OR estimates was found among different studies for 13 SNPs. The proportion of total genetic variance attributed by each SNP ranged between 0.2% and 0.9%. These 30 SNPs explained ∼13.5% of the total genetic variance of PCa risk in the Caucasian population. CONCLUSION This study provides more stable OR estimates for PCa risk-associated SNPs, which is an important baseline for the effect of these SNPs in risk prediction. These SNPs explain a considerable proportion of genetic variance, however, the majority of genetic variance has yet to be explained.
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Affiliation(s)
- Seong-Tae Kim
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Yu Cheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Fang-Chi Hsu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Tao Jin
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - A. Karim Kader
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - William B. Isaacs
- The Brady Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Address for correspondence: Dr. Jielin Sun, Center for Cancer Genomics, Medical Center Blvd, Winston-Salem, NC 27157, Phone: (336) 713-7500, Fax: (336) 713-7566,
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Chang BL, Spangler E, Gallagher S, Haiman CA, Henderson B, Isaacs W, Benford ML, Kidd LR, Cooney K, Strom S, Ingles SA, Stern MC, Corral R, Joshi AD, Xu J, Giri VN, Rybicki B, Neslund-Dudas C, Kibel AS, Thompson IM, Leach RJ, Ostrander EA, Stanford JL, Witte J, Casey G, Eeles R, Hsing AW, Chanock S, Hu JJ, John EM, Park J, Stefflova K, Zeigler-Johnson C, Rebbeck TR. Validation of genome-wide prostate cancer associations in men of African descent. Cancer Epidemiol Biomarkers Prev 2010; 20:23-32. [PMID: 21071540 DOI: 10.1158/1055-9965.epi-10-0698] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified numerous prostate cancer susceptibility alleles, but these loci have been identified primarily in men of European descent. There is limited information about the role of these loci in men of African descent. METHODS We identified 7,788 prostate cancer cases and controls with genotype data for 47 GWAS-identified loci. RESULTS We identified significant associations for SNP rs10486567 at JAZF1, rs10993994 at MSMB, rs12418451 and rs7931342 at 11q13, and rs5945572 and rs5945619 at NUDT10/11. These associations were in the same direction and of similar magnitude as those reported in men of European descent. Significance was attained at all reported prostate cancer susceptibility regions at chromosome 8q24, including associations reaching genome-wide significance in region 2. CONCLUSION We have validated in men of African descent the associations at some, but not all, prostate cancer susceptibility loci originally identified in European descent populations. This may be due to the heterogeneity in genetic etiology or in the pattern of genetic variation across populations. IMPACT The genetic etiology of prostate cancer in men of African descent differs from that of men of European descent.
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Affiliation(s)
- Bao-Li Chang
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, 217 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
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Wiklund F. Prostate cancer genomics: can we distinguish between indolent and fatal disease using genetic markers? Genome Med 2010; 2:45. [PMID: 20667146 PMCID: PMC2923737 DOI: 10.1186/gm166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 07/26/2010] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer is one of the most heritable cancers in men, and recent genome-wide association studies have revealed numerous genetic variants associated with disease. The risk variants identified using case-control designs that compared unaffected individuals with all types of patients with prostate cancer show little or no ability to discriminate between indolent and fatal forms of this disease. This suggests different genetic components are involved in the initiation as compared with the prognosis of prostate cancer. Future studies contrasting patients with more and less aggressive disease, and exploring association with disease progression and prognosis, should be more effective in detecting genetic risk factors for prostate cancer outcome.
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Affiliation(s)
- Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Bos 281, 171 77 Stockholm, Sweden.
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Helfand BT, Fought AJ, Loeb S, Meeks JJ, Kan D, Catalona WJ. Genetic prostate cancer risk assessment: common variants in 9 genomic regions are associated with cumulative risk. J Urol 2010; 184:501-5. [PMID: 20620408 DOI: 10.1016/j.juro.2010.04.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Indexed: 10/19/2022]
Abstract
PURPOSE Five genetic variants along chromosomes 8q24 and 17q have a cumulative association with prostate cancer risk. Our research group previously reported an association between these variants and clinicopathological characteristics. More recently 4 additional prostate cancer susceptibility variants were identified on chromosomes 2p15, 10q11, 11q13 and Xp11. We performed cumulative risk assessment incorporating all 9 genetic variants and determined the relationship of the new variants to clinicopathological tumor features. MATERIALS AND METHODS The genotype of 9 variants was determined in 687 men of European ancestry who underwent radical prostatectomy from 2002 to 2008 and in 777 healthy volunteer controls. We compared the incidence of these variants in prostate cancer cases and controls, and assessed their cumulative risk. We also determined the relationship of carrier status for the 4 new variants and clinicopathological tumor features. RESULTS Prostate cancer cases had an increased incidence of all 9 risk variants compared to controls. A cumulative model including the 9 single nucleotide polymorphisms provided greater prostate cancer risk stratification than a model restricted to the original 5 single nucleotide polymorphisms described. Specifically men with 6 or more variants were at greater than 6-fold increased risk for prostate cancer. Although 2p15 and 11q13 carriers were more likely to have aggressive features, other clinicopathological features were similar in carriers and noncarriers. CONCLUSIONS Genetic variants located in 9 regions have a cumulative association with prostate cancer risk. Identification of an increasing number of single nucleotide polymorphisms may provide greater understanding of their combined relationship with CaP risk and disease aggressiveness.
