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Orman MV, Sreekanth V, Laajala TD, Cramer SD, Costello JC. ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer. Front Pharmacol 2024; 15:1360352. [PMID: 38751776 PMCID: PMC11094266 DOI: 10.3389/fphar.2024.1360352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/13/2024] [Indexed: 05/18/2024] Open
Abstract
Background Prostate cancer is a leading cause of cancer-related deaths among men, marked by heterogeneous clinical and molecular characteristics. The complexity of the molecular landscape necessitates tools for identifying multi-gene co-alteration patterns that are associated with aggressive disease. The identification of such gene sets will allow for deeper characterization of the processes underlying prostate cancer progression and potentially lead to novel strategies for treatment. Methods We developed ProstaMine to systematically identify co-alterations associated with aggressiveness in prostate cancer molecular subtypes defined by high-fidelity alterations in primary prostate cancer. ProstaMine integrates genomic, transcriptomic, and clinical data from five primary and one metastatic prostate cancer cohorts to prioritize co-alterations enriched in metastatic disease and associated with disease progression. Results Integrated analysis of primary tumors defined a set of 17 prostate cancer alterations associated with aggressive characteristics. We applied ProstaMine to NKX3-1-loss and RB1-loss tumors and identified subtype-specific co-alterations associated with metastasis and biochemical relapse in these molecular subtypes. In NKX3-1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations known to regulate prostate cancer signaling pathways including MAPK, NF-kB, p53, PI3K, and Sonic hedgehog. In RB1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations involved in p53, STAT6, and MHC class I antigen presentation. Co-alterations impacting autophagy were noted in both molecular subtypes. Conclusion ProstaMine is a method to systematically identify novel subtype-specific co-alterations associated with aggressive characteristics in prostate cancer. The results from ProstaMine provide insights into potential subtype-specific mechanisms of prostate cancer progression which can be formed into testable experimental hypotheses. ProstaMine is publicly available at: https://bioinformatics.cuanschutz.edu/prostamine.
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Affiliation(s)
- Michael V. Orman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Teemu D. Laajala
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Scott D. Cramer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - James C. Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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2
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Ermis Akyuz E, Bell SM. The Diverse Role of CUB and Sushi Multiple Domains 1 (CSMD1) in Human Diseases. Genes (Basel) 2022; 13:genes13122332. [PMID: 36553598 PMCID: PMC9778380 DOI: 10.3390/genes13122332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
CUB and Sushi Multiple Domains 1 (CSMD1), a tumour suppressor gene, encodes a large membrane-bound protein including a single transmembrane domain. This transmembrane region has a potential tyrosine phosphorylation site, suggesting that CSMD1 is involved in controlling cellular functions. Although the specific mechanisms of action for CSMD1 have not yet been uncovered, it has been linked to a number of processes including development, complement control, neurodevelopment, and cancer progression. In this review, we summarise CSMD1 functions in the cellular processes involved in the complement system, metastasis, and Epithelial mesenchymal transition (EMT) and also in the diseases schizophrenia, Parkinson's disease, and cancer. Clarifying the association between CSMD1 and the aforementioned diseases will contribute to the development of new diagnosis and treatment methods for these diseases. Recent studies in certain cancer types, e.g., gastric cancer, oesophageal cancer, and head and neck squamous cell carcinomas, have indicated the involvement of CSMD1 in response to immunotherapy.
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3
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Sakellakis M, Flores L, Ramachandran S. Patterns of indolence in prostate cancer (Review). Exp Ther Med 2022; 23:351. [PMID: 35493432 PMCID: PMC9019743 DOI: 10.3892/etm.2022.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
Although prostate cancer is a major cause of cancer-related mortality worldwide, most patients will have a relatively indolent clinical course. Contrary to most other types of cancer, even the diagnosis of locally advanced or metastatic disease is not always lethal. The present review aimed to summarize what is known regarding the underlying mechanisms related to the indolent course of subsets of prostate cancer, at various stages. The data suggested that no specific gene alteration by itself was responsible for carcinogenesis or disease aggressiveness. However, pathway analysis identified genetic aberrations in multiple critical pathways that tend to accumulate over the course of the disease. The progression from indolence into aggressive disease is associated with a complex interplay in which genetic and epigenetic factors are involved. The effect of the immune tumor microenvironment is also very important. Emerging evidence has suggested that the upregulation of pathways related to cellular aging and senescence can identify patients with indolent disease. In addition, a number of tumors enter a long-lasting quiescent state. Further research will determine whether halting tumor evolution is a feasible option, and whether the life of patients can be markedly prolonged by inducing tumor senescence or long-term dormancy.
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Affiliation(s)
- Minas Sakellakis
- Fourth Oncology Department and Comprehensive Clinical Trials Center, Metropolitan Hospital, 18547 Athens, Greece
| | - Laura Flores
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, University of Texas, Houston, TX 77025, USA
| | - Sumankalai Ramachandran
- Department of Genitourinary Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX 77025, USA
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4
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Involvement of the MEN1 Gene in Hormone-Related Cancers: Clues from Molecular Studies, Mouse Models, and Patient Investigations. ENDOCRINES 2020. [DOI: 10.3390/endocrines1020007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MEN1 mutation predisposes patients to multiple endocrine neoplasia type 1 (MEN1), a genetic syndrome associated with the predominant co-occurrence of endocrine tumors. Intriguingly, recent evidence has suggested that MEN1 could also be involved in the development of breast and prostate cancers, two major hormone-related cancers. The first clues as to its possible role arose from the identification of the physical and functional interactions between the menin protein, encoded by MEN1, and estrogen receptor α and androgen receptor. In parallel, our team observed that aged heterozygous Men1 mutant mice developed cancerous lesions in mammary glands of female and in the prostate of male mutant mice at low frequencies, in addition to endocrine tumors. Finally, observations made both in MEN1 patients and in sporadic breast and prostate cancers further confirmed the role played by menin in these two cancers. In this review, we present the currently available data concerning the complex and multifaceted involvement of MEN1 in these two types of hormone-dependent cancers.
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5
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Kamel MG, Istanbuly S, Abd-Elhay FAE, Mohamed MYF, Huu-Hoai L, Sadik M, Dibas M, Huy NT. Examined and Positive Lymph Node Counts Are Associated with Mortality in Prostate Cancer: A Population-Based Analysis. Urol Int 2020; 104:699-709. [PMID: 32268338 DOI: 10.1159/000505410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/11/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is the third leading cause of death from cancer in the United States. We aimed to disclose the prognostic values of examined (dissected) lymph node (ELN), negative lymph node (NLN), and positive (metastatic) lymph node (PLN) counts and lymph node (LNs) ratio in PCa patients. METHODS We extracted data of PCa patients diagnosed between 2004 and 2015 from the Surveillance, Epidemiology, and End Results (SEER) program. We included patients with a histologically confirmed diagnosis having at least one ELN and with the PCa as the primary tumor only. RESULTS We have included 96,064 patients. Multivariable Cox proportional hazards regression modelsdisclosed that patients having more ELNs were associated with better survival. However, we demonstrated that patients having more PLNs were associated with worse survival. Additionally, older age, unmarried patients, with Gleason's score of 8-10, T4 and M1 stages and those who received chemotherapy and/or radiation but did not receive surgery were significantly associated with worse PCa survival. CONCLUSIONS We have disclosed several independent predictors affecting PCa patients including age, marital status, Gleason's score, T and N stages, having received therapy, surgery, and ELN and PLN counts. Moreover, we demonstrated that patients with lower ELN and higher PLN counts were a high-risk group. We strongly recommend adding the ELN and/or PLN counts into consideration during patient staging/treatment.
