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Deng X, Sun S, Yao W, Yue P, Guo F, Wang Y, Zhang Y. The association between three prevalent autoimmune disorders and the likelihood of developing prostate cancer: a Mendelian randomization study. Sci Rep 2024; 14:11755. [PMID: 38783043 PMCID: PMC11116512 DOI: 10.1038/s41598-024-62716-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
Numerous studies establish a significant correlation between autoimmune disorders (AIDs) and prostate cancer (PCa). Our Mendelian randomization (MR) analysis investigates the potential connection between rheumatoid arthritis (RA) and PCa, aiming to confirm causal links between systemic lupus erythematosus (SLE), hyperthyroidism, and PCa. Summary statistics from genome-wide association studies provided data on PCa and three AIDs. MR analysis, using IVW as the main approach, assessed causal relationships, validated by sensitivity analysis. IVW revealed a correlation between genetically anticipated RA and PCa, notably in Europeans (OR = 1.03; 95% CI 1.01-1.04, p = 2*10-5). Evidence supported a lower PCa risk in individuals with SLE (OR = 0.94; 95% CI 0.91-0.97, p = 2*10-4) and hyperthyroidism (OR = 0.02; 95% CI 0.001-0.2, p = 2*10-3). Weighted mode and median confirmed these findings. No pleiotropic effects were observed, and MR heterogeneity tests indicated dataset homogeneity. Our study establishes a causal link between RA, SLE, hyperthyroidism, and PCa.
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Affiliation(s)
- Xiaoqian Deng
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Shiwei Sun
- Department of Urology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, 030000, China
| | - Wei Yao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Peng Yue
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Fuyu Guo
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Yue Wang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Yangang Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China.
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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2
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Janaththani P, Tevz G, Fernando A, Malik A, Rockstroh A, Kryza T, Walpole C, Moya L, Lehman M, Nelson C, Srinivasan S, Clements J, Batra J. Unravelling the Role of Iroquois Homeobox 4 and its Interplay with Androgen Receptor in Prostate Cancer. RESEARCH SQUARE 2023:rs.3.rs-3295914. [PMID: 38076926 PMCID: PMC10705702 DOI: 10.21203/rs.3.rs-3295914/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Genome-wide association studies have linked Iroquois-Homeobox 4 (IRX4) as a robust expression quantitative-trait locus associated with prostate cancer (PCa) risk. However, the intricate mechanism and regulatory factors governing IRX4 expression in PCa remain poorly understood. Here, we unveil enrichment of androgen-responsive gene signatures in metastatic prostate tumors exhibiting heightened IRX4 expression. Furthermore, we uncover a novel interaction between IRX4 and the androgen receptor (AR) co-factor, FOXA1, suggesting that IRX4 modulates PCa cell behavior through AR cistrome alteration. Remarkably, we identified a distinctive short insertion-deletion polymorphism (INDEL), upstream of the IRX4 gene that differentially regulates IRX4 expression through the disruption of AR binding. This INDEL emerges as the most significant PCa risk-associated variant within the 5p15 locus, in a genetic analysis involving 82,591 PCa cases and 61,213 controls and was associated with PCa survival in patients undergoing androgen-deprivation therapy. These studies suggest the potential of this INDEL as a prognostic biomarker for androgen therapy in PCa and IRX4 as a potential therapeutic target in combination with current clinical management.
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Affiliation(s)
- Panchadsaram Janaththani
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, Victoria
| | - Gregor Tevz
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Achala Fernando
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Adil Malik
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Anja Rockstroh
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Thomas Kryza
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Mater Research UQ, Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Carina Walpole
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Mater Research UQ, Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Melanie Lehman
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada
| | - Colleen Nelson
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - The Australian Prostate Cancer BioResource
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | | | - Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
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3
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Ou J, Zhen K, Wu Y, Xue Z, Fang Y, Zhang Q, Bi H, Tian X, Ma L, Liu C. Systemic lupus erythematosus and prostate cancer risk: a pool of cohort studies and Mendelian randomization analysis. J Cancer Res Clin Oncol 2023; 149:9517-9528. [PMID: 37213031 PMCID: PMC10423167 DOI: 10.1007/s00432-023-04853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/13/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current observational studies suggest that there may be a causal relationship between systemic lupus erythematosus (SLE) and prostate cancer (PC). However, there is contradictory evidence. This study aimed to investigate and clarify the association between SLE and PC. METHODS We searched PubMed, Embase, Web of Science, and Scopus until May 2022. A meta-analysis was conducted on the standard incidence rate (SIR) and 95% CI. Subgroup analysis was performed based on the follow-up duration, study quality, and appropriate SLE diagnosis. Mendelian randomization (MR) of the two samples was used to determine whether genetically elevated SLE was causal for PC. Summary MR data were obtained from published GWASs, which included 1,959,032 individuals. The results were subjected to sensitivity analysis to verify their reliability. RESULTS In a meta-analysis of 79,316 participants from 14 trials, we discovered that patients with SLE had decreased PC risk (SIR, 0.78; 95% CI, 0.70-0.87) significantly. The MR results showed that a one-SD increase in genetic susceptibility to SLE significantly reduced PC risk (OR, 0.9829; 95% CI, 0.9715-0.9943; P = 0.003). Additional MR analyses suggested that the use of immunosuppressants (ISs) (OR, 1.1073; 95% CI, 1.0538-1.1634; P < 0.001), but not glucocorticoids (GCs) or non-steroidal anti-inflammatory drugs (NSAIDs), which were associated with increased PC risk. The results of the sensitivity analyses were stable, and there was no evidence of directional pleiotropy. CONCLUSIONS Our results suggest that patients with SLE have a lower risk of developing PC. Additional MR analyses indicated that genetic susceptibility to the use of ISs, but not GCs or NSAIDs, was associated with increased PC risk. This finding enriches our understanding of the potential risk factors for PC in patients with SLE. Further study is required to reach more definitive conclusions regarding these mechanisms.