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Affiliation(s)
- Brian T Helfand
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Abstract
The revelation of the entire human DNA sequence in 2001, and the launching of the international haplotype map (HapMap) project, made the identification of common markers of disease possible, dramatically transforming molecular epidemiology. In recent years, the development of, and discoveries within, human genome research have been rapid, highlighted by the current explosion of genome-wide association studies (GWAS). GWAS aim at finding germline changes that increase cancer risk. An equally important and rapid development had been seen in cancer genomics, with great strides being made in our understanding of somatic mutations that allow and accompany cancer development. In this review we discuss whether it is currently possible to use these new discoveries to aid the reduction of cancer mortality by reducing risk of disease, improving prognosis, and keeping complications due to treatment to a minimum. Findings from GWAS have mostly been used to predict risk, but there is the potential to use them for prognostication and even treatment prediction. Expression arrays have identified prognostic patterns for breast cancer, but few reliable patterns are available for treatment prediction. More importantly, virtually no genetic signatures are available to predict morbidity from treatment. Thus, there is a need to bring different biological techniques together and integrate them with existing clinical oncological care for a simultaneous risk and outcome assessment.
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Mandal RK, Gangwar R, Mandhani A, Mittal RD. DNA Repair Gene X-Ray Repair Cross-Complementing Group 1 and Xeroderma Pigmentosum Group D Polymorphisms and Risk of Prostate Cancer: A Study from North India. DNA Cell Biol 2010; 29:183-90. [DOI: 10.1089/dna.2009.0956] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Raju K. Mandal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Ruchika Gangwar
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Anil Mandhani
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Rama Devi Mittal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Hooker S, Hernandez W, Chen H, Robbins C, Torres JB, Ahaghotu C, Carpten J, Kittles RA. Replication of prostate cancer risk loci on 8q24, 11q13, 17q12, 19q33, and Xp11 in African Americans. Prostate 2010; 70:270-5. [PMID: 19902474 DOI: 10.1002/pros.21061] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Prostate cancer (Pca) is a common malignancy that disproportionately affects African American men (AA). Recently there have been several genome-wide association studies (GWAS) implicating new prostate cancer risk loci along chromosomes 2, 3, 6, 7, 8, 10, 11, 12, 17, 19, and X in populations of European ancestry. Given the higher incidence and mortality for AAs, and differences in allele frequencies and haplotype structures between African and European descent populations, it is important to assess the impact of these candidate risk loci in AAs. METHODS Here we evaluated 20 single nucleotide polymorphisms (SNPs) associated with prostate cancer risk in recent GWAS studies, in AA prostate cancer cases and controls. RESULTS We replicated five of the SNPs in our AA population, rs10896449 on 11q13.2 (P = 0.009), rs2735839 on 19q33.33 region, (P = 0.04), rs443076 on chromosome 17q12 (P = 0.008), rs5945572 on Xp11.22 (P = 0.05), as well as the rare variant specific to west African ancestry, bd11934905 in region 2 of 8q24 (P = 1 x 10(-4)). CONCLUSIONS While we were able to replicate a few of the previous GWAS SNPs, we were not able to confirm the vast majority of these associations in our AA population. This finding further supports the need to perform GWAS and additional fine mapping in AAs to locate additional susceptibility loci.