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Affiliation(s)
- Mohamed Gomaa Kamel
- Faculty of Medicine, Minia University, Minia, Egypt.,Online Research Club, Nagasaki, Japan
| | - Sedralmontaha Istanbuly
- Online Research Club, Nagasaki, Japan.,Faculty of Medicine, University of Aleppo, Aleppo, Syrian Arab Republic
| | | | | | - Le Huu-Hoai
- Online Research Club, Nagasaki, Japan.,Saigon General Hospital, Ho Chi Minh, Vietnam
| | - Mohamed Sadik
- Online Research Club, Nagasaki, Japan.,Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Mahmoud Dibas
- Online Research Club, Nagasaki, Japan.,Sulaiman Al Rajhi Colleges, Al Bukayriya, Saudi Arabia
| | - Nguyen Tien Huy
- Department of Clinical Product Development, Institute of Tropical Medicine (NEKKEN), School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan, .,Evidence Based Medicine Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh, Vietnam,
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6
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Xu Z, Ma T, Zhou J, Gao W, Li Y, Yu S, Wang Y, Chan FL. Nuclear receptor ERRα contributes to castration-resistant growth of prostate cancer via its regulation of intratumoral androgen biosynthesis. Theranostics 2020; 10:4201-4216. [PMID: 32226548 PMCID: PMC7086365 DOI: 10.7150/thno.35589] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 02/17/2020] [Indexed: 12/29/2022] Open
Abstract
Enhanced intratumoral androgen biosynthesis and persistent androgen receptor (AR) signaling are key factors responsible for the relapse growth of castration-resistant prostate cancer (CRPC). Residual intraprostatic androgens can be produced by de novo synthesis of androgens from cholesterol or conversion from adrenal androgens by steroidogenic enzymes expressed in prostate cancer cells via different steroidogenic pathways. However, the dysregulation of androgen biosynthetic enzymes in CRPC still remains poorly understood. This study aims to elucidate the role of the nuclear receptor, estrogen-related receptor alpha (ERRα, ESRRA), in the promotion of androgen biosynthesis in CRPC growth. Methods: ERRα expression in CRPC patients was analyzed using Gene Expression Omnibus (GEO) datasets and validated in established CRPC xenograft model. The roles of ERRα in the promotion of castration-resistant growth were elucidated by overexpression and knockdown studies and the intratumoral androgen levels were measured by UPLC-MS/MS. The effect of suppression of ERRα activity in the potentiation of sensitivity to androgen-deprivation was determined using an ERRα inverse agonist. Results: ERRα exhibited an increased expression in metastatic CRPC and CRPC xenograft model, could act to promote castration-resistant growth via direct transactivation of two key androgen synthesis enzymes CYP11A1 and AKR1C3, and hence enhance intraprostatic production of dihydrotestosterone (DHT) and activation of AR signaling in prostate cancer cells. Notably, inhibition of ERRα activity by an inverse agonist XCT790 could reduce the DHT production and suppress AR signaling in prostate cancer cells. Conclusion: Our study reveals a new role of ERRα in the intratumoral androgen biosynthesis in CRPC via its transcriptional control of steroidogenic enzymes, and also provides a novel insight that targeting ERRα could be a potential androgen-deprivation strategy for the management of CRPC.
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Affiliation(s)
- Zhenyu Xu
- Precision Medicine Centre, Yijishan Affiliated Hospital of Wannan Medical College, Wuhu, Anhui Province, PR China
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Taiyang Ma
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Jianfu Zhou
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
- Department of Urology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weijie Gao
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Youjia Li
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Shan Yu
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Yuliang Wang
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Franky Leung Chan
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
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7
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Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci 2019; 20:ijms20194711. [PMID: 31547595 PMCID: PMC6801775 DOI: 10.3390/ijms20194711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype-phenotype.
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8
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Das R, Feng FY, Selth LA. Long non-coding RNAs in prostate cancer: Biological and clinical implications. Mol Cell Endocrinol 2019; 480:142-152. [PMID: 30391670 DOI: 10.1016/j.mce.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/12/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022]
Abstract
Prostate cancer (PCa) is a major health issue in the Western world. Current clinical imperatives for this disease include better stratification of indolent versus aggressive disease to enable improved patient management, as well as the identification of more effective therapies for the prevention and treatment of metastatic and therapy-resistant PCa. The advent of next-generation transcriptomics led to the identification of an important class of molecules, long non-coding RNAs (lncRNAs). LncRNAs have critical functions in normal physiology, but their dysregulation has also been implicated in the development and progression of a variety of cancers, including PCa. Importantly, a subset of lncRNAs are highly prostate-specific, suggesting potential for utility as both biomarkers and therapeutic targets. In this review, we summarise the biology of lncRNAs and their mechanisms of action in the development and progression of prostate cancer. Additionally, we cast a critical eye over the potential for this class of molecules to impact on clinical practice.
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Affiliation(s)
- Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, USA.
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, USA; Department of Urology, University of California San Francisco, USA
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Freemasons Foundation Centre for Men's Health, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.
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9
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Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy. J Urol 2018; 199:719-725. [DOI: 10.1016/j.juro.2017.09.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 11/24/2022]
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10
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Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. Oncotarget 2018; 7:68688-68707. [PMID: 27626693 PMCID: PMC5356583 DOI: 10.18632/oncotarget.11925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/24/2016] [Indexed: 12/27/2022] Open
Abstract
To understand the heterogeneity of prostate cancer (PCa) and identify novel underlying drivers, we constructed integrative molecular Bayesian networks (IMBNs) for PCa by integrating gene expression and copy number alteration data from published datasets. After demonstrating such IMBNs with superior network accuracy, we identified multiple sub-networks within IMBNs related to biochemical recurrence (BCR) of PCa and inferred the corresponding key drivers. The key drivers regulated a set of common effectors including genes preferentially expressed in neuronal cells. NLGN4Y—a protein involved in synaptic adhesion in neurons—was ranked as the top gene closely linked to key drivers of myogenesis subnetworks. Lower expression of NLGN4Y was associated with higher grade PCa and an increased risk of BCR. We show that restoration of the protein expression of NLGN4Y in PC-3 cells leads to decreased cell proliferation, migration and inflammatory cytokine expression. Our results suggest that NLGN4Y is an important negative regulator in prostate cancer progression. More importantly, it highlights the value of IMBNs in generating biologically and clinically relevant hypotheses about prostate cancer that can be validated by independent studies.
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11
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Nowinski S, Santaolalla A, O'Leary B, Loda M, Mirchandani A, Emberton M, Van Hemelrijck M, Grigoriadis A. Systematic identification of functionally relevant risk alleles to stratify aggressive versus indolent prostate cancer. Oncotarget 2018; 9:12812-12824. [PMID: 29560112 PMCID: PMC5849176 DOI: 10.18632/oncotarget.24400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
Novel approaches for classification, including molecular features, are needed to direct therapy for men with low-grade prostate cancer (PCa), especially men on active surveillance. Risk alleles identified from genome-wide association studies (GWAS) could improve prognostication. Those risk alleles that coincided with genes and somatic copy number aberrations associated with progression of PCa were selected as the most relevant for prognostication. In a systematic literature review, a total of 698 studies were collated. Fifty-three unique SNPs residing in 29 genomic regions, including 8q24, 10q11 and 19q13, were associated with PCa progression. Functional studies implicated 21 of these single nucleotide polymorphisms (SNPs) as modulating the expression of genes in the androgen receptor pathway and several other oncogenes. In particular, 8q24, encompassing MYC, harbours a high density of SNPs conferring unfavourable pathological characteristics in low-grade PCa, while a copy number gain of MYC in low-grade PCa was associated with prostate-specific antigen recurrence after radical prostatectomy. By combining GWAS data with gene expression and structural rearrangements, risk alleles were identified that could provide a new basis for developing a prognostication tool to guide therapy for men with early prostate cancer.
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Affiliation(s)
- Salpie Nowinski
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Aida Santaolalla
- Translational Oncology & Urology Research, King's College London, London, UK
| | - Ben O'Leary
- Breast Cancer NOW Centre, The Institute of Cancer Research, The Royal Marsden Hospital, London, UK
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ayesha Mirchandani
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Mark Emberton
- Division of Surgery and Interventional Science, University College London, London, UK
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
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12
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Clinton TN, Bagrodia A, Lotan Y, Margulis V, Raj GV, Woldu SL. Tissue-based biomarkers in prostate cancer. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017; 2:249-260. [PMID: 29226251 PMCID: PMC5722240 DOI: 10.1080/23808993.2017.1372687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Prostate cancer is a heterogeneous disease. Existing risk stratification tools based on standard clinlicopathologic variables (prostate specific antigen [PSA], Gleason score, and tumor stage) provide a modest degree of predictive ability. Advances in high-throughput sequencing has led to the development of several novel tissue-based biomarkers that can improve prognostication in prostate cancer management. AREAS COVERED The authors review commercially-available, tissue-based biomarker assays that improve upon existing risk-stratification tools in several areas of prostate cancer management, including the appropriateness of active surveillance and aiding in decision making regarding the use of adjuvant therapy. Additionally, some of the obstacles to the widespread adoption of these biomarkers and discuss several investigational sources of new biomarkers are discussed. EXPERT COMMENTARY Work is ongoing to answer pertinent clinical questions in prostate cancer management including which patients should undergo biopsy, active surveillance, receive adjuvant therapy, and what systemic therapy is best in the first-line. Incorporation into novel biomarkers may allow for the incorporation of a 'personalized' approach to management. Further validation will be required and questions of cost must be considered before wide scale adoption of these biomarkers. Tumor heterogeneity may impose a ceiling on the prognostic ability of biomarkers using currently available techniques.