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Affiliation(s)
- Junyong Ou
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Kailan Zhen
- Department of Histology and Embryology, Southern Medical University, Guangzhou, 510515 China
| | - Yaqian Wu
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Zixuan Xue
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Yangyi Fang
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Qiming Zhang
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Hai Bi
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 85 Wujin Road, Shanghai, 200080 China
| | - Xiaojun Tian
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Lulin Ma
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
| | - Cheng Liu
- Department of Urology, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, 100191 China
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 85 Wujin Road, Shanghai, 200080 China
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4
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Ito S, Liu X, Ishikawa Y, Conti DD, Otomo N, Kote-Jarai Z, Suetsugu H, Eeles RA, Koike Y, Hikino K, Yoshino S, Tomizuka K, Horikoshi M, Ito K, Uchio Y, Momozawa Y, Kubo M, Kamatani Y, Matsuda K, Haiman CA, Ikegawa S, Nakagawa H, Terao C. Androgen receptor binding sites enabling genetic prediction of mortality due to prostate cancer in cancer-free subjects. Nat Commun 2023; 14:4863. [PMID: 37612283 PMCID: PMC10447511 DOI: 10.1038/s41467-023-39858-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 06/27/2023] [Indexed: 08/25/2023] Open
Abstract
Prostate cancer (PrCa) is the second most common cancer worldwide in males. While strongly warranted, the prediction of mortality risk due to PrCa, especially before its development, is challenging. Here, we address this issue by maximizing the statistical power of genetic data with multi-ancestry meta-analysis and focusing on binding sites of the androgen receptor (AR), which has a critical role in PrCa. Taking advantage of large Japanese samples ever, a multi-ancestry meta-analysis comprising more than 300,000 subjects in total identifies 9 unreported loci including ZFHX3, a tumor suppressor gene, and successfully narrows down the statistically finemapped variants compared to European-only studies, and these variants strongly enrich in AR binding sites. A polygenic risk scores (PRS) analysis restricting to statistically finemapped variants in AR binding sites shows among cancer-free subjects, individuals with a PRS in the top 10% have a strongly higher risk of the future death of PrCa (HR: 5.57, P = 4.2 × 10-10). Our findings demonstrate the potential utility of leveraging large-scale genetic data and advanced analytical methods in predicting the mortality of PrCa.
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Affiliation(s)
- Shuji Ito
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
- Department of Orthopedic Surgery, Shimane University, Izumo, Japan
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Yuki Ishikawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - David D Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nao Otomo
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, School of Medicine, Keio University, Tokyo, Japan
| | | | - Hiroyuki Suetsugu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Yoshinao Koike
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Keiko Hikino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Pharmacogenomics, Yokohama, Japan
| | - Soichiro Yoshino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohei Tomizuka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Momoko Horikoshi
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genomics of Diabetes and Metabolism, Yokohama, Japan
| | - Kaoru Ito
- RIKEN Center for Integrative Medical Sciences, The Cardiovascular Genomics and Informatics, Yokohama, Japan
| | - Yuji Uchio
- Department of Orthopedic Surgery, Shimane University, Izumo, Japan
| | - Yukihide Momozawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genotyping Development, Yokohama, Japan
| | | | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Laboratory of Genome Technology, Human Genome Center, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Tokyo, Japan
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shiro Ikegawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics, Yokohama, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan.
- Shizuoka General Hospital, The Clinical Research Center, Shizuoka, Japan.
- School of Pharmaceutical Sciences, University of Shizuoka, The Department of Applied Genetics, Shizuoka, Japan.
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5
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Gu D, Tang M, Wang Y, Cui H, Zhang M, Bai Y, Zeng Z, Tan Y, Wang X, Zhang B. The Causal Relationships Between Extrinsic Exposures and Risk of Prostate Cancer: A Phenome-Wide Mendelian Randomization Study. Front Oncol 2022; 12:829248. [PMID: 35237523 PMCID: PMC8882837 DOI: 10.3389/fonc.2022.829248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
Background Prostate cancer is the second most common cancer in males worldwide, and multitudes of factors have been reported to be associated with prostate cancer risk. Objectives We aim to conduct the phenome-wide exposed-omics analysis of the risk factors for prostate cancer and verify the causal associations between them. Methods We comprehensively searched published systematic reviews and meta-analyses of cohort studies and conducted another systematic review and meta-analysis of the Mendelian randomization studies investigating the associations between extrinsic exposures and prostate cancer, thus to find all of the potential risk factors for prostate cancer. Then, we launched a phenome-wide two-sample Mendelian randomization analysis to validate the potentially causal relationships using the PRACTICAL consortium and UK Biobank. Results We found a total of 55 extrinsic exposures for prostate cancer risk. The causal effect of 30 potential extrinsic exposures on prostate cancer were assessed, and the results showed docosahexaenoic acid (DHA) [odds ratio (OR)=0.806, 95% confidence interval (CI): 0.661-0.984, p=0.034], insulin-like growth factor binding protein 3 (IGFBP-3) (OR=1.0002, 95%CI: 1.00004-1.0004, p=0.016), systemic lupus erythematosus (SLE) (OR=0.9993, 95%CI: 0.9986-0.99997, p=0.039), and body mass index (BMI) (OR=0.995, 95%CI: 0.990-0.9999, p=0.046) were associated with prostate cancer risk. However, no association was found between the other 26 factors and prostate cancer risk. Conclusions Our study discovered the phenome-wide exposed-omics risk factors profile of prostate cancer, and verified that the IGFBP-3, DHA, BMI, and SLE were causally related to prostate cancer risk. The results may provide new insight into the study of the pathogenesis of prostate cancer.
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Affiliation(s)
- Dongqing Gu
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Min Zhang
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Ye Bai
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Ziqian Zeng
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yunhua Tan
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xin Wang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
- *Correspondence: Ben Zhang,
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7
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Valentini S, Gandolfi F, Carolo M, Dalfovo D, Pozza L, Romanel A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1335-1350. [PMID: 35061909 PMCID: PMC8860573 DOI: 10.1093/nar/gkac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 11/21/2022] Open
Abstract
In the last years, many studies were able to identify associations between common genetic variants and complex diseases. However, the mechanistic biological links explaining these associations are still mostly unknown. Common variants are usually associated with a relatively small effect size, suggesting that interactions among multiple variants might be a major genetic component of complex diseases. Hence, elucidating the presence of functional relations among variants may be fundamental to identify putative variants’ interactions. To this aim, we developed Polympact, a web-based resource that allows to explore functional relations among human common variants by exploiting variants’ functional element landscape, their impact on transcription factor binding motifs, and their effect on transcript levels of protein-coding genes. Polympact characterizes over 18 million common variants and allows to explore putative relations by combining clustering analysis and innovative similarity and interaction network models. The properties of the network models were studied and the utility of Polympact was demonstrated by analysing the rich sets of Breast Cancer and Alzheimer's GWAS variants. We identified relations among multiple variants, suggesting putative interactions. Polympact is freely available at bcglab.cibio.unitn.it/polympact.
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Affiliation(s)
- Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Carolo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lara Pozza
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- To whom correspondence should be addressed. Tel: +39 0461 285217; Fax: +39 0461 283937;
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8
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Valentini S, Marchioretti C, Bisio A, Rossi A, Zaccara S, Romanel A, Inga A. TranSNPs: A class of functional SNPs affecting mRNA translation potential revealed by fraction-based allelic imbalance. iScience 2021; 24:103531. [PMID: 34917903 PMCID: PMC8666669 DOI: 10.1016/j.isci.2021.103531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/27/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
Few studies have explored the association between SNPs and alterations in mRNA translation potential. We developed an approach to identify SNPs that can mark allele-specific protein expression levels and could represent sources of inter-individual variation in disease risk. Using MCF7 cells under different treatments, we performed polysomal profiling followed by RNA sequencing of total or polysome-associated mRNA fractions and designed a computational approach to identify SNPs showing a significant change in the allelic balance between total and polysomal mRNA fractions. We identified 147 SNPs, 39 of which located in UTRs. Allele-specific differences at the translation level were confirmed in transfected MCF7 cells by reporter assays. Exploiting breast cancer data from TCGA we identified UTR SNPs demonstrating distinct prognosis features and altering binding sites of RNA-binding proteins. Our approach produced a catalog of tranSNPs, a class of functional SNPs associated with allele-specific translation and potentially endowed with prognostic value for disease risk.