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Affiliation(s)
- Stanley Hooker
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
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Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. Proc Natl Acad Sci U S A 2010; 107:2136-40. [PMID: 20080650 DOI: 10.1073/pnas.0914061107] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Autopsy studies suggest that most aging men will develop lesions that, if detected clinically, would be diagnosed as prostate cancer (PCa). Most of these cancers are indolent and remain localized; however, a subset of PCa is aggressive and accounts for more than 27,000 deaths in the United States annually. Identification of factors specifically associated with risk for more aggressive PCa is urgently needed to reduce overdiagnosis and overtreatment of this common disease. To search for such factors, we compared the frequencies of SNPs among PCa patients who were defined as having either more aggressive or less aggressive disease in four populations examined in the Genetic Markers of Susceptibility (CGEMS) study performed by the National Cancer Institute. SNPs showing possible associations with disease severity were further evaluated in an additional three independent study populations from the United States and Sweden. In total, we studied 4,829 and 12,205 patients with more and less aggressive disease, respectively. We found that the frequency of the TT genotype of SNP rs4054823 at 17p12 was consistently higher among patients with more aggressive compared with less aggressive disease in each of the seven populations studied, with an overall P value of 2.1 x 10(-8) under a recessive model, exceeding the conservative genome-wide significance level. The difference in frequency was largest between patients with high-grade, non-organ-confined disease compared with those with low-grade, organ-confined disease. This study demonstrates that inherited variants predisposing to aggressive but not indolent PCa exist in the genome, and suggests that the clinical potential of such variants as potential early markers for risk of aggressive PCa should be evaluated.
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Kader AK, Sun J, Isaacs SD, Wiley KE, Yan G, Kim ST, Fedor H, DeMarzo AM, Epstein JI, Walsh PC, Partin AW, Trock B, Zheng SL, Xu J, Isaacs W. Individual and cumulative effect of prostate cancer risk-associated variants on clinicopathologic variables in 5,895 prostate cancer patients. Prostate 2009; 69:1195-205. [PMID: 19434657 PMCID: PMC2852875 DOI: 10.1002/pros.20970] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND More than a dozen single nucleotide polymorphisms (SNPs) have been associated with prostate cancer (PCa) risk from genome-wide association studies (GWAS). Their association with PCa aggressiveness and clinicopathologic variables is inconclusive. METHODS Twenty PCa risk SNPs implicated in GWAS and fine mapping studies were evaluated in 5,895 PCa cases treated by radical prostatectomy at Johns Hopkins Hospital, where each tumor was uniformly graded and staged using the same protocol. RESULTS For 18 of the 20 SNPs examined, no statistically significant differences (P > 0.05) were observed in risk allele frequencies between patients with more aggressive (Gleason scores > or =4 + 3, or stage > or =T3b, or N+) or less aggressive disease (Gleason scores < or =3 + 4, and stage < or =T2, and N0). For the two SNPs that had significant differences between more and less aggressive disease rs2735839 in KLK3 (P = 8.4 x 10(-7)) and rs10993994 in MSMB (P = 0.046), the alleles that are associated with increased risk for PCa were more frequent in patients with less aggressive disease. Since these SNPs are known to be associated with PSA levels in men without PCa diagnoses, these latter associations may reflect the enrichment of low grade, low stage cases diagnosed by contemporary disease screening with PSA. CONCLUSIONS The vast majority of PCa risk-associated SNPs are not associated with aggressiveness and clinicopathologic variables of PCa. Correspondingly, they have minimal utility in predicting the risk for developing more or less aggressive forms of PCa.
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Affiliation(s)
- A Karim Kader
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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Xu J, Kibel AS, Hu JJ, Turner AR, Pruett K, Zheng SL, Sun J, Isaacs SD, Wiley KE, Kim ST, Hsu FC, Wu W, Torti FM, Walsh PC, Chang BL, Isaacs WB. Prostate cancer risk associated loci in African Americans. Cancer Epidemiol Biomarkers Prev 2009; 18:2145-9. [PMID: 19549807 DOI: 10.1158/1055-9965.epi-09-0091] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Four genome-wide association studies, all in populations of European descent, have identified 20 independent single nucleotide polymorphisms (SNP) in 20 regions that are associated with prostate cancer risk. We evaluated these 20 SNPs in a combined African American (AA) study, with 868 prostate cancer patients and 878 control subjects. For 17 of these 20 SNPs, implicated risk-associated alleles were found to be more common in these AA cases than controls, significantly more than expected under the null hypothesis (P = 0.03). Two of these 17 SNPs, located at 3p12, and region 2 at 8q24, were significantly associated with prostate cancer risk (P < 0.05), and only SNP rs16901979 at region 2 of 8q24 remained significant after accounting for 20 tests. A multivariate analysis of additional SNPs across the broader 8q24 region revealed three independent prostate cancer risk-associated SNPs, including rs16901979, rs13254738, and rs10086908. The first two SNPs were approximately 20 kb apart and the last SNP, a novel finding from this study, was approximately 100 kb centromeric to the first two SNPs. These results suggest that a systematic evaluation of regions harboring known prostate cancer risk SNPs implicated in other races is an efficient approach to identify risk alleles for AA. However, studies with larger numbers of AA subjects are needed, and this will likely require a major collaborative effort to combine multiple AA study populations.
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Affiliation(s)
- Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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