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Affiliation(s)
- Timothy N Clinton
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
| | - Aditya Bagrodia
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
| | - Yair Lotan
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
| | - Vitaly Margulis
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
| | - Ganesh V Raj
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
| | - Solomon L Woldu
- University of Texas Southwestern Medical Center, Department of Urology, Dallas, Texas
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13
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Kamal M, Holliday DL, Morrison EE, Speirs V, Toomes C, Bell SM. Loss of CSMD1 expression disrupts mammary duct formation while enhancing proliferation, migration and invasion. Oncol Rep 2017; 38:283-292. [PMID: 28534981 DOI: 10.3892/or.2017.5656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
The CUB and sushi multiple domains 1 (CSMD1) gene maps to chromosome 8p23, a region deleted in many cancers. Loss of CSMD1 expression is associated with poor prognosis in breast cancer suggesting that it acts as a tumour suppressor in this cancer. However, the function of CSMD1 is largely unknown. Herein, we investigated CSMD1 functions in cell line models. CSMD1 expression was suppressed in MCF10A and LNCaP cells using short hairpin RNA. Functional assays were performed focusing on the 'normal' MCF10A cell line. Suppression of CSMD1 significantly increased the proliferation, cell migration and invasiveness of MCF10A cells compared to shcontrols. shCSMD1 cells also showed significantly reduced adhesion to Matrigel and fibronectin. In a three-dimensional Matrigel model of MCF10A cells, reduced CSMD1 expression resulted in the development of larger and more poorly differentiated breast acini-like structures that displayed impaired lumen formation. Loss of CSMD1 expression disrupts a model of mammary duct formation while enhancing proliferation, migration and invasion. Our data suggest that CSMD1 is involved in the suppression of a transformed phenotype.
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Affiliation(s)
- Mohamed Kamal
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Deborah L Holliday
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Valerie Speirs
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Sandra M Bell
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
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14
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Gao G, Johnson SH, Vasmatzis G, Pauley CE, Tombers NM, Kasperbauer JL, Smith DI. Common fragile sites (CFS) and extremely large CFS genes are targets for human papillomavirus integrations and chromosome rearrangements in oropharyngeal squamous cell carcinoma. Genes Chromosomes Cancer 2016; 56:59-74. [PMID: 27636103 DOI: 10.1002/gcc.22415] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 01/04/2023] Open
Abstract
Common fragile sites (CFS) are chromosome regions that are prone to form gaps or breaks in response to DNA replication stress. They are often found as hotspots for sister chromatid exchanges, deletions, and amplifications in different cancers. Many of the CFS regions are found to span genes whose genomic sequence is greater than 1 Mb, some of which have been demonstrated to function as important tumor suppressors. CFS regions are also hotspots for human papillomavirus (HPV) integrations in cervical cancer. We used mate-pair sequencing to examine HPV integration events and chromosomal structural variations in 34 oropharyngeal squamous cell carcinoma (OPSCC). We used endpoint PCR and Sanger sequencing to validate each HPV integration event and found HPV integrations preferentially occurred within CFS regions similar to what is observed in cervical cancer. We also found that many of the chromosomal alterations detected also occurred at or near the cytogenetic location of CFSs. Several large genes were also found to be recurrent targets of rearrangements, independent of HPV integrations, including CSMD1 (2.1Mb), LRP1B (1.9Mb), and LARGE1 (0.7Mb). Sanger sequencing revealed that the nucleotide sequences near to identified junction sites contained repetitive and AT-rich sequences that were shown to have the potential to form stem-loop DNA secondary structures that might stall DNA replication fork progression during replication stress. This could then cause increased instability in these regions which could lead to cancer development in human cells. Our findings suggest that CFSs and some specific large genes appear to play important roles in OPSCC. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN
| | - Sarah H Johnson
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - George Vasmatzis
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | - David I Smith
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN
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Abstract
Although most prostate cancer (PCa) cases are not life-threatening, approximately 293 000 men worldwide die annually due to PCa. These lethal cases are thought to be caused by coordinated genomic alterations that accumulate over time. Recent genome-wide analyses of DNA from subjects with PCa have revealed most, if not all, genetic changes in both germline and PCa tumor genomes. In this article, I first review the major, somatically acquired genomic characteristics of various subtypes of PCa. I then recap key findings on the relationships between genomic alterations and clinical parameters, such as biochemical recurrence or clinical relapse, metastasis and cancer-specific mortality. Finally, I outline the need for, and challenges with, validation of recent findings in prospective studies for clinical utility. It is clearer now than ever before that the landscape of somatically acquired aberrations in PCa is highlighted by DNA copy number alterations (CNAs) and TMPRSS2-ERG fusion derived from complex rearrangements, numerous single nucleotide variations or mutations, tremendous heterogeneity, and continuously punctuated evolution. Genome-wide CNAs, PTEN loss, MYC gain in primary tumors, and TP53 loss/mutation and AR amplification/mutation in advanced metastatic PCa have consistently been associated with worse cancer prognosis. With this recently gained knowledge, it is now an opportune time to develop DNA-based tests that provide more accurate patient stratification for prediction of clinical outcome, which will ultimately lead to more personalized cancer care than is possible at present.
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Affiliation(s)
- Wennuan Liu
- Program for Personalized Cancer Care, Research Institute, NorthShore University HealthSystem, Evanston, IL, USA
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16
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Abstract
Although prostate cancer is the most common malignancy to affect men in the Western world, the molecular mechanisms underlying its development and progression remain poorly understood. Like all cancers, prostate cancer is a genetic disease that is characterized by multiple genomic alterations, including point mutations, microsatellite variations, and chromosomal alterations such as translocations, insertions, duplications, and deletions. In prostate cancer, but not other carcinomas, these chromosome alterations result in a high frequency of gene fusion events. The development and application of novel high-resolution technologies has significantly accelerated the detection of genomic alterations, revealing the complex nature and heterogeneity of the disease. The clinical heterogeneity of prostate cancer can be partly explained by this underlying genetic heterogeneity, which has been observed between patients from different geographical and ethnic populations, different individuals within these populations, different tumour foci within the same patient, and different cells within the same tumour focus. The highly heterogeneous nature of prostate cancer provides a real challenge for clinical disease management and a detailed understanding of the genetic alterations in all cells, including small subpopulations, would be highly advantageous.
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Nordström T, Van Blarigan EL, Ngo V, Roy R, Weinberg V, Song X, Simko J, Carroll PR, Chan JM, Paris PL. Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer. Prostate 2016; 76:339-48. [PMID: 26585352 PMCID: PMC5493324 DOI: 10.1002/pros.23125] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/05/2015] [Indexed: 11/11/2022]
Abstract
BACKGROUND Carotenoids are a class of nutrients with antioxidant properties that have been purported to protect against cancer. However, the reported associations between carotenoids and prostate cancer have been heterogeneous and lacking data on interactions with nucleotide sequence variations and genomic biomarkers. OBJECTIVE To examine the associations between carotenoid levels and the risk of high-grade prostate cancer, also considering antioxidant-related genes and tumor instability. METHODS We measured plasma levels of carotenoids and genotyped 20 single nucleotide polymorphisms (SNP) in SOD1, SOD2, SOD3, XRCC1, and OGG1 among 559 men with non-metastatic prostate cancer undergoing radical prostatectomy. We performed copy number analysis in a subset of these men (n = 67) to study tumor instability assessed as Fraction of the Genome Altered (FGA). We examined associations between carotenoids, genotypes, tumor instability and risk of high-grade prostate cancer (Gleason grade ≥ 4 + 3) using logistic and linear regression. RESULTS Circulating carotenoid levels were inversely associated with the risk of high-grade prostate cancer; odds ratios (OR) and 95% confidence intervals (CI) comparing highest versus lowest quartiles were: 0.34 (95% CI: 0.18-0.66) for α-carotene, 0.31 (95% CI: 0.15-0.63) for β-carotene, 0.55 (0.28-1.08) for lycopene and 0.37 (0.18-0.75) for total carotenoids. SNPs rs25489 in XRCC1, rs699473 in SOD3 and rs1052133 in OGG1 modified these associations for α-carotene, β-carotene and lycopene, respectively (P ≤ 0.05). The proportion of men with a high degree of FGA increased with Gleason Score (P < 0.001). Among men with Gleason score ≤ 3 + 4, higher lycopene levels were associated with lower FGA (P = 0.04). CONCLUSION Circulating carotenoids at diagnosis, particularly among men carrying specific somatic variations, were inversely associated with risk of high-grade prostate cancer. In exploratory analyses, higher lycopene level was associated with less genomic instability among men with low-grade disease which is novel and supports the hypothesis that lycopene may inhibit progression of prostate cancer early in its natural history.
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Affiliation(s)
- Tobias Nordström
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Erin L. Van Blarigan
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Vy Ngo
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
| | - Ritu Roy
- Computational Biology Core, Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Vivian Weinberg
- Biostatistics Core, Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Xiaoling Song
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeffry Simko
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
- Department of Pathology, University of California, San Francisco, California
| | - Peter R. Carroll
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
| | - June M. Chan
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Pamela L. Paris
- Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, University of California, San Francisco, California
- Correspondence to: Pamela L. Paris, Department of Urology, Helen Diller Family Comprehensive Cancer Research Center, UCSF Box 3110, 1450 3rd Street (Rm HD384), San Francisco, CA 94158.