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Affiliation(s)
- Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Caterina Marchioretti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- Department of Biomedical Sciences (DBS), University of Padova, 35131 Padova, Italy
| | - Alessandra Bisio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Sara Zaccara
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- Weill Medical College, Cornell University, New York 10065, NY, USA
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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9
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Giambartolomei C, Seo JH, Schwarz T, Freund MK, Johnson RD, Spisak S, Baca SC, Gusev A, Mancuso N, Pasaniuc B, Freedman ML. H3K27ac HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility. Am J Hum Genet 2021; 108:2284-2300. [PMID: 34822763 PMCID: PMC8715276 DOI: 10.1016/j.ajhg.2021.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/02/2021] [Indexed: 12/26/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 200 prostate cancer (PrCa) risk regions, which provide potential insights into causal mechanisms. Multiple lines of evidence show that a significant proportion of PrCa risk can be explained by germline causal variants that dysregulate nearby target genes in prostate-relevant tissues, thus altering disease risk. The traditional approach to explore this hypothesis has been correlating GWAS variants with steady-state transcript levels, referred to as expression quantitative trait loci (eQTLs). In this work, we assess the utility of chromosome conformation capture (3C) coupled with immunoprecipitation (HiChIP) to identify target genes for PrCa GWAS risk loci. We find that interactome data confirm previously reported PrCa target genes identified through GWAS/eQTL overlap (e.g., MLPH). Interestingly, HiChIP identifies links between PrCa GWAS variants and genes well-known to play a role in prostate cancer biology (e.g., AR) that are not detected by eQTL-based methods. HiChIP predicted enhancer elements at the AR and NKX3-1 prostate cancer risk loci, and both were experimentally confirmed to regulate expression of the corresponding genes through CRISPR interference (CRISPRi) perturbation in LNCaP cells. Our results demonstrate that looping data harbor additional information beyond eQTLs and expand the number of PrCa GWAS loci that can be linked to candidate susceptibility genes.
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Affiliation(s)
- Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova 16163, Italy; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA; The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Malika Kumar Freund
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ruth Dolly Johnson
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sandor Spisak
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Sylvan C Baca
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Johnson Comprehensive Cancer Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA; The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02215, USA.
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10
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Ermini L, Francis JC, Rosa GS, Rose AJ, Ning J, Greaves M, Swain A. Evolutionary selection of alleles in the melanophilin gene that impacts on prostate organ function and cancer risk. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:311-321. [PMID: 34754452 PMCID: PMC8573191 DOI: 10.1093/emph/eoab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/03/2021] [Indexed: 11/21/2022]
Abstract
Background and objectives Several hundred inherited genetic variants or SNPs that alter the risk of cancer have been identified through genome-wide association studies. In populations of European ancestry, these variants are mostly present at relatively high frequencies. To gain insight into evolutionary origins, we screened a series of genes and SNPs linked to breast or prostate cancer for signatures of historical positive selection. Methodology We took advantage of the availability of the 1000 genome data and we performed genomic scans for positive selection in five different Caucasian populations as well as one African reference population. We then used prostate organoid cultures to provide a possible functional explanation for the interplay between the action of evolutionary forces and the disease risk association. Results Variants in only one gene showed genomic signatures of positive, evolutionary selection within Caucasian populations melanophilin (MLPH). Functional depletion of MLPH in prostate organoids, by CRISPR/Cas9 mutation, impacted lineage commitment of progenitor cells promoting luminal versus basal cell differentiation and on resistance to androgen deprivation. Conclusions and implications The MLPH variants influencing prostate cancer risk may have been historically selected for their adaptive benefit on skin pigmentation but MLPH is highly expressed in the prostate and the derivative, positively selected, alleles decrease the risk of prostate cancer. Our study suggests a potential functional mechanism via which MLPH and its genetic variants could influence risk of prostate cancer, as a serendipitous consequence of prior evolutionary benefits to another tissue. Lay Summary We screened a limited series of genomic variants associated with breast and prostate cancer risk for signatures of historical positive selection. Variants within the melanophilin (MLPH) gene fell into this category. Depletion of MLPH in prostate organoid cultures, suggested a potential functional mechanism for impacting on cancer risk, as a serendipitous consequence of prior evolutionary benefits to another tissue.
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Affiliation(s)
- Luca Ermini
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jeffrey C Francis
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Gabriel S Rosa
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Alexandra J Rose
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jian Ning
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.,Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Amanda Swain
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.,Tumour Profiling Unit, The Institute of Cancer Research, London, UK
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11
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Somatic Alterations Impact AR Transcriptional Activity and Efficacy of AR-Targeting Therapies in Prostate Cancer. Cancers (Basel) 2021; 13:cancers13163947. [PMID: 34439101 PMCID: PMC8393938 DOI: 10.3390/cancers13163947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary For patients whose prostate cancer spreads beyond the confines of the prostate, treatment options continue to increase. However, we are missing the information that is needed to choose for each patient the best treatment at each step of his cancer progression so we can ensure that maximal remissions and prolonged survival are achieved. In this review, we examine whether a better understanding of how the activity of the target for the default first treatment, the androgen receptor, is regulated in prostate cancer tissues can improve prostate cancer treatment plans. We consider the evidence for variability of androgen receptor activity among patients and examine the molecular basis for this variable action. We summarize clinical evidence supporting that information on a prostate cancer’s genomic composition may inform on its level of androgen receptor action, which may facilitate choice for the most effective first-line therapy and ultimately improve prostate cancer treatment plans overall. Abstract Inhibiting the activity of the ligand-activated transcription factor androgen receptor (AR) is the default first-line treatment for metastatic prostate cancer (CaP). Androgen deprivation therapy (ADT) induces remissions, however, their duration varies widely among patients. The reason for this heterogeneity is not known. A better understanding of its molecular basis may improve treatment plans and patient survival. AR’s transcriptional activity is regulated in a context-dependent manner and relies on an interplay between its associated transcriptional regulators, DNA recognition motifs, and ligands. Alterations in one or more of these factors induce shifts in the AR cistrome and transcriptional output. Significant variability in AR activity is seen in both castration-sensitive (CS) and castration-resistant CaP (CRPC). Several AR transcriptional regulators undergo somatic alterations that impact their function in clinical CaPs. Some alterations occur in a significant fraction of cases, resulting in CaP subtypes, while others affect only a few percent of CaPs. Evidence is emerging that these alterations may impact the response to CaP treatments such as ADT, radiation therapy, and chemotherapy. Here, we review the contribution of recurring somatic alterations on AR cistrome and transcriptional output and the efficacy of CaP treatments and explore strategies to use these insights to improve treatment plans and outcomes for CaP patients.