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18
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Lindquist KJ, Paris PL, Hoffmann TJ, Cardin NJ, Kazma R, Mefford JA, Simko JP, Ngo V, Chen Y, Levin AM, Chitale D, Helfand BT, Catalona WJ, Rybicki BA, Witte JS. Mutational Landscape of Aggressive Prostate Tumors in African American Men. Cancer Res 2016; 76:1860-8. [PMID: 26921337 DOI: 10.1158/0008-5472.can-15-1787] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/31/2015] [Indexed: 12/20/2022]
Abstract
Prostate cancer is the most frequently diagnosed and second most fatal nonskin cancer among men in the United States. African American men are two times more likely to develop and die of prostate cancer compared with men of other ancestries. Previous whole genome or exome tumor-sequencing studies of prostate cancer have primarily focused on men of European ancestry. In this study, we sequenced and characterized somatic mutations in aggressive (Gleason ≥7, stage ≥T2b) prostate tumors from 24 African American patients. We describe the locations and prevalence of small somatic mutations (up to 50 bases in length), copy number aberrations, and structural rearrangements in the tumor genomes compared with patient-matched normal genomes. We observed several mutation patterns consistent with previous studies, such as large copy number aberrations in chromosome 8 and complex rearrangement chains. However, TMPRSS2-ERG gene fusions and PTEN losses occurred in only 21% and 8% of the African American patients, respectively, far less common than in patients of European ancestry. We also identified mutations that appeared specific to or more common in African American patients, including a novel CDC27-OAT gene fusion occurring in 17% of patients. The genomic aberrations reported in this study warrant further investigation of their biologic significant role in the incidence and clinical outcomes of prostate cancer in African Americans. Cancer Res; 76(7); 1860-8. ©2016 AACR.
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Affiliation(s)
- Karla J Lindquist
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Pamela L Paris
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California. Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Niall J Cardin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rémi Kazma
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jeffrey P Simko
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Vy Ngo
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Yalei Chen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Dhananjay Chitale
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Brian T Helfand
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - William J Catalona
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California. Department of Urology, University of California San Francisco, San Francisco, California. Institute for Human Genetics, University of California San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California.
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19
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Takayama KI, Inoue S. The emerging role of noncoding RNA in prostate cancer progression and its implication on diagnosis and treatment. Brief Funct Genomics 2015; 15:257-65. [DOI: 10.1093/bfgp/elv057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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20
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Biomarkers for prostate cancer: present challenges and future opportunities. Future Sci OA 2015; 2:FSO72. [PMID: 28031932 PMCID: PMC5137959 DOI: 10.4155/fso.15.72] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 01/30/2023] Open
Abstract
Prostate cancer (PCa) has variable biological potential with multiple treatment options. A more personalized approach, therefore, is needed to better define men at higher risk of developing PCa, discriminate indolent from aggressive disease and improve risk stratification after treatment by predicting the likelihood of progression. This may improve clinical decision-making regarding management, improve selection for active surveillance protocols and minimize morbidity from treatment. Discovery of new biomarkers associated with prostate carcinogenesis present an opportunity to provide patients with novel genetic signatures to better understand their risk of developing PCa and help forecast their clinical course. In this review, we examine the current literature evaluating biomarkers in PCa. We also address current limitations and present several ideas for future studies.
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21
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The Molecular Taxonomy of Primary Prostate Cancer. Cell 2015; 163:1011-25. [PMID: 26544944 PMCID: PMC4695400 DOI: 10.1016/j.cell.2015.10.025] [Citation(s) in RCA: 2175] [Impact Index Per Article: 241.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/14/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022]
Abstract
There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1 mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner, with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects.
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22
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Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MHW, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet 2015; 47:736-45. [PMID: 26005866 DOI: 10.1038/ng.3315] [Citation(s) in RCA: 350] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/01/2015] [Indexed: 12/12/2022]
Abstract
Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We initially determined the copy number aberration (CNA) profiles of 74 patients with index tumors of Gleason score 7. Of these, 5 patients were subjected to whole-genome sequencing using DNA quantities achievable in diagnostic biopsies, with detailed spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity in focal genomics. Multifocal tumors are highly heterogeneous for single-nucleotide variants (SNVs), CNAs and genomic rearrangements. We identified and validated a new recurrent amplification of MYCL, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation. Moreover, we demonstrate divergent tumor evolution in multifocal cancer and, in some cases, tumors of independent clonal origin. These data represent the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome and inform the development of novel biomarkers that reflect individual prognosis.
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Affiliation(s)
- Paul C Boutros
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Dominique Trudel
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Emilie Lalonde
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alice Meng
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Amin Zia
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Natalie S Fox
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timothy A Beck
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cherry L Have
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Taryne Chong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle Sam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Ada Wong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trent T Simmons
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christine P'ng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gaetano Zafarana
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Francis Nguyen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Xuemei Luo
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kenneth C Chu
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Jenna Sykes
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alan Dal Pra
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Berlin
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Brown
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Lauren C Chong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gregory M Chen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Esther Jung
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Clement Fung
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Hanbo Chen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - James Hawley
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alister D'Costa
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melania Pintilie
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daryl Waggott
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faraz Hach
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Philippe Lambin
- Department of Radiotherapy, Maastricht University, Maastricht, the Netherlands
| | | | - Colin Cooper
- 1] Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK. [2] Department of Biological Sciences, University of East Anglia, Norwich, UK. [3] School of Medicine, University of East Anglia, Norwich, UK
| | - Rosalind Eeles
- 1] Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK. [2] Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - David Neal
- 1] Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK. [2] Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Bernard Tetu
- Department of Pathology, Laval University, Quebec City, Quebec, Canada
| | - Cenk Sahinalp
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Neil Fleshner
- Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sohrab P Shah
- 1] Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada. [2] Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada. [3] British Columbia Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - Colin C Collins
- 1] Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. [2] Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Robert G Bristow
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
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Zhu Q, Gong L, Liu X, Wang J, Ren P, Zhang W, Yao L, Han X, Zhu S, Lan M, Li Y, Zhang W. Loss of heterozygosity at D8S262: an early genetic event of hepatocarcinogenesis. Diagn Pathol 2015; 10:70. [PMID: 26076954 PMCID: PMC4469120 DOI: 10.1186/s13000-015-0308-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a multi-factor, multi-step, multi-gene and complicated process resulting from the accumulation of sequential genetic and epigenetic alterations. An important change among them is from precancerous lesions to HCC. However, only few studies have been reported about the sequential genetic changes during hepatocarcinogenesis. METHODS We observed firstly molecular karyotypes of 10 matched HCC using Affymetrix single-nucleotide polymorphism (SNP) 6.0 arrays, and found chromosomal fragments with high incidence (more than 70%) of loss of heterozygosity (LOH). Then, we selected 28 microsatellite markers at some gene spanning these chromosomal fragments, and examined the frequency of LOH of 128 matched HCC and 43 matched precancerous lesions-dysplastic nodules (DN) by a PCR-based analysis. Finally, we investigated the expression of proteins encoded by these genes in HCC, DN and the surrounding hepatic tissues. RESULTS The result of Affymetrix SNP6.0 arrays demonstrated that more than 70% (7/10) cases had chromosomal fragment deletion on 4q13.3-35.1, 8p23.2-21.2, 16q11.2-24.3, and 17p13.3-12. Among 28 microsatellite markers selected, LOH frequencies at D8S262 for DN and HCC were found to be the highest, 51.2% and 72.7%, respectively. Immunohistochemically, the positive rate of its adjacent gene CSMD1 in HCC, DN, and the surrounding hepatic tissues were 27.3% (35/128), 75% (33/44), and 82% (105/128), respectively. CONCLUSIONS LOH at D8S262 may be associated with an early genetic event of hepatocarcinogenesis, and a predictor for the monitor and prevention of HCC. VIRTUAL SLIDES The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1557074981159099 .
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Affiliation(s)
- Qiao Zhu
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Li Gong
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China.
| | - Xiaoyan Liu
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Jun Wang
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Pin Ren
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Wendong Zhang
- Department of Rehabilitation Medicine, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Li Yao
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Xiujuan Han
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Shaojun Zhu
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Miao Lan
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China
| | - Yanhong Li
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China. .,Department of Gynaecology and Obstetrics, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China.
| | - Wei Zhang
- The Helmholtz Sino-German Laboratory for Cancer Research, Department of Pathology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, People's Republic of China.
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24
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Boström PJ, Bjartell AS, Catto JWF, Eggener SE, Lilja H, Loeb S, Schalken J, Schlomm T, Cooperberg MR. Genomic Predictors of Outcome in Prostate Cancer. Eur Urol 2015; 68:1033-44. [PMID: 25913390 DOI: 10.1016/j.eururo.2015.04.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/03/2015] [Indexed: 01/09/2023]
Abstract
CONTEXT Given the highly variable behavior and clinical course of prostate cancer (PCa) and the multiple available treatment options, a personalized approach to oncologic risk stratification is important. Novel genetic approaches offer additional information to improve clinical decision making. OBJECTIVE To review the use of genomic biomarkers in the prognostication of PCa outcome and prediction of therapeutic response. EVIDENCE ACQUISITION Systematic literature review focused on human clinical studies reporting outcome measures with external validation. The literature search included all Medline, Embase, and Scopus articles from inception through July 2014. EVIDENCE SYNTHESIS An improved understanding of the genetic basis of prostate carcinogenesis has produced an increasing number of potential prognostic and predictive tools, such as transmembrane protease, serine2:v-ets avian erythroblastosis virus E26 oncogene homolog (TMPRSS2:ERG) gene fusion status, loss of the phosphatase and tensin homolog (PTEN) gene, and gene expression signatures utilizing messenger RNA from tumor tissue. Several commercially available gene panels with external validation are now available, although most have yet to be widely used. The most studied commercially available gene panels, Prolaris, Oncotype DX Genomic Prostate Score, and Decipher, may be used to estimate disease outcome in addition to clinical parameters or clinical nomograms. ConfirmMDx is an epigenetic test used to predict the results of repeat prostate biopsy after an initial negative biopsy. Additional future strategies include using genetic information from circulating tumor cells in the peripheral blood to guide treatment decisions at the initial diagnosis and at subsequent decision points. CONCLUSIONS Major advances have been made in our understanding of PCa biology in recent years. Our field is currently exploring the early stages of a personalized approach to augment traditional clinical decision making using commercially available genomic tools. A more comprehensive appreciation of value, limitations, and cost is important. PATIENT SUMMARY We summarized current advances in genomic testing in prostate cancer with a special focus on the estimation of disease outcome. Several commercial tests are currently available, but further understanding is needed to appreciate the potential benefits and limitations of these novel tests.
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Affiliation(s)
- Peter J Boström
- Department of Urology, Turku University Hospital, Turku, Finland.
| | - Anders S Bjartell
- Department of Urology, Skåne University Hospital Malmö, Lund University, Lund Sweden
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | | | - Hans Lilja
- Departments of Laboratory Medicine, Surgery (Urology), and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - Stacy Loeb
- Department of Urology and Population Health, New York University and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Jack Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthew R Cooperberg
- Departments of Urology and Epidemiology and Biostatistics, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
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Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2671-86. [PMID: 25131421 DOI: 10.1016/j.ajpath.2014.06.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 12/11/2022]
Abstract
Gauging the risk of developing progressive disease is a major challenge in prostate cancer patient management. We used genetic markers to understand genomic alteration dynamics during disease progression. By using a novel, advanced, multicolor fluorescence in situ hybridization approach, we enumerated copy numbers of six genes previously identified by array comparative genomic hybridization to be involved in aggressive prostate cancer [TBL1XR1, CTTNBP2, MYC (alias c-myc), PTEN, MEN1, and PDGFB] in six nonrecurrent and seven recurrent radical prostatectomy cases. An ERG break-apart probe to detect TMPRSS2-ERG fusions was included. Subsequent hybridization of probe panels and cell relocation resulted in signal counts for all probes in each individual cell analyzed. Differences in the degree of chromosomal and genomic instability (ie, tumor heterogeneity) or the percentage of cells with TMPRSS2-ERG fusion between samples with or without progression were not observed. Tumors from patients that progressed had more chromosomal gains and losses, and showed a higher degree of selection for a predominant clonal pattern. PTEN loss was the most frequent aberration in progressers (57%), followed by TBL1XR1 gain (29%). MYC gain was observed in one progresser, which was the only lesion with an ERG gain, but no TMPRSS2-ERG fusion. According to our results, a probe set consisting of PTEN, MYC, and TBL1XR1 would detect progressers with 86% sensitivity and 100% specificity. This will be evaluated further in larger studies.
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26
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Levin AM, Lindquist KJ, Avila A, Witte JS, Paris PL, Rybicki BA. Performance of the Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) tumor biomarker for identifying recurrent disease in African American patients. Cancer Epidemiol Biomarkers Prev 2014; 23:1677-82. [PMID: 24891551 PMCID: PMC4119547 DOI: 10.1158/1055-9965.epi-13-1124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Evaluation of prostate cancer prognosis after surgery is increasingly relying upon genomic analyses of tumor DNA. We assessed the ability of the biomarker panel Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) to predict biochemical recurrence in 33 European American and 28 African American prostate cancer cases using genome-wide copy number data from a previous study. "Biomarker positive" was defined as ≥20% of the 38 constituent copy number gain/loss GEMCaP loci affected in a given tumor; based on this threshold, the frequency of a positive biomarker was significantly lower in African Americans (n = 2; 7%) than European Americans (n = 11; 33%; P = 0.013). GEMCaP positivity was associated with risk of recurrence [hazard ratio (HR), 5.92; 95% confidence interval (CI), 2.32-15.11; P = 3 × 10(-4)] in the full sample and among European Americans (HR, 3.45; 95% CI, 1.13-10.51; P = 0.032) but was not estimable in African Americans due to the low rate of GEMCaP positivity. Overall, the GEMCaP recurrence positive predictive value (PPV) was 85%; in African Americans, PPV was 100%. When we expanded the definition of loss to include copy-neutral loss of heterozygosity (i.e., loss of one allele with concomitant duplication of the other), recurrence PPV was 83% for European American subjects. Under this definition, 5 African American subjects had a positive GEMCaP test value; 4 went on to develop biochemical recurrence (PPV = 80%). Our results suggest that the GEMCaP biomarker set could be an effective predictor for both European American and African American men diagnosed with localized prostate cancer who may benefit from immediate aggressive therapy after radical prostatectomy.
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Affiliation(s)
- Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | | | - Andrew Avila
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - John S Witte
- Department of Epidemiology and Biostatistics; and
| | - Pamela L Paris
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan;
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27
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Lapuk AV, Volik SV, Wang Y, Collins CC. The role of mRNA splicing in prostate cancer. Asian J Androl 2014; 16:515-21. [PMID: 24830689 PMCID: PMC4104073 DOI: 10.4103/1008-682x.127825] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/12/2014] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing (AS) is a crucial step in gene expression. It is subject to intricate regulation, and its deregulation in cancer can lead to a wide array of neoplastic phenotypes. A large body of evidence implicates splice isoforms in most if not all hallmarks of cancer, including growth, apoptosis, invasion and metastasis, angiogenesis, and metabolism. AS has important clinical implications since it can be manipulated therapeutically to treat cancer and represents a mechanism of resistance to therapy. In prostate cancer (PCa) AS also plays a prominent role and this review will summarize the current knowledge of alternatively spliced genes with important functional consequences. We will highlight accumulating evidence on AS of the components of the two critical pathways in PCa: androgen receptor (AR) and phosphoinositide 3-kinase (PI3K). These observations together with data on dysregulation of splice factors in PCa suggest that AR and PI3K pathways may be interconnected with previously unappreciated splicing regulatory networks. In addition, we will discuss several lines of evidence implicating splicing regulation in the development of the castration resistance.
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Affiliation(s)
- Anna V Lapuk
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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28
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Schinke EN, Bii V, Nalla A, Rae DT, Tedrick L, Meadows GG, Trobridge GD. A novel approach to identify driver genes involved in androgen-independent prostate cancer. Mol Cancer 2014; 13:120. [PMID: 24885513 PMCID: PMC4098713 DOI: 10.1186/1476-4598-13-120] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/13/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Insertional mutagenesis screens have been used with great success to identify oncogenes and tumor suppressor genes. Typically, these screens use gammaretroviruses (γRV) or transposons as insertional mutagens. However, insertional mutations from replication-competent γRVs or transposons that occur later during oncogenesis can produce passenger mutations that do not drive cancer progression. Here, we utilized a replication-incompetent lentiviral vector (LV) to perform an insertional mutagenesis screen to identify genes in the progression to androgen-independent prostate cancer (AIPC). METHODS Prostate cancer cells were mutagenized with a LV to enrich for clones with a selective advantage in an androgen-deficient environment provided by a dysregulated gene(s) near the vector integration site. We performed our screen using an in vitro AIPC model and also an in vivo xenotransplant model for AIPC. Our approach identified proviral integration sites utilizing a shuttle vector that allows for rapid rescue of plasmids in E. coli that contain LV long terminal repeat (LTR)-chromosome junctions. This shuttle vector approach does not require PCR amplification and has several advantages over PCR-based techniques. RESULTS Proviral integrations were enriched near prostate cancer susceptibility loci in cells grown in androgen-deficient medium (p < 0.001), and five candidate genes that influence AIPC were identified; ATPAF1, GCOM1, MEX3D, PTRF, and TRPM4. Additionally, we showed that RNAi knockdown of ATPAF1 significantly reduces growth (p < 0.05) in androgen-deficient conditions. CONCLUSIONS Our approach has proven effective for use in PCa, identifying a known prostate cancer gene, PTRF, and also several genes not previously associated with prostate cancer. The replication-incompetent shuttle vector approach has broad potential applications for cancer gene discovery, and for interrogating diverse biological and disease processes.
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Affiliation(s)
| | | | | | | | | | | | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210-1495, USA.