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12
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Adiba M, Das T, Paul A, Das A, Chakraborty S, Hosen MI, Nabi AN. In silico characterization of coding and non-coding SNPs of the androgen receptor gene. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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13
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Brandão A, Paulo P, Teixeira MR. Hereditary Predisposition to Prostate Cancer: From Genetics to Clinical Implications. Int J Mol Sci 2020; 21:E5036. [PMID: 32708810 PMCID: PMC7404100 DOI: 10.3390/ijms21145036] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PrCa) ranks among the top five cancers for both incidence and mortality worldwide. A significant proportion of PrCa susceptibility has been attributed to inherited predisposition, with 10-20% of cases expected to occur in a hereditary/familial context. Advances in DNA sequencing technologies have uncovered several moderate- to high-penetrance PrCa susceptibility genes, most of which have previously been related to known hereditary cancer syndromes, namely the hereditary breast and ovarian cancer (BRCA1, BRCA2, ATM, CHEK2, and PALB2) and Lynch syndrome (MLH1, MSH2, MSH6, and PMS2) genes. Additional candidate genes have also been suggested, but further evidence is needed to include them in routine genetic testing. Recommendations based on clinical features, family history, and ethnicity have been established for more cost-efficient genetic testing of patients and families who may be at an increased risk of developing PrCa. The identification of alterations in PrCa predisposing genes may help to inform screening strategies, as well as treatment options, in the metastatic setting. This review provides an overview of the genetic basis underlying hereditary predisposition to PrCa, the current genetic screening recommendations, and the implications for clinical management of the disease.
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Affiliation(s)
- Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
| | - Manuel R. Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
- Biomedical Sciences Institute Abel Salazar (ICBAS), University of Porto, 4200-072 Porto, Portugal
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14
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Pinto AR, Silva J, Pinto R, Medeiros R. Aggressive prostate cancer phenotype and genome-wide association studies: where are we now? Pharmacogenomics 2020; 21:487-503. [PMID: 32343194 DOI: 10.2217/pgs-2019-0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The majority of prostate cancer (PCa) is indolent, however, a percentage of patients are initially diagnosed with metastatic disease, for which there is a worse prognosis. There is a lack of biomarkers to identify men at greater risk for developing aggressive PCa. Genome-wide association studies (GWAS) scan the genome to search associations of SNPs with specific traits, like cancer. To date, eight GWAS have resulted in the reporting of 16 SNPs associated with aggressive PCa (p < 5.00 × 10-2). Still, validation studies need to be conducted to confirm the obtained results as GWAS can generate false-positive results. Furthermore, post-GWAS studies provide a better understanding of the functional consequences.
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Affiliation(s)
- Ana R Pinto
- Molecular Oncology & Viral Pathology Group, IPO-Porto Research Center, (CI-IPOP) Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-4072 Porto, Portugal.,ICBAS, Abel Salazar Institute for the Biomedical Sciences, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Jani Silva
- Molecular Oncology & Viral Pathology Group, IPO-Porto Research Center, (CI-IPOP) Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-4072 Porto, Portugal
| | - Ricardo Pinto
- Molecular Oncology & Viral Pathology Group, IPO-Porto Research Center, (CI-IPOP) Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-4072 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group, IPO-Porto Research Center, (CI-IPOP) Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-4072 Porto, Portugal.,Research Department, Portuguese League Against Cancer (NRNorte), Estrada Interior da Circunvalação, 6657, 4200-172 Porto, Portugal.,CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, Praça 9 de Abril, 349, 4249-004 Porto, Portugal
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15
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Fu WF, Li JJ, Kang SH, Song CG. The Expression, Clinicopathologic Characteristics, and Prognostic Value of Androgen Receptor in Breast Cancer: A Bioinformatics Analysis Using Public Databases. DNA Cell Biol 2020; 39:864-874. [PMID: 32181676 DOI: 10.1089/dna.2019.5192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The role of androgen receptor (AR) in breast cancer has been unveiled in succession for the past few years. In this study, we conducted a comprehensive analysis based on four online public databases of data from many previous studies. We found that the expression of AR is significantly related to age, histological grade, and subtype but not to lymph node status. The low expression level of AR is strongly associated with poor recurrence-free survival, especially with poor distance metastasis-free survival in luminal A patients, but inverse in HER2 (human epidermal growth factor receptor-2) enriched patients. AR might be a biomarker of chemosensitivity in the basal subtype. Besides, the expression of melanophilin (MLPH) is distinctly in accordance with that of AR. AR could play diverse roles in different subtypes of breast cancer.
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Affiliation(s)
- Wen-Fen Fu
- Department of Breast Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Juan-Juan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shao-Hong Kang
- Department of Breast Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Chuan-Gui Song
- Department of Breast Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
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16
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Dai JY, Wang X, Wang B, Sun W, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Feng Z, Stanford JL. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. PLoS Genet 2020; 16:e1008667. [PMID: 32226005 PMCID: PMC7145271 DOI: 10.1371/journal.pgen.1008667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 04/09/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction. Comparing eQTLs between tumors and benign samples, we show that 98 of the 147 risk SNPs were identified as eQTLs in the tumor-adjacent benign samples, and almost all 34 eQTL identified in tumor sets were also eQTLs in the benign samples. Three lines of results support the causal role of DNA methylation. First, nearly 100 of the 147 risk SNPs were identified as meQTLs in one tumor set, and almost all eQTLs in tumors were meQTLs. Second, the loss of eQTLs in tumors relative to benign samples was associated with altered DNA methylation. Third, among risk SNPs identified as both eQTLs and meQTLs, mediation analyses suggest that over two-thirds have evidence of a causal role for DNA methylation, mostly mediating genetic influence on gene expression. In summary, we provide a comprehensive catalog of eQTLs, meQTLs and putative cancer genes for known PrCa risk SNPs. We observe that a substantial portion of germline eQTL regulatory mechanisms are maintained in the tumor development, despite somatic alterations in tumor genome. Finally, our mediation analyses illuminate the likely intermediary role of CpG methylation in eQTL regulation of gene expression.
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Affiliation(s)
- James Y. Dai
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Sun
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Kristina M. Jordahl
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Yaw A. Nyame
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Ziding Feng
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, United States of America
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17
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Zhang T, Sun Y, Zheng T, Wang R, Jia D, Zhang W. MLPH Accelerates the Epithelial-Mesenchymal Transition in Prostate Cancer. Onco Targets Ther 2020; 13:701-708. [PMID: 32158222 PMCID: PMC6986253 DOI: 10.2147/ott.s225023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/20/2019] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION Prostate cancer (PC) is the second greatest cause of cancer deaths globally. PC presents a poor prognosis once it metastasizes. There is considerable proof of vital epithelial-mesenchymal transition (EMT) functionality in PC metastasis. Previous studies revealed that melanophilin (MLPH) is associated with PC; however, its role in PC remains poorly understood. METHODS Bioinformatics analyses were performed. The cellular responses to MLPH knockdown were examined in HCC cell lines via wound healing assay, migration and invasion assay, Western blotting. RESULTS Analysis of the PROGgeneV2 database revealed that high MLPH expression might indicate poor overall survival. MLPH knockdown reduced PC cell migration, proliferation, and invasion. MLPH downregulation in vivo resulted in a lower growth rate and fewer metastatic nodules in lung tissues. Furthermore, MLPH knockdown recovered downregulated expression of the mesenchymal marker N-cadherin and the epithelial marker E-cadherin following a decrease in β-catenin. CONCLUSION These results indicate that progression of PC is stimulated via MLPH-dependent initiation of the EMT.