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29
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Walsh AL, Tuzova AV, Bolton EM, Lynch TH, Perry AS. Long noncoding RNAs and prostate carcinogenesis: the missing 'linc'? Trends Mol Med 2014; 20:428-36. [PMID: 24836411 DOI: 10.1016/j.molmed.2014.03.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) are rapidly becoming essential pieces in the cancer puzzle. Our understanding of their functional capabilities is in its infancy. One certain fact, however, is that their molecular interactions extend beyond chromatin complexes into diverse biological processes. In prostate cancer, aberrant expression of lncRNAs is associated with disease progression. Overexpression of oncogenic lncRNAs promotes tumor-cell proliferation and metastasis through chromatin looping and distal engagement with the androgen receptor, antisense gene regulation, alternative splicing, and impeding DNA repair. Several lncRNAs, such as prostate cancer antigen 3 (PCA3), prostate cancer gene expression marker 1 (PCGEM1), and prostate cancer associated ncRNA transcript 1 (PCAT1), are highly prostate-specific, posing as attractive biomarkers. Herein we review the mechanisms of action of lncRNAs in prostate carcinogenesis and their potential clinical utility for disease.
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Affiliation(s)
- Anna L Walsh
- Prostate Molecular Oncology Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Department of Urology, St. James's Hospital, Dublin, Ireland
| | - Alexandra V Tuzova
- Prostate Molecular Oncology Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - Eva M Bolton
- Prostate Molecular Oncology Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Department of Urology, St. James's Hospital, Dublin, Ireland
| | - Thomas H Lynch
- Prostate Molecular Oncology Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Department of Urology, St. James's Hospital, Dublin, Ireland
| | - Antoinette S Perry
- Prostate Molecular Oncology Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland.
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30
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Zhang R, Song C. Loss of CSMD1 or 2 may contribute to the poor prognosis of colorectal cancer patients. Tumour Biol 2014; 35:4419-23. [DOI: 10.1007/s13277-013-1581-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022] Open
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31
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Lewinshtein DJ, Porter CR, Nelson PS. Genomic predictors of prostate cancer therapy outcomes. Expert Rev Mol Diagn 2014; 10:619-36. [DOI: 10.1586/erm.10.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Tang MR, Wang YX, Guo S, Han SY, Wang D. CSMD1 exhibits antitumor activity in A375 melanoma cells through activation of the Smad pathway. Apoptosis 2013; 17:927-37. [PMID: 22538441 DOI: 10.1007/s10495-012-0727-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this work, we studied the effects of CUB and Sushi multiple domains 1 gene (CSMD1) expression in A375 melanoma cells in vivo and in vitro. CSDM1 expression decreased proliferation and migration, and increased apoptosis and G(1) arrest in A375 cells in vitro. Expression of CSDM1 in established xenografted tumors decreased tumor size and weight, and decreased the density of intratumor microvessels. The survival rate of mice with tumors expressing CSMD1 was significantly higher than mice with tumors that did not express CSDM1. These results confirm the role of CSDM1 as a tumor suppressor gene in melanoma cells. Furthermore, we found that CSMD1 can interact with Smad3, activate Smad1, Smad2, and Smad3, and increase the expression of Smad4. These results might prove helpful for the development of novel therapies for melanoma treatment.
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Affiliation(s)
- Ming-Rui Tang
- Department of Plastic Surgery, The First Hospital of China Medical University, Nanjing North Street 155 Heping District, Shenyang City, 110001, China.
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33
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Okubo H, Ohori M, Ohno Y, Nakashima J, Inoue R, Nagao T, Tachibana M. Prediction of non-biochemical recurrence rate after radical prostatectomy in a Japanese cohort: Development of a postoperative nomogram. Int J Urol 2013; 21:479-83. [DOI: 10.1111/iju.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hidenori Okubo
- Department of Urology; Tokyo Medical University; Tokyo Japan
| | - Makoto Ohori
- Department of Urology; Tokyo Medical University; Tokyo Japan
| | - Yoshio Ohno
- Department of Urology; Tokyo Medical University; Tokyo Japan
| | - Jun Nakashima
- Department of Urology; Tokyo Medical University; Tokyo Japan
| | - Rie Inoue
- Department of Pathology; Tokyo Medical University; Tokyo Japan
| | - Toshitaka Nagao
- Department of Pathology; Tokyo Medical University; Tokyo Japan
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34
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Wyatt AW, Mo F, Wang Y, Collins CC. The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing. Asian J Androl 2013; 15:301-8. [PMID: 23503423 PMCID: PMC3739651 DOI: 10.1038/aja.2013.13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Prostate cancer is a leading cause of global cancer-related death but attempts to improve diagnoses and develop novel therapies have been confounded by significant patient heterogeneity. In recent years, the application of next-generation sequencing to hundreds of prostate tumours has defined novel molecular subtypes and characterized extensive genomic aberration underlying disease initiation and progression. It is now clear that the heterogeneity observed in the clinic is underpinned by a molecular landscape rife with complexity, where genomic rearrangements and rare mutations combine to amplify transcriptomic diversity. This review dissects our current understanding of prostate cancer 'omics', including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare. Therefore, it is critical that we continue to define individual tumour genomes, especially in the context of their expressed transcriptome. Only through improved characterisation of tumour to tumour variability can we advance to an age of precision therapy and personalized oncology.
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Affiliation(s)
- Alexander W Wyatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada.
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35
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Vang S, Wu HT, Fischer A, Miller DH, MacLaughlan S, Douglass E, Steinhoff M, Collins C, Smith PJS, Brard L, Brodsky AS. Identification of ovarian cancer metastatic miRNAs. PLoS One 2013; 8:e58226. [PMID: 23554878 PMCID: PMC3595263 DOI: 10.1371/journal.pone.0058226] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/31/2013] [Indexed: 12/31/2022] Open
Abstract
Serous epithelial ovarian cancer (EOC) patients often succumb to aggressive metastatic disease, yet little is known about the behavior and genetics of ovarian cancer metastasis. Here, we aim to understand how omental metastases differ from primary tumors and how these differences may influence chemotherapy. We analyzed the miRNA expression profiles of primary EOC tumors and their respective omental metastases from 9 patients using miRNA Taqman qPCR arrays. We find 17 miRNAs with differential expression in omental lesions compared to primary tumors. miR-21, miR-150, and miR-146a have low expression in most primary tumors with significantly increased expression in omental lesions, with concomitant decreased expression of predicted mRNA targets based on mRNA expression. We find that miR-150 and miR-146a mediate spheroid size. Both miR-146a and miR-150 increase the number of residual surviving cells by 2-4 fold when challenged with lethal cisplatin concentrations. These observations suggest that at least two of the miRNAs, miR-146a and miR-150, up-regulated in omental lesions, stimulate survival and increase drug tolerance. Our observations suggest that cancer cells in omental tumors express key miRNAs differently than primary tumors, and that at least some of these microRNAs may be critical regulators of the emergence of drug resistant disease.