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Affiliation(s)
- Tianbiao Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
| | - Yangyang Sun
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
| | - Tao Zheng
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
| | - Rui Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
| | - Donghui Jia
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
| | - Weixing Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, People’s Republic of China
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18
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Xiao F, Zhang P, Wang Y, Tian Y, James M, Huang CC, Wang L, Wang L. Single-nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4. Mol Carcinog 2019; 59:45-55. [PMID: 31659808 DOI: 10.1002/mc.23127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022]
Abstract
A prostate cancer risk single-nucleotide polymorphism (SNP), rs13426236, is significantly associated with melanophilin (MLPH) expression. To functionally characterize role of the rs13426236 in prostate cancer, we first performed splicing-specific expression quantitative trait loci analysis and refined the significant association of rs13426236 allele G with an increased expression of MLPH splicing transcript variant 4 (V4) (P = 7.61E-5) but not other protein-coding variants (V1-V3) (P > .05). We then performed an allele-specific reporter assay to determine if SNP-containing sequences functioned as an active enhancer. Compared to allele A, allele G of rs13426236 showed significantly higher luciferase activity on the promoter of the splicing transcript V4 (P < .03) but not on the promoter of transcript V1 (P > .05) in two prostate cancer cell lines (DU145 and 22Rv1). Cell transfection assays showed stronger effect of transcript V4 than V1 on promoting cell proliferation, invasion, and antiapoptotic activities. RNA profiling analysis demonstrated that transcript V4 overexpression caused significant expression changes in glycosylation/glycoprotein and metal-binding gene ontology pathways (FDR < 0.01). We also found that both transcripts V4 and V1 were significantly upregulated in prostate adenocarcinoma (P ≤ 2.49E-6) but only transcript V4 upregulation was associated with poor recurrence-free survival (P = .028, hazard ratio = 1.63, 95% confidence interval = 1.05-2.42) in The Cancer Genome Atlas data. This study provides strong evidence showing that prostate cancer risk SNP rs13426236 upregulates expression of MLPH transcript V4, which may function as a candidate oncogene in prostate cancer.
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Affiliation(s)
- Fankai Xiao
- Henan Key Laboratory for Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yuan Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yijun Tian
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael James
- Department of Surgery, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Chiang-Ching Huang
- Department of Biostatistics, University of Wisconsin, Milwaukee, Wisconsin
| | - Lidong Wang
- Henan Key Laboratory for Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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19
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Senapati D, Kumari S, Heemers HV. Androgen receptor co-regulation in prostate cancer. Asian J Urol 2019; 7:219-232. [PMID: 32742924 PMCID: PMC7385509 DOI: 10.1016/j.ajur.2019.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) progression relies on androgen receptor (AR) action. Preventing AR's ligand-activation is the frontline treatment for metastatic PCa. Androgen deprivation therapy (ADT) that inhibits AR ligand-binding initially induces remission but eventually fails, mainly because of adaptive PCa responses that restore AR action. The vast majority of castration-resistant PCa (CRPC) continues to rely on AR activity. Novel therapeutic strategies are being explored that involve targeting other critical AR domains such as those that mediate its constitutively active transactivation function, its DNA binding ability, or its interaction with co-operating transcriptional regulators. Considerable molecular and clinical variability has been found in AR's interaction with its ligands, DNA binding motifs, and its associated coregulators and transcription factors. Here, we review evidence that each of these levels of AR regulation can individually and differentially impact transcription by AR. In addition, we examine emerging insights suggesting that each can also impact the other, and that all three may collaborate to induce gene-specific AR target gene expression, likely via AR allosteric effects. For the purpose of this review, we refer to the modulating influence of these differential and/or interdependent contributions of ligands, cognate DNA-binding motifs and critical regulatory protein interactions on AR's transcriptional output, which may influence the efficiency of the novel PCa therapeutic approaches under consideration, as co-regulation of AR activity.
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Affiliation(s)
| | - Sangeeta Kumari
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Hannelore V Heemers
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA.,Department of Urology, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology/Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
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20
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Stelloo S, Bergman AM, Zwart W. Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers. Endocr Relat Cancer 2019; 26:R267-R285. [PMID: 30865928 DOI: 10.1530/erc-19-0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance. Genome-wide chromatin association studies revealed that transcriptional regulation by AR mainly depends on binding to distal regulatory enhancer elements that control gene expression through chromatin looping to gene promoters. Changes in the chromatin epigenetic landscape and DNA sequence can locally alter AR-DNA-binding capacity and consequently impact transcriptional output and disease outcome. The vast majority of reports describing AR chromatin interactions have been limited to cell lines, identifying numerous other factors and interacting transcription factors that impact AR chromatin interactions. Do these factors also impact AR cistromics - the genome-wide chromatin-binding landscape of AR - in vivo? Recent technological advances now enable researchers to identify AR chromatin-binding sites and their target genes in human specimens. In this review, we provide an overview of the different factors that influence AR chromatin binding in prostate cancer specimens, which is complemented with knowledge from cell line studies. Finally, we discuss novel perspectives on studying AR cistromics in clinical samples.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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21
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Chung CT, Marrano P, Swanson D, Dickson BC, Thorner PS. Fusion of ALK to the melanophilin gene MLPH in pediatric Spitz nevi. Hum Pathol 2019; 87:57-64. [PMID: 30857967 DOI: 10.1016/j.humpath.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Abstract
Spitzoid neoplasms typically affect young individuals and include Spitz nevus, atypical Spitz tumor, and Spitzoid melanoma. Spitz tumors can exhibit gene fusions involving the receptor tyrosine kinases NTRK1, NTRK3, ALK, ROS1, RET, or MET, or the serine-threonine kinase BRAF. Because most studies have been based on adult cases, we studied ALK fusions in Spitz nevi occurring in pediatric patients. Twenty-seven cases were screened for ALK expression by immunohistochemistry, and 6 positive cases were identified. These cases were studied further using the TruSight RNA Fusion Panel, and in 4 cases, exon 20 of the ALK gene was found to be fused to exon 14 of the MLPH (melanophilin) gene, a gene fusion that has only been reported in a Spitz nevus in an adult. The remaining 2 cases showed no fusion of ALK with any gene. The cases with the MLPH-ALK fusion showed a similar histology to that described for Spitz nevi with ALK fusions, with spindle-shaped and epithelioid melanocytes in fusiform nests with a plexiform growth pattern and infiltrative border. We created a breakapart fluorescence in situ hybridization assay for MLPH, and all 4 cases with the MLPH-ALK fusion were positive, whereas the other 23 cases in the study were negative. Thus, ALK and MLPH were fused only to each other in our series. Melanophilin is part of the melanosome trafficking apparatus together with MYO5a, TPM3, and RAB27a, all constitutively expressed in melanocytes. Kinase fusions involving MYO5A and TPM3 have been reported in Spitz tumors, and our series adds MLPH to this group.
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Affiliation(s)
- Catherine T Chung
- Division of Pathology, The Hospital for Sick Children, Toronto, M5G 1X8 Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8 Canada.
| | - Paula Marrano
- Division of Pathology, The Hospital for Sick Children, Toronto, M5G 1X8 Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount, Sinai Hospital, Toronto, M5G 1X5 Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8 Canada; Department of Pathology and Laboratory Medicine, Mount, Sinai Hospital, Toronto, M5G 1X5 Canada
| | - Paul Scott Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8 Canada
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22
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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23
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Watts EL, Appleby PN, Perez-Cornago A, Bueno-de-Mesquita HB, Chan JM, Chen C, Cohn BA, Cook MB, Flicker L, Freedman ND, Giles GG, Giovannucci E, Gislefoss RE, Hankey GJ, Kaaks R, Knekt P, Kolonel LN, Kubo T, Le Marchand L, Luben RN, Luostarinen T, Männistö S, Metter EJ, Mikami K, Milne RL, Ozasa K, Platz EA, Quirós JR, Rissanen H, Sawada N, Stampfer M, Stanczyk FZ, Stattin P, Tamakoshi A, Tangen CM, Thompson IM, Tsilidis KK, Tsugane S, Ursin G, Vatten L, Weiss NS, Yeap BB, Allen NE, Key TJ, Travis RC. Low Free Testosterone and Prostate Cancer Risk: A Collaborative Analysis of 20 Prospective Studies. Eur Urol 2018; 74:585-594. [PMID: 30077399 PMCID: PMC6195673 DOI: 10.1016/j.eururo.2018.07.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/13/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Experimental and clinical evidence implicates testosterone in the aetiology of prostate cancer. Variation across the normal range of circulating free testosterone concentrations may not lead to changes in prostate biology, unless circulating concentrations are low. This may also apply to prostate cancer risk, but this has not been investigated in an epidemiological setting. OBJECTIVE To examine whether men with low concentrations of circulating free testosterone have a reduced risk of prostate cancer. DESIGN, SETTING, AND PARTICIPANTS Analysis of individual participant data from 20 prospective studies including 6933 prostate cancer cases, diagnosed on average 6.8 yr after blood collection, and 12 088 controls in the Endogenous Hormones, Nutritional Biomarkers and Prostate Cancer Collaborative Group. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Odds ratios (ORs) of incident overall prostate cancer and subtypes by stage and grade, using conditional logistic regression, based on study-specific tenths of calculated free testosterone concentration. RESULTS AND LIMITATIONS Men in the lowest tenth of free testosterone concentration had a lower risk of overall prostate cancer (OR=0.77, 95% confidence interval [CI] 0.69-0.86; p<0.001) compared with men with higher concentrations (2nd-10th tenths of the distribution). Heterogeneity was present by tumour grade (phet=0.01), with a lower risk of low-grade disease (OR=0.76, 95% CI 0.67-0.88) and a nonsignificantly higher risk of high-grade disease (OR=1.56, 95% CI 0.95-2.57). There was no evidence of heterogeneity by tumour stage. The observational design is a limitation. CONCLUSIONS Men with low circulating free testosterone may have a lower risk of overall prostate cancer; this may be due to a direct biological effect, or detection bias. Further research is needed to explore the apparent differential association by tumour grade. PATIENT SUMMARY In this study, we looked at circulating testosterone levels and risk of developing prostate cancer, finding that men with low testosterone had a lower risk of prostate cancer.
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Affiliation(s)
- Eleanor L Watts
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Paul N Appleby
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - H Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands; Department of Epidemiology and Biostatistics, Imperial College London, London, UK; Department of Social & Preventive Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - June M Chan
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, CA, USA; Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Chu Chen
- Public Health Sciences Division, Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA, USA
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, USA
| | - Leon Flicker
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Western Australian Centre for Health and Ageing, Centre for Medical Research, University of Western Australia, Perth, Western Australia, Australia
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, USA
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Edward Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Randi E Gislefoss
- Cancer Registry of Norway, Institute for Epidemiological Cancer Research, Oslo, Norway
| | - Graeme J Hankey
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Paul Knekt
- National Institute for Health and Welfare, Helsinki, Finland
| | | | - Tatsuhiko Kubo
- Department of Preventive Medicine and Community Health, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | - Robert N Luben
- Strangeways Research Laboratory, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Tapio Luostarinen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - E Jeffrey Metter
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kazuya Mikami
- Department of Urology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Kotaro Ozasa
- Department of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Harri Rissanen
- National Institute for Health and Welfare, Helsinki, Finland
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Meir Stampfer
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Frank Z Stanczyk
- Division of Reproductive Endocrinology and Infertility, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Akiko Tamakoshi
- Department of Public Health, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M Thompson
- Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, TX, USA
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Giske Ursin
- Cancer Registry of Norway, Institute for Epidemiological Cancer Research, Oslo, Norway; Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Noel S Weiss
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Bu B Yeap
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Endocrinology and Diabetes, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Naomi E Allen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
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24
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Mancuso N, Gayther S, Gusev A, Zheng W, Penney KL, Kote-Jarai Z, Eeles R, Freedman M, Haiman C, Pasaniuc B. Large-scale transcriptome-wide association study identifies new prostate cancer risk regions. Nat Commun 2018; 9:4079. [PMID: 30287866 PMCID: PMC6172280 DOI: 10.1038/s41467-018-06302-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022] Open
Abstract
Although genome-wide association studies (GWAS) for prostate cancer (PrCa) have identified more than 100 risk regions, most of the risk genes at these regions remain largely unknown. Here we integrate the largest PrCa GWAS (N = 142,392) with gene expression measured in 45 tissues (N = 4458), including normal and tumor prostate, to perform a multi-tissue transcriptome-wide association study (TWAS) for PrCa. We identify 217 genes at 84 independent 1 Mb regions associated with PrCa risk, 9 of which are regions with no genome-wide significant SNP within 2 Mb. 23 genes are significant in TWAS only for alternative splicing models in prostate tumor thus supporting the hypothesis of splicing driving risk for continued oncogenesis. Finally, we use a Bayesian probabilistic approach to estimate credible sets of genes containing the causal gene at a pre-defined level; this reduced the list of 217 associations to 109 genes in the 90% credible set. Overall, our findings highlight the power of integrating expression with PrCa GWAS to identify novel risk loci and prioritize putative causal genes at known risk loci.