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Affiliation(s)
- Souriya Vang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Hsin-Ta Wu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Department of Computer Science, Brown University, Providence, Rhode Island, United States of America
| | - Andrew Fischer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Daniel H. Miller
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Shannon MacLaughlan
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women and Infants' Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Elijah Douglass
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Margaret Steinhoff
- Department of Pathology, Women and Infants' Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Colin Collins
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Peter J. S. Smith
- Institute of Life Sciences, University of Southampton, Southampton, England
| | - Laurent Brard
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Alexander S. Brodsky
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Genomics and Proteomics, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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36
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Genomic Signatures Associated with the Development, Progression, and Outcome of Prostate Cancer. Mol Diagn Ther 2012; 11:345-54. [DOI: 10.1007/bf03256258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol 2012; 227:286-97. [PMID: 22553170 DOI: 10.1002/path.4047] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The current paradigm of cancer care relies on predictive nomograms which integrate detailed histopathology with clinical data. However, when predictions fail, the consequences for patients are often catastrophic, especially in prostate cancer where nomograms influence the decision to therapeutically intervene. We hypothesized that the high dimensional data afforded by massively parallel sequencing (MPS) is not only capable of providing biological insights, but may aid molecular pathology of prostate tumours. We assembled a cohort of six patients with high-risk disease, and performed deep RNA and shallow DNA sequencing in primary tumours and matched metastases where available. Our analysis identified copy number abnormalities, accurately profiled gene expression levels, and detected both differential splicing and expressed fusion genes. We revealed occult and potentially dormant metastases, unambiguously supporting the patients' clinical history, and implicated the REST transcriptional complex in the development of neuroendocrine prostate cancer, validating this finding in a large independent cohort. We massively expand on the number of novel fusion genes described in prostate cancer; provide fresh evidence for the growing link between fusion gene aetiology and gene expression profiles; and show the utility of fusion genes for molecular pathology. Finally, we identified chromothripsis in a patient with chronic prostatitis. Our results provide a strong foundation for further development of MPS-based molecular pathology.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/secondary
- Adenocarcinoma/therapy
- Aged
- Alternative Splicing
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- British Columbia
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cluster Analysis
- Decision Support Techniques
- Gene Dosage
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Gene Fusion
- Genetic Predisposition to Disease
- Humans
- Lymphatic Metastasis
- Male
- Middle Aged
- Neoplasm Grading
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Neoplasms, Hormone-Dependent/pathology
- Neoplasms, Hormone-Dependent/therapy
- Neuroendocrine Cells/metabolism
- Neuroendocrine Cells/pathology
- Nomograms
- Oligonucleotide Array Sequence Analysis
- Patient Selection
- Phenotype
- Precision Medicine
- Prognosis
- Prostate-Specific Antigen/blood
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Prostatic Neoplasms/therapy
- RNA Interference
- Transfection
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Affiliation(s)
- Anna V Lapuk
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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38
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Yuan X, Zhang J, Yang L, Zhang S, Chen B, Geng Y, Wang Y. TAGCNA: a method to identify significant consensus events of copy number alterations in cancer. PLoS One 2012; 7:e41082. [PMID: 22815924 PMCID: PMC3399811 DOI: 10.1371/journal.pone.0041082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 06/17/2012] [Indexed: 01/20/2023] Open
Abstract
Somatic copy number alteration (CNA) is a common phenomenon in cancer genome. Distinguishing significant consensus events (SCEs) from random background CNAs in a set of subjects has been proven to be a valuable tool to study cancer. In order to identify SCEs with an acceptable type I error rate, better computational approaches should be developed based on reasonable statistics and null distributions. In this article, we propose a new approach named TAGCNA for identifying SCEs in somatic CNAs that may encompass cancer driver genes. TAGCNA employs a peel-off permutation scheme to generate a reasonable null distribution based on a prior step of selecting tag CNA markers from the genome being considered. We demonstrate the statistical power of TAGCNA on simulated ground truth data, and validate its applicability using two publicly available cancer datasets: lung and prostate adenocarcinoma. TAGCNA identifies SCEs that are known to be involved with proto-oncogenes (e.g. EGFR, CDK4) and tumor suppressor genes (e.g. CDKN2A, CDKN2B), and provides many additional SCEs with potential biological relevance in these data. TAGCNA can be used to analyze the significance of CNAs in various cancers. It is implemented in R and is freely available at http://tagcna.sourceforge.net/.
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Affiliation(s)
- Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, People’s Republic of China
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, People’s Republic of China
- * E-mail: (JZ); (YW)
| | - Liying Yang
- School of Computer Science and Technology, Xidian University, Xi'an, People’s Republic of China
| | - Shengli Zhang
- Department of Mathematics, Xidian University, Xi'an, People’s Republic of China
| | - Baodi Chen
- School of Computer Science and Technology, Xidian University, Xi'an, People’s Republic of China
| | - Yaojun Geng
- School of Computer Science and Technology, Xidian University, Xi'an, People’s Republic of China
| | - Yue Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America
- * E-mail: (JZ); (YW)
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Abstract
Rad9 plays a crucial role in maintaining genomic stability by regulating cell cycle checkpoints, DNA repair, telomere stability, and apoptosis. Rad9 controls these processes mainly as part of the heterotrimeric 9-1-1 (Rad9-Hus1-Rad1) complex. However, in recent years it has been demonstrated that Rad9 can also act independently of the 9-1-1 complex as a transcriptional factor, participate in immunoglobulin class switch recombination, and show 3'-5' exonuclease activity. Aberrant Rad9 expression has been associated with prostate, breast, lung, skin, thyroid, and gastric cancers. High expression of Rad9 is causally related to, at least, human prostate cancer growth. On the other hand, deletion of Mrad9, the mouse homolog, is responsible for increased skin cancer incidence. These results reveal that Rad9 can act as an oncogene or tumor suppressor. Which of the many functions of Rad9 are causally related to initiation and progression of tumorigenesis and the mechanistic details by which Rad9 induces or suppresses tumorigenesis are presently not known, but are crucial for the development of targeted therapeutic interventions.
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Affiliation(s)
- Constantinos G Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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40
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Zhang X, Jing Y, Qin Y, Hunsucker S, Meng H, Sui J, Jiang Y, Gao L, An G, Yang N, Orlowski RZ, Yang L. The zinc finger transcription factor ZKSCAN3 promotes prostate cancer cell migration. Int J Biochem Cell Biol 2012; 44:1166-73. [PMID: 22531714 DOI: 10.1016/j.biocel.2012.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/03/2012] [Accepted: 04/09/2012] [Indexed: 12/01/2022]
Abstract
In our previous studies, ZKSCAN3 was demonstrated to be over-expressed in invasive colonic tumor cells and their liver metastases, but minimally expressed in adjacent non-transformed tissues. Further preliminary data showed that ZKSCAN3 was expressed in a majority of prostate cancer patient samples, but not in normal prostate tissues. Moreover, the ZKSCAN3 protein is highly expressed in the PC3 prostate cancer cell line, which has high metastatic potential, but little expression was observed in non-metastatic prostate cancer cell lines. Thus, we hypothesized that ZKSCAN3 could participate in tumor metastasis by regulating tumor cell migration. To test this hypothesis, ZKSCAN3 mRNA was knocked down by ZKSCAN3 specific shRNA in PC3 cells and a significant decrease in cell motility was observed. In contrast, when ZKSCAN3 cDNA was overexpressed in PC3 cells, cell detachment was observed and suspension culture induced apoptosis was greatly decreased, suggesting that ZKSCAN3 is able to enhance PC3 cell survival under anoikis stress. Additional wound healing and invasion assays showed that cell migration was enhanced by ZKSCAN3 expression. Interestingly, the ZKSCAN3 gene was amplified in 26% (5/19) of metastatic prostate cancers and 20% (1/5) of lymph node metastases, but there was no amplification found in primary prostate cancers, further supporting the role of ZKSCAN3 in tumor cell migration. In vivo studies using orthotopic tumor models indicated that overexpression of ZKSCAN3 significantly enhanced tumorigenicity. Taken together, we provide evidence that ZKSCAN3, a zinc finger transcription factor, plays a critical role in promoting prostate cancer cell migration.
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Affiliation(s)
- Xingding Zhang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, Jiangsu, PR China
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41
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Oncogenic CUL4A determines the response to thalidomide treatment in prostate cancer. J Mol Med (Berl) 2012; 90:1121-32. [PMID: 22422151 DOI: 10.1007/s00109-012-0885-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 12/23/2022]
Abstract
Thalidomide is experimentally used to treat various human cancers; however, clinical responses to thalidomide are sporadic. Here we demonstrate that CUL4A plays an oncogenic role in prostate cancer development and prostate cancer cells with higher level of CUL4A are particularly sensitive to thalidomide treatment. We show that CUL4A is frequently overexpressed in human primary prostate cancer and cell lines. Notably, subjects with tumors that highly expressed CUL4A had poor overall survival. CUL4A downregulation inhibited cell proliferation and induced apoptosis in vitro and in vivo, whereas CUL4A overexpression transformed human normal prostate epithelial cells and promoted invasion, which was attenuated by the extracellular signal-regulated kinase (ERK) inhibitor. We further show that the sensitivity to thalidomide is positively correlated with CUL4A expression in a panel of prostate cell lines. Ectopic CUL4A expression greatly enhanced sensitivity to thalidomide, while its downregulation conferred resistance to this drug. Mechanistically, thalidomide decreased CUL4A in a time- and dose-dependent manner, consequently leading to inaction of ERK pathway. Finally, we show that cereblon level is correlated with CUL4A expression and downregulated in thalidomide-resistant prostate cancer cell. Our results offer the first evidence that CUL4A is a potential therapeutic target for prostate cancer and may serve as a biomarker for assessing prognosis of human prostate cancer and response to thalidomide treatment.
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42
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Lee JS, Kim JH, Park YY, Mills GB. Systems biology approaches to decoding the genome of liver cancer. Cancer Res Treat 2011; 43:205-11. [PMID: 22247704 PMCID: PMC3253861 DOI: 10.4143/crt.2011.43.4.205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 11/14/2011] [Indexed: 12/13/2022] Open
Abstract
Molecular classification of cancers has been significantly improved patient outcomes through the implementation of treatment protocols tailored to the abnormalities present in each patient's cancer cells. Breast cancer represents the poster child with marked improvements in outcome occurring due to the implementation of targeted therapies for estrogen receptor or human epidermal growth factor receptor-2 positive breast cancers. Important subtypes with characteristic molecular features as potential therapeutic targets are likely to exist for all tumor lineages including hepatocellular carcinoma (HCC) but have yet to be discovered and validated as targets. Because each tumor accumulates hundreds or thousands of genomic and epigenetic alterations of critical genes, it is challenging to identify and validate candidate tumor aberrations as therapeutic targets or biomarkers that predict prognosis or response to therapy. Therefore, there is an urgent need to devise new experimental and analytical strategies to overcome this problem. Systems biology approaches integrating multiple data sets and technologies analyzing patient tissues holds great promise for the identification of novel therapeutic targets and linked predictive biomarkers allowing implementation of personalized medicine for HCC patients.