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Affiliation(s)
- Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
| | - Simon Gayther
- The Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, 90048, CA, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, 37232, TN, USA
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, 02115, MA, USA
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, 02215, MA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90015, CA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, 90095, CA, USA
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25
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Wallis CJD, Krakowsky Y, Finelli A. Low Testosterone and Prostate Cancer: Is the Protection Real? Eur Urol 2018; 74:595-596. [PMID: 30195834 DOI: 10.1016/j.eururo.2018.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Christopher J D Wallis
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yonah Krakowsky
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Women's College Hospital and Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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26
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Watts EL, Appleby PN, Albanes D, Black A, Chan JM, Chen C, Cirillo PM, Cohn BA, Cook MB, Donovan JL, Ferrucci L, Garland CF, Giles GG, Goodman PJ, Habel LA, Haiman CA, Holly JMP, Hoover RN, Kaaks R, Knekt P, Kolonel LN, Kubo T, Le Marchand L, Luostarinen T, MacInnis RJ, Mäenpää HO, Männistö S, Metter EJ, Milne RL, Nomura AMY, Oliver SE, Parsons JK, Peeters PH, Platz EA, Riboli E, Ricceri F, Rinaldi S, Rissanen H, Sawada N, Schaefer CA, Schenk JM, Stanczyk FZ, Stampfer M, Stattin P, Stenman UH, Tjønneland A, Trichopoulou A, Thompson IM, Tsugane S, Vatten L, Whittemore AS, Ziegler RG, Allen NE, Key TJ, Travis RC. Circulating sex hormones in relation to anthropometric, sociodemographic and behavioural factors in an international dataset of 12,300 men. PLoS One 2017; 12:e0187741. [PMID: 29281666 PMCID: PMC5744924 DOI: 10.1371/journal.pone.0187741] [Citation(s) in RCA: 28] [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: 06/12/2017] [Accepted: 10/25/2017] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Sex hormones have been implicated in the etiology of a number of diseases. To better understand disease etiology and the mechanisms of disease-risk factor associations, this analysis aimed to investigate the associations of anthropometric, sociodemographic and behavioural factors with a range of circulating sex hormones and sex hormone-binding globulin. METHODS Statistical analyses of individual participant data from 12,330 male controls aged 25-85 years from 25 studies involved in the Endogenous Hormones Nutritional Biomarkers and Prostate Cancer Collaborative Group. Analysis of variance was used to estimate geometric means adjusted for study and relevant covariates. RESULTS Older age was associated with higher concentrations of sex hormone-binding globulin and dihydrotestosterone and lower concentrations of dehydroepiandrosterone sulfate, free testosterone, androstenedione, androstanediol glucuronide and free estradiol. Higher body mass index was associated with higher concentrations of free estradiol, androstanediol glucuronide, estradiol and estrone and lower concentrations of dihydrotestosterone, testosterone, sex hormone-binding globulin, free testosterone, androstenedione and dehydroepiandrosterone sulfate. Taller height was associated with lower concentrations of androstenedione, testosterone, free testosterone and sex hormone-binding globulin and higher concentrations of androstanediol glucuronide. Current smoking was associated with higher concentrations of androstenedione, sex hormone-binding globulin and testosterone. Alcohol consumption was associated with higher concentrations of dehydroepiandrosterone sulfate, androstenedione and androstanediol glucuronide. East Asians had lower concentrations of androstanediol glucuronide and African Americans had higher concentrations of estrogens. Education and marital status were modestly associated with a small number of hormones. CONCLUSION Circulating sex hormones in men are strongly associated with age and body mass index, and to a lesser extent with smoking status and alcohol consumption.
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Affiliation(s)
- Eleanor L. Watts
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Paul N. Appleby
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, United States of America
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, United States of America
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, CA, United States of America
- Department of Urology, University of California-San Francisco, San Francisco, CA, United States of America
| | - Chu Chen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Piera M. Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, CA, United States of America
| | - Barbara A. Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA, United States of America
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, United States of America
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Luigi Ferrucci
- Intramural Research Program, National Institute on Aging, Bethesda, MD, United States of America
| | - Cedric F. Garland
- Department of Family Medicine and Public Health, University of California, San Diego, CA, United States of America
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Laurel A. Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jeff M. P. Holly
- School of Clinical Sciences, Faculty of Health Science, University of Bristol, Bristol, United Kingdom
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, United States of America
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Paul Knekt
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Laurence N. Kolonel
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States of America
| | - Tatsuhiko Kubo
- Department of Public Health, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Loïc Le Marchand
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States of America
| | - Tapio Luostarinen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Robert J. MacInnis
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Hanna O. Mäenpää
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - E. Jeffrey Metter
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Abraham M. Y. Nomura
- Japan-Hawaii Cancer Study, Kuakini Medical Center, Honolulu, HI, United States of America
| | - Steven E. Oliver
- Department of Health Sciences, University of York, York, United Kingdom
| | - J. Kellogg Parsons
- Division of Urologic Oncology, University of California San Diego Moores Cancer Center, San Diego, CA, United States of America
| | - Petra H. Peeters
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | - Elizabeth A. Platz
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Fulvio Ricceri
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
- Unit of Epidemiology, Regional Health Service ASL TO3, Grugliasco, Italy
| | - Sabina Rinaldi
- Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Harri Rissanen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Catherine A. Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, United States of America
| | - Jeannette M. Schenk
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Frank Z. Stanczyk
- Division of Reproductive Endocrinology and Infertility, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States of America
| | - Meir Stampfer
- Departments of Nutrition and Epidemiology, Harvard University T.H. Chan School of Public Health, Boston, MA, United States of America
- The Channing Division of Network Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Pär Stattin
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, Medicum, University of Helsinki, Helsinki, Finland
| | - Anne Tjønneland
- Department of Diet, Genes and Environment, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Ian M. Thompson
- CHRISTUS Medical Center Hospital, San Antonio, TX, United States of America
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Lars Vatten
- Department of Public Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, United States of America
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States of America
| | - Regina G. Ziegler
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, MD, United States of America
| | - Naomi E. Allen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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27
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Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nat Commun 2017; 8:48. [PMID: 28663546 PMCID: PMC5491529 DOI: 10.1038/s41467-017-00046-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/13/2017] [Accepted: 04/28/2017] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate heritable facilitators of somatic genomic events in the context of the androgen receptor signaling. Here, we use a ranking score and benign prostate transcriptomes to identify a non-coding polymorphic regulatory element at 7p14.3 that associates with DNA repair and hormone-regulated transcript levels and with an early recurrent prostate cancer-specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene. The locus shows allele-specific activity that is concomitantly modulated by androgen receptor and by CCAAT/enhancer-binding protein (C/EBP) beta (CEBPB). Deletion of this locus via CRISPR-Cas9 leads to deregulation of the genes predicted to interact with the 7p14.3 locus by Hi-C chromosome conformation capture data. This study suggests that a polymorphism at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone-dependent DNA damage response. Prostate cancer is a heterogeneous disease, and many cases show somatic mutations of SPOP. Here, the authors show that a non-coding polymorphic regulatory element at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone dependent DNA damage response.