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Affiliation(s)
- Ju-Seog Lee
- Department of Systems Biology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
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43
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Friedlander TW, Roy R, Tomlins SA, Ngo VT, Kobayashi Y, Azameera A, Rubin MA, Pienta KJ, Chinnaiyan A, Ittmann MM, Ryan CJ, Paris PL. Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res 2011; 72:616-25. [PMID: 22158653 DOI: 10.1158/0008-5472.can-11-2079] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Progression of primary prostate cancer to castration-resistant prostate cancer (CRPC) is associated with numerous genetic and epigenetic alterations that are thought to promote survival at metastatic sites. In this study, we investigated gene copy number and CpG methylation status in CRPC to gain insight into specific pathophysiologic pathways that are active in this advanced form of prostate cancer. Our analysis defined and validated 495 genes exhibiting significant differences in CRPC in gene copy number, including gains in androgen receptor (AR) and losses of PTEN and retinoblastoma 1 (RB1). Significant copy number differences existed between tumors with or without AR gene amplification, including a common loss of AR repressors in AR-unamplified tumors. Simultaneous gene methylation and allelic deletion occurred frequently in RB1 and HSD17B2, the latter of which is involved in testosterone metabolism. Lastly, genomic DNA from most CRPC was hypermethylated compared with benign prostate tissue. Our findings establish a comprehensive methylation signature that couples epigenomic and structural analyses, thereby offering insights into the genomic alterations in CRPC that are associated with a circumvention of hormonal therapy. Genes identified in this integrated genomic study point to new drug targets in CRPC, an incurable disease state which remains the chief therapeutic challenge.
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Affiliation(s)
- Terence W Friedlander
- Division on Genitourinary Medical Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
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44
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Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I. Calling amplified haplotypes in next generation tumor sequence data. Genome Res 2011; 22:362-74. [PMID: 22090379 DOI: 10.1101/gr.122564.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
During tumor initiation and progression, cancer cells acquire a selective advantage, allowing them to outcompete their normal counterparts. Identification of the genetic changes that underlie these tumor acquired traits can provide deeper insights into the biology of tumorigenesis. Regions of copy number alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor "prefers" to have amplified. Next-generation sequencing of tumor and matched normal tissues provides a high-resolution platform to identify and analyze such somatic amplicons. Within an amplicon, examination of informative (e.g., heterozygous) sites deviating from a 1:1 ratio may suggest selection of that allele. A naive approach examines the reads for each heterozygous site in isolation; however, this ignores available valuable linkage information across sites. We, therefore, present a novel hidden Markov model-based method-Haplotype Amplification in Tumor Sequences (HATS)-that analyzes tumor and normal sequence data, along with training data for phasing purposes, to infer amplified alleles and haplotypes in regions of copy number gain. Our method is designed to handle rare variants and biases in read data. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons in real data. We demonstrate that HATS infers the amplified alleles more accurately than does the naive approach, especially at low to intermediate coverage levels and in cases (including high coverage) possessing stromal contamination or allelic bias.
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Affiliation(s)
- Ninad Dewal
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
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45
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Barros-Silva JD, Ribeiro FR, Rodrigues Â, Cruz R, Martins AT, Jerónimo C, Henrique R, Teixeira MR. Relative 8q gain predicts disease-specific survival irrespective of the TMPRSS2-ERG fusion status in diagnostic biopsies of prostate cancer. Genes Chromosomes Cancer 2011; 50:662-671. [DOI: 10.1002/gcc.20888] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ. Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinformatics 2011; 12:114. [PMID: 21510904 PMCID: PMC3112242 DOI: 10.1186/1471-2105-12-114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 04/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs), including deletions, amplifications, and other rearrangements, are common in human and cancer genomes. Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants. Comparison of copy number data from multiple individuals reveals recurrent variants. Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant. RESULTS We introduce Neighborhood Breakpoint Conservation (NBC), an algorithm for identifying rearrangement breakpoints that are highly conserved at the same locus in multiple individuals. NBC detects recurrent breakpoints at varying levels of resolution, including breakpoints whose location is exactly conserved and breakpoints whose location varies within a gene. NBC also identifies pairs of recurrent breakpoints such as those that result from fusion genes. We apply NBC to aCGH data from 36 primary prostate tumors and identify 12 novel rearrangements, one of which is the well-known TMPRSS2-ERG fusion gene. We also apply NBC to 227 glioblastoma tumors and predict 93 novel rearrangements which we further classify as gene truncations, germline structural variants, and fusion genes. A number of these variants involve the protein phosphatase PTPN12 suggesting that deregulation of PTPN12, via a variety of rearrangements, is common in glioblastoma. CONCLUSIONS We demonstrate that NBC is useful for detection of recurrent breakpoints resulting from copy number variants or other structural variants, and in particular identifies recurrent breakpoints that result in gene truncations or fusion genes. Software is available at http://http.//cs.brown.edu/people/braphael/software.html.
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Affiliation(s)
- Anna Ritz
- Department of Computer Science, Brown University, Providence, RI, USA.
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47
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Varier RA, Timmers HTM. Histone lysine methylation and demethylation pathways in cancer. Biochim Biophys Acta Rev Cancer 2010; 1815:75-89. [PMID: 20951770 DOI: 10.1016/j.bbcan.2010.10.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 12/21/2022]
Abstract
The genetic changes leading to the development of human cancer are accompanied by alterations in the structure and modification status of chromatin, which represent powerful regulatory mechanisms for gene expression and genome stability. These epigenetic alterations have sparked interest into deciphering the regulatory pathways and function of post-translational modifications of histones during the initiation and progression of cancer. In this review we describe and summarize the current knowledge of several histone lysine methyltransferase and demethylase pathways relevant to cancer. Mechanistic insight into histone modifications will pave the way for the development and therapeutic application of "epidrugs" in cancer.
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Affiliation(s)
- Radhika A Varier
- Department of Physiological Chemistry, University Medical Centre, Utrecht, The Netherlands
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48
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Pickard MR, Edwards SE, Cooper CS, Williams GT. Apoptosis regulators Fau and Bcl-G are down-regulated in prostate cancer. Prostate 2010; 70:1513-23. [PMID: 20687224 DOI: 10.1002/pros.21186] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The molecular control of cell death through apoptosis is compromised in prostate cancer cells, resulting in inappropriate cell survival and resistance to cytotoxic therapy. Reduced expression of the functionally connected apoptosis-regulators and candidate tumor suppressors Fau and Bcl-G has recently been implicated in oncogenesis in other tissues. The present study examines the hypothesis that reduced expression of these genes may be involved in prostate cancer. METHODS Fau and Bcl-G mRNA levels were determined by real time RT-PCR in two independent prostate tissue collections. In experiments in vitro, Fau and Bcl-G levels in prostate cancer cell lines were reduced using RNA interference and the effects on sensitivity to UVC irradiation were determined. RESULTS Fau and Bcl-G mRNA levels were both lower in prostate cancer tissue than in normal prostate and Benign Prostate Hyperplasia. Active down-regulation of Fau and Bcl-G expression in vitro resulted in decreased sensitivity to UVC-induced cytotoxicity. Simultaneous down-regulation of Fau and Bcl-G produced a decrease in sensitivity which was similar to either gene alone. CONCLUSIONS Fau and Bcl-G mRNA levels are both decreased in prostate cancer. In prostate cancer cell lines in vitro such down-regulation results in reduced sensitivity to UVC-induced cytotoxicity, consistent with the putative roles of these genes as candidate prostate tumor suppressors. The absence of an additive effect when Fau and Bcl-G were down-regulated simultaneously is consistent with the two genes acting in the same apoptosis pathway, for example, with the pro-apoptotic effects of Fau being mediated through modulation of Bcl-G.
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Affiliation(s)
- Mark R Pickard
- Institute for Science and Technology in Medicine, School of Life Sciences, Keele University, Huxley Building, Keele, UK
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49
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Karimpour-Fard A, Dumas L, Phang T, Sikela JM, Hunter LE. A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation. Hum Genomics 2010; 4:421-7. [PMID: 20846932 PMCID: PMC3525224 DOI: 10.1186/1479-7364-4-6-421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 08/27/2010] [Indexed: 11/10/2022] Open
Abstract
Copy number variants (CNVs) create a major source of variation among individuals and populations. Array-based comparative genomic hybridisation (aCGH) is a powerful method used to detect and compare the copy numbers of DNA sequences at high resolution along the genome. In recent years, several informatics tools for accurate and efficient CNV detection and assessment have been developed. In this paper, most of the well known algorithms, analysis software and the limitations of that software will be briefly reviewed.
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Affiliation(s)
- Anis Karimpour-Fard
- Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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50
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The progress on genetic analysis of nasopharyngeal carcinoma. Comp Funct Genomics 2010:57513. [PMID: 18288251 PMCID: PMC2233780 DOI: 10.1155/2007/57513] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 12/09/2007] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research.
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