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Affiliation(s)
- Alessandro Romanel
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Sonia Garritano
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Blerta Stringa
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Mirjam Blattner
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Davide Dalfovo
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Dimple Chakravarty
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - David Soong
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kellie A Cotter
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - Gianluca Petris
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Paola Gasperini
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Anna Cereseto
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - Ekta Khurana
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Alberto Inga
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy. .,Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.
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28
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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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29
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Luef B, Handle F, Kharaishvili G, Hager M, Rainer J, Janetschek G, Hruby S, Englberger C, Bouchal J, Santer FR, Culig Z. The AR/NCOA1 axis regulates prostate cancer migration by involvement of PRKD1. Endocr Relat Cancer 2016; 23:495-508. [PMID: 27255895 DOI: 10.1530/erc-16-0160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 12/25/2022]
Abstract
Due to the urgent need for new prostate cancer (PCa) therapies, the role of androgen receptor (AR)-interacting proteins should be investigated. In this study we aimed to address whether the AR coactivator nuclear receptor coactivator 1 (NCOA1) is involved in PCa progression. Therefore, we tested the effect of long-term NCOA1 knockdown on processes relevant to metastasis formation. [(3)H]-thymidine incorporation assays revealed a reduced proliferation rate in AR-positive MDA PCa 2b and LNCaP cells upon knockdown of NCOA1, whereas AR-negative PC3 cells were not affected. Furthermore, Boyden chamber assays showed a strong decrease in migration and invasion upon NCOA1 knockdown, independently of the cell line's AR status. In order to understand the mechanistic reasons for these changes, transcriptome analysis using cDNA microarrays was performed. Protein kinase D1 (PRKD1) was found to be prominently up-regulated by NCOA1 knockdown in MDA PCa 2b, but not in PC3 cells. Inhibition of PRKD1 reverted the reduced migratory potential caused by NCOA1 knockdown. Furthermore, PRKD1 was negatively regulated by AR. Immunohistochemical staining of PCa patient samples revealed a strong increase in NCOA1 expression in primary tumors compared with normal prostate tissue, while no final conclusion could be drawn for PRKD1 expression in tumor specimens. Thus, our findings directly associate the AR/NCOA1 complex with PRKD1 regulation and cellular migration and support the concept of therapeutic inhibition of NCOA1 in PCa.
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Affiliation(s)
- Birgit Luef
- Division of Experimental UrologyDepartment of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Handle
- Division of Experimental UrologyDepartment of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gvantsa Kharaishvili
- Department of Clinical and Molecular Pathology and Institute of Molecular and Translational MedicineFaculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Martina Hager
- Department of PathologyParacelsus Medical University, Salzburg, Austria
| | - Johannes Rainer
- Division of Molecular PathophysiologyBiocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Günter Janetschek
- Department of UrologyParacelsus Medical University, Salzburg, Austria
| | - Stephan Hruby
- Department of UrologyParacelsus Medical University, Salzburg, Austria
| | | | - Jan Bouchal
- Department of Clinical and Molecular Pathology and Institute of Molecular and Translational MedicineFaculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Frédéric R Santer
- Division of Experimental UrologyDepartment of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zoran Culig
- Division of Experimental UrologyDepartment of Urology, Medical University of Innsbruck, Innsbruck, Austria
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30
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Nurminen R, Rantapero T, Wong SC, Fischer D, Lehtonen R, Tammela TL, Nykter M, Visakorpi T, Wahlfors T, Schleutker J. Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifiesDGAT2as a new target gene. Genes Chromosomes Cancer 2016; 55:661-73. [DOI: 10.1002/gcc.22368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/17/2016] [Accepted: 04/20/2016] [Indexed: 01/17/2023] Open
Affiliation(s)
- Riikka Nurminen
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere University Hospital; Tampere Finland
| | - Tommi Rantapero
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere University Hospital; Tampere Finland
| | - Swee C. Wong
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Daniel Fischer
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere University Hospital; Tampere Finland
| | - Rainer Lehtonen
- Institute of Biomedicine & Genome-Scale Biology Research Program, Faculty of Medicine, Biomedicum, University of Helsinki; Helsinki Finland
| | - Teuvo L.J. Tammela
- Department of Urology and Prostate Cancer Research Center; University of Tampere and Tampere University Hospital; Tampere Finland
| | - Matti Nykter
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
| | - Tapio Visakorpi
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere University Hospital; Tampere Finland
| | - Tiina Wahlfors
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere University Hospital; Tampere Finland
| | - Johanna Schleutker
- BioMediTech and Prostate Cancer Research Center; University of Tampere; Tampere Finland
- Department of Medical Biochemistry and Genetics; University of Turku; Turku Finland
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital; Turku Finland
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31
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Handle F, Erb HHH, Luef B, Hoefer J, Dietrich D, Parson W, Kristiansen G, Santer FR, Culig Z. SOCS3 Modulates the Response to Enzalutamide and Is Regulated by Androgen Receptor Signaling and CpG Methylation in Prostate Cancer Cells. Mol Cancer Res 2016; 14:574-85. [PMID: 27053681 DOI: 10.1158/1541-7786.mcr-15-0495] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/23/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED The proinflammatory cytokine IL6 is associated with bad prognosis in prostate cancer and implicated in progression to castration resistance. Suppressor of cytokine signaling 3 (SOCS3) is an IL6-induced negative feedback regulator of the IL6/Janus kinase (JAK)/STAT3 pathway. This study reveals that the SOCS3 promoter is hypermethylated in cancerous regions compared with adjacent benign tissue in prostate cancer using methylation-specific qPCR. A series of in vitro experiments was performed to assess the functional impact of low SOCS3 expression during anti-androgen treatment. Using lentivirus-mediated knockdown, it was demonstrated for the first time that SOCS3 regulates IL6/JAK/STAT3 signaling in androgen receptor-positive LNCaP cells. In addition, SOCS3 mRNA is upregulated by the anti-androgens bicalutamide and enzalutamide. This effect is caused by androgen receptor-mediated suppression of IL6ST and JAK1 expression, which leads to altered STAT3 signaling. Functionally, knockdown of SOCS3 led to enhanced androgen receptor activity after 3 weeks of enzalutamide treatment in an inflammatory setting. Furthermore, the stemness/self-renewal associated genes SOX2 and NANOG were strongly upregulated by the long-term treatment, and modulation of SOCS3 expression was sufficient to counteract this effect. These findings prove that SOCS3 plays an important role during anti-androgen treatment in an inflammatory environment. IMPLICATIONS SOCS3 is frequently inactivated by promoter hypermethylation in prostate cancer, which disrupts the feedback regulation of IL6 signaling and leads to reduced efficacy of enzalutamide in the presence of inflammatory cytokines. Mol Cancer Res; 14(6); 574-85. ©2016 AACR.
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Affiliation(s)
- Florian Handle
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Holger H H Erb
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria. Yorkshire Cancer Research Unit, University of York, York, United Kingdom
| | - Birgit Luef
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Julia Hoefer
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Frédéric R Santer
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Zoran Culig
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria.
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